Echinoderm Anatomy and Development Ontology
type: Ontology
version IRI: ecao.owl
description: None
license: https://creativecommons.org/licenses/by/3.0/

definition
type: AnnotationProperty
IAO_0000114: IAO_0000122

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.

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
IAO_0000111: is part of
IAO_0000112: my brain is part of my body (continuant parthood, two material entities)
IAO_0000112: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
IAO_0000112: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
IAO_0000116: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
IAO_0000118: part_of
RO_0001900: RO_0001901
RO_0040042: continuant
RO_0040042: occurrent
RO_0040042: independent continuant
RO_0040042: BFO_0000017
RO_0040042: BFO_0000019
RO_0040042: BFO_0000020
RO_0040042: BFO_0000031
database_cross_reference: BFO:0000050
has OBO namespace: uberon
id: part_of
shorthand: 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 https://code.google.com/p/obo-relations/wiki/ROAndTime
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
IAO_0000118: has_part
RO_0001900: RO_0001901
database_cross_reference: BFO:0000051
has OBO namespace: uberon
id: has_part
shorthand: has_part

preceded_by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
IAO_0000111: preceded by
definition: X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
IAO_0000116: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
IAO_0000118: is preceded by
IAO_0000118: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
database_cross_reference: BFO:0000062
has_exact_synonym: is preceded by
has_exact_synonym: takes place after
has OBO namespace: uberon
id: preceded_by
in subset: ro-eco
shorthand: preceded_by
label: preceded by

Axiom
annotated source: preceded_by
annotated property: has_exact_synonym
annotated target: is preceded by
database_cross_reference: SIO:000249

Axiom
annotated source: preceded_by
annotated property: has_exact_synonym
annotated target: takes place after
database_cross_reference: Allen:precedes

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.
database_cross_reference: BFO:0000063
has OBO namespace: uberon
id: precedes
in subset: ro-eco
shorthand: precedes

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

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

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
IAO_0000111: participates in
IAO_0000112: this blood clot participates in this blood coagulation
IAO_0000112: this input material (or this output material) participates in this process
IAO_0000112: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
IAO_0000118: participates_in

has participant
type: ObjectProperty
domain: occurrent
range: continuant
property chain axiom: has part
IAO_0000111: has participant
IAO_0000112: this blood coagulation has participant this blood clot
IAO_0000112: this investigation has participant this investigator
IAO_0000112: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
IAO_0000116: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
IAO_0000118: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
definition: A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
created by: dos
creation date: 2017-05-24T09:30:46Z

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

has positive regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: positively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
created by: dos
creation date: 2017-05-24T09:31:17Z
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.

has component activity
type: ObjectProperty
sub property of: has component process
created by: dos
creation date: 2017-05-24T09:44:33Z
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

has component process
type: ObjectProperty
sub property of: has component
domain: process
range: process
definition: w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
created by: dos
creation date: 2017-05-24T09:49:21Z

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

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

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

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

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

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

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

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

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
definition: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
IAO_0000117: David Osumi-Sutherland
IAO_0000118: starts_at_end_of
UBPROP_0000001: A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
database_cross_reference: RO:0002087
has_exact_synonym: directly preceded by
has_exact_synonym: is directly preceded by
has_exact_synonym: is immediately preceded by
has_exact_synonym: starts_at_end_of
has OBO namespace: uberon
id: immediately_preceded_by
shorthand: immediately_preceded_by
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
label: immediately preceded by

Axiom
annotated source: immediately_preceded_by
annotated property: UBPROP_0000001
annotated target: A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
source: SIO:000251

Axiom
annotated source: immediately_preceded_by
annotated property: has_exact_synonym
annotated target: is immediately preceded by
database_cross_reference: SIO:000251

immediately precedes
type: ObjectProperty
sub property of: precedes
IAO_0000117: David Osumi-Sutherland
IAO_0000118: ends_at_start_of
IAO_0000118: meets
RO_0002575: precedes
in subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

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

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

has component
type: ObjectProperty
sub property of: has part
IAO_0000114: IAO_0000125
definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
IAO_0000116: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
IAO_0000232: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO_0001900: RO_0001901
in subset: ro-eco

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
property chain axiom: part of
IAO_0000114: IAO_0000125
definition: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Melissa Haendel
IAO_0000117: Terry Meehan
database_cross_reference: RO:0002202
has OBO namespace: uberon
id: develops_from
shorthand: develops_from
comment: This is the transitive form of the develops from relation
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
IAO_0000114: IAO_0000125
definition: inverse of develops from
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Terry Meehan
database_cross_reference: RO:0002203
has OBO namespace: uberon
id: develops_into
in subset: RO_0002259
shorthand: develops_into
label: develops into

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: directly regulates
IAO_0000114: IAO_0000125
definition: process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
IAO_0000116: We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
IAO_0000117: Chris Mungall
IAO_0000117: David Hill
IAO_0000117: Tanya Berardini
IAO_0000119: causal-relations
IAO_0000119: GO
IAO_0000232: Regulation precludes parthood; the regulatory process may not be within the regulated process.
IAO_0000589: regulates (processual)
IAO_0000600: false

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
definition: Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: negatively regulates (process to process)
RO_0004050: regulates

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
definition: Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: positively regulates (process to process)
RO_0004049: regulates

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
IAO_0000112: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
IAO_0000112: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
IAO_0000117: Chris Mungall
IAO_0000118: has function realized in
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20123131
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/21208450
IAO_0000232: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
IAO_0000424: RO_0000053 some (RO_0000054 only ?Y)
in subset: ro-eco

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
IAO_0000117: Chris Mungall
IAO_0000118: has function in
IAO_0000424: RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))

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

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
IAO_0000114: IAO_0000125
IAO_0000117: Chris Mungall
IAO_0000119: Allen's interval algebra
IAO_0000232: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

starts
type: ObjectProperty
sub property of: part of
inverse of: starts with
definition: Relation between occurrents, shares a start boundary with.
database_cross_reference: RO:0002223
has OBO namespace: uberon
id: starts
shorthand: starts

Axiom
annotated source: starts
annotated property: definition
annotated target: Relation between occurrents, shares a start boundary with.
database_cross_reference: https://orcid.org/0000-0002-6601-2165
database_cross_reference: Allen:starts

starts with
type: ObjectProperty
sub property of: has part
type: TransitiveProperty
database_cross_reference: RO:0002224
has OBO namespace: uberon
id: starts_with
shorthand: starts_with

ends
type: ObjectProperty
sub property of: part of
definition: Relation between occurrents, shares an end boundary with.
database_cross_reference: RO:0002229
has_exact_synonym: finishes
has OBO namespace: uberon
id: ends
shorthand: ends

Axiom
annotated source: ends
annotated property: definition
annotated target: Relation between occurrents, shares an end boundary with.
database_cross_reference: https://orcid.org/0000-0002-6601-2165
database_cross_reference: Allen:starts
database_cross_reference: ZFS:finishes

ends with
type: ObjectProperty
sub property of: has part
type: TransitiveProperty
database_cross_reference: RO:0002230
has OBO namespace: uberon
id: ends_with
shorthand: ends_with

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
range: material entity
IAO_0000114: IAO_0000125
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
IAO_0000117: Chris Mungall
IAO_0000118: consumes
in subset: ro-eco

has developmental contribution from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally_contributes_to
type: TransitiveProperty
domain: anatomical entity
range: anatomical entity
property chain axiom: has part
property chain axiom: develops_from
IAO_0000112: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
IAO_0000114: IAO_0000125
definition: x has developmental contribution from y iff x has some part z such that z develops from y
IAO_0000117: Chris Mungall
database_cross_reference: RO:0002254
has OBO namespace: uberon
id: has_developmental_contribution_from
shorthand: has_developmental_contribution_from

developmentally_contributes_to
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to
property chain axiom: develops_into
property chain axiom: part of
IAO_0000114: IAO_0000125
definition: inverse of has developmental contribution from
IAO_0000117: Chris Mungall
database_cross_reference: RO:0002255
has OBO namespace: uberon
id: developmentally_contributes_to
in subset: RO_0002259
shorthand: developmentally_contributes_to
label: developmentally contributes to

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: continuant
range: continuant
IAO_0000114: IAO_0000125
definition: Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
IAO_0000116: false
IAO_0000117: Chris Mungall
IAO_0000232: In general you should not use this relation to make assertions - use one of the more specific relations below this one
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from

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

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

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

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
RO_0004049: causally upstream of
creator: cjm
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
RO_0004050: causally upstream of
creator: cjm
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

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

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
IAO_0000112: a particular instances of akt-2 enables some instance of protein kinase activity
IAO_0000117: Chris Mungall
IAO_0000118: catalyzes
IAO_0000118: executes
IAO_0000118: has
IAO_0000118: is catalyzing
IAO_0000118: is executing
IAO_0000232: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
IAO_0000232: This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
IAO_0000117: Chris Mungall
IAO_0000232: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
IAO_0000117: Chris Mungall
IAO_0000118: false

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

involved in
type: ObjectProperty
sub property of: participates in
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: part of
definition: c involved_in p if and only if c enables some process p', and p' is part of p
IAO_0000117: Chris Mungall
IAO_0000118: actively involved in
IAO_0000118: enables part of

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
definition: inverse of enables
IAO_0000117: Chris Mungall

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

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

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

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

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: anatomical entity
range: anatomical entity
IAO_0000114: IAO_0000428
definition: x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
IAO_0000117: Chris Mungall

has potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
definition: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
IAO_0000117: Chris Mungall
database_cross_reference: RO:0002385
has OBO namespace: uberon
id: has_potential_to_developmentally_contribute_to
shorthand: has_potential_to_developmentally_contribute_to

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
IAO_0000117: Chris Mungall
database_cross_reference: RO:0002387
has OBO namespace: uberon
id: has_potential_to_develop_into
shorthand: has_potential_to_develop_into

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
IAO_0000114: IAO_0000428
definition: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
IAO_0000117: Chris Mungall

causally downstream of
type: ObjectProperty
sub property of: preceded_by
sub property of: causally downstream of or within
inverse of: causally upstream of
IAO_0000114: IAO_0000428
definition: inverse of upstream of
IAO_0000117: Chris Mungall

immediately causally downstream of
type: ObjectProperty
sub property of: immediately_preceded_by
sub property of: causally downstream of
inverse of: immediately causally upstream of
IAO_0000114: IAO_0000428
IAO_0000117: Chris Mungall

causally related to
type: ObjectProperty
IAO_0000114: IAO_0000428
definition: This relation groups causal relations between material entities and causal relations between processes
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 yiel…
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
IAO_0000114: IAO_0000428
definition: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
IAO_0000117: Chris Mungall

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
IAO_0000114: IAO_0000428
definition: p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
IAO_0000117: Chris Mungall
RO_0002575: causally upstream of

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
definition: p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
IAO_0000116: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
IAO_0000117: Chris Mungall
IAO_0000118: influences (processual)
has related synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
in subset: RO_0002259

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' regulates some p
IAO_0000117: Chris Mungall

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
IAO_0000117: Chris Mungall
RO_0004049: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
IAO_0000117: Chris Mungall
RO_0004050: involved in regulation of

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
definition: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
IAO_0000116: OWL does not allow defining object properties via a Union
IAO_0000117: Chris Mungall
IAO_0000118: involved in or reguates

is active in
type: ObjectProperty
sub property of: overlaps
sub property of: functionally related to
property chain axiom: enables
property chain axiom: occurs in
IAO_0000112: A protein that enables activity in a cytosol.
definition: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
IAO_0000117: Chris Mungall
IAO_0000118: executes activity in
has_exact_synonym: enables activity in

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

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

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

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
definition: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
IAO_0000117: Chris Mungall
IAO_0000118: binds
IAO_0000118: molecularly binds with

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: Chris Mungall
IAO_0000118: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
has_exact_synonym: molecularly controls

directly negatively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000118: directly inhibits
has_exact_synonym: molecularly decreases activity of

directly positively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000118: directly activates
has_exact_synonym: molecularly increases activity of

helper property (not for use in curation)
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000232: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.

has part that occurs in
type: ObjectProperty
domain: occurrent
range: independent continuant
property chain axiom: has part
property chain axiom: occurs in
definition: p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
IAO_0000117: Chris Mungall
in subset: ro-eco

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

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

relation between physical entity and a process or stage
type: ObjectProperty
domain: independent continuant
domain: Class
  union of: material anatomical entity
  union of: immaterial anatomical entity
range: occurrent
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.

existence starts during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence starts during or after
property chain axiom: part of
definition: Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
definition: x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
IAO_0000117: Chris Mungall
database_cross_reference: RO:0002488
has_exact_synonym: begins_to_exist_during
has OBO namespace: uberon
id: RO:0002488
id: existence_starts_during
shorthand: existence_starts_during

Axiom
annotated source: existence starts during
annotated property: definition
annotated target: Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

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

existence ends during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence ends during or before
property chain axiom: part of
definition: Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
definition: x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
IAO_0000117: Chris Mungall
database_cross_reference: RO:0002492
has_exact_synonym: ceases_to_exist_during
has OBO namespace: uberon
id: RO:0002492
id: existence_ends_during
shorthand: existence_ends_during
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

Axiom
annotated source: existence ends during
annotated property: definition
annotated target: Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

existence starts during or after
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: developmentally preceded by
property chain axiom: preceded_by
definition: x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
IAO_0000117: Chris Mungall
database_cross_reference: RO:0002496
has OBO namespace: uberon
id: existence_starts_during_or_after
shorthand: existence_starts_during_or_after
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends during or before
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: developmentally succeeded by
property chain axiom: precedes
definition: x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
IAO_0000117: Chris Mungall
database_cross_reference: RO:0002497
has OBO namespace: uberon
id: existence_ends_during_or_before
shorthand: existence_ends_during_or_before
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

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

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

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

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: causally influenced by (entity-centric)

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)
IAO_0000117: Chris Mungall

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

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

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: Process(P1) directly regulates process(P2) 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.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: directly regulates (processual)
RO_0002575: regulates

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has part
property chain axiom: capable of
IAO_0000112: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
IAO_0000117: Chris Mungall

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

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

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

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

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

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: Process(P1) directly postively regulates process(P2) 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 P1 directly positively regulates P2.
IAO_0000119: causal-relations
IAO_0000589: directly positively regulates (process to process)
RO_0004049: directly regulates

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: Process(P1) directly negatively regulates process(P2) 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 P1 directly negatively regulates P2.
IAO_0000119: causal-relations
IAO_0000589: directly negatively regulates (process to process)
RO_0004050: directly 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: cjm
creation date: 2018-01-25T23:20:13Z

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
RO_0004049: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:30Z

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
RO_0004050: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:51Z

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
definition: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
RO_0004049: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:14Z

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
definition: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
RO_0004050: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:22Z

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

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

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

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

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

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

continuant
type: Class
subclass of: entity
subclass of: Restriction
  on property: part of
  all values from: continuant
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO_0000179: continuant
BFO_0000180: Continuant
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
IAO_0000116: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
IAO_0000116: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
IAO_0000600: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
IAO_0000601: if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
IAO_0000601: if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
IAO_0000601: if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
IAO_0000602: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
IAO_0000602: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
IAO_0000602: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
IAO_0000602: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: IAO_0000116
annotated target: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: IAO_0000600
annotated target: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: IAO_0000601
annotated target: if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: IAO_0000601
annotated target: if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: IAO_0000601
annotated target: if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/011-002

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

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

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

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

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

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: independent continuant
BFO_0000179: ic
BFO_0000180: IndependentContinuant
IAO_0000112: a chair
IAO_0000112: a heart
IAO_0000112: a leg
IAO_0000112: a molecule
IAO_0000112: a spatial region
IAO_0000112: an atom
IAO_0000112: an orchestra.
IAO_0000112: an organism
IAO_0000112: the bottom right portion of a human torso
IAO_0000112: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
IAO_0000601: For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
IAO_0000601: For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
IAO_0000602: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
IAO_0000602: (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
IAO_0000602: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: IAO_0000601
annotated target: For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: IAO_0000601
annotated target: For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/018-002

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

Axiom
annotated source: independent continuant
annotated property: IAO_0000602
annotated target: (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/018-002

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

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

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

Axiom
annotated source: material entity
annotated property: IAO_0000600
annotated target: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/019-002

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

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

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

Axiom
annotated source: material entity
annotated property: IAO_0000602
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: IAO_0000602
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/020-002

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

anatomical entity
type: Class
subclass of: biological entity
IAO_0000412: caro.owl

material anatomical entity
type: Class
subclass of: material entity
subclass of: anatomical entity
IAO_0000412: caro.owl

immaterial anatomical entity
type: Class
subclass of: immaterial entity

biological entity
type: Class
subclass of: independent continuant

root node
type: Class

life cycle period
type: Class

gametogenesis
type: Class
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: life cycle period
definition: Biological process during which certain cells of a female or male individual (parent) are transformed into specialized reproductive cells (gametes) that will initiate development of a progeny individual (offspring) upon fertilization.
has OBO namespace: ecao_developmental_stage

oogenesis period
type: Class
subclass of: Restriction
  on property: part of
  some values from: gametogenesis
definition: Period during which female gametes (or oocytes, or eggs) develop and mature from primordial female germ cells to generate cells competent to further development upon fertilization by a mature spermatozoid.
has_exact_synonym: ovogenesis period
has OBO namespace: ecao_developmental_stage

previtellogenic primary oocyte stage
type: Class
subclass of: Restriction
  on property: part of
  some values from: oogenesis period
definition: A female gamete that is small in size, i.e. about 10??m in diameter, and that is at the previtellogenic stage.
has OBO namespace: ecao_developmental_stage

not fully grown oocyte stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: oogenesis period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: previtellogenic primary oocyte stage
definition: A developing female gamete that started growing in size by accumulation of yolk proteins. At this stage, it is characterized by the presence of a large nucleus, the germinal vesicle, which contains a prominent nucleolus and occupies most of the cytoplasm.
has OBO namespace: ecao_developmental_stage

fully grown oocyte with centered germinal vesicle stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: oogenesis period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: not fully grown oocyte stage
definition: A developing female gamete that has reached its full size. It has grown up to ten times its original size, i.e. 80 to 100??m. It also displays a large germinal vesicle that is centered, but it is still not competent for fertilization.
has OBO namespace: ecao_developmental_stage

fully grown oocyte with off-centered germinal vesicle stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: oogenesis period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: fully grown oocyte with centered germinal vesicle stage
definition: A developing female gamete that has reached its full size and in which the germinal vesicle has moved asymmetrically to the cell periphery. The germinal vesicle is now close to the animal pole.
has_exact_synonym: primary oocyte
has OBO namespace: ecao_developmental_stage

fully grown oocyte with no nucleus stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: oogenesis period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: fully grown oocyte with off-centered germinal vesicle stage
definition: A developing female gamete in which the germinal vesicle has broken down. The germinal vesicle is no longer visible. However, the female gamete is still not mature. It is undergoing meiotic maturation, extruding successively a first and a second polar body.
has OBO namespace: ecao_developmental_stage

mature oocyte stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: oogenesis period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: fully grown oocyte with no nucleus stage
definition: A mature female gamete that has achieved its meiotic maturation and in which the female pronucleus is visible. The mature oocyte is arrested in G1 phase and its average size is 80 to 100 µm. It is surrounded by a transparent jelly coat that is about 30 µm thick. It is competent to fertilization and it is located in the female gonad where it may be stored for weeks to months before its release in sea water by spawning. In the P. lividus species, the mature female gametes are characterized by the presence of pigment granules concentrated in a subequatorial band. This band is classically called the pigment band and allows to visualize the first embryonic axis, i.e. the animal-vegetal axis, which is perpendicular to the band.
has_exact_synonym: spawned egg
has_exact_synonym: unfertilized egg
has OBO namespace: ecao_developmental_stage

spermatogenesis period
type: Class
subclass of: Restriction
  on property: part of
  some values from: gametogenesis
definition: Period during which male gametes (or spermatozoa, or spermatozoid) develop and mature from primordial male germ cells to generate cells competent to further development upon fertilization of a mature oocyte.
has OBO namespace: ecao_developmental_stage

developing spermatozoa stage
type: Class
subclass of: Restriction
  on property: part of
  some values from: spermatogenesis period
definition: A developing, immature male gamete undergoing mitosis and meiosis to ultimately produce mature spermatozoa.
has_exact_synonym: spermatid
has OBO namespace: ecao_developmental_stage

mature spermatozoid stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: spermatogenesis period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: developing spermatozoa stage
definition: A mature male gamete that is composed of a head, encompassing a compact nucleus, a neck, a middle piece, and a tail (or flagellum) that propels it towards the oocyte upon spawning.
has_exact_synonym: spermatozoa
has_exact_synonym: sperm
has OBO namespace: ecao_developmental_stage

embryogenesis
type: Class
subclass of: occurrent
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: life cycle period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: gametogenesis
definition: Biological process during which the embryo forms. This process starts with the fertilization of a mature oocyte by a mature spermatozoid. It is characterized by a succession of rapid mitotic divisions with no significant growth, but with axis establishment and cellular differentiation, thereby leading to the development of a multicellular embryo.
has OBO namespace: ecao_developmental_stage

1-cell stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: embryogenesis
definition: A fertilized egg, right after fertilization. The embryo is characterized morphologically by the fact that it is a single diploid cell surrounded by a fertilization envelope. This stage corresponds to an embryo of age 0 hour post-fertilization.
database_cross_reference: UBERON:0000106
has_exact_synonym: fertilized egg
has_exact_synonym: zygote stage
has OBO namespace: ecao_developmental_stage

cleavage period
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: embryogenesis
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: 1-cell stage
definition: Period during which the fertilized egg undergoes a succession of rapid cell divisions with no significant growth.
database_cross_reference: UBERON:0000107
has OBO namespace: ecao_developmental_stage

2-cell stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: cleavage period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: 1-cell stage
definition: An embryo that is composed of two cells and is surrounded by a fertilization envelope. The first cleavage plane took place meridionally (i.e. along the animal-vegetal axis), thereby generating two blastomeres of equal size, each containing both animal and vegetal cytoplasm.
database_cross_reference: UBERON:0007232
has_exact_synonym: 2c
has OBO namespace: ecao_developmental_stage

4-cell stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: cleavage period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: 2-cell stage
definition: An embryo that is composed of four cells and is surrounded by a fertilization envelope. The second cleavage plane was meridional and perpendicular to the first one, thereby producing four blastomeres of equal size, each containing both animal and vegetal cytoplasm.
database_cross_reference: UBERON:0007233
has_exact_synonym: 4c
has OBO namespace: ecao_developmental_stage

8-cell stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: cleavage period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: 4-cell stage
definition: An embryo that is composed of eight cells and is surrounded by a fertilization envelope. The third cleavage took place perpendicular to the first two cleavage planes and was equatorial. It thus generated an animal and a vegetal hemisphere each composed of a quartet of four cells of equal volume.
database_cross_reference: UBERON:0007236
has_exact_synonym: 8c
has OBO namespace: ecao_developmental_stage

16-cell stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: cleavage period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: 8-cell stage
definition: An embryo that is composed of 16 cells and is surrounded by a fertilization envelope. Note for euechinoid indirect developers: although the fourth cleavage occurred simultaneously in all cells, the pattern of cell division differed in the animal and vegetal blastomeres. In the animal hemisphere the four cells divided meridionally, producing eight blastomeres of equal volume arrayed in a single tier. These cells are called the mesomeres. In the vegetal hemisphere, the four cells underwent an unequal, equatorial cleavage, producing a tier of four large cells, the macromeres, and a tier of four small cells, the micromeres, located at the vegetal pole. At the 16-cell stage, the embryo is hence composed of three groups of cells with distinct sizes. In most sea urchin species,this is the first morphological indication of the animal-vegetal axis.
has_exact_synonym: 16c
has OBO namespace: ecao_developmental_stage

28-cell stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: cleavage period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: 16-cell stage
definition: An embryo that is composed of 28 cells and is surrounded by a fertilization envelope. Note for euechinoid indirect developers: In most sea urchin species, the fifth cleavage signed the end of cell division synchrony, with the mesomeres and macromeres dividing prior to the micromeres with a significant time difference. In the animal hemisphere, the mesomeres underwent an equal and equatorial cleavage, giving rise to two animal cell tiers, each composed of eight blastomeres of equal size: the an1 tier located at the animal pole and the an2 tier located below an1. In parallel, the macromeres divided meridionally, forming a ring of eight cells of equal volume located below the an2 tier. At that stage, the micromeres have not yet divided and are still at a number of four cells.
has_exact_synonym: 28c
has OBO namespace: ecao_developmental_stage

32-cell stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: cleavage period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: 28-cell stage
definition: An embryo that is composed of 32 cells and is surrounded by a fertilization envelope. Note for euechinoid indirect developers: The micromeres have undergone a fifth cleavage (and this has occurred prior to a subsequent division of the other cells). This cleavage was unequal and equatorial, thereby producing four large micromeres and four small micromeres, the smallest cells still marking the vegetal pole.
has_exact_synonym: 32c
has OBO namespace: ecao_developmental_stage

56-cell stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: cleavage period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: 32-cell stage
definition: An embryo that is composed of 56 cells and is surrounded by a fertilization envelope. Note for euechinoid indirect developers: In the animal hemisphere, cells of the an1 and an2 tiers underwent an additional meridional division, producing tiers composed of 16 cells. The macromeres divided equatorially and equally, generating two vegetal cell tiers, each composed of 8 cells of equal volume, namely the veg1 tier (located below an2) and the veg2 tier (located below veg1 and above the large micromeres). At that stage, the large and small micromeres (4 cells each) have not undergone yet a sixth division.
has_exact_synonym: 56c
has OBO namespace: ecao_developmental_stage

60-cell stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: cleavage period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: 56-cell stage
definition: An embryo that is composed of 60 cells and is surrounded by a fertilization envelope. Note for euechinoid indirect developers: The large micromeres have achieved a sixth cleavage, which was meridional, thereby generating a ring of 8 cells. At that stage, from the animal to the vegetal pole, the embryo is composed of: 16 an1-cells, 16 an2-cells, 8 veg1-cells, 8 veg2-cells, 8 large micromeres and 4 small micromeres.
has_exact_synonym: 60c
has OBO namespace: ecao_developmental_stage

blastula period
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: embryogenesis
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: cleavage period
definition: Period during which the embryo is transformed into a hollow sphere that is one cell layer thick and encompasses a central, fluid-filled cavity called the blastocoel. During this period, every cell of the embryo is in contact on the inside with the blastocoel and on the outside with the hyaline layer.
database_cross_reference: UBERON:0000307
has OBO namespace: ecao_developmental_stage

very early blastula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: blastula period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: 60-cell stage
definition: The embryo is composed of 110-120 cells, as most blastomeres have completed an additional mitotic division after the 60-cell stage. The embryo is surrounded by a fertilization envelope. All cells are about the same size and there are no obvious morphological indications of embryonic polarity or embryonic territories. All cells have begun to acquire apico-basal polarity, and the embryo is beginning to transform into a hollow sphere with a wall that is one cell layer thick and a fluid-filled cavity (the blastocoel) in the center. Note for euechinoid indirect developers: the micromere progeny divide more slowly than other cells of the embryo. Molecular labelling typically indicates the presence of 8 large micromere descendants and 4 small micromeres at this stage .
has_exact_synonym: 120-cell stage
has_exact_synonym: B1
has_exact_synonym: vEB
has OBO namespace: ecao_developmental_stage

early blastula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: blastula period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: very early blastula stage
definition: The embryo is composed of slightly more than 200 cells, as most blastomeres have completed an additional mitotic division after the very early blastula stage. The embryo is surrounded by a fertilization envelope. The embryo remains spherical and one cell layer thick, and the blastocoel has expanded slightly since the very early blastula stage, without increasing though the size of the embryo. The synchrony of cell divisions between animal and vegetal cell tiers, as well as within cell tiers, is becoming less pronounced. Note for euechinoid indirect developers: Molecular labeling typically indicates the presence of 16 large micromere descendants and 4 small micromeres at this stage .
has_exact_synonym: B2
has_exact_synonym: EB
has OBO namespace: ecao_developmental_stage

mid-blastula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: blastula period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: early blastula stage
definition: The embryo is composed of about 300 cells and is surrounded by a fertilization envelope. Cell divisions are less synchronous than at earlier stages. The cells have flattened slightly on their inner (basal) surface, further contributing to the enlargement of the blastocoel. In some species, cells have started to form cilia on their outer surface. The embryo is still spherical and does not display any obvious morphological landmarks that indicate the primary or secondary embryonic axes. Note for euechinoid indirect developers: molecular labeling typically indicates the presence of 16 to 32 large micromere descendant cells and 4 to 8 small micromere descendants at this stage .
has_exact_synonym: B3
has_exact_synonym: midB
has_exact_synonym: mid-B
has OBO namespace: ecao_developmental_stage

late blastula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: blastula period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: mid-blastula stage
definition: The embryo is composed of about 400 cells and is surrounded by a fertilization envelope. The embryo is still spherical but the wall is thinner and smoother than at previous stages. The vegetal plate has not formed. Many cells are ciliated, and in some species (e.g. P. lividus) the embryo has begun to rotate within the fertilization envelope, while in others (e.g. S. purpuratus) it is still non-motile. Note for euechinoid indirect developers: molecular labeling typically indicates the presence of 32 large micromere descendants and 4 to 8 small micromere descendants at this stage .
has_exact_synonym: B4
has_exact_synonym: LB
has_exact_synonym: pre-HB
has_exact_synonym: prehatched blastula
has_exact_synonym: Late-B
has OBO namespace: ecao_developmental_stage

hatched blastula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: blastula period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: late blastula stage
definition: The embryo is composed of about 800 cells and is surrounded by a fertilization envelope. The fertilization envelope has started to break down due to the secretion by ectodermal cells of the hatching enzyme, a metalloprotease that digests the fertilization envelope and frees the embryo. The vegetal plate has not formed. The embryo rotates within the envelope or swims away as soon as it is free. At the animal pole, a tuft of long and immotile cilia has started growing.
has_exact_synonym: B5
has_exact_synonym: very late blastula stage
has_exact_synonym: HB
has OBO namespace: ecao_developmental_stage

swimming blastula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: blastula period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: hatched blastula stage
definition: The embryo has hatched from the fertilization envelope and swims freely. It is still a hollow sphere that is one cell layer thick, but the cells constituting the vegetal plate (i.e. located at the vegetal pole) have started thickening along the apico-basal axis, thereby creating a morphological landmark that enables orienting the embryo along the animal-vegetal axis. In addition, at the animal pole, the apical tuft composed of long and immotile cilia has continued expending.
has_exact_synonym: SB
has OBO namespace: ecao_developmental_stage

late swimming blastula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: blastula period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: swimming blastula stage
definition: The embryo has started elongated along the animal-vegetal axis. Its vegetal region has further continued to thicken and it is marked by a characteristic 'V' shape formed by the blastocoel at the level of the cells constituting the vegetal plate, thereby pointing to the vegetal pole. At the animal pole, the embryo is characterized by the presence of an apical tuft.
has_exact_synonym: late-SB
has OBO namespace: ecao_developmental_stage

gastrula period
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: embryogenesis
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: blastula period
definition: Period during which complex and coordinated cellular movements take place and ultimately generate a three-layered embryo with inner tissues. A portion of cells will ingress, invaginate and/or migrate within the embryo and form the two inner layers (i.e. the endoderm and the mesoderm). The cells that remained outside will instead spread over the whole surface of the embryo and form the outer layer (i.e. the ectoderm).
database_cross_reference: UBERON:0000109
has OBO namespace: ecao_developmental_stage

mesenchyme blastula phase
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: gastrula period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: blastula period
definition: The phase during which skeletogenic primary mesenchyme cells (PMCs) move from the vegetal plate into the blastocoel (ingress) but before the vegetal plate has started to invaginate.
has OBO namespace: ecao_developmental_stage

early mesenchyme blastula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: blastula period
definition: The vegetal plate is apparent and skeletogenic primary mesenchyme cells (PMCs) are in the process of ingression, a type of epithelial–mesenchymal transition (EMT). The epithelial wall of the embryo has thickened at the animal pole, where a tuft of long, non-motile cilia has formed.
has_exact_synonym: eMB
has OBO namespace: ecao_developmental_stage

mid-mesenchyme blastula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: early mesenchyme blastula stage
definition: All skeletogenic primary mesenchyme cells (PMCs) have ingressed into the blastocoel, leaving behind a reformed vegetal plate containing at its center the 8 small micromere descendants surrounded by non-skeletogenic mesoderm cells. The PMCs are organized in a mound on the vegetal plate but have not begun to disperse. The thickened apical pole domain with its tuft of long, non-motile cilia is still apparent.
has_exact_synonym: mid-MB
has OBO namespace: ecao_developmental_stage

late mesenchyme blastula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: mid-mesenchyme blastula stage
definition: The skeletogenic primary mesenchyme cells (PMCs) have migrated away from the vegetal plate by extending filopodia and moving along the blastocoel wall. The vegetal plate has flattened but has not started to invaginate. The apical pole domain still bears an apical tuft of long, non-motile cilia.
has OBO namespace: ecao_developmental_stage

invagination phase
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: gastrula period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: mesenchyme blastula phase
definition: Period during which the inpocketing and elongation of the archenteron takes place.
has OBO namespace: ecao_developmental_stage

blastopore formation stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: invagination phase
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: late mesenchyme blastula stage
definition: The embryo is characterized morphologically by a slight invagination of the vegetal plate and the dispersal of the skeletogenic primary mesenchyme cells (PMCs) along the blastocoel wall at the periphery of the invaginating region. The PMCs are just beginning to adopt a characteristic, ring-like arrangement near the equator of the embryo. Within the vegetal plate, the peripheral non-skeletogenic mesoderm cells have started to indent, undergoing important cell shape changes, but the center of the vegetal plate (composed of small micromeres) has not started to elevate. Invagination has generated the blastopore (an opening that will give rise to the larval anus) as well as the anterior portion of the archenteron (a region that will give rise to the coelomic pouches). At the animal pole, the apical pole domain is still marked by an enlarged epithelium bearing long and immotile cilia.
has_exact_synonym: blastopore gastrula stage
has_exact_synonym: blasto-G
has OBO namespace: ecao_developmental_stage

early gastrula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: invagination phase
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: blastopore formation stage
definition: The embryo is mainly characterized morphologically by the presence in the blastocoel of a small archenteron (i.e. primitive digestive tract) that is about a third of its finally size. Following the initial invagination of the vegetal plate, the archenteron has slightly been extended, within the blastocoel, by the subsequent invagination of additional non-skeletogenic mesoderm cells and of some endoderm cells. In parallel, the skeletogenic mesenchyme cells (or SM cells, primary mesenchyme cells or PMC) have by now started migrating along the blastocoel wall, towards the animal pole, thereby creating two lateral chains (one left and one right), while around the developing archenteron, they have gathered into two ventrolateral clusters separated by an oral (or ventral) and an aboral (or dorsal) chain defined by the remaining skeletogenic mesenchyme cells. Within the oral and aboral skeletogenic mesenchyme chains, the cells have further started to fuse to form syncytial filopodial cables within which skeletal calcification will subsequently take place. At the animal pole, the animal neuroectoderm territory is still marked by an enlarged epithelium bearing long and immotile cilia.
has_exact_synonym: EG
has_exact_synonym: eG
has OBO namespace: ecao_developmental_stage

mid-gastrula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: invagination phase
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: early gastrula stage
definition: The embryo is mainly characterized morphologically by the presence of an archenteron (i.e. primitive digestive tract) that has reached one-half its way into the blastocoel. A second phase of archenteron elongation has taken place by invagination of additional cells into the blastocoel, by cell division or by convergent-extension movements depending on the sea urchin species. Non-skeletogenic mesoderm cells that are present at the tip of the archenteron have further started ingressing into the blastocoel, generating the non-skeletogenic mesenchyme cells (or NSM cells, secondary mesenchyme cells or SMC). The oral ectoderm has also started to flatten and to become thicker, providing the first morphological indicator of the oral-aboral (or ventro-dorsal) axis of the embryo. As a consequence the oral chain formed by a portion of the skeletogenic mesenchyme cells has also flattened. Finally, skeletal calcification has further begun within the skeletogenic mesenchyme ventrolateral clusters, marked by the presence of the first calcified structures, which appear as small dots at that stage. At the animal pole, the animal neuroectoderm territory is still marked by an enlarged epithelium bearing long and immotile cilia.
has_exact_synonym: mid-G
has_exact_synonym: G
has OBO namespace: ecao_developmental_stage

late gastrula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: invagination phase
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: mid-gastrula stage
definition: The embryo is mainly characterized morphologically by the presence in the blastocoel of a fully extended archenteron (i.e. primitive digestive tract) that has now reached the roof of the blastocoel. The third and last extension phase of the archenteron has been ensured by pulling forces exerted by non-skeletogenic mesoderm cells that are still present at the tip of the archenteron. These cells have produced filopodia that extended towards the animal pole, attached the wall, and then shortened, thereby pulling up the archenteron. In some sea urchin species, this pulling force is already orienting the tip of the archenteron towards the oral ectoderm, where the future mouth of the larvae will form. In parallel, in the blastocoel, additional non-skeletogenic mesoderm cells continued ingressing from the tip of the archenteron and the skeletal calcified structures present in the skeletogenic mesenchyme ventrolateral clusters have further grown, forming now the primary triradiate skeletal rudiments (or spicules). At the animal pole, the animal neuroectoderm territory is still marked by an enlarged epithelium bearing long and immotile cilia.
has_exact_synonym: late-G
has_exact_synonym: LG
has OBO namespace: ecao_developmental_stage

organogenesis period
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: embryogenesis
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: gastrula period
definition: To be written
has OBO namespace: ecao_developmental_stage

prism stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: organogenesis period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: late gastrula stage
definition: The embryo is mainly characterized morphologically by a typical triangular shape, the beginning of the tripatition of the digestive tract and the presence of pigmented cells. The oral (or ventral) ectoderm has by now even more flattened, making an almost perfect right angle with the blastoporal side of the embryo. By contrast, on the opposite side, the aboral (or dorsal) ectoderm has round up and slightly elongated, thereby forming the primitive apex of the future larvae. These changes have conferred the embryo a typical and easy recognizable triangular shape. In the oral ectoderm, a small depression has further appeared, called the stomodeum, which will later fuse with the tip of the archenteron to form the mouth. In the blastocoel, the digestive tract has also by now bended toward the stomodeum and started to become tripartite. The cardiac sphincter has started forming, separating the future esophagus from the future stomach. The triradiate spicules have also continued elongating, thereby forming by now, towards the animal pole, the right and left dorsoventral connecting rods, towards the apex, the body rods, and along the vegetal, oral ectoderm the left and right ventral transverse rods. Moreover, some non-skeletogenic mesenchyme cells (or NSM cells, secondary mesenchyme cells or SMC) have started becoming pigmented and inserted into the aboral ectoderm. These cells represent part of the future immune system of the larvae along with other blastocoelar cells that are present in the blastocoel around the gut. In the vicinity of the future esophagus, other non-skeletogenic mesoderm descendant cells along with some endoderm cells have further arranged to form a single unpaired coelomic pouch. At the animal pole, the apical pole domain has also started to flatten making the embryo look like a square when viewed from the oral side, and it still arbors a tuft a long and immotile cilia. Finally, within the apical pole domain, but not yet in the ciliary band, molecular la…
has_exact_synonym: D
has_exact_synonym: Pr
has OBO namespace: ecao_developmental_stage

larval development
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: life cycle period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: embryogenesis
has OBO namespace: ecao_developmental_stage

early feeding larva period
type: Class
subclass of: occurrent
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: larval development
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: organogenesis period
definition: Biological process during which the specific outcome is the progression of a free-living larva before the development of the adult. Indirect development represents the mainstream developmental mode of metazoans. This process usually starts with the emergence of a larva that is planktonic and stops at the end of metamorphosis once the animal assumes adult characters.
database_cross_reference: UBERON:0000069
has OBO namespace: ecao_developmental_stage

early pluteus larva stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: early feeding larva period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: prism stage
definition: The embryo is by now a fully formed pluteus larva. The mouth has opened and the digestive tract is becoming functional. On the ventral side, the mouth is surrounded anteriorly by an oral hood and posteriorly by two postoral arms. On the dorsal side, the apex has lengthened. The skeleton has indeed continued extending, expending the dorsoventral connecting rods, the body rods, and the ventral transverse rods as well as developing the anterolateral rods and the postoral rods. Within the larva, the tripartition of the digestive tract has further progressed. The cardiac sphincter is now fully formed in between the esophagus and the stomach, and the pyloric sphincter in between the stomach and the intestine and the anal sphincter at the level of the anus have also started forming. Around the esophagus, the coelomic pouch has further developed into two bilobed sacs (or pouches), one on each side of the digestive tract. Finally, within the apical pole domain, as well as within the ciliary band, differentiated neurons with their extended axons can also now be distinguished by immunostaining. In parallel, the apical tuft of long and immotile cilia remains discernable at the tip of the oral hood, while in parallel the ciliary band has further started growing a concentrated number of intermediate size motile cilia, which will be used by the larva to swim directionally.
database_cross_reference: UBERON:0008265
has_exact_synonym: 2-arm pluteus stage
has_exact_synonym: early pluteus stage
has_exact_synonym: Eplut
has OBO namespace: ecao_developmental_stage

4-arm pluteus larva stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: early feeding larva period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: early pluteus larva stage
definition: The 4-arm pluteus larva is mainly characterized morphologically by the presence, on the ventral side, of four extended arms (two anterolateral arms at the level of the oral hood and two postoral arms) and on the dorsal side by a sleeked apex. The larva now possesses a completely tripartite and functional digestive tract composed of an esophagus, a stomach, and an intestine, respectively limited by a cardiac sphincter, a pyloric sphincter, and an anal sphincter. Around the esophagus, the right and left coelomic pouches have further started to grow in size and elongate. The first morphological indicator of a left-right asymmetry becomes apparent at that stage, the left coelomic pouch being slightly more elongated than the right one. Furthermore, a thin protrusion of non-skeletogenic mesenchyme cells can be seen extending from the left coelomic pouch to the anterior ectoderm. This is the primary pore canal, which opens to the exterior environment by the hydropore. The larva further now possesses, all around the esophagus, a network of contractile muscles allowing it to swallow and feed. Finally, the apical tuft previously observed at the animal pole has by now disappeared, leaving behind only the concentrated stretch of intermediate size cilia borne by the ciliary band.
database_cross_reference: UBERON:0008265
has_exact_synonym: P
has_exact_synonym: Plut
has_exact_synonym: Plut4a
has_exact_synonym: pluteus larva
has_exact_synonym: Pluteus
has OBO namespace: ecao_developmental_stage

late feeding larva period
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: larval development
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: early feeding larva period
definition: To be written
has OBO namespace: ecao_developmental_stage

6-arm pluteus larva stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: late feeding larva period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: 4-arm pluteus larva stage
definition: The 6-arm pluteus larva is mainly characterized morphologically by the presence, on the ventral side, of six arms, and by the development, on the anterior midline of the esophagus, of the dorsal arch. The larva has indeed extended on the ventral side two additional posterodorsal arms and has developed on the anterior side an additional skeletal element called the dorsal arch. In addition, at the basis of the postoral and posterodorsal arms, four small patches of ciliary band have by now cut off and migrated toward the apex, forming four patches of ciliated structures called the epaulettes (one posterior and one anterior pair). The nervous system of the larva has also become more complex with cell bodies and axons being present all along the arms and for the latter as well throughout the apex. The left and right coelomic pouches have continued to elongate on each side of the digestive tract. As a note this stage is relatively fleeting.
database_cross_reference: UBERON:0008265
has_exact_synonym: Plut6a
has OBO namespace: ecao_developmental_stage

8-arm pluteus larva stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: late feeding larva period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: 6-arm pluteus larva stage
definition: The 8-arm pluteus larva is mainly characterized morphologically by the presence on the ventral side of the larva of eight arms and by the development within the larva, on the left side of the stomach, of the adult rudiment. This stage is relatively long. It includes distinct changes occurring to the larva as well as within the larva, although the larva consistently exhibits 8 arms. In addition, it should be highlighted that the sequence of events taking place at the level of the larva compared to that occurring on the left side of the stomach to form the rudiment are heterochronic, meaning that differences are observed among individuals in the relative timing of these events. From the larval point of view, at that stage, on the anterior side, the dorsal arch has extended out of the oral hood, thereby forming two additional arms above the mouth, i.e. the preoral arms. In parallel, across the apex, the epaulettes have continued developing, thereby generating four large structures rich in cilia and perpendicular to the ventro-dorsal axis. At the tip of the apex, the suture of the body rods has also eventually ruptured, considerably enlarging the larval apex and reducing the angle between the postoral and posterodorsal arms. In parallel, inside the larva, the left coelomic pouch has also by now been partitioned into three parts: the axocoel (upper part, close to the esophagus), the hydrocoel (middle part) and the somatocoel (lower part, next to the stomach). Likewise, on the opposite side, the right coelomic pouch has also been partitioned into a right axohydrocoel and a right somatocoel, although the right axohydrocoel remains in a rudimentary state compared to its left counterparts. In addition, at the basis of the posterodorsal arm on the left side, a small portion of the ectoderm has thickened, invaginated, and came into contact with the left hydocoel. This structure is called the vestibule and together with the left hydrocoel and the left stomatocoel they have furt…
database_cross_reference: UBERON:0008265
has_exact_synonym: Plut8a
has OBO namespace: ecao_developmental_stage

competent pluteus larva stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: late feeding larva period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: 8-arm pluteus larva stage
definition: The competent pluteus larva is mainly characterized morphologically by the presence, on the ventral size, of still 8 arms and by the presence on the left side of the stomach of the rudiment that is now the size of or even bigger than the stomach. The rudiment further harbors by now five long primary podia (i.e. tube feet), five quartets of definitive spines located between the primary podia and five pairs of immature spines at the basis of the primary podia, while on the opposite side, i.e. on the right side of the larva, five to seven immature spines have further developed, supported by the genital plates, along with one to four pedicaellariae. At the level of the larva, in parallel, the anterior and posterior pairs of epaulettes have also considerably increased in size by now and even fused dorsally to the hydropore and to the anus respectively, thereby leaving exempt of cilia two lateral fields in between them. At the center of the left lateral field, the vestibular roof has also by now ruptured and this opening has created the vestibular pore, through which some primary podia of the rudiment protrude outside the larva and scrutinize the substrate looking for the adequate cues to begin metamorphosis. At that stage, the larva is thus exhibiting a typical substrate-test behavior, going to the sea bottom and scrutinizing the substrate. This behavior is characteristic of a larva named competent to metamorphosis, which it will accomplish providing that it is adequately stimulated by environmental factors.
database_cross_reference: UBERON:0008265
has_exact_synonym: Cpt8a
has_exact_synonym: cPlut
has OBO namespace: ecao_developmental_stage

metamorphic larva stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: late feeding larva period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: competent pluteus larva stage
definition: The metamorphic larva stage consists essentially of the evagination of the echinoid rudiment. It is characterized by the execution of conspicuous and relatively abrupt physical changes that take place quite quickly, in about one hour, and during which the planktonic larva is transformed into a benthic juvenile. At that stage, the larva is settled on the substrate and is firmly attached to it by the primary podia of the rudiment. The ectodermal epithelium of its arms has started to collapse, making the spicules supporting the larval arms piercing through the epidermis. The larval mouth and anus have further closed, while in parallel, within the larva, the rudiment spines have lifted up thereby distending the vestibular wall and wide opening the vestibular pore. Following these movements, the rudiment has farther down accomplished and finalized its complete eversion, encapsulating the digestive tract and reaching the right side of the larval body. During this process, the genital plates and the associated pedicellariae and immature spines present on the right side of the larva have further completed the production of the aboral part of the adult body. At the end of metamorphosis, hence at the end of the metamorphic larva stage, the individual has thus become benthic, it is settled in the substrate, and it looks like an adult pentaradial sea urchin although it is smaller in size, deprived of a functional digestive system and sexually immature.
has_exact_synonym: meta
has_exact_synonym: metamorphosis
has OBO namespace: ecao_developmental_stage

adulthood
type: Class
subclass of: occurrent
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: life cycle period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: larval development
definition: Biological process during which changes occur in biological and psychological domains to generate a sexually mature animal.
has OBO namespace: ecao_developmental_stage

juvenile period
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: adulthood
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: metamorphic larva stage
definition: Period during which a young individual, posing as a small adult, grows but remains unable to reproduce.
database_cross_reference: UBERON:0034919
has OBO namespace: ecao_developmental_stage

early juvenile stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: juvenile period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: metamorphic larva stage
definition: The early juvenile is morphologically similar to both the late rudiment and a miniature sea urchin adult. Like the rudiment, it harbors five primary podia (or tube feet), five quartet of definitive spines, five pairs of immature spines located at the basis of the primary podia, 5 to 7 immature spines supported by the genital plates as well as 1 to 4 pedicellariae. Like the adult, it displays a pentarial symmetry and is settled on the substrate. An early juvenile is about 300 µm in diameter. On its aboral side, it still exhibits some remaining larval rods and tissues, although these will soon disappear. In addition, the plates forming its endoskeleton are still rather light and porous making it looking relatively clear, although it bears lots of red-pigmented cells. However, the postlarva is still deprived of a mouth and an anus, hence of a functional digestive tract. The early juvenile is thus endotrophic, meaning that its growth and development solely relies on energy derived from internal sources. Furthermore, the early juvenile is sexually immature.
database_cross_reference: UBERON:0007021
has_exact_synonym: endotrophic juvenile
has_exact_synonym: postlarva
has_exact_synonym: PLJuv
has OBO namespace: ecao_developmental_stage

late juvenile stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: juvenile period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: early juvenile stage
definition: The late juvenile really looks like a small adult. The plates of its endoskeleton have by now densified providing it with a dark shell. In addition, it has finally developed a functional digestive tract. The digestive tract inherited from the larva has indeed by now undergone a complete reorganization, progressively bending within the perivisceral cavity to form two successive loops. The buccal plates and the aristotle lantern have further finished developing, creating a new mouth that has opened on the oral side at the center of the aristotle's lantern, while a new anus has also opened in the periproct, i.e. at the center of the five genital plates. The late juvenile can thus feed and starts growing in size, by grazing on the substrate. The late juvenile is exotrophic, meaning that its growth and development rely on energy derived from external sources. In addition, the primary podia have started to regress by that stage and will eventually disappear, while secondary podia have emerged and are functional, allowing the juvenile to move. Similarly, the immature spines have also started to be lost and be replaced by definitive spines. The genital plate CD has further differentiated into the madreporite and sphaeridia have formed. However, this individual is still sexually immature.
database_cross_reference: UBERON:0007021
has_exact_synonym: ExJuv
has OBO namespace: ecao_developmental_stage

adult period
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: adulthood
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: juvenile period
definition: Period during which the animal reaches sexual maturity.
database_cross_reference: UBERON:0000066
has OBO namespace: ecao_developmental_stage

adult stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: adult period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: late juvenile stage
definition: This stage corresponds to a fully formed pentaradial sea urchin that has reached sexual maturity. The gonads have developed within the perivisceral cavity and are connected to the outside by the genital pores pierced into the genital plates. The young adult has grown up to about several centimeters in diameter and is now producing gametes. Time after fertilization is unknown, between several months to one year depending on the sea urchin species and the rate and type of feeding.
database_cross_reference: UBERON:0000113
has_exact_synonym: gravid sea urchin
has_exact_synonym: sexual mature sea urchin
has OBO namespace: ecao_developmental_stage

very late blastula stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: blastula period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: late blastula stage
definition: The embryo is composed of about 800 cells and is surrounded by a fertilization envelope. The wall of the embryo is thinner and smoother than at previous stages. The vegetal plate has not formed. Many cells are ciliated but the embryo has not begun to rotate within the fertilization envelope. Note for euechinoid indirect developers: molecular labeling typically indicates the presence of 32 large micromere descendants and 4 small micromere descendants at this stage.
has_exact_synonym: vLB
has OBO namespace: ecao_developmental_stage

vegetal plate stage
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  some values from: blastula period
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: very late blastula stage
definition: Stage when the vegetal plate is apparent but primary mesenchyme cells (PMCs) have not started to ingress. Embryos are motile due ciliary beating but have not completed hatching.
has_exact_synonym: VP
has OBO namespace: ecao_developmental_stage

echinoderm anatomy
type: Class
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.
database_cross_reference: UBERON:0001062
has OBO namespace: echinoderm_anatomy

anatomical structure
type: Class
subclass of: Restriction
  on property: part of
  some values from: echinoderm anatomy
definition: Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome
database_cross_reference: UBERON:0000061
has OBO namespace: echinoderm_anatomy

anatomical system
type: Class
subclass of: Restriction
  on property: part of
  some values from: echinoderm anatomy
definition: A system that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity. Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function
database_cross_reference: UBERON:0000467
has_exact_synonym: body system
has_exact_synonym: connected anatomical system
has_exact_synonym: organ system
has OBO namespace: echinoderm_anatomy

anatomical region
type: Class
subclass of: Restriction
  on property: part of
  some values from: echinoderm anatomy
definition: A region of the whole organism without well-defined compartmental boundaries
database_cross_reference: UBERON:0000475
has_exact_synonym: organism subdivision
has OBO namespace: echinoderm_anatomy

anatomical space
type: Class
subclass of: Restriction
  on property: part of
  some values from: echinoderm anatomy
database_cross_reference: UBERON:0000464
has OBO namespace: echinoderm_anatomy

whole organism
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: existence starts during
  some values from: previtellogenic primary oocyte stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
definition: Anatomical structure that is an individual member of a species and consists of one cell or more
has OBO namespace: echinoderm_anatomy

multicellular organism
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: 2-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
definition: Anatomical structure that is an individual member of a species and consists of more than one cell
database_cross_reference: UBERON:0000468
has OBO namespace: echinoderm_anatomy

embryo
type: Class
subclass of: multicellular organism
subclass of: Restriction
  on property: existence starts during
  some values from: 1-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
definition: Anatomical entity that comprises the animal in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems
database_cross_reference: UBERON:0000922
has OBO namespace: echinoderm_anatomy

larva
type: Class
subclass of: anatomical entity
subclass of: multicellular organism
subclass of: Restriction
  on property: develops_from
  some values from: embryo
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
database_cross_reference: UBERON:0002548
has OBO namespace: echinoderm_anatomy

juvenile
type: Class
subclass of: anatomical entity
subclass of: multicellular organism
subclass of: Restriction
  on property: develops_from
  some values from: larva
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
database_cross_reference: UBERON:0034919
has OBO namespace: echinoderm_anatomy

adult
type: Class
subclass of: anatomical entity
subclass of: multicellular organism
subclass of: Restriction
  on property: develops_from
  some values from: juvenile
subclass of: Restriction
  on property: existence starts during
  some values from: adult stage
database_cross_reference: UBERON:0007023
has OBO namespace: echinoderm_anatomy

digestive system
type: Class
subclass of: independent continuant
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: blastopore formation stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
definition: Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
database_cross_reference: UBERON:0001007
has OBO namespace: echinoderm_anatomy

embryonic digestive system
type: Class
subclass of: digestive system
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
definition: The gastrointestinal tract that is being formed during embryonic development starting with the formation of the primitive gut tube (or archenteron)
has OBO namespace: echinoderm_anatomy

larval digestive system
type: Class
subclass of: anatomical entity
subclass of: digestive system
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: develops_from
  some values from: embryonic digestive system
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
definition: Organ system responsible for the food uptake and processing in the larva
has OBO namespace: echinoderm_anatomy

juvenile digestive system
type: Class
subclass of: anatomical entity
subclass of: digestive system
subclass of: Restriction
  on property: part of
  some values from: juvenile
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
has OBO namespace: echinoderm_anatomy

adult digestive system
type: Class
subclass of: anatomical entity
subclass of: digestive system
subclass of: Restriction
  on property: part of
  some values from: adult
subclass of: Restriction
  on property: develops_from
  some values from: juvenile digestive system
subclass of: Restriction
  on property: existence starts during
  some values from: adult stage
definition: Anatomical system that processes ingested substances in the adult
has OBO namespace: echinoderm_anatomy

immune system
type: Class
subclass of: independent continuant
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: late gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0002405
has OBO namespace: echinoderm_anatomy

embryonic immune system
type: Class
subclass of: immune system
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has OBO namespace: echinoderm_anatomy

larval immune system
type: Class
subclass of: anatomical entity
subclass of: immune system
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has OBO namespace: echinoderm_anatomy

juvenile immune system
type: Class
subclass of: anatomical entity
subclass of: immune system
subclass of: Restriction
  on property: part of
  some values from: juvenile
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
has OBO namespace: echinoderm_anatomy

adult immune system
type: Class
subclass of: anatomical entity
subclass of: immune system
subclass of: Restriction
  on property: part of
  some values from: adult
subclass of: Restriction
  on property: existence starts during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

reproductive system
type: Class
subclass of: independent continuant
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
definition: Anatomical system that has as its parts the organs concerned with reproduction, i.e. the male and female gonads.
database_cross_reference: UBERON:0000990
has OBO namespace: echinoderm_anatomy

nervous system
type: Class
subclass of: independent continuant
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0001016
has OBO namespace: echinoderm_anatomy

embryonic nervous system
type: Class
subclass of: nervous system
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
definition: The sum of all the structures in the embryo that will develop into the larval nervous system
has OBO namespace: echinoderm_anatomy

larval nervous system
type: Class
subclass of: anatomical entity
subclass of: nervous system
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: develops_from
  some values from: embryonic nervous system
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
definition: The sum of all the neural structures present in the larva
has OBO namespace: echinoderm_anatomy

juvenile nervous system
type: Class
subclass of: anatomical entity
subclass of: nervous system
subclass of: Restriction
  on property: part of
  some values from: juvenile
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
has OBO namespace: echinoderm_anatomy

adult nervous system
type: Class
subclass of: anatomical entity
subclass of: nervous system
subclass of: Restriction
  on property: part of
  some values from: adult
subclass of: Restriction
  on property: develops_from
  some values from: juvenile nervous system
subclass of: Restriction
  on property: existence starts during
  some values from: adult stage
database_cross_reference: UBERON:6003559
has OBO namespace: echinoderm_anatomy

muscular system
type: Class
subclass of: independent continuant
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0000383
has OBO namespace: echinoderm_anatomy

larval muscular system
type: Class
subclass of: anatomical entity
subclass of: muscular system
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has OBO namespace: echinoderm_anatomy

juvenile muscular system
type: Class
subclass of: anatomical entity
subclass of: muscular system
subclass of: Restriction
  on property: part of
  some values from: juvenile
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
has OBO namespace: echinoderm_anatomy

adult muscular system
type: Class
subclass of: anatomical entity
subclass of: muscular system
subclass of: Restriction
  on property: part of
  some values from: adult
subclass of: Restriction
  on property: develops_from
  some values from: juvenile muscular system
subclass of: Restriction
  on property: existence starts during
  some values from: adult stage
database_cross_reference: UBERON:6003218
has OBO namespace: echinoderm_anatomy

endoskeleton
type: Class
subclass of: independent continuant
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
definition: Internal support structure of an animal composed of mineralized tissue. It gives shape, support and protection to the body.
database_cross_reference: UBERON:0001434
has OBO namespace: echinoderm_anatomy

embryonic endoskeleton
type: Class
subclass of: endoskeleton
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has OBO namespace: echinoderm_anatomy

larval endoskeleton
type: Class
subclass of: anatomical entity
subclass of: endoskeleton
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has OBO namespace: echinoderm_anatomy

rudiment endoskeleton
type: Class
subclass of: anatomical entity
subclass of: endoskeleton
subclass of: Restriction
  on property: part of
  some values from: rudiment
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has_exact_synonym: skeletal rudiment
has OBO namespace: echinoderm_anatomy

juvenile endoskeleton
type: Class
subclass of: anatomical entity
subclass of: endoskeleton
subclass of: Restriction
  on property: part of
  some values from: juvenile
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
has OBO namespace: echinoderm_anatomy

adult endoskeleton
type: Class
subclass of: anatomical entity
subclass of: endoskeleton
subclass of: Restriction
  on property: part of
  some values from: adult
subclass of: Restriction
  on property: existence starts during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

water vascular system
type: Class
subclass of: independent continuant
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
definition: The water vascular system is a hydraulic system used by sea urchins for locomotion, food and waste transportation, and respiration. The system is composed of canals connecting numerous tube feet.
database_cross_reference: UBERON:0008251
has OBO namespace: echinoderm_anatomy

hemal system
type: Class
subclass of: independent continuant
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
definition: The hemal system contains the blood. It is composed of a complex network of vessels mainly located around the gut.
has_exact_synonym: haemal system
has OBO namespace: echinoderm_anatomy

animal hemisphere
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: mature oocyte stage
subclass of: Restriction
  on property: existence ends during
  some values from: vegetal plate stage
definition: Anatomical region that corresponds to the upper half of the embryo, which later is composed of the mesomeres, and ultimately encompasses the presumptive ectoderm
database_cross_reference: UBERON:0012284
has_exact_synonym: upper half
has_exact_synonym: upper hemisphere
has_exact_synonym: animal half
has OBO namespace: echinoderm_anatomy

vegetal hemisphere
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: mature oocyte stage
subclass of: Restriction
  on property: existence ends during
  some values from: vegetal plate stage
definition: Anatomical region that corresponds to the lower half of the embryo, which later is composed of the macromeres and the micromeres, and ultimately encompasses the endoderm and mesoderm
database_cross_reference: UBERON:0012285
has_exact_synonym: lower half
has_exact_synonym: lower hemisphere
has_exact_synonym: vegetal half
has OBO namespace: echinoderm_anatomy

cell cortex
type: Class
subclass of: cell part
subclass of: Restriction
  on property: existence starts during
  some values from: mature oocyte stage
has OBO namespace: echinoderm_anatomy

cleavage furrow
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: existence starts during
  some values from: 1-cell stage
has OBO namespace: echinoderm_anatomy

animal cortex
type: Class
subclass of: cell cortex
subclass of: Restriction
  on property: part of
  some values from: animal hemisphere
subclass of: Restriction
  on property: existence starts during
  some values from: fully grown oocyte with centered germinal vesicle stage
subclass of: Restriction
  on property: existence ends during
  some values from: 1-cell stage
definition: Cell component comprising the outermost layer of the animal region of the oocyte. It consists of a phospholipid bilayer and associated proteins
has OBO namespace: echinoderm_anatomy

vegetal cortex
type: Class
subclass of: cell cortex
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: existence starts during
  some values from: fully grown oocyte with centered germinal vesicle stage
subclass of: Restriction
  on property: existence ends during
  some values from: 1-cell stage
definition: Cell component comprising the outermost layer of the vegetal region of the oocyte. It consists of a phospholipid bilayer and associated proteins
has OBO namespace: echinoderm_anatomy

animal pole
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: fully grown oocyte with centered germinal vesicle stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
definition: The apical region of the animal hemisphere
has OBO namespace: echinoderm_anatomy

vegetal pole
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: fully grown oocyte with centered germinal vesicle stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
definition: The apical most region of the vegetal hemisphere. Once cleavages have started the vegetal pole is characterized by the presence of the micromeres initially and then that of the small micromeres
has OBO namespace: echinoderm_anatomy

animal pole domain
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: existence starts during
  some values from: very early blastula stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has_exact_synonym: animal plate
has_exact_synonym: anterior neuroectoderm
has_exact_synonym: apical plate
has_exact_synonym: neurogenic ectoderm
has_exact_synonym: apical pole domain
has OBO namespace: echinoderm_anatomy

blastopore
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: embryonic digestive system
subclass of: Restriction
  on property: existence starts during
  some values from: blastopore formation stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
database_cross_reference: UBERON:0000100
has OBO namespace: echinoderm_anatomy

blastopore lip
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: blastopore
subclass of: Restriction
  on property: existence starts during
  some values from: blastopore formation stage
database_cross_reference: UBERON:3010455
has OBO namespace: echinoderm_anatomy

bottle cell
type: Class
subclass of: embryonic cell
subclass of: Restriction
  on property: part of
  some values from: vegetal plate
subclass of: Restriction
  on property: existence starts during
  some values from: blastopore formation stage
subclass of: Restriction
  on property: existence ends during
  some values from: blastopore formation stage
has OBO namespace: echinoderm_anatomy

embryonic cell
type: Class
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: existence starts during
  some values from: 2-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has OBO namespace: echinoderm_anatomy

vegetal plate
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: existence starts during
  some values from: vegetal plate stage
subclass of: Restriction
  on property: existence ends during
  some values from: late mesenchyme blastula stage
has OBO namespace: echinoderm_anatomy

cell
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: existence starts during
  some values from: previtellogenic primary oocyte stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
definition: Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane
has OBO namespace: echinoderm_anatomy

cell part
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: cell
subclass of: Restriction
  on property: existence starts during
  some values from: previtellogenic primary oocyte stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
definition: Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher.
has OBO namespace: echinoderm_anatomy

digestive system element
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: digestive system
subclass of: Restriction
  on property: existence starts during
  some values from: blastopore formation stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
definition: Any of the organs or elements that are part of the digestive system
database_cross_reference: UBERON:0013765
has OBO namespace: echinoderm_anatomy

skeletal element
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: endoskeleton
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0004765
has OBO namespace: echinoderm_anatomy

embryonic structure
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: existence starts during
  some values from: 1-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
definition: Any anatomical structure that is part of an embryo
database_cross_reference: UBERON:0002050
has OBO namespace: echinoderm_anatomy

larval structure
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
definition: Any anatomical structure that is part of a larva
has OBO namespace: echinoderm_anatomy

juvenile structure
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: juvenile
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
definition: Any anatomical structure that is part of a juvenile
has OBO namespace: echinoderm_anatomy

adult structure
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: adult
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
definition: Any anatomical structure that is part of an adult
has OBO namespace: echinoderm_anatomy

tissue
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: multicellular organism
subclass of: Restriction
  on property: existence starts during
  some values from: 60-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0000479
has OBO namespace: echinoderm_anatomy

rudiment
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has_exact_synonym: imaginal adult rudiment
has_exact_synonym: adult rudiment
has OBO namespace: echinoderm_anatomy

rudiment structure
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: rudiment
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has OBO namespace: echinoderm_anatomy

non-rudiment adult structure
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has OBO namespace: echinoderm_anatomy

intracellular part
type: Class
subclass of: cell part
has OBO namespace: echinoderm_anatomy

cytoskeleton
type: Class
subclass of: intracellular part
has OBO namespace: echinoderm_anatomy

microtubule
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: part of
  some values from: cytoskeleton
has OBO namespace: echinoderm_anatomy

nucleus
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: existence starts during
  some values from: mature oocyte stage
definition: A membrane-bounded organelle of in which chromosomes are housed and replicated. In most cells, it contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some specialized cell types, RNA metabolism or DNA replication may be absent
has OBO namespace: echinoderm_anatomy

oocyte
type: Class
subclass of: gamete
subclass of: Restriction
  on property: existence starts during
  some values from: oogenesis period
subclass of: Restriction
  on property: existence ends during
  some values from: oogenesis period
definition: A female haploid germ cell.
has OBO namespace: echinoderm_anatomy

germinal vesicle
type: Class
subclass of: anatomical entity
subclass of: nucleus
subclass of: Restriction
  on property: part of
  some values from: oocyte
subclass of: Restriction
  on property: existence starts during
  some values from: not fully grown oocyte stage
subclass of: Restriction
  on property: existence ends during
  some values from: fully grown oocyte with off-centered germinal vesicle stage
definition: The enlarged, fluid filled nucleus of a primary oocyte, the development of which is suspended in prophase I of the first meiotic division between embryohood and sexual maturity
has OBO namespace: echinoderm_anatomy

equatorial pigment band
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: existence starts during
  some values from: fully grown oocyte with centered germinal vesicle stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
definition: The subequatorial accumulation of pigment granules (the so-called ‘pigment band’) in eggs or early stage embryos, which constitutes an unambiguous marker of animal-vegetal polarity
has_exact_synonym: pigmented band
has_exact_synonym: pigment band
has OBO namespace: echinoderm_anatomy

cytoplasm
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: existence starts during
  some values from: not fully grown oocyte stage
definition: All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures
has OBO namespace: echinoderm_anatomy

centrosome
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: existence starts during
  some values from: fully grown oocyte with off-centered germinal vesicle stage
has OBO namespace: echinoderm_anatomy

mitotic spindle
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: existence starts during
  some values from: 1-cell stage
has OBO namespace: echinoderm_anatomy

meiotic spindle
type: Class
subclass of: anatomical entity
subclass of: intracellular part
subclass of: Restriction
  on property: part of
  some values from: oocyte
subclass of: Restriction
  on property: existence starts during
  some values from: fully grown oocyte with off-centered germinal vesicle stage
subclass of: Restriction
  on property: existence ends during
  some values from: fully grown oocyte with off-centered germinal vesicle stage
has OBO namespace: echinoderm_anatomy

fertilization envelope
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: existence ends during
  some values from: late blastula stage
definition: A structure that lies outside the plasma membrane and surrounds the egg. The fertilization envelope forms from the vitelline membrane after fertilization as a result of cortical granule release
has_exact_synonym: fertilization membrane
has OBO namespace: echinoderm_anatomy

spermatozoid
type: Class
subclass of: gamete
subclass of: Restriction
  on property: existence starts during
  some values from: spermatogenesis period
subclass of: Restriction
  on property: existence ends during
  some values from: spermatogenesis period
definition: A mature male germ cell
has_exact_synonym: male gamete
has_exact_synonym: mature sperm cell
has_exact_synonym: spermatozoa
has_exact_synonym: spermatozoan
has_exact_synonym: sperm
has OBO namespace: echinoderm_anatomy

aster
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: part of
  some values from: cytoskeleton
subclass of: Restriction
  on property: existence starts during
  some values from: fully grown oocyte with off-centered germinal vesicle stage
has_exact_synonym: mitotic aster
has_exact_synonym: spindle aster
has OBO namespace: echinoderm_anatomy

sperm aster
type: Class
subclass of: anatomical entity
subclass of: aster
subclass of: Restriction
  on property: part of
  some values from: spermatozoid
subclass of: Restriction
  on property: existence starts during
  some values from: mature spermatozoid stage
subclass of: Restriction
  on property: existence ends during
  some values from: mature spermatozoid stage
has_exact_synonym: spermatozoid aster
has OBO namespace: echinoderm_anatomy

acellular membrane
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: existence starts during
  some values from: mature oocyte stage
subclass of: Restriction
  on property: existence ends during
  some values from: mature oocyte stage
database_cross_reference: UBERON:0005764
has OBO namespace: echinoderm_anatomy

vitelline membrane
type: Class
subclass of: anatomical entity
subclass of: acellular membrane
subclass of: Restriction
  on property: part of
  some values from: oocyte
database_cross_reference: UBERON:0003125
has_exact_synonym: vitelline envelope
has_exact_synonym: vitelline layer
has OBO namespace: echinoderm_anatomy

hyaline layer
type: Class
subclass of: acellular membrane
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: existence starts during
  some values from: 1-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has_exact_synonym: hyaline membrane
has OBO namespace: echinoderm_anatomy

microvillus
type: Class
subclass of: cell part
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: 1-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: 1-cell stage
has OBO namespace: echinoderm_anatomy

apical lamina
type: Class
subclass of: acellular membrane
subclass of: Restriction
  on property: part of
  some values from: hyaline layer
subclass of: Restriction
  on property: existence starts during
  some values from: 1-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has_exact_synonym: fibropellin layer
has OBO namespace: echinoderm_anatomy

secretory vesicle
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: 1-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: 1-cell stage
has OBO namespace: echinoderm_anatomy

cilium
type: Class
subclass of: cell part
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: vegetal plate stage
has OBO namespace: echinoderm_anatomy

filopodium
type: Class
subclass of: cell part
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: existence starts during
  some values from: early mesenchyme blastula stage
subclass of: Restriction
  on property: existence ends during
  some values from: late gastrula stage
has OBO namespace: echinoderm_anatomy

basal lamina
type: Class
subclass of: acellular membrane
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence ends during
  some values from: 4-arm pluteus larva stage
database_cross_reference: UBERON:0000482
has OBO namespace: echinoderm_anatomy

basal laminar vesicle
type: Class
subclass of: secretory vesicle
subclass of: Restriction
  on property: existence starts during
  some values from: mature oocyte stage
subclass of: Restriction
  on property: existence ends during
  some values from: 4-arm pluteus larva stage
has_exact_synonym: basal vesicle
has_exact_synonym: basal lamina vesicle
has OBO namespace: echinoderm_anatomy

apical vesicle
type: Class
subclass of: secretory vesicle
subclass of: Restriction
  on property: existence starts during
  some values from: mature oocyte stage
has OBO namespace: echinoderm_anatomy

cortical granule
type: Class
subclass of: secretory vesicle
subclass of: Restriction
  on property: existence starts during
  some values from: mature oocyte stage
has_exact_synonym: cortical vesicle
has OBO namespace: echinoderm_anatomy

echinonectin vesicle
type: Class
subclass of: secretory vesicle
subclass of: Restriction
  on property: existence starts during
  some values from: mature oocyte stage
has_exact_synonym: echinonectin granule
has_exact_synonym: nectosome
has OBO namespace: echinoderm_anatomy

mitochondrion
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: part of
  some values from: whole organism
has OBO namespace: echinoderm_anatomy

actin cytoskeleton
type: Class
subclass of: cytoskeleton
has OBO namespace: echinoderm_anatomy

actin filament
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: part of
  some values from: actin cytoskeleton
has_exact_synonym: F-actin filament
has_exact_synonym: microfilament
has OBO namespace: echinoderm_anatomy

nuclear part
type: Class
subclass of: intracellular part
subclass of: Restriction
  on property: part of
  some values from: nucleus
subclass of: Restriction
  on property: existence starts during
  some values from: mature oocyte stage
has OBO namespace: echinoderm_anatomy

nucleoplasm
type: Class
subclass of: nuclear part
has OBO namespace: echinoderm_anatomy

nuclear envelope
type: Class
subclass of: nuclear part
has OBO namespace: echinoderm_anatomy

endoplasmic reticulum
type: Class
subclass of: intracellular part
has OBO namespace: echinoderm_anatomy

spermatozoid entry point
type: Class
subclass of: cell part
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: mature oocyte stage
subclass of: Restriction
  on property: existence ends during
  some values from: 1-cell stage
has OBO namespace: echinoderm_anatomy

plasma membrane
type: Class
subclass of: cell part
subclass of: Restriction
  on property: part of
  some values from: whole organism
has_exact_synonym: cell membrane
has OBO namespace: echinoderm_anatomy

polar body
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: oocyte
subclass of: Restriction
  on property: existence starts during
  some values from: fully grown oocyte with off-centered germinal vesicle stage
subclass of: Restriction
  on property: existence ends during
  some values from: fully grown oocyte with no nucleus stage
definition: A small cell formed by the meiotic division of an oocyte
has OBO namespace: echinoderm_anatomy

spermatozoid part
type: Class
subclass of: anatomical entity
subclass of: cell part
subclass of: Restriction
  on property: part of
  some values from: spermatozoid
subclass of: Restriction
  on property: existence starts during
  some values from: spermatogenesis period
subclass of: Restriction
  on property: existence ends during
  some values from: spermatogenesis period
has_exact_synonym: sperm part
has OBO namespace: echinoderm_anatomy

spermatozoid head
type: Class
subclass of: spermatozoid part
definition: The part of the late spermatid or spermatozoon that contains the nucleus and acrosome.
has OBO namespace: echinoderm_anatomy

spermatozoid flagellum
type: Class
subclass of: spermatozoid part
definition: A microtubule-based flagellum (or cilium) that is part of a sperm, a mature male germ cell that develops from a spermatid
has_exact_synonym: sperm tail
has OBO namespace: echinoderm_anatomy

acrosomal vesicle
type: Class
subclass of: anatomical entity
subclass of: secretory vesicle
subclass of: Restriction
  on property: part of
  some values from: spermatozoid head
subclass of: Restriction
  on property: existence starts during
  some values from: spermatogenesis period
subclass of: Restriction
  on property: existence ends during
  some values from: spermatogenesis period
definition: An organelle that develops over the anterior half of the head in the spermatozoa
has_exact_synonym: acrosome
has OBO namespace: echinoderm_anatomy

small micromere descendant cell
type: Class
subclass of: anatomical entity
subclass of: blastomere
subclass of: Restriction
  on property: develops_from
  some values from: small micromere
subclass of: Restriction
  on property: existence starts during
  some values from: very early blastula stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has_exact_synonym: presumptive primordial germ cell
has OBO namespace: echinoderm_anatomy

presumptive primordial germ cell
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: develops_from
  some values from: small micromere descendant cell
subclass of: Restriction
  on property: existence starts during
  some values from: 32-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has OBO namespace: echinoderm_anatomy

primordial germ cell
type: Class
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: reproductive system
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
has OBO namespace: echinoderm_anatomy

germ cell
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: reproductive system
subclass of: Restriction
  on property: develops_from
  some values from: primordial germ cell
subclass of: Restriction
  on property: existence starts during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

gamete
type: Class
subclass of: germ cell
subclass of: Restriction
  on property: existence starts during
  some values from: gametogenesis
subclass of: Restriction
  on property: existence ends during
  some values from: gametogenesis
has OBO namespace: echinoderm_anatomy

immature occyte
type: Class
subclass of: oocyte
subclass of: Restriction
  on property: part of
  some values from: primordial germ cell
subclass of: Restriction
  on property: existence ends during
  some values from: fully grown oocyte with no nucleus stage
has_exact_synonym: immature egg
has OBO namespace: echinoderm_anatomy

mature oocyte
type: Class
subclass of: oocyte
subclass of: Restriction
  on property: part of
  some values from: germ cell
subclass of: Restriction
  on property: develops_from
  some values from: immature occyte
subclass of: Restriction
  on property: existence starts during
  some values from: mature oocyte stage
subclass of: Restriction
  on property: existence ends during
  some values from: mature oocyte stage
definition: A mature female gamet that has entered meiosis.
has_exact_synonym: female gamete
has_exact_synonym: female germ cell
has_exact_synonym: unfertilized egg
has_exact_synonym: egg
has OBO namespace: echinoderm_anatomy

blastomere
type: Class
subclass of: embryonic cell
subclass of: Restriction
  on property: existence ends during
  some values from: 60-cell stage
definition: An undifferentiated cell produced by early cleavages of the fertilized egg (zygote)
has_exact_synonym: blastoderm cell
has OBO namespace: echinoderm_anatomy

blastomere of 2-cell embryo
type: Class
subclass of: blastomere
subclass of: Restriction
  on property: existence ends during
  some values from: 2-cell stage
has OBO namespace: echinoderm_anatomy

blastomere of 4-cell embryo
type: Class
subclass of: blastomere
subclass of: Restriction
  on property: existence starts during
  some values from: 4-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: 4-cell stage
has OBO namespace: echinoderm_anatomy

mesomere
type: Class
subclass of: blastomere
subclass of: Restriction
  on property: part of
  some values from: animal hemisphere
subclass of: Restriction
  on property: existence starts during
  some values from: 16-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: 16-cell stage
definition: Intermediate size blastomere forming the animal hemisphere of the cleaving embryo
has_exact_synonym: mesomeres
has OBO namespace: echinoderm_anatomy

macromere
type: Class
subclass of: blastomere
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: existence starts during
  some values from: 16-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: 16-cell stage
definition: Larger blastomere of the vegetal hemisphere of the cleaving embryo located below the equator
has_exact_synonym: macromeres
has OBO namespace: echinoderm_anatomy

cell tier
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: existence starts during
  some values from: 8-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: late blastula stage
has_exact_synonym: blastomere tier
has OBO namespace: echinoderm_anatomy

macromere daughter cell tier
type: Class
subclass of: cell tier
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: existence starts during
  some values from: 28-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: 32-cell stage
has OBO namespace: echinoderm_anatomy

micromere
type: Class
subclass of: blastomere
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: existence starts during
  some values from: 16-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: 28-cell stage
definition: Small blastomere of the vegetal hemisphere of the cleaving embryo located at to the vegetal pole
has_exact_synonym: micromeres
has OBO namespace: echinoderm_anatomy

large micromere
type: Class
subclass of: anatomical entity
subclass of: blastomere
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: develops_from
  some values from: micromere
subclass of: Restriction
  on property: existence starts during
  some values from: 32-cell stage
has OBO namespace: echinoderm_anatomy

large micromere descendant cell
type: Class
subclass of: anatomical entity
subclass of: blastomere
subclass of: Restriction
  on property: develops_from
  some values from: large micromere
subclass of: Restriction
  on property: existence starts during
  some values from: very early blastula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early mesenchyme blastula stage
has_exact_synonym: presumptive PMC
has_exact_synonym: presumptive primary mesenchyme cell
has_exact_synonym: presumptive skeletogenic mesenchyme cell
has_exact_synonym: large micromere progeny
has OBO namespace: echinoderm_anatomy

small micromere
type: Class
subclass of: anatomical entity
subclass of: blastomere
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: develops_from
  some values from: micromere
subclass of: Restriction
  on property: existence starts during
  some values from: 32-cell stage
has_exact_synonym: SM
has OBO namespace: echinoderm_anatomy

presumptive neuron
type: Class
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: nervous system
subclass of: Restriction
  on property: existence starts during
  some values from: late blastula stage
definition: A progenitor cell of the nervous system that will develop into a neuron
has_exact_synonym: neuronal progenitor cell
has OBO namespace: echinoderm_anatomy

animal pole domain presumptive neuron
type: Class
subclass of: presumptive neuron
subclass of: Restriction
  on property: part of
  some values from: embryonic nervous system
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has_exact_synonym: animal pole domain neuronal progenitor cell
has_exact_synonym: apical pole domain presumptive neuron
has OBO namespace: echinoderm_anatomy

ectoderm presumptive neuron
type: Class
subclass of: presumptive neuron
subclass of: Restriction
  on property: part of
  some values from: embryonic nervous system
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has_exact_synonym: ectoderm neuronal progenitor cell
has OBO namespace: echinoderm_anatomy

ciliary band presumptive neuron
type: Class
subclass of: presumptive neuron
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has_exact_synonym: ciliary band neuronal progenitor cell
has OBO namespace: echinoderm_anatomy

endoderm associated presumptive neuron
type: Class
subclass of: presumptive neuron
subclass of: Restriction
  on property: existence starts during
  some values from: prism stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has_exact_synonym: endoderm associated neuronal progenitor cell
has OBO namespace: echinoderm_anatomy

neuron
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: nervous system
subclass of: Restriction
  on property: develops_from
  some values from: presumptive neuron
subclass of: Restriction
  on property: existence starts during
  some values from: prism stage
has_exact_synonym: nerve cell
has OBO namespace: echinoderm_anatomy

larval neuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: larval nervous system
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

serotonergic neuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: develops_from
  some values from: animal pole domain presumptive neuron
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

synaptotagmin-B neuron
type: Class
subclass of: neuron
has OBO namespace: echinoderm_anatomy

dopaminergic neuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: develops_from
  some values from: ectoderm presumptive neuron
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has OBO namespace: echinoderm_anatomy

GABAergic neuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has OBO namespace: echinoderm_anatomy

sensory neuron
type: Class
subclass of: neuron
has_exact_synonym: sensory cell
has OBO namespace: echinoderm_anatomy

biopolar neuron
type: Class
subclass of: neuron
has OBO namespace: echinoderm_anatomy

multipolar neuron
type: Class
subclass of: neuron
has OBO namespace: echinoderm_anatomy

neural structure
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: nervous system
subclass of: Restriction
  on property: existence starts during
  some values from: prism stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has_exact_synonym: neuronal structure
has OBO namespace: echinoderm_anatomy

axon tract
type: Class
subclass of: neural structure
database_cross_reference: UBERON:0001018
has_exact_synonym: axon bundle
has_exact_synonym: axonal tract
has OBO namespace: echinoderm_anatomy

ciliary band neuron
type: Class
subclass of: larval neuron
subclass of: Restriction
  on property: develops_from
  some values from: ciliary band presumptive neuron
has_exact_synonym: peripheral neuron
has OBO namespace: echinoderm_anatomy

ectoderm
type: Class
subclass of: germ layer
subclass of: Restriction
  on property: existence starts during
  some values from: 60-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
definition: Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
database_cross_reference: UBERON:0000924
has OBO namespace: echinoderm_anatomy

presumptive ciliary band cell
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: develops_from
  some values from: ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: late blastula stage
subclass of: Restriction
  on property: existence ends during
  some values from: late gastrula stage
has OBO namespace: echinoderm_anatomy

endoderm associated neuron
type: Class
subclass of: larval neuron
subclass of: Restriction
  on property: develops_from
  some values from: endoderm associated presumptive neuron
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
has OBO namespace: echinoderm_anatomy

ganglion
type: Class
subclass of: neural structure
database_cross_reference: UBERON:0000045
has OBO namespace: echinoderm_anatomy

apical ganglion
type: Class
subclass of: anatomical entity
subclass of: ganglion
subclass of: Restriction
  on property: part of
  some values from: larval nervous system
subclass of: Restriction
  on property: develops_from
  some values from: animal pole domain
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has_exact_synonym: apical organ
has OBO namespace: echinoderm_anatomy

adult neuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: part of
  some values from: adult nervous system
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
has OBO namespace: echinoderm_anatomy

circumoral nerve ring
type: Class
subclass of: anatomical entity
subclass of: neural structure
subclass of: Restriction
  on property: part of
  some values from: adult nervous system
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
has OBO namespace: echinoderm_anatomy

enteric nerve plexus
type: Class
subclass of: anatomical entity
subclass of: neural structure
subclass of: Restriction
  on property: part of
  some values from: adult nervous system
subclass of: Restriction
  on property: existence starts during
  some values from: late juvenile stage
database_cross_reference: UBERON:0000429
has_exact_synonym: digestive nerve plexus
has_exact_synonym: enteric plexus
has OBO namespace: echinoderm_anatomy

radial nerve cord
type: Class
subclass of: anatomical entity
subclass of: neural structure
subclass of: Restriction
  on property: part of
  some values from: adult nervous system
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
has OBO namespace: echinoderm_anatomy

primary podia associated neuron
type: Class
subclass of: adult neuron
subclass of: Restriction
  on property: part of
  some values from: adult neuron
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
has OBO namespace: echinoderm_anatomy

secondary podia associated neuron
type: Class
subclass of: adult neuron
subclass of: Restriction
  on property: part of
  some values from: adult neuron
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
has OBO namespace: echinoderm_anatomy

definitive spine associated neuron
type: Class
subclass of: adult neuron
has OBO namespace: echinoderm_anatomy

pedicellaria associated neuron
type: Class
subclass of: adult neuron
has OBO namespace: echinoderm_anatomy

basiepidermal nerve plexus
type: Class
subclass of: anatomical entity
subclass of: neural structure
subclass of: Restriction
  on property: part of
  some values from: adult nervous system
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
has OBO namespace: echinoderm_anatomy

animal quartet
type: Class
subclass of: cell tier
subclass of: Restriction
  on property: part of
  some values from: animal hemisphere
subclass of: Restriction
  on property: existence ends during
  some values from: 8-cell stage
definition: Group of four cells of equal size forming the animal hemisphere of an eight-cell stage embryo
has OBO namespace: echinoderm_anatomy

vegetal quartet
type: Class
subclass of: cell tier
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: existence ends during
  some values from: 8-cell stage
definition: Group of four cells of equal size forming the vegetal hemisphere of an eight-cell stage embryo
has OBO namespace: echinoderm_anatomy

animal tier 1
type: Class
subclass of: anatomical entity
subclass of: cell tier
subclass of: Restriction
  on property: part of
  some values from: animal hemisphere
subclass of: Restriction
  on property: develops_from
  some values from: mesomere
subclass of: Restriction
  on property: existence starts during
  some values from: 28-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: 60-cell stage
has_exact_synonym: an1
has OBO namespace: echinoderm_anatomy

animal tier 2
type: Class
subclass of: anatomical entity
subclass of: cell tier
subclass of: Restriction
  on property: part of
  some values from: animal hemisphere
subclass of: Restriction
  on property: develops_from
  some values from: mesomere
subclass of: Restriction
  on property: existence starts during
  some values from: 28-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: 60-cell stage
has_exact_synonym: an2
has OBO namespace: echinoderm_anatomy

vegetal tier 1
type: Class
subclass of: anatomical entity
subclass of: cell tier
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: develops_from
  some values from: macromere
subclass of: Restriction
  on property: existence starts during
  some values from: 56-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: early blastula stage
has_exact_synonym: ectoendoderm
has_exact_synonym: veg1
has OBO namespace: echinoderm_anatomy

vegetal tier 2
type: Class
subclass of: anatomical entity
subclass of: cell tier
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: develops_from
  some values from: macromere
subclass of: Restriction
  on property: existence starts during
  some values from: 56-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: early blastula stage
has_exact_synonym: endomesoderm
has_exact_synonym: veg2
has OBO namespace: echinoderm_anatomy

vegetal tier 1 upper
type: Class
subclass of: anatomical entity
subclass of: cell tier
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: develops_from
  some values from: vegetal tier 1
subclass of: Restriction
  on property: existence starts during
  some values from: mid-blastula stage
has_exact_synonym: presumptive vegetal ectoderm
has_exact_synonym: veg1 upper
has_exact_synonym: veg1U
has OBO namespace: echinoderm_anatomy

vegetal tier 1 lower
type: Class
subclass of: anatomical entity
subclass of: cell tier
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: develops_from
  some values from: vegetal tier 1
subclass of: Restriction
  on property: existence starts during
  some values from: mid-blastula stage
has_exact_synonym: veg1 lower
has_exact_synonym: veg1L
has OBO namespace: echinoderm_anatomy

vegetal tier 2 upper
type: Class
subclass of: anatomical entity
subclass of: cell tier
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: develops_from
  some values from: vegetal tier 2
subclass of: Restriction
  on property: existence starts during
  some values from: mid-blastula stage
has_exact_synonym: veg2 upper
has_exact_synonym: veg2U
has OBO namespace: echinoderm_anatomy

vegetal tier 2 lower
type: Class
subclass of: anatomical entity
subclass of: cell tier
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: develops_from
  some values from: vegetal tier 2
subclass of: Restriction
  on property: existence starts during
  some values from: mid-blastula stage
has_exact_synonym: presumptive non-skeletogenic mesoderm
has_exact_synonym: veg2 lower
has_exact_synonym: veg2L
has OBO namespace: echinoderm_anatomy

germ layer
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: existence starts during
  some values from: early mesenchyme blastula stage
database_cross_reference: UBERON:0000923
has_exact_synonym: embryonic germ layer
has_exact_synonym: primary germ layer
has OBO namespace: echinoderm_anatomy

embryonic tissue
type: Class
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: existence starts during
  some values from: 16-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
database_cross_reference: UBERON:0005291
has OBO namespace: echinoderm_anatomy

presumptive ectoderm
type: Class
subclass of: anatomical entity
subclass of: embryonic tissue
subclass of: Restriction
  on property: part of
  some values from: animal hemisphere
subclass of: Restriction
  on property: develops_from
  some values from: mesomere
subclass of: Restriction
  on property: existence ends during
  some values from: vegetal plate stage
database_cross_reference: UBERON:0006601
has OBO namespace: echinoderm_anatomy

animal ectoderm
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: develops_from
  some values from: animal hemisphere
subclass of: Restriction
  on property: existence starts during
  some values from: 60-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: vegetal plate stage
has OBO namespace: echinoderm_anatomy

vegetal ectoderm
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: develops_from
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: existence starts during
  some values from: early blastula stage
subclass of: Restriction
  on property: existence ends during
  some values from: vegetal plate stage
has OBO namespace: echinoderm_anatomy

ventral ectoderm
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: 60-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has_exact_synonym: oral ectoderm
has OBO namespace: echinoderm_anatomy

dorsal ectoderm
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: 60-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has_exact_synonym: aboral ectoderm
has OBO namespace: echinoderm_anatomy

ectoendoderm
type: Class
subclass of: anatomical entity
subclass of: germ layer
subclass of: Restriction
  on property: develops_from
  some values from: vegetal tier 1
subclass of: Restriction
  on property: existence starts during
  some values from: 60-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: very late blastula stage
has_exact_synonym: veg1
has_exact_synonym: vegetal tier 1
has OBO namespace: echinoderm_anatomy

endomesoderm
type: Class
subclass of: anatomical entity
subclass of: germ layer
subclass of: Restriction
  on property: develops_from
  some values from: vegetal tier 2
subclass of: Restriction
  on property: existence starts during
  some values from: 60-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: very late blastula stage
has_exact_synonym: mesoendoderm
has_exact_synonym: veg2
has_exact_synonym: vegetal tier 2
has OBO namespace: echinoderm_anatomy

inner animal pole domain
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: animal pole domain
subclass of: Restriction
  on property: develops_from
  some values from: animal tier 1
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has_exact_synonym: inner apical pole domain
has OBO namespace: echinoderm_anatomy

outer animal pole domain
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: animal pole domain
subclass of: Restriction
  on property: develops_from
  some values from: animal tier 1
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has_exact_synonym: outer apical pole domain
has OBO namespace: echinoderm_anatomy

central ectoderm
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: late blastula stage
subclass of: Restriction
  on property: existence ends during
  some values from: late gastrula stage
has OBO namespace: echinoderm_anatomy

border ectoderm
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: develops_from
  some values from: ectoendoderm
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: mesenchyme blastula phase
has_exact_synonym: BE
has OBO namespace: echinoderm_anatomy

near-apical ectoderm
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: invagination phase
has OBO namespace: echinoderm_anatomy

apical ectoderm
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: blastula period
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has OBO namespace: echinoderm_anatomy

veg1-lateral ectoderm
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: invagination phase
has OBO namespace: echinoderm_anatomy

veg-1 oral ectoderm
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: invagination phase
has OBO namespace: echinoderm_anatomy

lateral ectoderm
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: invagination phase
has OBO namespace: echinoderm_anatomy

right lateral ectoderm
type: Class
subclass of: lateral ectoderm
has OBO namespace: echinoderm_anatomy

left lateral ectoderm
type: Class
subclass of: lateral ectoderm
has OBO namespace: echinoderm_anatomy

arm tip ectoderm
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

dorsal arm tip ectoderm
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: arm tip ectoderm
subclass of: Restriction
  on property: develops_from
  some values from: border ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

ventral arm tip ectoderm
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: arm tip ectoderm
subclass of: Restriction
  on property: develops_from
  some values from: border ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

apical tuft
type: Class
subclass of: anatomical entity
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: animal pole domain
subclass of: Restriction
  on property: develops_from
  some values from: animal tier 1
subclass of: Restriction
  on property: existence starts during
  some values from: very late blastula stage
has OBO namespace: echinoderm_anatomy

larval tissue
type: Class
subclass of: anatomical entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

rudiment tissue
type: Class
subclass of: anatomical entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: rudiment
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has OBO namespace: echinoderm_anatomy

juvenile tissue
type: Class
subclass of: anatomical entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: juvenile
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
has OBO namespace: echinoderm_anatomy

adult tissue
type: Class
subclass of: anatomical entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: adult
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
has OBO namespace: echinoderm_anatomy

presumptive stomodeum
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: ventral ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
has OBO namespace: echinoderm_anatomy

stomodeum
type: Class
subclass of: anatomical entity
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: ventral ectoderm
subclass of: Restriction
  on property: develops_from
  some values from: presumptive stomodeum
subclass of: Restriction
  on property: existence starts during
  some values from: prism stage
database_cross_reference: UBERON:0000930
has_exact_synonym: presumptive mouth
has OBO namespace: echinoderm_anatomy

ciliary band
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

oral hood ciliary band
type: Class
subclass of: larval structure
subclass of: Restriction
  on property: part of
  some values from: ciliary band
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

arm ciliary band
type: Class
subclass of: larval structure
subclass of: Restriction
  on property: part of
  some values from: ciliary band
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

animal pole ciliary band
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: ciliary band
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
has OBO namespace: echinoderm_anatomy

vegetal ciliary band
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: ciliary band
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
has OBO namespace: echinoderm_anatomy

lateral ciliary band
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: ciliary band
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
has OBO namespace: echinoderm_anatomy

oral hood
type: Class
subclass of: larval structure
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has_exact_synonym: PL
has_exact_synonym: preoral lobe
has_exact_synonym: oh
has OBO namespace: echinoderm_anatomy

apex
type: Class
subclass of: larval structure
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

larval arm
type: Class
subclass of: larval structure
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

right anterolateral arm
type: Class
subclass of: larval arm
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
has_exact_synonym: ALA
has_exact_synonym: AL
has OBO namespace: echinoderm_anatomy

left anterolateral arm
type: Class
subclass of: larval arm
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
has_exact_synonym: ALA
has_exact_synonym: AL
has OBO namespace: echinoderm_anatomy

right postoral arm
type: Class
subclass of: larval arm
has_exact_synonym: PO
has OBO namespace: echinoderm_anatomy

left postoral arm
type: Class
subclass of: larval arm
has_exact_synonym: PO
has OBO namespace: echinoderm_anatomy

right posterodorsal arm
type: Class
subclass of: larval arm
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
has_exact_synonym: PD
has OBO namespace: echinoderm_anatomy

left posterodorsal arm
type: Class
subclass of: larval arm
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
has_exact_synonym: PD
has OBO namespace: echinoderm_anatomy

right preoral arm
type: Class
subclass of: larval arm
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
has_exact_synonym: PRO
has_exact_synonym: PR
has OBO namespace: echinoderm_anatomy

left preoral arm
type: Class
subclass of: larval arm
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
has_exact_synonym: PRO
has_exact_synonym: PR
has OBO namespace: echinoderm_anatomy

spicule rudiment
type: Class
subclass of: skeletal element
has OBO namespace: echinoderm_anatomy

spicule granule
type: Class
subclass of: spicule rudiment
has_exact_synonym: spicule dot
has OBO namespace: echinoderm_anatomy

triradiate spicule rudiment
type: Class
subclass of: anatomical entity
subclass of: spicule rudiment
subclass of: Restriction
  on property: develops_from
  some values from: spicule granule
has_exact_synonym: spicule primordium
has OBO namespace: echinoderm_anatomy

right ventrolateral triradiate spicule rudiment
type: Class
subclass of: triradiate spicule rudiment
subclass of: Restriction
  on property: existence ends during
  some values from: late gastrula stage
has_exact_synonym: triradiate spicule
has OBO namespace: echinoderm_anatomy

left ventrolateral triradiate spicule rudiment
type: Class
subclass of: triradiate spicule rudiment
subclass of: Restriction
  on property: existence ends during
  some values from: late gastrula stage
has OBO namespace: echinoderm_anatomy

hexaradiate spicule rudiment
type: Class
subclass of: anatomical entity
subclass of: spicule rudiment
subclass of: Restriction
  on property: develops_from
  some values from: spicule granule
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
has_exact_synonym: hexaradiate spicule
has OBO namespace: echinoderm_anatomy

larval spicule
type: Class
subclass of: anatomical entity
subclass of: skeletal element
subclass of: Restriction
  on property: part of
  some values from: larval endoskeleton
subclass of: Restriction
  on property: develops_from
  some values from: triradiate spicule rudiment
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
definition: A triradiate or hexaradiate minute calcareous skeletal element that initiates most if not all skeletal structures found within the sea urchin embryo, larva and adult.
has_exact_synonym: primary triradiate skeletal rudiment
has OBO namespace: echinoderm_anatomy

embryonic skeletogenic mesenchyme
type: Class
subclass of: anatomical entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: develops_from
  some values from: embryonic skeletogenic mesoderm
subclass of: Restriction
  on property: existence starts during
  some values from: early mesenchyme blastula stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
definition: The embryonic tissue made up of loosely connected mesoderm cells that will produce all of the skeletal elements.
has_exact_synonym: primary mesenchyme
has_exact_synonym: SM
has OBO namespace: echinoderm_anatomy

skeletal rod
type: Class
subclass of: anatomical entity
subclass of: skeletal element
subclass of: Restriction
  on property: develops_from
  some values from: embryonic skeletogenic mesenchyme
subclass of: Restriction
  on property: existence starts during
  some values from: late gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early juvenile stage
has_exact_synonym: spicule rod
has OBO namespace: echinoderm_anatomy

anonymous rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

right anonymous rod
type: Class
subclass of: anonymous rod
subclass of: Restriction
  on property: develops_from
  some values from: right ventrolateral triradiate spicule rudiment
has OBO namespace: echinoderm_anatomy

left anonymous rod
type: Class
subclass of: anonymous rod
subclass of: Restriction
  on property: develops_from
  some values from: left ventrolateral triradiate spicule rudiment
has OBO namespace: echinoderm_anatomy

right dorsoventral connecting rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: develops_from
  some values from: right ventrolateral triradiate spicule rudiment
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

right anterolateral rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: develops_from
  some values from: right dorsoventral connecting rod
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

left dorsoventral connecting rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: develops_from
  some values from: left ventrolateral triradiate spicule rudiment
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

left anterolateral rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: develops_from
  some values from: left dorsoventral connecting rod
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

right postoral rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: develops_from
  some values from: right anonymous rod
subclass of: Restriction
  on property: existence starts during
  some values from: prism stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

left postoral rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: develops_from
  some values from: left anonymous rod
subclass of: Restriction
  on property: existence starts during
  some values from: prism stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

right posterodorsal rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: part of
  some values from: larval endoskeleton
subclass of: Restriction
  on property: develops_from
  some values from: triradiate spicule rudiment
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

left posterodorsal rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: part of
  some values from: larval endoskeleton
subclass of: Restriction
  on property: develops_from
  some values from: triradiate spicule rudiment
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

dorsal arch
type: Class
subclass of: anatomical entity
subclass of: skeletal element
subclass of: Restriction
  on property: part of
  some values from: larval endoskeleton
subclass of: Restriction
  on property: develops_from
  some values from: triradiate spicule rudiment
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

right preoral rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: part of
  some values from: larval endoskeleton
subclass of: Restriction
  on property: develops_from
  some values from: dorsal arch
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

left preoral rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: part of
  some values from: larval endoskeleton
subclass of: Restriction
  on property: develops_from
  some values from: dorsal arch
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

right ventral transverse rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: develops_from
  some values from: right ventrolateral triradiate spicule rudiment
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

left ventral transverse rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: develops_from
  some values from: left ventrolateral triradiate spicule rudiment
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

posterior tip of body rod
type: Class
subclass of: anatomical entity
subclass of: skeletal element
subclass of: Restriction
  on property: part of
  some values from: body rod
subclass of: Restriction
  on property: existence starts during
  some values from: prism stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

scheitel
type: Class
subclass of: anatomical entity
subclass of: skeletal element
subclass of: Restriction
  on property: part of
  some values from: larval endoskeleton
subclass of: Restriction
  on property: develops_from
  some values from: posterior tip of body rod
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has_exact_synonym: body rod end
has OBO namespace: echinoderm_anatomy

body rod
type: Class
subclass of: anatomical entity
subclass of: skeletal element
subclass of: Restriction
  on property: part of
  some values from: larval endoskeleton
subclass of: Restriction
  on property: existence starts during
  some values from: prism stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

left body rod
type: Class
subclass of: body rod
subclass of: Restriction
  on property: develops_from
  some values from: left anonymous rod
has OBO namespace: echinoderm_anatomy

right body rod
type: Class
subclass of: body rod
subclass of: Restriction
  on property: develops_from
  some values from: right anonymous rod
has OBO namespace: echinoderm_anatomy

posterior tip of left body rod
type: Class
subclass of: posterior tip of body rod
subclass of: Restriction
  on property: part of
  some values from: left body rod
has OBO namespace: echinoderm_anatomy

posteror tip of right body rod
type: Class
subclass of: posterior tip of body rod
subclass of: Restriction
  on property: part of
  some values from: right body rod
has OBO namespace: echinoderm_anatomy

right recurrent rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: part of
  some values from: larval endoskeleton
subclass of: Restriction
  on property: develops_from
  some values from: right dorsoventral connecting rod
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

left recurrent rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: part of
  some values from: larval endoskeleton
subclass of: Restriction
  on property: develops_from
  some values from: left dorsoventral connecting rod
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

posterior transverse rod
type: Class
subclass of: skeletal rod
subclass of: Restriction
  on property: part of
  some values from: larval endoskeleton
subclass of: Restriction
  on property: develops_from
  some values from: triradiate spicule rudiment
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

mouth
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0000165
has OBO namespace: echinoderm_anatomy

larval mouth
type: Class
subclass of: anatomical entity
subclass of: mouth
subclass of: Restriction
  on property: part of
  some values from: larval digestive system
subclass of: Restriction
  on property: develops_from
  some values from: stomodeum
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

anus
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0001245
has OBO namespace: echinoderm_anatomy

larval anus
type: Class
subclass of: anatomical entity
subclass of: anus
subclass of: Restriction
  on property: part of
  some values from: larval digestive system
subclass of: Restriction
  on property: develops_from
  some values from: blastopore
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

presumptive endoderm
type: Class
subclass of: embryonic tissue
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: existence starts during
  some values from: early blastula stage
subclass of: Restriction
  on property: existence ends during
  some values from: vegetal plate stage
database_cross_reference: UBERON:0006595
has_exact_synonym: prospective endoderm
has OBO namespace: echinoderm_anatomy

endoderm
type: Class
subclass of: anatomical entity
subclass of: germ layer
subclass of: Restriction
  on property: develops_from
  some values from: presumptive endoderm
subclass of: Restriction
  on property: existence starts during
  some values from: mid-blastula stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
database_cross_reference: UBERON:0000925
has OBO namespace: echinoderm_anatomy

archenteron
type: Class
subclass of: anatomical entity
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: digestive system
subclass of: Restriction
  on property: develops_from
  some values from: vegetal plate
subclass of: Restriction
  on property: existence starts during
  some values from: blastopore formation stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
database_cross_reference: UBERON:0004735
has_exact_synonym: primitive gut
has_exact_synonym: embryonic gut
has OBO namespace: echinoderm_anatomy

hindgut
type: Class
subclass of: anatomical entity
subclass of: digestive system element
subclass of: Restriction
  on property: part of
  some values from: archenteron
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: late gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
database_cross_reference: UBERON:0001046
has OBO namespace: echinoderm_anatomy

dorsal hindgut
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: hindgut
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: late gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

ventral hindgut
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: hindgut
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: late gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

midgut
type: Class
subclass of: anatomical entity
subclass of: digestive system element
subclass of: Restriction
  on property: part of
  some values from: archenteron
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
database_cross_reference: UBERON:0001045
has OBO namespace: echinoderm_anatomy

ventral midgut
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: midgut
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

dorsal midgut
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: midgut
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

anterior midgut
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: midgut
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

posterior midgut
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: midgut
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

anterior hindgut
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: hindgut
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: late gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

posterior hindgut
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: hindgut
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: late gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

foregut
type: Class
subclass of: anatomical entity
subclass of: digestive system element
subclass of: Restriction
  on property: part of
  some values from: archenteron
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
database_cross_reference: UBERON:0001041
has_exact_synonym: tip of the digestive tract
has OBO namespace: echinoderm_anatomy

ventral foregut
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: foregut
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

dorsal foregut
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: foregut
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

anterior foregut
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: foregut
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

posterior foregut
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: foregut
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

tip of archenteron
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: archenteron
subclass of: Restriction
  on property: develops_from
  some values from: vegetal plate
subclass of: Restriction
  on property: existence starts during
  some values from: early gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
database_cross_reference: UBERON:3010432
has_exact_synonym: archenteron roof
has OBO namespace: echinoderm_anatomy

presumptive mesoderm
type: Class
subclass of: anatomical entity
subclass of: embryonic tissue
subclass of: Restriction
  on property: part of
  some values from: vegetal hemisphere
subclass of: Restriction
  on property: develops_from
  some values from: vegetal plate
subclass of: Restriction
  on property: existence ends during
  some values from: vegetal plate stage
database_cross_reference: UBERON:0006603
has_exact_synonym: prospective mesoderm
has OBO namespace: echinoderm_anatomy

mesoderm
type: Class
subclass of: anatomical entity
subclass of: germ layer
subclass of: Restriction
  on property: develops_from
  some values from: presumptive mesoderm
subclass of: Restriction
  on property: existence starts during
  some values from: 16-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
database_cross_reference: UBERON:0000926
has OBO namespace: echinoderm_anatomy

embryonic skeletogenic mesoderm
type: Class
subclass of: anatomical entity
subclass of: embryonic tissue
subclass of: Restriction
  on property: part of
  some values from: mesoderm
subclass of: Restriction
  on property: develops_from
  some values from: large micromere
subclass of: Restriction
  on property: existence starts during
  some values from: 32-cell stage
subclass of: Restriction
  on property: existence ends during
  some values from: very late blastula stage
definition: The subset of the embryonic mesoderm that will later give rise to the skeletogenic mesenchyme and embryonic skeleton.
has OBO namespace: echinoderm_anatomy

embryonic skeletogenic mesenchyme cell
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: embryonic skeletogenic mesenchyme
subclass of: Restriction
  on property: develops_from
  some values from: large micromere
subclass of: Restriction
  on property: existence starts during
  some values from: early mesenchyme blastula stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has_exact_synonym: primary mesenchyme cell
has_exact_synonym: PMC
has OBO namespace: echinoderm_anatomy

syncytium
type: Class
subclass of: cell
has_exact_synonym: multinucleated cell
has_exact_synonym: syncytial cell
has_exact_synonym: syncytium
has_exact_synonym: multinucleate cell
has OBO namespace: echinoderm_anatomy

embryonic skeletogenic mesenchyme syncytium
type: Class
subclass of: anatomical entity
subclass of: syncytium
subclass of: Restriction
  on property: part of
  some values from: endoskeleton
subclass of: Restriction
  on property: develops_from
  some values from: embryonic skeletogenic mesenchyme
subclass of: Restriction
  on property: existence starts during
  some values from: early gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
definition: Anatomical structure composed of skeletogenic mesenchyme cells that have fused to form a single syncytial network.
has OBO namespace: echinoderm_anatomy

subequatorial skeletogenic mesenchyme ring
type: Class
subclass of: anatomical entity
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: embryonic skeletogenic mesenchyme syncytium
subclass of: Restriction
  on property: develops_from
  some values from: embryonic skeletogenic mesenchyme
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
has_exact_synonym: PMC ring
has_exact_synonym: primary mesenchyme cell ring
has_exact_synonym: subequatorial PMC ring
has_exact_synonym: subequatorial SM ring
has_exact_synonym: subequatorial primary mesenchyme cell ring
has_exact_synonym: SM ring
has OBO namespace: echinoderm_anatomy

ventral skeletogenic mesenchyme chain
type: Class
subclass of: anatomical entity
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: subequatorial skeletogenic mesenchyme ring
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
definition: Subpopulation of skeletogenic mesenchyme forming a chain on the oral (i.e. ventral) side of the embryo.
has OBO namespace: echinoderm_anatomy

dorsal skeletogenic mesenchyme chain
type: Class
subclass of: anatomical entity
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: subequatorial skeletogenic mesenchyme ring
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
definition: Subpopulation of skeletogenic mesenchyme forming a chain on the aboral (i.e. dorsal) side of the embryo.
has OBO namespace: echinoderm_anatomy

right ventrolateral skeletogenic mesenchyme cluster
type: Class
subclass of: anatomical entity
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: subequatorial skeletogenic mesenchyme ring
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
definition: Subpopulation of skeletogenic mesenchyme forming a cluster (i.e. a group of cells) in the ventrolateral region of the embryo.
has OBO namespace: echinoderm_anatomy

left ventrolateral skeletogenic mesenchyme cluster
type: Class
subclass of: anatomical entity
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: subequatorial skeletogenic mesenchyme ring
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
has OBO namespace: echinoderm_anatomy

lateral chain of skeletogenic mesenchyme
type: Class
subclass of: anatomical entity
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: embryonic skeletogenic mesenchyme syncytium
subclass of: Restriction
  on property: existence starts during
  some values from: mid-gastrula stage
definition: Subpopulation of skeletogenic mesenchyme forming a chain on either side of the developing digestive tract, along the blastocoel wall and towards the animal pole.
has OBO namespace: echinoderm_anatomy

right lateral chain of skeletogenic mesenchyme
type: Class
subclass of: anatomical entity
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: lateral chain of skeletogenic mesenchyme
subclass of: Restriction
  on property: develops_from
  some values from: subequatorial skeletogenic mesenchyme ring
subclass of: Restriction
  on property: existence starts during
  some values from: late gastrula stage
definition: Subpopulation of skeletogenic mesenchyme forming a chain along the blastocoel wall towards the animal pole on the right side of the embryo.
has OBO namespace: echinoderm_anatomy

left lateral chain of skeletogenic mesenchyme
type: Class
subclass of: anatomical entity
subclass of: embryonic structure
subclass of: Restriction
  on property: part of
  some values from: lateral chain of skeletogenic mesenchyme
subclass of: Restriction
  on property: develops_from
  some values from: subequatorial skeletogenic mesenchyme ring
subclass of: Restriction
  on property: existence starts during
  some values from: late gastrula stage
definition: Subpopulation of skeletogenic mesenchyme forming a chain along the blastocoel wall towards the animal pole on the left side of the embryo.
has OBO namespace: echinoderm_anatomy

embryonic non-skeletogenic mesoderm
type: Class
subclass of: anatomical entity
subclass of: embryonic tissue
subclass of: Restriction
  on property: part of
  some values from: mesoderm
subclass of: Restriction
  on property: develops_from
  some values from: vegetal tier 2
subclass of: Restriction
  on property: existence starts during
  some values from: very late blastula stage
subclass of: Restriction
  on property: existence ends during
  some values from: late gastrula stage
has OBO namespace: echinoderm_anatomy

ventral non-skeletogenic mesoderm
type: Class
subclass of: anatomical entity
subclass of: embryonic tissue
subclass of: Restriction
  on property: part of
  some values from: embryonic non-skeletogenic mesoderm
subclass of: Restriction
  on property: develops_from
  some values from: vegetal tier 2
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: early gastrula stage
has OBO namespace: echinoderm_anatomy

dorsal non-skeletogenic mesoderm
type: Class
subclass of: anatomical entity
subclass of: embryonic tissue
subclass of: Restriction
  on property: part of
  some values from: embryonic non-skeletogenic mesoderm
subclass of: Restriction
  on property: develops_from
  some values from: vegetal tier 2
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: early gastrula stage
has OBO namespace: echinoderm_anatomy

embryonic non-skeletogenic mesenchyme
type: Class
subclass of: anatomical entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: develops_from
  some values from: vegetal tier 2
subclass of: Restriction
  on property: existence starts during
  some values from: early gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has_exact_synonym: NSM
has_exact_synonym: secondary mesenchyme
has OBO namespace: echinoderm_anatomy

embryonic non-skeletogenic mesenchyme cell
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: embryonic non-skeletogenic mesenchyme
subclass of: Restriction
  on property: develops_from
  some values from: vegetal tier 2
subclass of: Restriction
  on property: existence starts during
  some values from: early gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has_exact_synonym: secondary mesenchyme cell
has_exact_synonym: SMC
has OBO namespace: echinoderm_anatomy

larval non-skeletogenic mesenchyme
type: Class
subclass of: anatomical entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

larval non-skeletogenic mesenchyme cell
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: larval non-skeletogenic mesenchyme
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

presumptive blastocoelar cell
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: embryonic non-skeletogenic mesoderm
subclass of: Restriction
  on property: develops_from
  some values from: vegetal tier 2
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: late gastrula stage
has OBO namespace: echinoderm_anatomy

presumptive pigment cell
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: embryonic non-skeletogenic mesoderm
subclass of: Restriction
  on property: existence starts during
  some values from: mesenchyme blastula phase
subclass of: Restriction
  on property: existence ends during
  some values from: late gastrula stage
has_exact_synonym: presumptive immunocyte
has_exact_synonym: presumptive pigmented cell
has OBO namespace: echinoderm_anatomy

pigment cell
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: immune system
subclass of: Restriction
  on property: develops_from
  some values from: presumptive pigment cell
subclass of: Restriction
  on property: existence starts during
  some values from: early gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
definition: a cell that contains red coloring matter
has_exact_synonym: pigmented immunocyte
has_exact_synonym: pigmented cell
has OBO namespace: echinoderm_anatomy

embryonic pigment cell
type: Class
subclass of: pigment cell
subclass of: Restriction
  on property: part of
  some values from: embryonic immune system
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has OBO namespace: echinoderm_anatomy

larval pigment cell
type: Class
subclass of: pigment cell
subclass of: Restriction
  on property: part of
  some values from: larval immune system
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has OBO namespace: echinoderm_anatomy

juvenile pigment cell
type: Class
subclass of: pigment cell
subclass of: Restriction
  on property: part of
  some values from: juvenile immune system
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
has OBO namespace: echinoderm_anatomy

rudiment pigment cell
type: Class
subclass of: pigment cell
subclass of: Restriction
  on property: part of
  some values from: rudiment
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has OBO namespace: echinoderm_anatomy

blastocoelar cell
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: immune system
subclass of: Restriction
  on property: develops_from
  some values from: presumptive blastocoelar cell
subclass of: Restriction
  on property: existence starts during
  some values from: late gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has OBO namespace: echinoderm_anatomy

globular cell
type: Class
subclass of: blastocoelar cell
subclass of: Restriction
  on property: part of
  some values from: larval immune system
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

filopodial cell
type: Class
subclass of: blastocoelar cell
subclass of: Restriction
  on property: part of
  some values from: larval immune system
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

ovoid cell
type: Class
subclass of: blastocoelar cell
subclass of: Restriction
  on property: part of
  some values from: larval immune system
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

amoeboid cell
type: Class
subclass of: blastocoelar cell
subclass of: Restriction
  on property: part of
  some values from: larval immune system
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
has OBO namespace: echinoderm_anatomy

muscle precursor cell
type: Class
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: muscular system
subclass of: Restriction
  on property: existence starts during
  some values from: late gastrula stage
subclass of: Restriction
  on property: existence ends during
  some values from: early pluteus larva stage
has_exact_synonym: presumptive muscle cell
has OBO namespace: echinoderm_anatomy

muscle
type: Class
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: muscular system
has OBO namespace: echinoderm_anatomy

larval muscle
type: Class
subclass of: larval tissue
subclass of: Restriction
  on property: part of
  some values from: larval muscular system
has_exact_synonym: contractile muscle
has OBO namespace: echinoderm_anatomy

rudiment muscle
type: Class
subclass of: rudiment tissue
subclass of: Restriction
  on property: part of
  some values from: muscular system
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
has OBO namespace: echinoderm_anatomy

juvenile muscle
type: Class
subclass of: juvenile tissue
subclass of: Restriction
  on property: part of
  some values from: juvenile muscular system
has OBO namespace: echinoderm_anatomy

adult muscle
type: Class
subclass of: adult tissue
subclass of: Restriction
  on property: part of
  some values from: adult muscular system
subclass of: Restriction
  on property: existence starts during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

blastocoel
type: Class
subclass of: independent continuant
subclass of: anatomical space
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: existence starts during
  some values from: very early blastula stage
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
database_cross_reference: UBERON:0000090
has OBO namespace: echinoderm_anatomy

sphincter
type: Class
subclass of: digestive system element
subclass of: Restriction
  on property: existence starts during
  some values from: prism stage
has OBO namespace: echinoderm_anatomy

pyloric sphincter
type: Class
subclass of: anatomical entity
subclass of: sphincter
subclass of: Restriction
  on property: part of
  some values from: larval digestive system
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has_exact_synonym: midgut-hindgut constriction
has OBO namespace: echinoderm_anatomy

cardiac sphincter
type: Class
subclass of: anatomical entity
subclass of: sphincter
subclass of: Restriction
  on property: part of
  some values from: larval digestive system
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has_exact_synonym: foregut-midgut constriction
has OBO namespace: echinoderm_anatomy

anal sphincter
type: Class
subclass of: anatomical entity
subclass of: sphincter
subclass of: Restriction
  on property: part of
  some values from: larval digestive system
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has_exact_synonym: hindgut-ectoderm constriction
has OBO namespace: echinoderm_anatomy

sphincter muscle
type: Class
subclass of: anatomical entity
subclass of: muscle
subclass of: Restriction
  on property: part of
  some values from: larval digestive system
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
database_cross_reference: UBERON:0004590
has OBO namespace: echinoderm_anatomy

sphincter muscle cell
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: sphincter muscle
subclass of: Restriction
  on property: develops_from
  some values from: archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
has_exact_synonym: myoepithelial cell
has OBO namespace: echinoderm_anatomy

pyloric sphincteric muscle
type: Class
subclass of: sphincter muscle
subclass of: Restriction
  on property: part of
  some values from: pyloric sphincter
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
database_cross_reference: UBERON:0001202
has_exact_synonym: pyloric sphincter
has OBO namespace: echinoderm_anatomy

cardiac sphincteric muscle
type: Class
subclass of: sphincter muscle
subclass of: Restriction
  on property: part of
  some values from: cardiac sphincter
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has_exact_synonym: cardiac sphincter
has OBO namespace: echinoderm_anatomy

anal sphincteric muscle
type: Class
subclass of: sphincter muscle
subclass of: Restriction
  on property: part of
  some values from: anal sphincter
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
database_cross_reference: UBERON:0004916
has_exact_synonym: anal sphincter
has OBO namespace: echinoderm_anatomy

larval esophagus
type: Class
subclass of: anatomical entity
subclass of: digestive system element
subclass of: Restriction
  on property: part of
  some values from: larval digestive system
subclass of: Restriction
  on property: develops_from
  some values from: foregut
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

circumesophageal muscle
type: Class
subclass of: larval muscle
subclass of: Restriction
  on property: part of
  some values from: larval esophagus
subclass of: Restriction
  on property: develops_from
  some values from: tip of archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
has OBO namespace: echinoderm_anatomy

circumesophageal muscle cell
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: circumesophageal muscle
subclass of: Restriction
  on property: develops_from
  some values from: tip of archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has_exact_synonym: presumptive circumesophageal muscle cell
has OBO namespace: echinoderm_anatomy

larval stomach
type: Class
subclass of: anatomical entity
subclass of: digestive system element
subclass of: Restriction
  on property: part of
  some values from: larval digestive system
subclass of: Restriction
  on property: develops_from
  some values from: midgut
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

larval intestine
type: Class
subclass of: anatomical entity
subclass of: digestive system element
subclass of: Restriction
  on property: part of
  some values from: larval digestive system
subclass of: Restriction
  on property: develops_from
  some values from: hindgut
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

larval skeletogenic mesenchyme
type: Class
subclass of: anatomical entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
definition: The mesenchyme cells that produce new skeletal elements (i.e., the posterodorsal rods, dorsal arch, and preoral rods) in the larva after feeding begins
has OBO namespace: echinoderm_anatomy

larval skeletogenic mesenchyme cell
type: Class
subclass of: anatomical entity
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: larval skeletogenic mesenchyme
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

coelom
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: develops_from
  some values from: tip of archenteron
subclass of: Restriction
  on property: existence starts during
  some values from: prism stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0011997
has OBO namespace: echinoderm_anatomy

unpaired coelomic pouch
type: Class
subclass of: coelom
subclass of: Restriction
  on property: part of
  some values from: embryo
subclass of: Restriction
  on property: existence ends during
  some values from: prism stage
has_exact_synonym: unpaired coelomic rudiment
has OBO namespace: echinoderm_anatomy

right coelomic pouch
type: Class
subclass of: coelom
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: develops_from
  some values from: unpaired coelomic pouch
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: 6-arm pluteus larva stage
has OBO namespace: echinoderm_anatomy

left coelomic pouch
type: Class
subclass of: coelom
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: develops_from
  some values from: unpaired coelomic pouch
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: 6-arm pluteus larva stage
has_exact_synonym: left coelomic sac
has OBO namespace: echinoderm_anatomy

right coelomic constriction
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: right coelomic pouch
subclass of: Restriction
  on property: develops_from
  some values from: unpaired coelomic pouch
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: 6-arm pluteus larva stage
has OBO namespace: echinoderm_anatomy

left coelomic constriction
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: left coelomic pouch
subclass of: Restriction
  on property: develops_from
  some values from: unpaired coelomic pouch
subclass of: Restriction
  on property: existence starts during
  some values from: early pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: 6-arm pluteus larva stage
has OBO namespace: echinoderm_anatomy

larval epithelium
type: Class
subclass of: larval tissue
subclass of: Restriction
  on property: existence ends during
  some values from: metamorphic larva stage
has OBO namespace: echinoderm_anatomy

vestibule
type: Class
subclass of: larval structure
subclass of: Restriction
  on property: part of
  some values from: larval epithelium
subclass of: Restriction
  on property: develops_from
  some values from: ventral ectoderm
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: 8-arm pluteus larva stage
has_exact_synonym: amniotic sac
has OBO namespace: echinoderm_anatomy

oral epithelium
type: Class
subclass of: larval tissue
subclass of: Restriction
  on property: part of
  some values from: larval epithelium
database_cross_reference: UBERON:0002424
has_exact_synonym: circumoral ectoderm
has_exact_synonym: circumoral epithelium
has_exact_synonym: oral epidermis
has OBO namespace: echinoderm_anatomy

aboral epithelium
type: Class
subclass of: larval tissue
subclass of: Restriction
  on property: part of
  some values from: larval epithelium
has OBO namespace: echinoderm_anatomy

left lateral field
type: Class
subclass of: lateral field
definition: The left lateral field is the lateral field located on the left side of the larva
has OBO namespace: echinoderm_anatomy

vestibular pore
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: develops_from
  some values from: left lateral field
subclass of: Restriction
  on property: existence starts during
  some values from: competent pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
definition: Opening located in the left lateral field
has OBO namespace: echinoderm_anatomy

axocoel
type: Class
subclass of: coelom
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: 8-arm pluteus larva stage
has_exact_synonym: anterior coelom
has OBO namespace: echinoderm_anatomy

left axocoel
type: Class
subclass of: axocoel
subclass of: Restriction
  on property: develops_from
  some values from: left coelomic pouch
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

axial coelom
type: Class
subclass of: coelom
subclass of: Restriction
  on property: part of
  some values from: adult
subclass of: Restriction
  on property: develops_from
  some values from: left axocoel
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
has OBO namespace: echinoderm_anatomy

hydrocoel
type: Class
subclass of: coelom
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: 8-arm pluteus larva stage
has_exact_synonym: central coelom
has OBO namespace: echinoderm_anatomy

somatocoel
type: Class
subclass of: coelom
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: 8-arm pluteus larva stage
has_exact_synonym: posterior coelom
has OBO namespace: echinoderm_anatomy

left hydrocoel
type: Class
subclass of: hydrocoel
subclass of: Restriction
  on property: develops_from
  some values from: left coelomic pouch
has OBO namespace: echinoderm_anatomy

left somatocoel
type: Class
subclass of: somatocoel
subclass of: Restriction
  on property: develops_from
  some values from: left coelomic pouch
has OBO namespace: echinoderm_anatomy

right axohydrocoel
type: Class
subclass of: coelom
subclass of: Restriction
  on property: part of
  some values from: larva
subclass of: Restriction
  on property: develops_from
  some values from: right coelomic pouch
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: 8-arm pluteus larva stage
has_exact_synonym: anterior sac
has OBO namespace: echinoderm_anatomy

right somatocoel
type: Class
subclass of: somatocoel
subclass of: Restriction
  on property: develops_from
  some values from: right coelomic pouch
has OBO namespace: echinoderm_anatomy

axial complex
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: water vascular system
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

stone canal
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: axial complex
subclass of: Restriction
  on property: develops_from
  some values from: left coelomic pouch
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

ring canal
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: water vascular system
subclass of: Restriction
  on property: develops_from
  some values from: left hydrocoel
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

radial canal
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: water vascular system
subclass of: Restriction
  on property: develops_from
  some values from: left hydrocoel
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

primary pore canal
type: Class
subclass of: larval structure
subclass of: Restriction
  on property: part of
  some values from: water vascular system
subclass of: Restriction
  on property: develops_from
  some values from: embryonic non-skeletogenic mesenchyme
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: 4-arm pluteus larva stage
has_exact_synonym: hydropore canal
has OBO namespace: echinoderm_anatomy

hydropore
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: water vascular system
subclass of: Restriction
  on property: existence starts during
  some values from: 4-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

right axocoel
type: Class
subclass of: axocoel
subclass of: Restriction
  on property: develops_from
  some values from: right axohydrocoel
has OBO namespace: echinoderm_anatomy

right hydrocoel
type: Class
subclass of: hydrocoel
subclass of: Restriction
  on property: develops_from
  some values from: right axohydrocoel
has OBO namespace: echinoderm_anatomy

axial sinus
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: axial complex
subclass of: Restriction
  on property: develops_from
  some values from: right hydrocoel
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

axial organ
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: axial complex
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

dorsal sac
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: axial complex
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

ciliated epaulette
type: Class
subclass of: larval structure
subclass of: Restriction
  on property: part of
  some values from: larval epithelium
subclass of: Restriction
  on property: develops_from
  some values from: ciliary band
subclass of: Restriction
  on property: existence starts during
  some values from: 6-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

anterior ciliated epaulette
type: Class
subclass of: larval structure
subclass of: Restriction
  on property: part of
  some values from: ciliated epaulette
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

posterior ciliated epaulette
type: Class
subclass of: larval structure
subclass of: Restriction
  on property: part of
  some values from: ciliated epaulette
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
has OBO namespace: echinoderm_anatomy

lateral field
type: Class
subclass of: anatomical entity
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: larval epithelium
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: competent pluteus larva stage
definition: The lateral field is located in the aboral ectoderm of the larva. It separates the anterior and posterior pairs of epaulettes
has OBO namespace: echinoderm_anatomy

right lateral field
type: Class
subclass of: lateral field
definition: The right lateral field is the lateral field located on the right side of the larva
has OBO namespace: echinoderm_anatomy

ambulacral plate
type: Class
subclass of: skeletal element
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
has OBO namespace: echinoderm_anatomy

adult skeletogenic mesenchyme
type: Class
subclass of: anatomical entity
subclass of: tissue
subclass of: Restriction
  on property: part of
  some values from: adult
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
definition: The mesenchyme cells that produce biomineralized elements (e.g., spines, test plates, and teeth) in the juvenile and adult.
has OBO namespace: echinoderm_anatomy

interambulacral plate
type: Class
subclass of: skeletal element
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
has_exact_synonym: int
has OBO namespace: echinoderm_anatomy

ambulacra
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

interambulacra
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

genital plate
type: Class
subclass of: skeletal element
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
has OBO namespace: echinoderm_anatomy

appendage
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: whole organism
has OBO namespace: echinoderm_anatomy

pedicellaria
type: Class
subclass of: appendage
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0008261
has OBO namespace: echinoderm_anatomy

ocular plate
type: Class
subclass of: skeletal element
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
has_exact_synonym: terminal plate
has OBO namespace: echinoderm_anatomy

buccal plate
type: Class
subclass of: skeletal element
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
has OBO namespace: echinoderm_anatomy

genital plate AB
type: Class
subclass of: genital plate
has OBO namespace: echinoderm_anatomy

genital plate BC
type: Class
subclass of: genital plate
has OBO namespace: echinoderm_anatomy

genital plate CD
type: Class
subclass of: genital plate
has OBO namespace: echinoderm_anatomy

genital plate DE
type: Class
subclass of: genital plate
has OBO namespace: echinoderm_anatomy

genital plate EA
type: Class
subclass of: genital plate
has OBO namespace: echinoderm_anatomy

podia
type: Class
subclass of: appendage
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0008247
has_exact_synonym: tube foot
has OBO namespace: echinoderm_anatomy

primary podia
type: Class
subclass of: podia
subclass of: Restriction
  on property: part of
  some values from: appendage
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
has_exact_synonym: primary tube foot
has OBO namespace: echinoderm_anatomy

disk of primary podia
type: Class
subclass of: skeletal element
subclass of: Restriction
  on property: part of
  some values from: primary podia
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
has OBO namespace: echinoderm_anatomy

secondary podia
type: Class
subclass of: podia
subclass of: Restriction
  on property: part of
  some values from: appendage
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
has_exact_synonym: secondary tube foot
has OBO namespace: echinoderm_anatomy

disk of secondary podia
type: Class
subclass of: skeletal element
subclass of: Restriction
  on property: part of
  some values from: secondary podia
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
has OBO namespace: echinoderm_anatomy

buccal podia
type: Class
subclass of: primary podia associated neuron
subclass of: Restriction
  on property: part of
  some values from: appendage
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
has OBO namespace: echinoderm_anatomy

spine
type: Class
subclass of: appendage
subclass of: Restriction
  on property: existence starts during
  some values from: 8-arm pluteus larva stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0008260
has_exact_synonym: spine appendage
has OBO namespace: echinoderm_anatomy

juvenile spine
type: Class
subclass of: spine
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
has_exact_synonym: splayed spines
has OBO namespace: echinoderm_anatomy

definitive spine
type: Class
subclass of: spine
has_exact_synonym: adult spine
has OBO namespace: echinoderm_anatomy

sphaeridium
type: Class
subclass of: appendage
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

ampulla
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: water vascular system
subclass of: Restriction
  on property: develops_from
  some values from: radial canal
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0008252
has_exact_synonym: tube foot ampulla
has OBO namespace: echinoderm_anatomy

adult mouth
type: Class
subclass of: anatomical entity
subclass of: mouth
subclass of: Restriction
  on property: part of
  some values from: adult digestive system
subclass of: Restriction
  on property: existence starts during
  some values from: late juvenile stage
has OBO namespace: echinoderm_anatomy

adult anus
type: Class
subclass of: anatomical entity
subclass of: anus
subclass of: Restriction
  on property: part of
  some values from: adult digestive system
subclass of: Restriction
  on property: existence starts during
  some values from: late juvenile stage
has OBO namespace: echinoderm_anatomy

Aristotles lantern
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: digestive system
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0008253
has OBO namespace: echinoderm_anatomy

tooth
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: Aristotles lantern
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

madreporite
type: Class
subclass of: anatomical entity
subclass of: genital plate
subclass of: Restriction
  on property: develops_from
  some values from: genital plate CD
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
database_cross_reference: UBERON:0009476
has OBO namespace: echinoderm_anatomy

gonopore
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: genital plate
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has_exact_synonym: genital pore
has OBO namespace: echinoderm_anatomy

gonad
type: Class
subclass of: adult structure
subclass of: Restriction
  on property: part of
  some values from: reproductive system
subclass of: Restriction
  on property: existence starts during
  some values from: adult stage
database_cross_reference: UBERON:0000991
has OBO namespace: echinoderm_anatomy

ovary
type: Class
subclass of: gonad
database_cross_reference: UBERON:0000992
has OBO namespace: echinoderm_anatomy

testis
type: Class
subclass of: gonad
database_cross_reference: UBERON:0000473
has OBO namespace: echinoderm_anatomy

juvenile digestive tract
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: juvenile digestive system
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: late juvenile stage
has OBO namespace: echinoderm_anatomy

adult digestive tract
type: Class
subclass of: anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: adult digestive system
subclass of: Restriction
  on property: develops_from
  some values from: larval digestive system
subclass of: Restriction
  on property: existence starts during
  some values from: adult stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

mesentery
type: Class
subclass of: independent continuant
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: muscular system
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
database_cross_reference: UBERON:0002095
has OBO namespace: echinoderm_anatomy

perivisceral cavity
type: Class
subclass of: independent continuant
subclass of: anatomical region
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
subclass of: Restriction
  on property: existence ends during
  some values from: adult stage
has OBO namespace: echinoderm_anatomy

photosensory cell
type: Class
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: whole organism
subclass of: Restriction
  on property: existence starts during
  some values from: early juvenile stage
has_exact_synonym: photoreceptor cell
has OBO namespace: echinoderm_anatomy

molecular_function
type: Class
subclass of: process
IAO_0000589: molecular process

catalytic activity
type: Class
subclass of: molecular_function

biological_process
type: Class
subclass of: process

kinase activity
type: Class
subclass of: transferase activity, transferring phosphorus-containing groups
subclass of: Restriction
  on property: is kinase activity
  has self: true

transferase activity
type: Class
subclass of: catalytic activity

transferase activity, transferring phosphorus-containing groups
type: Class
subclass of: transferase activity

processual entity
type: Class
disjoint with: anatomical entity
definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
has OBO namespace: uberon
id: UBERON:0000000
in subset: upper level

Axiom
annotated source: processual entity
annotated property: definition
annotated target: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
database_cross_reference: span:ProcessualEntity

fully formed stage
type: Class
subclass of: occurrent
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: post-embryonic stage
subclass of: Restriction
  on property: preceded_by
  some values from: organogenesis stage
subclass of: Restriction
  on property: precedes
  some values from: death stage
definition: The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
has broad synonym: adult stage
database_cross_reference: BTO:0001043
database_cross_reference: BilaDO:0000004
database_cross_reference: EFO:0001272
database_cross_reference: FBdv:00005369
database_cross_reference: WBls:0000041
database_cross_reference: XtroDO:0000084
has_exact_synonym: fully formed animal stage
has_exact_synonym: juvenile-adult stage
has OBO namespace: uberon
id: UBERON:0000066
in subset: efo slim

Axiom
annotated source: fully formed stage
annotated property: definition
annotated target: The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

embryo stage
type: Class
subclass of: occurrent
subclass of: life cycle stage
subclass of: Restriction
  on property: precedes
  some values from: fully formed stage
subclass of: Restriction
  on property: precedes
  some values from: post-embryonic stage
disjoint with: post-embryonic stage
definition: A life cycle stage that starts with fertilization and ends with the fully formed embryo.
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/296280003
database_cross_reference: BilaDO:0000002
database_cross_reference: EV:0300001
database_cross_reference: FBdv:00005289
database_cross_reference: FMA:72652
database_cross_reference: HsapDv:0000002
database_cross_reference: MmusDv:0000002
database_cross_reference: OGES:000000
database_cross_reference: OGES:000022
database_cross_reference: WBls:0000003
database_cross_reference: WBls:0000092
database_cross_reference: WBls:0000102
database_cross_reference: XAO:1000012
has_exact_synonym: embryonic stage
has OBO namespace: uberon
has related synonym: embryogenesis
id: UBERON:0000068

Axiom
annotated source: embryo stage
annotated property: definition
annotated target: A life cycle stage that starts with fertilization and ends with the fully formed embryo.
database_cross_reference: http://orcid.org/0000-0002-6601-2165

death stage
type: Class
subclass of: life cycle stage
subclass of: Restriction
  on property: ends
  some values from: life cycle
definition: End of the life of an organism.
UBPROP_0000012: ncit:Death is an outcome
database_cross_reference: XAO:0000437
database_cross_reference: XtroDO:0000085
has OBO namespace: uberon
has related synonym: death
id: UBERON:0000071

Axiom
annotated source: death stage
annotated property: definition
annotated target: End of the life of an organism.
database_cross_reference: XAO:0000437

Axiom
annotated source: death stage
annotated property: UBPROP_0000012
annotated target: ncit:Death is an outcome
external ontology: ncit

post-embryonic stage
type: Class
subclass of: occurrent
subclass of: life cycle stage
subclass of: Restriction
  on property: preceded_by
  some values from: embryo stage
definition: stage succeeding embryo, including mature structure
UBPROP_0000008: In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
database_cross_reference: BilaDO:0000003
database_cross_reference: OGES:000010
database_cross_reference: OGES:000014
database_cross_reference: OGES:000024
database_cross_reference: WBls:0000022
database_cross_reference: WBls:0000093
database_cross_reference: WBls:0000103
has_exact_synonym: postembryonic stage
has narrow synonym: post-hatching stage
has OBO namespace: uberon
has related synonym: postembryonic
id: UBERON:0000092

Axiom
annotated source: post-embryonic stage
annotated property: definition
annotated target: stage succeeding embryo, including mature structure
database_cross_reference: https://orcid.org/0000-0002-6601-2165

life cycle
type: Class
subclass of: processual entity
subclass of: Restriction
  on property: has part
  some values from: life cycle stage
subclass of: Restriction
  on property: starts with
  some values from: zygote stage
subclass of: Restriction
  on property: ends with
  some values from: death stage
definition: An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
database_cross_reference: FBdv:00000000
database_cross_reference: HsapDv:0000001
database_cross_reference: MmusDv:0000001
database_cross_reference: OGES:000011
database_cross_reference: ncithesaurus:Life
has_exact_synonym: entire life cycle
has_exact_synonym: entire lifespan
has_exact_synonym: life
has_exact_synonym: lifespan
has OBO namespace: uberon
id: UBERON:0000104
in subset: upper level

Axiom
annotated source: life cycle
annotated property: definition
annotated target: An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

life cycle stage
type: Class
subclass of: processual entity
subclass of: Restriction
  on property: part of
  some values from: life cycle
definition: A spatiotemporal region encompassing some part of the life cycle of an organism.
IAO_0000116: this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
UBPROP_0000012: the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
UBPROP_0000012: we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
database_cross_reference: BILS:0000105
database_cross_reference: EFO:0000399
database_cross_reference: FBdv:00007012
database_cross_reference: FMA:24120
database_cross_reference: HsapDv:0000000
database_cross_reference: MmusDv:0000000
database_cross_reference: OlatDv:0000010
database_cross_reference: PdumDv:0000090
database_cross_reference: WBls:0000002
database_cross_reference: XAO:1000000
database_cross_reference: ZFS:0000000
database_cross_reference: ZFS:0100000
database_cross_reference: ncithesaurus:Developmental_Stage
has narrow synonym: developmental stage
has narrow synonym: stage
has OBO namespace: uberon
id: UBERON:0000105
in subset: efo slim
in subset: upper level

Axiom
annotated source: life cycle stage
annotated property: definition
annotated target: A spatiotemporal region encompassing some part of the life cycle of an organism.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

zygote stage
type: Class
subclass of: occurrent
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: embryo stage
subclass of: Restriction
  on property: starts
  some values from: life cycle
definition: A stage at which the organism is a single cell produced by means of sexual reproduction.
UBPROP_0000003: As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
database_cross_reference: Zygote
database_cross_reference: BILS:0000106
database_cross_reference: BilaDO:0000005
database_cross_reference: EFO:0001322
database_cross_reference: EHDAA:27
database_cross_reference: FBdv:00005288
database_cross_reference: NCIT:C12601
database_cross_reference: PdumDv:0000100
database_cross_reference: VHOG:0000745
database_cross_reference: XAO:1000001
database_cross_reference: ZFS:0000001
has_exact_synonym: 1-cell stage
has_exact_synonym: fertilized egg stage
has_exact_synonym: one cell stage
has OBO namespace: uberon
has related synonym: fertilized egg stage
has related synonym: one-cell stage
has related synonym: zygote
has related synonym: zygotum
id: UBERON:0000106
in subset: efo slim

Axiom
annotated source: zygote stage
annotated property: definition
annotated target: A stage at which the organism is a single cell produced by means of sexual reproduction.
database_cross_reference: Zygote

Axiom
annotated source: zygote stage
annotated property: UBPROP_0000003
annotated target: As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000745
ontology: VHOG
source: bgee.unil.ch
source: ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107

Axiom
annotated source: zygote stage
annotated property: has_exact_synonym
annotated target: fertilized egg stage
database_cross_reference: BTO:0000854

Axiom
annotated source: zygote stage
annotated property: hasRelatedSynonym
annotated target: one-cell stage
database_cross_reference: VHOG:0000745

Axiom
annotated source: zygote stage
annotated property: hasRelatedSynonym
annotated target: zygote
database_cross_reference: VHOG:0000745

Axiom
annotated source: zygote stage
annotated property: hasRelatedSynonym
annotated target: zygotum
database_cross_reference: Zygote
has synonym type: LATIN

cleavage stage
type: Class
subclass of: occurrent
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: embryo stage
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: zygote stage
definition: The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
database_cross_reference: Cleavage (embryo)
database_cross_reference: BILS:0000107
database_cross_reference: BilaDO:0000006
database_cross_reference: EFO:0001290
database_cross_reference: FBdv:00000054
database_cross_reference: MESH:A16.254.270
database_cross_reference: MmusDv:0000004
database_cross_reference: OGES:000015
database_cross_reference: OGES:000020
database_cross_reference: PdumDv:0000200
database_cross_reference: XAO:1000004
database_cross_reference: ZFS:0000046
has OBO namespace: uberon
id: UBERON:0000107
in subset: efo slim

Axiom
annotated source: cleavage stage
annotated property: definition
annotated target: The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
database_cross_reference: Cleavage (embryo)
database_cross_reference: GO:0040016

blastula stage
type: Class
subclass of: occurrent
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: embryo stage
subclass of: Restriction
  on property: preceded_by
  some values from: cleavage stage
definition: An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
IAO_0000116: consider adding a preceding stage 'morula stage' as part of cleavage
database_cross_reference: Blastula
database_cross_reference: BILS:0000108
database_cross_reference: BilaDO:0000007
database_cross_reference: EFO:0001282
database_cross_reference: HsapDv:0000006
database_cross_reference: MmusDv:0000007
database_cross_reference: OGES:000003
database_cross_reference: OGES:000016
database_cross_reference: OGES:000021
database_cross_reference: OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg
database_cross_reference: WBls:0000005
database_cross_reference: XAO:1000003
database_cross_reference: ZFS:0000045
has OBO namespace: uberon
id: UBERON:0000108
in subset: efo slim

Axiom
annotated source: blastula stage
annotated property: definition
annotated target: An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
database_cross_reference: Blastula

gastrula stage
type: Class
subclass of: occurrent
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: embryo stage
subclass of: Restriction
  on property: preceded_by
  some values from: blastula stage
definition: A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
database_cross_reference: BILS:0000109
database_cross_reference: BilaDO:0000008
database_cross_reference: EFO:0001296
database_cross_reference: FBdv:00005317
database_cross_reference: HsapDv:0000010
database_cross_reference: MmusDv:0000013
database_cross_reference: OGES:000004
database_cross_reference: OGES:000019
database_cross_reference: WBls:0000010
database_cross_reference: XAO:1000005
database_cross_reference: ZFS:0000047
has OBO namespace: uberon
has related synonym: blastocystis trilaminaris stage
has related synonym: trilaminar blastocyst stage
has related synonym: trilaminar blastoderm stage
has related synonym: trilaminar disk stage
has related synonym: trilaminar germ stage
has related synonym: trilaminar stage
id: UBERON:0000109
in subset: efo slim

Axiom
annotated source: gastrula stage
annotated property: subClassOf
annotated target: Restriction
  on property: preceded_by
  some values from: blastula stage
source: BILS

Axiom
annotated source: gastrula stage
annotated property: definition
annotated target: A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
database_cross_reference: GO:0007369

Axiom
annotated source: gastrula stage
annotated property: hasRelatedSynonym
annotated target: blastocystis trilaminaris stage
database_cross_reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: gastrula stage
annotated property: hasRelatedSynonym
annotated target: trilaminar blastocyst stage
database_cross_reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: gastrula stage
annotated property: hasRelatedSynonym
annotated target: trilaminar blastoderm stage
database_cross_reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: gastrula stage
annotated property: hasRelatedSynonym
annotated target: trilaminar disk stage
database_cross_reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: gastrula stage
annotated property: hasRelatedSynonym
annotated target: trilaminar germ stage
database_cross_reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: gastrula stage
annotated property: hasRelatedSynonym
annotated target: trilaminar stage
database_cross_reference: https://orcid.org/0000-0002-6601-2165

neurula stage
type: Class
subclass of: occurrent
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: embryo stage
subclass of: Restriction
  on property: preceded_by
  some values from: gastrula stage
definition: Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
database_cross_reference: BILS:0000110
database_cross_reference: BilaDO:0000009
database_cross_reference: HsapDv:0000012
database_cross_reference: MmusDv:0000017
database_cross_reference: XAO:1000006
has OBO namespace: uberon
id: UBERON:0000110

Axiom
annotated source: neurula stage
annotated property: definition
annotated target: Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
database_cross_reference: GO:0001841

organogenesis stage
type: Class
subclass of: occurrent
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: embryo stage
subclass of: Restriction
  on property: preceded_by
  some values from: neurula stage
definition: A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
database_cross_reference: Organogenesis
database_cross_reference: BILS:0000111
database_cross_reference: BilaDO:0000010
database_cross_reference: HsapDv:0000015
database_cross_reference: MmusDv:0000018
database_cross_reference: OGES:000005
database_cross_reference: OGES:000032
has OBO namespace: uberon
has related synonym: segmentation stage
id: UBERON:0000111

Axiom
annotated source: organogenesis stage
annotated property: definition
annotated target: A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
database_cross_reference: Organogenesis

anatomical entity
type: Class
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.
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1515976
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BILA:0000000
database_cross_reference: BIRNLEX:6
database_cross_reference: CARO:0000000
database_cross_reference: EHDAA2:0002229
database_cross_reference: FBbt:10000000
database_cross_reference: FBbt_root:00000000
database_cross_reference: FMA:62955
database_cross_reference: HAO:0000000
database_cross_reference: MA:0000001
database_cross_reference: NCIT:C12219
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
database_cross_reference: UMLS:C1515976
database_cross_reference: WBbt:0000100
database_cross_reference: XAO:0000000
database_cross_reference: ZFA:0100000
has OBO namespace: uberon
id: UBERON:0001062
in subset: upper level

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.
database_cross_reference: http://orcid.org/0000-0001-9114-8737
database_cross_reference: FMA:62955

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

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

Imp
comment: This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps"
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: occurs in
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: part of
  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