None
Echinoderm Anatomy and Development Ontology
definition
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
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.
is a defining property chain axiom where second argument is reflexive
database_cross_reference
has_exact_synonym
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
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.
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
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'.
part_of
BFO:0000050
uberon
part_of
part_of
part of
part of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
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.
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
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'.
has_part
BFO:0000051
uberon
has_part
has_part
has part
has part
preceded by
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
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.
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.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
BFO:0000062
is preceded by
takes place after
uberon
preceded_by
preceded_by
preceded by
preceded_by
is preceded by
SIO:000249
takes place after
Allen:precedes
precedes
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.
BFO:0000063
uberon
precedes
precedes
precedes
precedes
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
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
site of
[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
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
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.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
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.
dos
2017-05-24T09:30:46Z
has regulatory component activity
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.
dos
2017-05-24T09:31:01Z
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 negative regulatory component activity
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.
dos
2017-05-24T09:31:17Z
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 positive regulatory component activity
dos
2017-05-24T09:44:33Z
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
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.
dos
2017-05-24T09:49:21Z
has component process
dos
2017-09-17T13:52:24Z
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.
directly regulated by
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.
GOC:dos
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.
dos
2017-09-17T13:52:38Z
directly negatively regulated by
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.
GOC:dos
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.
dos
2017-09-17T13:52:47Z
directly positively regulated by
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.
GOC:dos
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.
dos
2017-09-22T14:14:36Z
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
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.
GOC:dos
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
David Osumi-Sutherland
starts_at_end_of
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].
RO:0002087
directly preceded by
is directly preceded by
is immediately preceded by
starts_at_end_of
uberon
immediately_preceded_by
immediately_preceded_by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
immediately_preceded_by
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].
SIO:000251
is immediately preceded by
SIO:000251
David Osumi-Sutherland
ends_at_start_of
meets
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
true
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.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
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.
has component
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
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
Terry Meehan
RO:0002202
uberon
develops_from
develops_from
This is the transitive form of the develops from relation
develops from
develops_from
inverse of develops from
Chris Mungall
David Osumi-Sutherland
Terry Meehan
RO:0002203
uberon
develops_into
develops_into
develops into
develops_into
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.
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
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
regulates
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.
Chris Mungall
negatively regulates (process to process)
negatively regulates
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.
Chris Mungall
positively regulates (process to process)
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
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.
Chris Mungall
has function realized in
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)".
RO_0000053 some (RO_0000054 only ?Y)
capable of
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.
Chris Mungall
has function in
RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
capable of part of
true
Chris Mungall
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.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
Relation between occurrents, shares a start boundary with.
RO:0002223
uberon
starts
starts
starts
Relation between occurrents, shares a start boundary with.
Allen:starts
RO:0002224
uberon
starts_with
starts_with
starts with
Relation between occurrents, shares an end boundary with.
RO:0002229
finishes
uberon
ends
ends
ends
Relation between occurrents, shares an end boundary with.
Allen:starts
ZFS:finishes
RO:0002230
uberon
ends_with
ends_with
ends with
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.
Chris Mungall
consumes
has input
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
Chris Mungall
RO:0002254
uberon
has_developmental_contribution_from
has_developmental_contribution_from
has developmental contribution from
has developmental contribution from
inverse of has developmental contribution from
Chris Mungall
RO:0002255
uberon
developmentally_contributes_to
developmentally_contributes_to
developmentally contributes to
developmentally_contributes_to
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
false
Chris Mungall
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
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.
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
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
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.
affects
acts upstream of or within
Inverse of developmentally preceded by
Chris Mungall
developmentally succeeded by
cjm
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, positive effect
cjm
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
causally upstream of, negative effect
A mereological relationship or a topological relationship
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
a particular instances of akt-2 enables some instance of protein kinase activity
Chris Mungall
catalyzes
executes
has
is catalyzing
is executing
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.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
Chris Mungall
false
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
Chris Mungall
actively involved in
enables part of
involved in
inverse of enables
Chris Mungall
enabled by
inverse of regulates
Chris Mungall
regulated by (processual)
regulated by
inverse of negatively regulates
Chris Mungall
negatively regulated by
inverse of positively regulates
Chris Mungall
positively regulated by
inverse of has input
Chris Mungall
input of
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).
Chris Mungall
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
Chris Mungall
RO:0002385
uberon
has_potential_to_developmentally_contribute_to
has_potential_to_developmentally_contribute_to
has potential to developmentally contribute to
has potential to developmentally contribute to
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
Chris Mungall
RO:0002387
uberon
has_potential_to_develop_into
has_potential_to_develop_into
has potential to develop into
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
Chris Mungall
has potential to directly develop into
inverse of upstream of
Chris Mungall
causally downstream of
Chris Mungall
immediately causally downstream of
This relation groups causal relations between material entities and causal relations between processes
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 yield a cross-product of different relation types.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
causally upstream of
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.
Chris Mungall
immediately causally upstream of
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.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
affects
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
Chris Mungall
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
Chris Mungall
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
Chris Mungall
involved in negative regulation of
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
OWL does not allow defining object properties via a Union
Chris Mungall
involved in or reguates
involved in or involved in regulation of
A protein that enables activity in a cytosol.
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.
Chris Mungall
executes activity in
enables activity in
is active in
true
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.
GOC:cjm
GOC:dos
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
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.
Chris Mungall
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.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/MI_0914
https://github.com/oborel/obo-relations/wiki/InteractionRelations
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.
Chris Mungall
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
Axiomatization to GO to be added later
Chris Mungall
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
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.
Chris Mungall
Vasundra Touré
molecularly controls
directly regulates activity of
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.
Chris Mungall
Vasundra Touré
directly inhibits
molecularly decreases activity of
directly negatively regulates activity of
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.
Chris Mungall
Vasundra Touré
directly activates
molecularly increases activity of
directly positively regulates activity of
Chris Mungall
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
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.
Chris Mungall
has part that occurs in
true
Chris Mungall
is kinase activity
Chris Mungall
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.
relation between physical entity and a process or stage
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
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).
Chris Mungall
RO:0002488
begins_to_exist_during
uberon
RO:0002488
existence_starts_during
existence_starts_during
existence starts during
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
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))
Chris Mungall
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 overlaps
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.
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).
Chris Mungall
RO:0002492
ceases_to_exist_during
uberon
RO:0002492
existence_ends_during
existence_ends_during
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
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.
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).
Chris Mungall
RO:0002496
uberon
existence_starts_during_or_after
existence_starts_during_or_after
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence starts during or after
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.
Chris Mungall
RO:0002497
uberon
existence_ends_during_or_before
existence_ends_during_or_before
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
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in process
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.
Chris Mungall
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 processes
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
Chris Mungall
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
Chris Mungall
causally influenced by (entity-centric)
causally influenced by
Chris Mungall
interaction relation helper property
https://github.com/oborel/obo-relations/wiki/InteractionRelations
Chris Mungall
molecular interaction relation helper property
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).
Chris Mungall
Vasundra Touré
causally influences (entity-centric)
causally influences
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.
Chris Mungall
directly regulates (processual)
directly regulates
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
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
Chris Mungall
has part structure that is capable of
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.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
capable of positively regulating
Inverse of 'causal agent in process'
process has causal agent
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.
directly positively regulates (process to process)
directly positively regulates
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.
directly negatively regulates (process to process)
directly negatively regulates
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
cjm
2018-01-25T23:20:13Z
enables subfunction
cjm
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
cjm
2018-01-26T23:49:51Z
acts upstream of or within, negative effect
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
cjm
2018-01-26T23:53:14Z
acts upstream of, positive effect
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
cjm
2018-01-26T23:53:22Z
acts upstream of, negative effect
cjm
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
cjm
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
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.
Vasundra Touré
regulates activity of
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
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
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
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
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
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
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.
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
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
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])
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])
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])
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])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
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
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])
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])
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])
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])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
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])
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])
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])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(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]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
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])
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])
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])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(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]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
material
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
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
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.
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.
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])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(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]
(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]
material entity
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])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(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]
(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]
immaterial entity
anatomical entity
material anatomical entity
immaterial anatomical entity
biological entity
root node
life cycle period
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.
gametogenesis
ecao_developmental_stage
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.
ovogenesis period
oogenesis period
ecao_developmental_stage
A female gamete that is small in size, i.e. about 10??m in diameter, and that is at the previtellogenic stage.
previtellogenic primary oocyte stage
ecao_developmental_stage
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.
not fully grown oocyte stage
ecao_developmental_stage
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.
fully grown oocyte with centered germinal vesicle stage
ecao_developmental_stage
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.
primary oocyte
fully grown oocyte with off-centered germinal vesicle stage
ecao_developmental_stage
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.
fully grown oocyte with no nucleus stage
ecao_developmental_stage
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.
spawned egg
unfertilized egg
mature oocyte stage
ecao_developmental_stage
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.
spermatogenesis period
ecao_developmental_stage
A developing, immature male gamete undergoing mitosis and meiosis to ultimately produce mature spermatozoa.
spermatid
developing spermatozoa stage
ecao_developmental_stage
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.
spermatozoa
sperm
mature spermatozoid stage
ecao_developmental_stage
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.
embryogenesis
ecao_developmental_stage
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.
UBERON:0000106
fertilized egg
zygote stage
1-cell stage
ecao_developmental_stage
Period during which the fertilized egg undergoes a succession of rapid cell divisions with no significant growth.
UBERON:0000107
cleavage period
ecao_developmental_stage
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.
UBERON:0007232
2c
2-cell stage
ecao_developmental_stage
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.
UBERON:0007233
4c
4-cell stage
ecao_developmental_stage
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.
UBERON:0007236
8c
8-cell stage
ecao_developmental_stage
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.
16c
16-cell stage
ecao_developmental_stage
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.
28c
28-cell stage
ecao_developmental_stage
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.
32c
32-cell stage
ecao_developmental_stage
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.
56c
56-cell stage
ecao_developmental_stage
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.
60c
60-cell stage
ecao_developmental_stage
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.
UBERON:0000307
blastula period
ecao_developmental_stage
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 .
120-cell stage
B1
vEB
very early blastula stage
ecao_developmental_stage
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 .
B2
EB
early blastula stage
ecao_developmental_stage
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 .
B3
midB
mid-B
mid-blastula stage
ecao_developmental_stage
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 .
B4
LB
pre-HB
prehatched blastula
Late-B
late blastula stage
ecao_developmental_stage
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.
B5
very late blastula stage
HB
hatched blastula stage
ecao_developmental_stage
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.
SB
swimming blastula stage
ecao_developmental_stage
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.
late-SB
late swimming blastula stage
ecao_developmental_stage
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).
UBERON:0000109
gastrula period
ecao_developmental_stage
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.
mesenchyme blastula phase
ecao_developmental_stage
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.
eMB
early mesenchyme blastula stage
ecao_developmental_stage
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.
mid-MB
mid-mesenchyme blastula stage
ecao_developmental_stage
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.
late mesenchyme blastula stage
ecao_developmental_stage
Period during which the inpocketing and elongation of the archenteron takes place.
invagination phase
ecao_developmental_stage
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.
blastopore gastrula stage
blasto-G
blastopore formation stage
ecao_developmental_stage
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.
EG
eG
early gastrula stage
ecao_developmental_stage
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.
mid-G
G
mid-gastrula stage
ecao_developmental_stage
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.
late-G
LG
late gastrula stage
ecao_developmental_stage
To be written
organogenesis period
ecao_developmental_stage
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 labeling surveys also start by this stage to reveal the presence of differentiating neuronal cells.
D
Pr
prism stage
ecao_developmental_stage
larval development
ecao_developmental_stage
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.
UBERON:0000069
early feeding larva period
ecao_developmental_stage
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.
UBERON:0008265
2-arm pluteus stage
early pluteus stage
Eplut
early pluteus larva stage
ecao_developmental_stage
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.
UBERON:0008265
P
Plut
Plut4a
pluteus larva
Pluteus
4-arm pluteus larva stage
ecao_developmental_stage
To be written
late feeding larva period
ecao_developmental_stage
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.
UBERON:0008265
Plut6a
6-arm pluteus larva stage
ecao_developmental_stage
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 further subsequently fused to form the adult rudiment. The formation of the rudiment has overall taken some time, giving rise first to a pentaradial disc and then to a pentaradial complex structure harboring podia (i.e. tube feet) and spines. In parallel, on the right size of the larva, a variable number of pedicellariae (one to four) and endoskeletal elements (i.e. the five genital plates) have further formed, which will also later contribute to the composition of the adult body.
UBERON:0008265
Plut8a
8-arm pluteus larva stage
ecao_developmental_stage
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.
UBERON:0008265
Cpt8a
cPlut
competent pluteus larva stage
ecao_developmental_stage
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.
meta
metamorphosis
metamorphic larva stage
ecao_developmental_stage
Biological process during which changes occur in biological and psychological domains to generate a sexually mature animal.
adulthood
ecao_developmental_stage
Period during which a young individual, posing as a small adult, grows but remains unable to reproduce.
UBERON:0034919
juvenile period
ecao_developmental_stage
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.
UBERON:0007021
endotrophic juvenile
postlarva
PLJuv
early juvenile stage
ecao_developmental_stage
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.
UBERON:0007021
ExJuv
late juvenile stage
ecao_developmental_stage
Period during which the animal reaches sexual maturity.
UBERON:0000066
adult period
ecao_developmental_stage
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.
UBERON:0000113
gravid sea urchin
sexual mature sea urchin
adult stage
ecao_developmental_stage
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.
vLB
very late blastula stage
ecao_developmental_stage
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.
VP
vegetal plate stage
ecao_developmental_stage
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.
UBERON:0001062
echinoderm anatomy
echinoderm_anatomy
Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome
UBERON:0000061
anatomical structure
echinoderm_anatomy
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
UBERON:0000467
body system
connected anatomical system
organ system
anatomical system
echinoderm_anatomy
A region of the whole organism without well-defined compartmental boundaries
UBERON:0000475
organism subdivision
anatomical region
echinoderm_anatomy
UBERON:0000464
anatomical space
echinoderm_anatomy
Anatomical structure that is an individual member of a species and consists of one cell or more
whole organism
echinoderm_anatomy
Anatomical structure that is an individual member of a species and consists of more than one cell
UBERON:0000468
multicellular organism
echinoderm_anatomy
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
UBERON:0000922
embryo
echinoderm_anatomy
UBERON:0002548
larva
echinoderm_anatomy
UBERON:0034919
juvenile
echinoderm_anatomy
UBERON:0007023
adult
echinoderm_anatomy
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
UBERON:0001007
digestive system
echinoderm_anatomy
The gastrointestinal tract that is being formed during embryonic development starting with the formation of the primitive gut tube (or archenteron)
embryonic digestive system
echinoderm_anatomy
Organ system responsible for the food uptake and processing in the larva
larval digestive system
echinoderm_anatomy
juvenile digestive system
echinoderm_anatomy
Anatomical system that processes ingested substances in the adult
adult digestive system
echinoderm_anatomy
UBERON:0002405
immune system
echinoderm_anatomy
embryonic immune system
echinoderm_anatomy
larval immune system
echinoderm_anatomy
juvenile immune system
echinoderm_anatomy
adult immune system
echinoderm_anatomy
Anatomical system that has as its parts the organs concerned with reproduction, i.e. the male and female gonads.
UBERON:0000990
reproductive system
echinoderm_anatomy
UBERON:0001016
nervous system
echinoderm_anatomy
The sum of all the structures in the embryo that will develop into the larval nervous system
embryonic nervous system
echinoderm_anatomy
The sum of all the neural structures present in the larva
larval nervous system
echinoderm_anatomy
juvenile nervous system
echinoderm_anatomy
UBERON:6003559
adult nervous system
echinoderm_anatomy
UBERON:0000383
muscular system
echinoderm_anatomy
larval muscular system
echinoderm_anatomy
juvenile muscular system
echinoderm_anatomy
UBERON:6003218
adult muscular system
echinoderm_anatomy
Internal support structure of an animal composed of mineralized tissue. It gives shape, support and protection to the body.
UBERON:0001434
endoskeleton
echinoderm_anatomy
embryonic endoskeleton
echinoderm_anatomy
larval endoskeleton
echinoderm_anatomy
skeletal rudiment
rudiment endoskeleton
echinoderm_anatomy
juvenile endoskeleton
echinoderm_anatomy
adult endoskeleton
echinoderm_anatomy
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.
UBERON:0008251
water vascular system
echinoderm_anatomy
The hemal system contains the blood. It is composed of a complex network of vessels mainly located around the gut.
haemal system
hemal system
echinoderm_anatomy
Anatomical region that corresponds to the upper half of the embryo, which later is composed of the mesomeres, and ultimately encompasses the presumptive ectoderm
UBERON:0012284
upper half
upper hemisphere
animal half
animal hemisphere
echinoderm_anatomy
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
UBERON:0012285
lower half
lower hemisphere
vegetal half
vegetal hemisphere
echinoderm_anatomy
cell cortex
echinoderm_anatomy
cleavage furrow
echinoderm_anatomy
Cell component comprising the outermost layer of the animal region of the oocyte. It consists of a phospholipid bilayer and associated proteins
animal cortex
echinoderm_anatomy
Cell component comprising the outermost layer of the vegetal region of the oocyte. It consists of a phospholipid bilayer and associated proteins
vegetal cortex
echinoderm_anatomy
The apical region of the animal hemisphere
animal pole
echinoderm_anatomy
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
vegetal pole
echinoderm_anatomy
animal plate
anterior neuroectoderm
apical plate
neurogenic ectoderm
apical pole domain
animal pole domain
echinoderm_anatomy
UBERON:0000100
blastopore
echinoderm_anatomy
UBERON:3010455
blastopore lip
echinoderm_anatomy
bottle cell
echinoderm_anatomy
embryonic cell
echinoderm_anatomy
vegetal plate
echinoderm_anatomy
Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane
cell
echinoderm_anatomy
Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher.
cell part
echinoderm_anatomy
Any of the organs or elements that are part of the digestive system
UBERON:0013765
digestive system element
echinoderm_anatomy
UBERON:0004765
skeletal element
echinoderm_anatomy
Any anatomical structure that is part of an embryo
UBERON:0002050
embryonic structure
echinoderm_anatomy
Any anatomical structure that is part of a larva
larval structure
echinoderm_anatomy
Any anatomical structure that is part of a juvenile
juvenile structure
echinoderm_anatomy
Any anatomical structure that is part of an adult
adult structure
echinoderm_anatomy
UBERON:0000479
tissue
echinoderm_anatomy
imaginal adult rudiment
adult rudiment
rudiment
echinoderm_anatomy
rudiment structure
echinoderm_anatomy
non-rudiment adult structure
echinoderm_anatomy
intracellular part
echinoderm_anatomy
cytoskeleton
echinoderm_anatomy
microtubule
echinoderm_anatomy
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
nucleus
echinoderm_anatomy
A female haploid germ cell.
oocyte
echinoderm_anatomy
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
germinal vesicle
echinoderm_anatomy
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
pigmented band
pigment band
equatorial pigment band
echinoderm_anatomy
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures
cytoplasm
echinoderm_anatomy
centrosome
echinoderm_anatomy
mitotic spindle
echinoderm_anatomy
meiotic spindle
echinoderm_anatomy
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
fertilization membrane
fertilization envelope
echinoderm_anatomy
A mature male germ cell
male gamete
mature sperm cell
spermatozoa
spermatozoan
sperm
spermatozoid
echinoderm_anatomy
mitotic aster
spindle aster
aster
echinoderm_anatomy
spermatozoid aster
sperm aster
echinoderm_anatomy
UBERON:0005764
acellular membrane
echinoderm_anatomy
UBERON:0003125
vitelline envelope
vitelline layer
vitelline membrane
echinoderm_anatomy
hyaline membrane
hyaline layer
echinoderm_anatomy
microvillus
echinoderm_anatomy
fibropellin layer
apical lamina
echinoderm_anatomy
secretory vesicle
echinoderm_anatomy
cilium
echinoderm_anatomy
filopodium
echinoderm_anatomy
UBERON:0000482
basal lamina
echinoderm_anatomy
basal vesicle
basal lamina vesicle
basal laminar vesicle
echinoderm_anatomy
apical vesicle
echinoderm_anatomy
cortical vesicle
cortical granule
echinoderm_anatomy
echinonectin granule
nectosome
echinonectin vesicle
echinoderm_anatomy
mitochondrion
echinoderm_anatomy
actin cytoskeleton
echinoderm_anatomy
F-actin filament
microfilament
actin filament
echinoderm_anatomy
nuclear part
echinoderm_anatomy
nucleoplasm
echinoderm_anatomy
nuclear envelope
echinoderm_anatomy
endoplasmic reticulum
echinoderm_anatomy
spermatozoid entry point
echinoderm_anatomy
cell membrane
plasma membrane
echinoderm_anatomy
A small cell formed by the meiotic division of an oocyte
polar body
echinoderm_anatomy
sperm part
spermatozoid part
echinoderm_anatomy
The part of the late spermatid or spermatozoon that contains the nucleus and acrosome.
spermatozoid head
echinoderm_anatomy
A microtubule-based flagellum (or cilium) that is part of a sperm, a mature male germ cell that develops from a spermatid
sperm tail
spermatozoid flagellum
echinoderm_anatomy
An organelle that develops over the anterior half of the head in the spermatozoa
acrosome
acrosomal vesicle
echinoderm_anatomy
presumptive primordial germ cell
small micromere descendant cell
echinoderm_anatomy
presumptive primordial germ cell
echinoderm_anatomy
primordial germ cell
echinoderm_anatomy
germ cell
echinoderm_anatomy
gamete
echinoderm_anatomy
immature egg
immature occyte
echinoderm_anatomy
A mature female gamet that has entered meiosis.
female gamete
female germ cell
unfertilized egg
egg
mature oocyte
echinoderm_anatomy
An undifferentiated cell produced by early cleavages of the fertilized egg (zygote)
blastoderm cell
blastomere
echinoderm_anatomy
blastomere of 2-cell embryo
echinoderm_anatomy
blastomere of 4-cell embryo
echinoderm_anatomy
Intermediate size blastomere forming the animal hemisphere of the cleaving embryo
mesomeres
mesomere
echinoderm_anatomy
Larger blastomere of the vegetal hemisphere of the cleaving embryo located below the equator
macromeres
macromere
echinoderm_anatomy
blastomere tier
cell tier
echinoderm_anatomy
macromere daughter cell tier
echinoderm_anatomy
Small blastomere of the vegetal hemisphere of the cleaving embryo located at to the vegetal pole
micromeres
micromere
echinoderm_anatomy
large micromere
echinoderm_anatomy
presumptive PMC
presumptive primary mesenchyme cell
presumptive skeletogenic mesenchyme cell
large micromere progeny
large micromere descendant cell
echinoderm_anatomy
SM
small micromere
echinoderm_anatomy
A progenitor cell of the nervous system that will develop into a neuron
neuronal progenitor cell
presumptive neuron
echinoderm_anatomy
animal pole domain neuronal progenitor cell
apical pole domain presumptive neuron
animal pole domain presumptive neuron
echinoderm_anatomy
ectoderm neuronal progenitor cell
ectoderm presumptive neuron
echinoderm_anatomy
ciliary band neuronal progenitor cell
ciliary band presumptive neuron
echinoderm_anatomy
endoderm associated neuronal progenitor cell
endoderm associated presumptive neuron
echinoderm_anatomy
nerve cell
neuron
echinoderm_anatomy
larval neuron
echinoderm_anatomy
serotonergic neuron
echinoderm_anatomy
synaptotagmin-B neuron
echinoderm_anatomy
dopaminergic neuron
echinoderm_anatomy
GABAergic neuron
echinoderm_anatomy
sensory cell
sensory neuron
echinoderm_anatomy
biopolar neuron
echinoderm_anatomy
multipolar neuron
echinoderm_anatomy
neuronal structure
neural structure
echinoderm_anatomy
UBERON:0001018
axon bundle
axonal tract
axon tract
echinoderm_anatomy
peripheral neuron
ciliary band neuron
echinoderm_anatomy
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
UBERON:0000924
ectoderm
echinoderm_anatomy
presumptive ciliary band cell
echinoderm_anatomy
endoderm associated neuron
echinoderm_anatomy
UBERON:0000045
ganglion
echinoderm_anatomy
apical organ
apical ganglion
echinoderm_anatomy
adult neuron
echinoderm_anatomy
circumoral nerve ring
echinoderm_anatomy
UBERON:0000429
digestive nerve plexus
enteric plexus
enteric nerve plexus
echinoderm_anatomy
radial nerve cord
echinoderm_anatomy
primary podia associated neuron
echinoderm_anatomy
secondary podia associated neuron
echinoderm_anatomy
definitive spine associated neuron
echinoderm_anatomy
pedicellaria associated neuron
echinoderm_anatomy
basiepidermal nerve plexus
echinoderm_anatomy
Group of four cells of equal size forming the animal hemisphere of an eight-cell stage embryo
animal quartet
echinoderm_anatomy
Group of four cells of equal size forming the vegetal hemisphere of an eight-cell stage embryo
vegetal quartet
echinoderm_anatomy
an1
animal tier 1
echinoderm_anatomy
an2
animal tier 2
echinoderm_anatomy
ectoendoderm
veg1
vegetal tier 1
echinoderm_anatomy
endomesoderm
veg2
vegetal tier 2
echinoderm_anatomy
presumptive vegetal ectoderm
veg1 upper
veg1U
vegetal tier 1 upper
echinoderm_anatomy
veg1 lower
veg1L
vegetal tier 1 lower
echinoderm_anatomy
veg2 upper
veg2U
vegetal tier 2 upper
echinoderm_anatomy
presumptive non-skeletogenic mesoderm
veg2 lower
veg2L
vegetal tier 2 lower
echinoderm_anatomy
UBERON:0000923
embryonic germ layer
primary germ layer
germ layer
echinoderm_anatomy
UBERON:0005291
embryonic tissue
echinoderm_anatomy
UBERON:0006601
presumptive ectoderm
echinoderm_anatomy
animal ectoderm
echinoderm_anatomy
vegetal ectoderm
echinoderm_anatomy
oral ectoderm
ventral ectoderm
echinoderm_anatomy
aboral ectoderm
dorsal ectoderm
echinoderm_anatomy
veg1
vegetal tier 1
ectoendoderm
echinoderm_anatomy
mesoendoderm
veg2
vegetal tier 2
endomesoderm
echinoderm_anatomy
inner apical pole domain
inner animal pole domain
echinoderm_anatomy
outer apical pole domain
outer animal pole domain
echinoderm_anatomy
central ectoderm
echinoderm_anatomy
BE
border ectoderm
echinoderm_anatomy
near-apical ectoderm
echinoderm_anatomy
apical ectoderm
echinoderm_anatomy
veg1-lateral ectoderm
echinoderm_anatomy
veg-1 oral ectoderm
echinoderm_anatomy
lateral ectoderm
echinoderm_anatomy
right lateral ectoderm
echinoderm_anatomy
left lateral ectoderm
echinoderm_anatomy
arm tip ectoderm
echinoderm_anatomy
dorsal arm tip ectoderm
echinoderm_anatomy
ventral arm tip ectoderm
echinoderm_anatomy
apical tuft
echinoderm_anatomy
larval tissue
echinoderm_anatomy
rudiment tissue
echinoderm_anatomy
juvenile tissue
echinoderm_anatomy
adult tissue
echinoderm_anatomy
presumptive stomodeum
echinoderm_anatomy
UBERON:0000930
presumptive mouth
stomodeum
echinoderm_anatomy
ciliary band
echinoderm_anatomy
oral hood ciliary band
echinoderm_anatomy
arm ciliary band
echinoderm_anatomy
animal pole ciliary band
echinoderm_anatomy
vegetal ciliary band
echinoderm_anatomy
lateral ciliary band
echinoderm_anatomy
PL
preoral lobe
oh
oral hood
echinoderm_anatomy
apex
echinoderm_anatomy
larval arm
echinoderm_anatomy
ALA
AL
right anterolateral arm
echinoderm_anatomy
ALA
AL
left anterolateral arm
echinoderm_anatomy
PO
right postoral arm
echinoderm_anatomy
PO
left postoral arm
echinoderm_anatomy
PD
right posterodorsal arm
echinoderm_anatomy
PD
left posterodorsal arm
echinoderm_anatomy
PRO
PR
right preoral arm
echinoderm_anatomy
PRO
PR
left preoral arm
echinoderm_anatomy
spicule rudiment
echinoderm_anatomy
spicule dot
spicule granule
echinoderm_anatomy
spicule primordium
triradiate spicule rudiment
echinoderm_anatomy
triradiate spicule
right ventrolateral triradiate spicule rudiment
echinoderm_anatomy
left ventrolateral triradiate spicule rudiment
echinoderm_anatomy
hexaradiate spicule
hexaradiate spicule rudiment
echinoderm_anatomy
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.
primary triradiate skeletal rudiment
larval spicule
echinoderm_anatomy
The embryonic tissue made up of loosely connected mesoderm cells that will produce all of the skeletal elements.
primary mesenchyme
SM
embryonic skeletogenic mesenchyme
echinoderm_anatomy
spicule rod
skeletal rod
echinoderm_anatomy
anonymous rod
echinoderm_anatomy
right anonymous rod
echinoderm_anatomy
left anonymous rod
echinoderm_anatomy
right dorsoventral connecting rod
echinoderm_anatomy
right anterolateral rod
echinoderm_anatomy
left dorsoventral connecting rod
echinoderm_anatomy
left anterolateral rod
echinoderm_anatomy
right postoral rod
echinoderm_anatomy
left postoral rod
echinoderm_anatomy
right posterodorsal rod
echinoderm_anatomy
left posterodorsal rod
echinoderm_anatomy
dorsal arch
echinoderm_anatomy
right preoral rod
echinoderm_anatomy
left preoral rod
echinoderm_anatomy
right ventral transverse rod
echinoderm_anatomy
left ventral transverse rod
echinoderm_anatomy
posterior tip of body rod
echinoderm_anatomy
body rod end
scheitel
echinoderm_anatomy
body rod
echinoderm_anatomy
left body rod
echinoderm_anatomy
right body rod
echinoderm_anatomy
posterior tip of left body rod
echinoderm_anatomy
posteror tip of right body rod
echinoderm_anatomy
right recurrent rod
echinoderm_anatomy
left recurrent rod
echinoderm_anatomy
posterior transverse rod
echinoderm_anatomy
UBERON:0000165
mouth
echinoderm_anatomy
larval mouth
echinoderm_anatomy
UBERON:0001245
anus
echinoderm_anatomy
larval anus
echinoderm_anatomy
UBERON:0006595
prospective endoderm
presumptive endoderm
echinoderm_anatomy
UBERON:0000925
endoderm
echinoderm_anatomy
UBERON:0004735
primitive gut
embryonic gut
archenteron
echinoderm_anatomy
UBERON:0001046
hindgut
echinoderm_anatomy
dorsal hindgut
echinoderm_anatomy
ventral hindgut
echinoderm_anatomy
UBERON:0001045
midgut
echinoderm_anatomy
ventral midgut
echinoderm_anatomy
dorsal midgut
echinoderm_anatomy
anterior midgut
echinoderm_anatomy
posterior midgut
echinoderm_anatomy
anterior hindgut
echinoderm_anatomy
posterior hindgut
echinoderm_anatomy
UBERON:0001041
tip of the digestive tract
foregut
echinoderm_anatomy
ventral foregut
echinoderm_anatomy
dorsal foregut
echinoderm_anatomy
anterior foregut
echinoderm_anatomy
posterior foregut
echinoderm_anatomy
UBERON:3010432
archenteron roof
tip of archenteron
echinoderm_anatomy
UBERON:0006603
prospective mesoderm
presumptive mesoderm
echinoderm_anatomy
UBERON:0000926
mesoderm
echinoderm_anatomy
The subset of the embryonic mesoderm that will later give rise to the skeletogenic mesenchyme and embryonic skeleton.
embryonic skeletogenic mesoderm
echinoderm_anatomy
primary mesenchyme cell
PMC
embryonic skeletogenic mesenchyme cell
echinoderm_anatomy
multinucleated cell
syncytial cell
syncytium
multinucleate cell
syncytium
echinoderm_anatomy
Anatomical structure composed of skeletogenic mesenchyme cells that have fused to form a single syncytial network.
embryonic skeletogenic mesenchyme syncytium
echinoderm_anatomy
PMC ring
primary mesenchyme cell ring
subequatorial PMC ring
subequatorial SM ring
subequatorial primary mesenchyme cell ring
SM ring
subequatorial skeletogenic mesenchyme ring
echinoderm_anatomy
Subpopulation of skeletogenic mesenchyme forming a chain on the oral (i.e. ventral) side of the embryo.
ventral skeletogenic mesenchyme chain
echinoderm_anatomy
Subpopulation of skeletogenic mesenchyme forming a chain on the aboral (i.e. dorsal) side of the embryo.
dorsal skeletogenic mesenchyme chain
echinoderm_anatomy
Subpopulation of skeletogenic mesenchyme forming a cluster (i.e. a group of cells) in the ventrolateral region of the embryo.
right ventrolateral skeletogenic mesenchyme cluster
echinoderm_anatomy
left ventrolateral skeletogenic mesenchyme cluster
echinoderm_anatomy
Subpopulation of skeletogenic mesenchyme forming a chain on either side of the developing digestive tract, along the blastocoel wall and towards the animal pole.
lateral chain of skeletogenic mesenchyme
echinoderm_anatomy
Subpopulation of skeletogenic mesenchyme forming a chain along the blastocoel wall towards the animal pole on the right side of the embryo.
right lateral chain of skeletogenic mesenchyme
echinoderm_anatomy
Subpopulation of skeletogenic mesenchyme forming a chain along the blastocoel wall towards the animal pole on the left side of the embryo.
left lateral chain of skeletogenic mesenchyme
echinoderm_anatomy
embryonic non-skeletogenic mesoderm
echinoderm_anatomy
ventral non-skeletogenic mesoderm
echinoderm_anatomy
dorsal non-skeletogenic mesoderm
echinoderm_anatomy
NSM
secondary mesenchyme
embryonic non-skeletogenic mesenchyme
echinoderm_anatomy
secondary mesenchyme cell
SMC
embryonic non-skeletogenic mesenchyme cell
echinoderm_anatomy
larval non-skeletogenic mesenchyme
echinoderm_anatomy
larval non-skeletogenic mesenchyme cell
echinoderm_anatomy
presumptive blastocoelar cell
echinoderm_anatomy
presumptive immunocyte
presumptive pigmented cell
presumptive pigment cell
echinoderm_anatomy
a cell that contains red coloring matter
pigmented immunocyte
pigmented cell
pigment cell
echinoderm_anatomy
embryonic pigment cell
echinoderm_anatomy
larval pigment cell
echinoderm_anatomy
juvenile pigment cell
echinoderm_anatomy
rudiment pigment cell
echinoderm_anatomy
blastocoelar cell
echinoderm_anatomy
globular cell
echinoderm_anatomy
filopodial cell
echinoderm_anatomy
ovoid cell
echinoderm_anatomy
amoeboid cell
echinoderm_anatomy
presumptive muscle cell
muscle precursor cell
echinoderm_anatomy
muscle
echinoderm_anatomy
contractile muscle
larval muscle
echinoderm_anatomy
rudiment muscle
echinoderm_anatomy
juvenile muscle
echinoderm_anatomy
adult muscle
echinoderm_anatomy
UBERON:0000090
blastocoel
echinoderm_anatomy
sphincter
echinoderm_anatomy
midgut-hindgut constriction
pyloric sphincter
echinoderm_anatomy
foregut-midgut constriction
cardiac sphincter
echinoderm_anatomy
hindgut-ectoderm constriction
anal sphincter
echinoderm_anatomy
UBERON:0004590
sphincter muscle
echinoderm_anatomy
myoepithelial cell
sphincter muscle cell
echinoderm_anatomy
UBERON:0001202
pyloric sphincter
pyloric sphincteric muscle
echinoderm_anatomy
cardiac sphincter
cardiac sphincteric muscle
echinoderm_anatomy
UBERON:0004916
anal sphincter
anal sphincteric muscle
echinoderm_anatomy
larval esophagus
echinoderm_anatomy
circumesophageal muscle
echinoderm_anatomy
presumptive circumesophageal muscle cell
circumesophageal muscle cell
echinoderm_anatomy
larval stomach
echinoderm_anatomy
larval intestine
echinoderm_anatomy
The mesenchyme cells that produce new skeletal elements (i.e., the posterodorsal rods, dorsal arch, and preoral rods) in the larva after feeding begins
larval skeletogenic mesenchyme
echinoderm_anatomy
larval skeletogenic mesenchyme cell
echinoderm_anatomy
UBERON:0011997
coelom
echinoderm_anatomy
unpaired coelomic rudiment
unpaired coelomic pouch
echinoderm_anatomy
right coelomic pouch
echinoderm_anatomy
left coelomic sac
left coelomic pouch
echinoderm_anatomy
right coelomic constriction
echinoderm_anatomy
left coelomic constriction
echinoderm_anatomy
larval epithelium
echinoderm_anatomy
amniotic sac
vestibule
echinoderm_anatomy
UBERON:0002424
circumoral ectoderm
circumoral epithelium
oral epidermis
oral epithelium
echinoderm_anatomy
aboral epithelium
echinoderm_anatomy
The left lateral field is the lateral field located on the left side of the larva
left lateral field
echinoderm_anatomy
Opening located in the left lateral field
vestibular pore
echinoderm_anatomy
anterior coelom
axocoel
echinoderm_anatomy
left axocoel
echinoderm_anatomy
axial coelom
echinoderm_anatomy
central coelom
hydrocoel
echinoderm_anatomy
posterior coelom
somatocoel
echinoderm_anatomy
left hydrocoel
echinoderm_anatomy
left somatocoel
echinoderm_anatomy
anterior sac
right axohydrocoel
echinoderm_anatomy
right somatocoel
echinoderm_anatomy
axial complex
echinoderm_anatomy
stone canal
echinoderm_anatomy
ring canal
echinoderm_anatomy
radial canal
echinoderm_anatomy
hydropore canal
primary pore canal
echinoderm_anatomy
hydropore
echinoderm_anatomy
right axocoel
echinoderm_anatomy
right hydrocoel
echinoderm_anatomy
axial sinus
echinoderm_anatomy
axial organ
echinoderm_anatomy
dorsal sac
echinoderm_anatomy
ciliated epaulette
echinoderm_anatomy
anterior ciliated epaulette
echinoderm_anatomy
posterior ciliated epaulette
echinoderm_anatomy
The lateral field is located in the aboral ectoderm of the larva. It separates the anterior and posterior pairs of epaulettes
lateral field
echinoderm_anatomy
The right lateral field is the lateral field located on the right side of the larva
right lateral field
echinoderm_anatomy
ambulacral plate
echinoderm_anatomy
The mesenchyme cells that produce biomineralized elements (e.g., spines, test plates, and teeth) in the juvenile and adult.
adult skeletogenic mesenchyme
echinoderm_anatomy
int
interambulacral plate
echinoderm_anatomy
ambulacra
echinoderm_anatomy
interambulacra
echinoderm_anatomy
genital plate
echinoderm_anatomy
appendage
echinoderm_anatomy
UBERON:0008261
pedicellaria
echinoderm_anatomy
terminal plate
ocular plate
echinoderm_anatomy
buccal plate
echinoderm_anatomy
genital plate AB
echinoderm_anatomy
genital plate BC
echinoderm_anatomy
genital plate CD
echinoderm_anatomy
genital plate DE
echinoderm_anatomy
genital plate EA
echinoderm_anatomy
UBERON:0008247
tube foot
podia
echinoderm_anatomy
primary tube foot
primary podia
echinoderm_anatomy
disk of primary podia
echinoderm_anatomy
secondary tube foot
secondary podia
echinoderm_anatomy
disk of secondary podia
echinoderm_anatomy
buccal podia
echinoderm_anatomy
UBERON:0008260
spine appendage
spine
echinoderm_anatomy
splayed spines
juvenile spine
echinoderm_anatomy
adult spine
definitive spine
echinoderm_anatomy
sphaeridium
echinoderm_anatomy
UBERON:0008252
tube foot ampulla
ampulla
echinoderm_anatomy
adult mouth
echinoderm_anatomy
adult anus
echinoderm_anatomy
UBERON:0008253
Aristotles lantern
echinoderm_anatomy
tooth
echinoderm_anatomy
UBERON:0009476
madreporite
echinoderm_anatomy
genital pore
gonopore
echinoderm_anatomy
UBERON:0000991
gonad
echinoderm_anatomy
UBERON:0000992
ovary
echinoderm_anatomy
UBERON:0000473
testis
echinoderm_anatomy
juvenile digestive tract
echinoderm_anatomy
adult digestive tract
echinoderm_anatomy
UBERON:0002095
mesentery
echinoderm_anatomy
perivisceral cavity
echinoderm_anatomy
photoreceptor cell
photosensory cell
echinoderm_anatomy
molecular process
molecular_function
catalytic activity
biological_process
true
kinase activity
transferase activity
transferase activity, transferring phosphorus-containing groups
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
uberon
UBERON:0000000
processual entity
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
span:ProcessualEntity
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
adult stage
BTO:0001043
BilaDO:0000004
EFO:0001272
FBdv:00005369
WBls:0000041
XtroDO:0000084
fully formed animal stage
juvenile-adult stage
uberon
UBERON:0000066
fully formed stage
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
BilaDO:0000002
EV:0300001
FBdv:00005289
FMA:72652
HsapDv:0000002
MmusDv:0000002
OGES:000000
OGES:000022
WBls:0000003
WBls:0000092
WBls:0000102
XAO:1000012
embryonic stage
uberon
embryogenesis
UBERON:0000068
embryo stage
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
End of the life of an organism.
ncit:Death is an outcome
XAO:0000437
XtroDO:0000085
uberon
death
UBERON:0000071
death stage
End of the life of an organism.
XAO:0000437
ncit:Death is an outcome
ncit
stage succeeding embryo, including mature structure
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
BilaDO:0000003
OGES:000010
OGES:000014
OGES:000024
WBls:0000022
WBls:0000093
WBls:0000103
postembryonic stage
post-hatching stage
uberon
postembryonic
UBERON:0000092
post-embryonic stage
stage succeeding embryo, including mature structure
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
FBdv:00000000
HsapDv:0000001
MmusDv:0000001
OGES:000011
ncithesaurus:Life
entire life cycle
entire lifespan
life
lifespan
uberon
UBERON:0000104
life cycle
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
BILS:0000105
EFO:0000399
FBdv:00007012
FMA:24120
HsapDv:0000000
MmusDv:0000000
OlatDv:0000010
PdumDv:0000090
WBls:0000002
XAO:1000000
ZFS:0000000
ZFS:0100000
ncithesaurus:Developmental_Stage
developmental stage
stage
uberon
UBERON:0000105
life cycle stage
A spatiotemporal region encompassing some part of the life cycle of an organism.
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
BILS:0000106
BilaDO:0000005
EFO:0001322
EHDAA:27
FBdv:00005288
NCIT:C12601
PdumDv:0000100
VHOG:0000745
XAO:1000001
ZFS:0000001
1-cell stage
fertilized egg stage
one cell stage
uberon
fertilized egg stage
one-cell stage
zygote
zygotum
UBERON:0000106
zygote stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
2012-09-17
VHOG:0000745
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107
fertilized egg stage
BTO:0000854
one-cell stage
VHOG:0000745
zygote
VHOG:0000745
zygotum
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.
BILS:0000107
BilaDO:0000006
EFO:0001290
FBdv:00000054
MESH:A16.254.270
MmusDv:0000004
OGES:000015
OGES:000020
PdumDv:0000200
XAO:1000004
ZFS:0000046
uberon
UBERON:0000107
cleavage stage
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.
GO:0040016
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.
consider adding a preceding stage 'morula stage' as part of cleavage
BILS:0000108
BilaDO:0000007
EFO:0001282
HsapDv:0000006
MmusDv:0000007
OGES:000003
OGES:000016
OGES:000021
OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg
WBls:0000005
XAO:1000003
ZFS:0000045
uberon
UBERON:0000108
blastula stage
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.
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.
BILS:0000109
BilaDO:0000008
EFO:0001296
FBdv:00005317
HsapDv:0000010
MmusDv:0000013
OGES:000004
OGES:000019
WBls:0000010
XAO:1000005
ZFS:0000047
uberon
blastocystis trilaminaris stage
trilaminar blastocyst stage
trilaminar blastoderm stage
trilaminar disk stage
trilaminar germ stage
trilaminar stage
UBERON:0000109
gastrula stage
BILS
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.
GO:0007369
blastocystis trilaminaris stage
trilaminar blastocyst stage
trilaminar blastoderm stage
trilaminar disk stage
trilaminar germ stage
trilaminar stage
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.
BILS:0000110
BilaDO:0000009
HsapDv:0000012
MmusDv:0000017
XAO:1000006
uberon
UBERON:0000110
neurula stage
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.
GO:0001841
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
BILS:0000111
BilaDO:0000010
HsapDv:0000015
MmusDv:0000018
OGES:000005
OGES:000032
uberon
segmentation stage
UBERON:0000111
organogenesis stage
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
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.
AAO:0010841
AEO:0000000
BILA:0000000
BIRNLEX:6
CARO:0000000
EHDAA2:0002229
FBbt:10000000
FBbt_root:00000000
FMA:62955
HAO:0000000
MA:0000001
NCIT:C12219
TAO:0100000
TGMA:0001822
UMLS:C1515976
WBbt:0000100
XAO:0000000
ZFA:0100000
uberon
UBERON:0001062
anatomical entity
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.
FMA:62955
UMLS:C1515976
ncithesaurus:Anatomic_Structure_System_or_Substance
true
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
infer input from direct reg
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'
enabling an MF enables its parts
true
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'
involved in BP
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"
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.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).