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).