None Echinoderm Anatomy and Development Ontology definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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 An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 quality spatial uberon part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of https://wiki.geneontology.org/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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 quality spatial uberon has_part has_part has part has part has_part preceded by 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 uberon preceded_by preceded_by preceded by preceded by 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 X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. BSPO:0000120 NCIT:C25229 spatial uberon in_left_side_of in_left_side_of in left side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. BSPO:PATO_mtg_2009 X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. BSPO:0000121 NCIT:C25228 spatial uberon in_right_side_of in_right_side_of in right side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. BSPO:PATO_mtg_2009 X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure BSPO:0000126 spatial uberon in_lateral_side_of in_lateral_side_of in lateral side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure UBERON:cjm inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in RO:0000052 characteristic_of Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 has_characteristic has characteristic has characteristic https://github.com/oborel/obo-relations/pull/284 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 RO:0000056 uberon participates_in participates_in 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 RO:0000057 has_participant has participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of RO:0000079 function_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of RO:0000080 quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of RO:0000081 role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function RO:0000085 has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality RO:0000086 uberon has_quality has_quality has quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role RO:0000087 has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence RO:0000091 has_disposition has disposition inverse of has disposition RO:0000092 disposition_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of 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. 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity 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. 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity 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. 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity 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 2017-05-24T09:44:33Z RO:0002017 has_component_activity 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. 2017-05-24T09:49:21Z RO:0002018 has_component_process has component process 2017-09-17T13:52:24Z RO:0002022 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. 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. 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. 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by 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. 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. 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by 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. 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. 2017-09-22T14:14:36Z RO:0002025 has_effector_activity 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. David Osumi-Sutherland <= RO:0002081 before_or_simultaneous_with Primitive instance level timing relation between events before or simultaneous with x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), 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 and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 uberon simultaneous_with simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with simultaneous with David Osumi-Sutherland RO:0002086 ends_after X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of RO:0002087 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 David Osumi-Sutherland ends_at_start_of meets RO:0002090 immediately_precedes 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 x overlaps y iff they have some part in common. http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 spatial uberon overlaps overlaps "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF [] overlaps overlaps true x overlaps y iff they have some part in common. BSPO:cjm lactation SubClassOf 'only in taxon' some 'Mammalia' x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria RO:0002160 uberon only_in_taxon only_in_taxon only in taxon x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. RO:0002162 uberon in_taxon in_taxon Connects a biological entity to its taxon of origin. in taxon 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. RO:0002180 uberon has_component has_component has component 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 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 RO:0002203 uberon develops_into develops_into develops into develops into p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 regulates regulates regulates (processual) p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates (process to process) RO:0002212 negatively_regulates negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates (process to process) RO:0002213 positively_regulates 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. 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:0002215 uberon capable_of capable_of capable of 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. has function in RO:0002216 uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true 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 RO:0002222 temporally_related_to A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to inverse of starts with Chris Mungall Allen RO:0002223 uberon starts starts starts starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(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. Chris Mungall started by RO:0002224 uberon starts_with starts_with starts with starts with inverse of ends with Chris Mungall RO:0002229 uberon ends ends ends ends x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(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. Chris Mungall finished by RO:0002230 uberon ends_with 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. consumes RO:0002233 has_input has input https://wiki.geneontology.org/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 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 RO:0002255 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 In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by 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. RO:0002263 acts_upstream_of 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. RO:0002264 affects acts_upstream_of_or_within acts upstream of or within https://wiki.geneontology.org/Acts_upstream_of_or_within Inverse of developmentally preceded by RO:0002286 developmentally_succeeded_by developmentally succeeded by p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. RO:0002295 results_in_developmental_progression_of results in developmental progression of every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. http://www.geneontology.org/GO.doc.development.shtml RO:0002296 results_in_development_of results in development of p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. RO:0002304 causally_upstream_of,_positive_effect 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 p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. RO:0002305 causally_upstream_of,_negative_effect causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of RO:0002314 characteristic_of_part_of characteristic of part of true an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity GOC:mtg_berkeley_2013 RO:0002315 results_in_acquisition_of_features_of results in acquisition of features of A relationship that holds via some environmental process Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. RO:0002320 evolutionarily_related_to evolutionarily related to A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 mereotopologically_related_to mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally_related_to developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. 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. RO:0002327 enables enables https://wiki.geneontology.org/Enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. false RO:0002329 part_of_structure_that_is_capable_of 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 actively involved in enables part of RO:0002331 involved_in involved in https://wiki.geneontology.org/Involved_in inverse of enables RO:0002333 enabled_by enabled by enabled by https://wiki.geneontology.org/Enabled_by inverse of regulates regulated by (processual) RO:0002334 regulated_by regulated by inverse of negatively regulates RO:0002335 negatively_regulated_by negatively regulated by inverse of positively regulates RO:0002336 positively_regulated_by positively regulated by inverse of has input RO:0002352 uberon input_of input_of input of 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). RO:0002384 has_developmental_potential_involving 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 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 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 RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into inverse of upstream of RO:0002404 causally_downstream_of causally downstream of RO:0002405 immediately_causally_downstream_of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates RO:0002407 indirectly_positively_regulates indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits RO:0002409 indirectly_negatively_regulates indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. 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. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. RO:0002411 causally_upstream_of causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. RO:0002412 immediately_causally_upstream_of immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 influences (processual) RO:0002418 affects causally_upstream_of_or_within causally upstream of or within inverse of causally upstream of or within RO:0002427 causally_downstream_of_or_within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p RO:0002428 involved_in_regulation_of involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p RO:0002429 involved_in_positive_regulation_of involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p RO:0002430 involved_in_negative_regulation_of 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 involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of involved in or involved in regulation of 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. 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. RO:0002434 in pairwise interaction with interacts_with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 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. binds molecularly binds with RO:0002436 molecularly_interacts_with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates 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. RO:0002448 molecularly controls directly_regulates_activity_of 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. directly inhibits RO:0002449 molecularly decreases activity of directly_negatively_regulates_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. directly activates RO:0002450 molecularly increases activity of directly_positively_regulates_activity_of directly positively regulates activity of This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. RO:0002464 helper_property_(not_for_use_in_curation) helper property (not for use in curation) RO:0002481 is_kinase_activity is kinase activity 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. RO:0002487 relation_between_physical_entity_and_a_process_or_stage relation between physical entity and a process or stage 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). RO:0002488 uberon existence_starts_during existence_starts_during existence starts during x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). RO:0002489 uberon existence_starts_with existence_starts_with existence starts with 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)) RO:0002490 existence_overlaps 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). RO:0002492 ceases_to_exist_during uberon 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. https://orcid.org/0000-0002-6601-2165 x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). RO:0002493 uberon existence_ends_with existence_ends_with 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 with 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). 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. 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 RO:0002500 causal_agent_in_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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 causal_relation_between_processes causal relation between processes RO:0002502 depends_on depends on 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 Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 causal_relation_between_entities causal relation between entities causally influenced by (entity-centric) RO:0002559 causally_influenced_by causally influenced by RO:0002563 interaction_relation_helper_property interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ RO:0002564 molecular_interaction_relation_helper_property 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). causally influences (entity-centric) RO:0002566 causally_influences causally influences p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) RO:0002578 directly_regulates 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 RO:0002584 has_part_structure_that_is_capable_of 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. RO:0002595 causal_relation_between_material_entity_and_a_process 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. RO:0002596 capable_of_regulating capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. RO:0002597 capable_of_negatively_regulating 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. RO:0002598 capable_of_positively_regulating capable of positively regulating Inverse of 'causal agent in process' RO:0002608 process_has_causal_agent process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) RO:0002629 directly_positively_regulates directly positively regulates https://wiki.geneontology.org/Directly_positively_regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) RO:0002630 directly_negatively_regulates directly negatively regulates https://wiki.geneontology.org/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. 2018-01-25T23:20:13Z RO:0004031 enables_subfunction enables subfunction 2018-01-26T23:49:30Z RO:0004032 acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect 2018-01-26T23:49:51Z RO:0004033 acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect https://wiki.geneontology.org/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 2018-01-26T23:53:14Z RO:0004034 acts_upstream_of,_positive_effect acts upstream of, positive effect https://wiki.geneontology.org/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 2018-01-26T23:53:22Z RO:0004035 acts_upstream_of,_negative_effect acts upstream of, negative effect https://wiki.geneontology.org/Acts_upstream_of,_negative_effect 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect 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. RO:0011002 regulates_activity_of regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates indirectly regulates A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes RO:0017001 device_utilizes_material device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. RO:0019000 regulates_characteristic regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. RO:0019001 positively_regulates_characteristic positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. RO:0019002 negatively_regulates_characteristic negatively regulates characteristic p has anatomical participant c iff p has participant c, and c is an anatomical entity 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure results in changes to anatomical or cellular structure 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] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. processual entity (BFO) An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] 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 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]) anatomical entity (BFO) 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] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. characteristic specifically dependent continuant https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] 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] 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. spatial CARO:0000000 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. CARO:MAH A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FBbt:00007002 FMA:68646 GO:0005623 KUPO:0000002 MESH:D002477 VHOG:0001533 WBbt:0004017 XAO:0003012 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CARO:mah A cell that lacks a nucleus. FMA:68647 non-nucleated cell anucleate cell A cell that lacks a nucleus. FB:ma A cell with a single nucleus. single nucleate cell A cell with a single nucleus. FB:ma GOC:tfm binucleate cell A cell with more than one nucleus. AEO:0000203 WBbt:0008074 syncitium syncytial cell syncytium multinucleate cell A cell with more than one nucleus. FB:ma MESH:D005057 eukaryotic cell fungal cell A cell containing at least one nucleus. 2010-09-07T03:32:33Z FMA:67513 nucleate cell A cell containing at least one nucleus. GOC:tfm A cell that, by division or terminal differentiation, can give rise to other cell types. Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell A cell that, by division or terminal differentiation, can give rise to other cell types. GOC:dos 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 microm 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 100microm. 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 open mouth stage open mouth stage ecao_developmental_stage early prism stage early prism stage ecao_developmental_stage late prism stage late prism stage ecao_developmental_stage early pluteus stage early pluteus stage ecao_developmental_stage early organogenesis stage early organogenesis stage ecao_developmental_stage mid-organogenesis stage mid-organogenesis stage ecao_developmental_stage late organogenesis stage late organogenesis stage ecao_developmental_stage very late organogenesis stage very late organogenesis stage ecao_developmental_stage mesenchyme blastula stage mesenchyme blastula 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 A population of embryonic cells that share a common developmental fate or program of gene expression and comprising a region that lacks clear morphological boundaries embryonic territory echinoderm_anatomy A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. UBERON:0007023 adult organism echinoderm_anatomy The muscle system of the embryo. embryonic muscular system echinoderm_anatomy A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. extracellular matrix echinoderm_anatomy A blastomere of an 8-cell embryo. blastomere of 8-cell embryo echinoderm_anatomy A blastomere of a 16-cell embryo. blastomere of 16-cell embryo echinoderm_anatomy A cell that will develop into a neuron of the animal pole domain. animal pole domain neuronal progenitor cell apical pole domain presumptive neuron presumptive animal pole domain neuron echinoderm_anatomy An ectodermal cell that will develop into a neuron. ectoderm neuronal progenitor cell presumptive ectoderm neuron echinoderm_anatomy A cell that will develop into a neuron of the ciliary band. ciliary band neuronal progenitor cell presumptive ciliary band neuron echinoderm_anatomy An endodermal cell that will develop into a neuron. endoderm-ssociated neuronal progenitor cell presumptive endodermal neuron presumptive endoderm-associated neuron echinoderm_anatomy A neuron located near the base of an oral arm and outside the ciliary band. postoral neuron echinoderm_anatomy A cell that will give rise to a postoral neuron. presumptive postoral neuron echinoderm_anatomy A neuron that produces the synaptotagmin-B protein. synaptotagmin-positive neuron synaptotagmin- B neuron synaptotagmin-B-expressing neuron echinoderm_anatomy A neuron that produces the nitric oxide synthase protein. nitric oxide synthase-expressing neuron echinoderm_anatomy A neuron that uses acetylcholine as a vesicular neurotransmitter. cholinergic neuron echinoderm_anatomy A neuron that uses both acetylcholine and catecholamines as vesicular neurotransmitters. catecholaminergic/cholinergic neuron echinoderm_anatomy A neuron derived from endoderm. endodermal neuron endoderm-associated neuron echinoderm_anatomy One of two bilateral ganglia that arise in the oral ectoderm near the ciliary band. lateral ganglion echinoderm_anatomy The lateral ganglion that forms on the right side of the embryo. right lateral ganglion echinoderm_anatomy The lateral ganglion that forms on the left side of the embryo. left lateral ganglion echinoderm_anatomy The part of the blastula that will give rise to ventral ectoderm. presumptive oral ectoderm presumptive ventral ectoderm echinoderm_anatomy The part of the blastula that will give rise to dorsal ectoderm. presumptive aboral ectoderm presumptive dorsal ectoderm echinoderm_anatomy A dynamic terriritory within the prospective ectoderm of the early embryo, located at the anterior (animal) end of the embryo and shaped by Wnt signaling, that contains cells with neurogenic potential. ANE animal ectoderm anterior neuroectoderm echinoderm_anatomy A dynamic territory within the prospective ectoderm of the early embryo, located between the anterior neuroectoderm and the endomesoderm. equatorial ectoderm echinoderm_anatomy The innermost part of the anterior neuroectoderm, immediately surrounding the animal pole. inner apical pole domain inner ANE inner anterior neuroectoderm echinoderm_anatomy A torus shaped region comprising the outer part of the anterior neuroectoderm. outer apical pole domain outer ANE outer anterior neuroectoderm echinoderm_anatomy A region of the ectoderm derived from the animal hemisphere (i.e., mesomere descendants) and located just above the equator on the ventral side of the embryo. central oral ectoderm central ventral ectoderm echinoderm_anatomy A region of the ectoderm derived from the animal hemisphere (i.e., mesomere descendants) and located between the central ventral ectoderm and the animal pole domain on the ventral side of the embryo. near apical ectoderm echinoderm_anatomy A region of border ectoderm located on a lateral surface of the embryo. lateral BE veg1 lateral ectoderm lateral border ectoderm echinoderm_anatomy A region of border ectoderm located on the ventral side of the embryo. oral BE oral border ectoderm ventral BE veg1 oral ectoderm ventral border ectoderm echinoderm_anatomy A region of border ectoderm located on the dorsal side of the embryo. aboral BE aboral border ectoderm dorsal BE veg1 aboral ectoderm dorsal border ectoderm echinoderm_anatomy A region of ectoderm derived from the animal hemisphere and located laterally at the boundary between hte ventral and dorsal ectoderm; this region overlaps with part of the prospective ciliary band. animal lateral ectoderm echinoderm_anatomy The animal lateral ectoderm on the right side of the embryo. right animal lateral ectoderm echinoderm_anatomy The animal lateral ectoderm on the left side of the embryo. left animal lateral ectoderm echinoderm_anatomy A portion of the ectoderm located at the tip of a postoral arm. postoral arm tip ectoderm echinoderm_anatomy A portion of the ectoderm located at the tip of the right postoral arm. right postoral arm tip ectoderm echinoderm_anatomy A portion of the ectoderm located at the tip of the left postoral arm. left postoral arm tip ectoderm echinoderm_anatomy The cells that will give rise to the ciliary band. presumptive ciliated band presumptive ciliary band echinoderm_anatomy An elongated extension of the embryo on the ventral side, supported by a simple or fenestrated skeletal rod and often covered in part by a ciliary band. Arms develop in bilaterally symmetrical pairs. arm echinoderm_anatomy A type of arm that projects from the oral hood; forms after the postoral arms appear and prior to the appearance of the preoral and posterodorsal arms. anterolateral arm echinoderm_anatomy A type of arm that forms between the equator and the posterior pole, near the position of the skeletal rudiment; the first type of arm to appear. postoral arm echinoderm_anatomy A rod that forms by the branching or pronounced curving of the anterior tip of a dorsoventral connecting rod and that projects ventrally from the oral hood, supporting an anterolateral arm. anterolateral rod echinoderm_anatomy A rod that forms by the branching of the anonymous rod and projects ventrally, supporting a postoral arm. postoral rod echinoderm_anatomy A rod that initially forms as one of the three arms of the embryonic triradiate spicule rudiment; this rod extends toward the animal pole before branching or curving to form the anterolateral rod and, in some species, the recurrent rod. dorsoventral connecting rod echinoderm_anatomy A rod that initially forms as one of the three arms of the embryonic triradiate spicule rudiment; this rod projects toward the ventral midline and ceases growth early in development without branching. ventral transverse rod echinoderm_anatomy The growing tip of the body rod as it extends dorsally. distal tip of body rod echinoderm_anatomy The distal tip of the body rod that forms on the right side of the embryo. distal tip of right body rod echinoderm_anatomy The distal tip of the body rod that forms on the left side of the embryo.. distal tip of left body rod echinoderm_anatomy A rod that forms from the branching of a dorsoventral transverse rod and extends dorsally. recurrent rod echinoderm_anatomy The part of the embryonic presumptive mesoderm that will later give rise to the skeletogenic mesenchyme and embryonic skeleton. presumptive embryonic skeletogenic mesoderm echinoderm_anatomy A cluster of skeletogenic cell bodies that forms in the ventrolateral region of the subequatorial skeletogenic mesenchyme ring; one triradiate spicule rudiment will form in each of two ventrolateral clusters. ventrolateral skeletogenic mesenchyme cluster echinoderm_anatomy Embryonic cells tin the epithelial wall of the vegetal plate or the archenteron that will give rise to mesodermal derivatives other than skeleton. NSM presumptive embryonic non-skeletogenic mesoderm echinoderm_anatomy The presumptive embryonic non-skeletogenic mesoderm on the ventral side of the embryo. ventral presumptive embryonic non-skeletogenic mesoderm echinoderm_anatomy The presumptive embryonic non-skeletogenic mesoderm on the dorsal side of the embryo. dorsal presumptive embryonic non-skeletogenic mesoderm echinoderm_anatomy A cell that will give rise to a muscle cell. muscle precursor cell presumptive muscle cell echinoderm_anatomy A cell that is part of a muscle. muscle cell echinoderm_anatomy The inner, extracellular space between blastomeres of the cleavage stage embryo that will gradually expand and form the blastocoel. presumptive blastocoel echinoderm_anatomy A cell that is part of the pyloric sphincter. pyloric sphincter muscle cell echinoderm_anatomy A cell that is part of the cardiac sphincter. cardiac sphincter muscle cell echinoderm_anatomy A cell that is part of the anal sphincter. UBERON:0004916 anal pore muscle cell anal sphincter muscle cell echinoderm_anatomy A strand of mesenchyme cells that extends from the left coelom to the ectoderm and that will give rise to the primary pore canal. presumptive hydropore canal primary pore canal rudiment echinoderm_anatomy An evagination of the midgut that will contribute to the coelom. posterior enterocoel echinoderm_anatomy In species with a posterior enterocoel, the left coelomic pouch that evaginates from the unpaired coelomic pouch at the anterior end of the archenteron. left anterior coelomic pouch echinoderm_anatomy In species with a posterior enterocoel, the right coelomic pouch that evaginates from the unpaired coelomic pouch at the anterior end of the archenteron. right anterior coelomic pouch echinoderm_anatomy In species with two separate ciliary bands, a ciliary band that surrounds the anterior-ventral end of the embryo, anterior to the mouth. preoral ciliary band echinoderm_anatomy In species with two separate ciliary bands, a ciliary band that surrounds the posterior-dorsal end of the embryo, posterior to the mouth. postoral ciliary band echinoderm_anatomy A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. GO:0005554 molecular function molecular_function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. This is the same as GO molecular function gene product or complex activity molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. GOC:pdt Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. Wikipedia:Enzyme enzyme activity molecular_function GO:0003824 catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GOC:vw ISBN:0198506732 enzyme activity GOC:dph GOC:tb A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). GOC:pdt subcellular entity NIF_Subcellular:nlx_subcell_100315 A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. https://github.com/geneontology/go-ontology/issues/17776 Wikipedia:Intracellular internal to cell intracellular protoplasm cellular_component nucleocytoplasm protoplast GO:0005622 intracellular anatomical structure A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. ISBN:0198506732 nucleocytoplasm GOC:mah protoplast GOC:mah A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus cellular_component GO:0005634 nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. GOC:go_curators horsetail nucleus GOC:al GOC:mah GOC:vw PMID:15030757 The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). GO:0005636 Wikipedia:Nuclear_envelope cellular_component GO:0005635 nuclear envelope The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). ISBN:0198547684 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. https://github.com/geneontology/go-ontology/issues/23023 Wikipedia:Cytoplasm cellular_component GO:0005737 cytoplasm The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. ISBN:0198547684 A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. Wikipedia:Vacuole cellular_component vacuolar carboxypeptidase Y GO:0005773 vacuole A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. GOC:mtg_sensu ISBN:0198506732 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0005887 GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane cell membrane cellular membrane cytoplasmic membrane plasmalemma bacterial inner membrane inner endospore membrane integral component of plasma membrane integral to plasma membrane plasma membrane lipid bilayer cellular_component GO:0005886 plasma membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. ISBN:0716731363 cellular membrane NIF_Subcellular:sao6433132645 plasma membrane lipid bilayer GOC:mah The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. https://github.com/geneontology/go-ontology/issues/26298 Wikipedia:Cell_cortex ectoplasm cellular_component cell periphery peripheral cytoplasm GO:0005938 cell cortex The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. GOC:mah ISBN:0815316194 The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). https://github.com/geneontology/go-ontology/issues/21234 biological_process GO:0007275 Note that this term was 'developmental process'. multicellular organism development The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:dph GOC:ems GOC:isa_complete GOC:tb A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 A biological process is an evolved process Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological process biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis embryonal development biological_process GO:0009790 embryo development The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. GOC:go_curators GOC:isa_complete GOC:mtg_sensu The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development. biological_process GO:0009791 post-embryonic development The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development. GOC:go_curators Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. jl 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. Wikipedia:Endomembrane_system cellular_component GO:0012505 endomembrane system A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. GOC:lh A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z GO:0016021 GO:0098589 GO:0098805 Wikipedia:Biological_membrane Wikipedia:Transmembrane_protein integral component of membrane integral to membrane membrane region region of membrane whole membrane cellular_component transmembrane GO:0016020 membrane A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GOC:dos GOC:mah ISBN:0815316194 transmembrane GOC:mah true Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity molecular_function GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. EC:2.-.-.- Reactome:R-HSA-1483089 Reactome:R-HSA-1483186 Reactome:R-HSA-5668414 Reactome:R-HSA-8868783 molecular_function GO:0016740 transferase activity Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. ISBN:0198506732 Reactome:R-HSA-1483089 PE is converted to PS by PTDSS2 Reactome:R-HSA-1483186 PC is converted to PS by PTDSS1 Reactome:R-HSA-5668414 TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK Reactome:R-HSA-8868783 TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). EC:2.7.-.- molecular_function GO:0016772 Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. transferase activity, transferring phosphorus-containing groups Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. https://github.com/geneontology/go-ontology/issues/24390 Wikipedia:Cellular_differentiation biological_process GO:0030154 cell differentiation The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. ISBN:0198506732 A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. NIF_Subcellular:sao830981606 cellular_component intracellular membrane GO:0031090 organelle membrane A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. GOC:dos GOC:mah intracellular membrane NIF_Subcellular:sao830981606 Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. NIF_Subcellular:sao1687101204 cellular_component GO:0031965 nuclear membrane Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. GOC:mah GOC:pz A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. cellular_component GO:0031967 organelle envelope A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. GOC:mah GOC:pz A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. cellular_component GO:0031975 envelope A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. GOC:mah GOC:pz Any biological process, occurring at the level of a multicellular organism, pertinent to its function. jl 2012-09-19T16:07:47Z GO:0044707 GO:0050874 organismal physiological process biological_process single-multicellular organism process GO:0032501 multicellular organismal process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. GOC:curators GOC:dph GOC:isa_complete GOC:tb A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. jl 2012-12-19T12:21:31Z GO:0044767 development biological_process single-organism developmental process GO:0032502 developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. GOC:isa_complete Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. NIF_Subcellular:sao1539965131 Wikipedia:Organelle cellular_component GO:0043226 organelle Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. cellular_component GO:0043229 intracellular organelle Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. intracellular membrane-enclosed organelle cellular_component GO:0043231 intracellular membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place. https://github.com/geneontology/go-ontology/issues/24390 biological_process terminal differentiation GO:0048468 cell development The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place. GOC:go_curators terminal differentiation GOC:dph GOC:tb Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. https://github.com/geneontology/go-ontology/issues/25943 Wikipedia:Organogenesis development of an organ organogenesis biological_process GO:0048513 animal organ development Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GOC:dph GOC:jid The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. https://github.com/geneontology/go-ontology/issues/26424 development of an anatomical structure biological_process GO:0048856 anatomical structure development The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GO_REF:0000021 A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. biological_process GO:0048869 cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. GOC:isa_complete The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. mah 2010-10-04T01:51:47Z cellular_component GO:0071944 cell periphery The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. GOC:pdt A membrane that is a (regional) part of the plasma membrane. dos 2014-03-06T11:55:32Z region of plasma membrane cellular_component GO:0098590 Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass. plasma membrane region A membrane that is a (regional) part of the plasma membrane. GOC:dos Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. cellular_component GO:0099568 cytoplasmic region Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. GOC:dos The complete extent of cell cortex that underlies some some region of the plasma membrane. perimembrane region cellular_component GO:0099738 cell cortex region The complete extent of cell cortex that underlies some some region of the plasma membrane. GOC:dos A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 kmv 2019-08-12T18:01:37Z cellular_component GO:0110165 cellular anatomical entity A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. GOC:kmv data item data item information content entity information content entity curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type GC_ID:1 PMID:30365038 PMID:32761142 ncbi_taxonomy all NCBITaxon:1 root all GC_ID:1 ncbi_taxonomy biota NCBITaxon:131567 cellular organisms biota GC_ID:1 true yeasts ncbi_taxonomy NCBITaxon:147537 Saccharomycotina true yeasts GC_ID:1 ncbi_taxonomy Archiascomycota NCBITaxon:147554 Schizosaccharomycetes Archiascomycota GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11542017 PMID:11542087 PMID:11760965 PMID:12054223 PMID:2112744 PMID:270744 PMID:32628106 PMID:36748408 PMID:7520741 PMID:8123559 PMID:8186100 PMID:8590690 PMID:9103655 PMID:9336922 eubacteria ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bacteria prokaryote prokaryotes NCBITaxon:2 Bacteria eubacteria Monera Procaryotae Prokaryota Prokaryotae bacteria prokaryote prokaryotes GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11541975 PMID:11542064 PMID:11542149 PMID:11760965 PMID:12054223 PMID:2112744 PMID:25527841 PMID:270744 PMID:32628106 PMID:36748408 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 ncbi_taxonomy Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes NCBITaxon:2157 Archaea Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes GC_ID:1 PMID:23020233 PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes NCBITaxon:2759 Eukaryota eucaryotes eukaryotes Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes GC_ID:1 ncbi_taxonomy Fungi/Metazoa group opisthokonts NCBITaxon:33154 Opisthokonta Fungi/Metazoa group opisthokonts GC_ID:1 metazoans multicellular animals ncbi_taxonomy Animalia animals NCBITaxon:33208 Metazoa metazoans multicellular animals Animalia animals GC_ID:1 ncbi_taxonomy NCBITaxon:33213 Bilateria GC_ID:1 ncbi_taxonomy NCBITaxon:34346 Schizosaccharomycetales GC_ID:1 PMID:15689432 PMID:16151185 PMID:17010206 PMID:17051209 PMID:17572334 ncbi_taxonomy NCBITaxon:451864 Dikarya GC_ID:1 ncbi_taxonomy NCBITaxon:451866 Taphrinomycotina GC_ID:1 PMID:11062127 PMID:12684019 ncbi_taxonomy Mycota fungi NCBITaxon:4751 Fungi Mycota fungi GC_ID:1 PMID:17572334 ascomycetes sac fungi ncbi_taxonomy ascomycete fungi NCBITaxon:4890 Ascomycota ascomycetes sac fungi ascomycete fungi GC_ID:1 ncbi_taxonomy Hemiascomycetes NCBITaxon:4891 Saccharomycetes Hemiascomycetes GC_ID:1 ncbi_taxonomy Endomycetales budding yeasts NCBITaxon:4892 Saccharomycetales Endomycetales budding yeasts NCBITaxon:221665 NCBITaxon:44280 GC_ID:1 ncbi_taxonomy NCBITaxon:4893 Saccharomycetaceae GC_ID:1 fission yeasts ncbi_taxonomy Schizosaccharomycetoideae NCBITaxon:4894 Schizosaccharomycetaceae fission yeasts Schizosaccharomycetoideae GC_ID:1 ncbi_taxonomy NCBITaxon:4895 Schizosaccharomyces NCBITaxon:45042 GC_ID:1 fission yeast ncbi_taxonomy Schizosaccharomyces malidevorans NCBITaxon:4896 Schizosaccharomyces pombe fission yeast Schizosaccharomyces malidevorans NCBITaxon:36915 GC_ID:1 ncbi_taxonomy Pachytichospora NCBITaxon:4930 Saccharomyces Pachytichospora NCBITaxon:41870 GC_ID:1 Saccharomyces cerevisiae 'var. diastaticus' baker's yeast brewer's yeast ncbi_taxonomy Candida robusta Mycoderma cerevisiae Saccharomyces capensis Saccharomyces diastaticus Saccharomyces italicus Saccharomyces oviformis Saccharomyces uvarum var. melibiosus NCBITaxon:4932 Saccharomyces cerevisiae Saccharomyces cerevisiae 'var. diastaticus' baker's yeast brewer's yeast Candida robusta Mycoderma cerevisiae Saccharomyces capensis Saccharomyces diastaticus Saccharomyces italicus Saccharomyces oviformis Saccharomyces uvarum var. melibiosus GC_ID:1 ncbi_taxonomy NCBITaxon:6072 Eumetazoa GC_ID:1 ncbi_taxonomy NCBITaxon:716545 saccharomyceta A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATO:0000072 quality PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality A quality which inheres in a continuant. PATOC:GVG A monadic quality of continuant that exists at the cellular level of organisation. quality PATO:0001396 cellular quality A monadic quality of continuant that exists at the cellular level of organisation. PATOC:GVG A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. quality PATO:0001404 nucleate quality A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. PATOC:GVG A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. quality PATO:0001405 anucleate A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. Biology-online:Biology-online A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. quality PATO:0001406 binucleate A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. Biology-online:Biology-online A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. quality PATO:0001407 mononucleate A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. Biology-online:Biology-online A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. quality PATO:0001908 multinucleate A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. PATOC:GVG An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. quality PATO:0001992 cellularity An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. PATOC:GVG A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. quality PATO:0001993 multicellular A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. PATOC:GVG A quality that inheres in an entire organism or part of an organism. quality PATO:0001995 organismal quality A quality that inheres in an entire organism or part of an organism. PATOC:CJM A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. 2013-10-21T05:44:34Z quality PATO:0002505 nucleated A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. PATOC:GVG A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components. http://orcid.org/0000-0001-7258-9596 quality PATO:0070044 anatomical structure quality An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. BFO:0000003 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 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 SCTID:362889002 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 http://dbpedia.org/ontology/AnatomicalStructure biological structure connected biological structure uberon UBERON:0000061 anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 FBbt:00007001 connected biological structure CARO:0000003 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 https://github.com/obophenotype/uberon/issues/566 The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. https://orcid.org/0000-0002-6601-2165 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 SCTID:296280003 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. http://orcid.org/0000-0002-6601-2165 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 https://github.com/obophenotype/uberon/issues/344 Stage succeeding embryo, including mature structure. https://orcid.org/0000-0002-6601-2165 An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with 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 https://github.com/obophenotype/uberon/issues/532 An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism. https://orcid.org/0000-0002-6601-2165 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 MESH:D008018 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. https://orcid.org/0000-0002-6601-2165 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 IDOMAL:0000302 NCIT:C12601 PdumDv:0000100 VHOG:0000745 Wikipedia:Zygote 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. Wikipedia:Zygote 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 http://bgee.unil.ch/ IDOMAL:0000302 https://github.com/biopragmatics/biomappings fertilized egg stage BTO:0000854 one-cell stage VHOG:0000745 zygote VHOG:0000745 zygotum Wikipedia:Zygote 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 Wikipedia:Organogenesis uberon segmentation stage UBERON:0000111 organogenesis stage https://github.com/obophenotype/developmental-stage-ontologies/issues/84 https://github.com/obophenotype/uberon/issues/533 A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. Wikipedia:Organogenesis Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 FBbt:00007016 Anatomical structure that is an individual member of a species and consists of more than one cell. TODO - split body and mc organism? body continues after death stage organismal organism AAO:0010026 AEO:0000191 BILA:0000012 BIRNLEX:18 BSA:0000038 BTO:0000042 CARO:0000012 EFO:0002906 EHDAA2:0003103 EHDAA2:0003191 EHDAA:1 EMAPA:25765 EV:0100016 FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 SCTID:243928005 TADS:0000001 TAO:0001094 TGMA:0001832 VHOG:0000671 WBbt:0007833 Wikipedia:Multi-cellular_organism XAO:0003004 ZFA:0001094 galen:Organism ncithesaurus:Whole_Organism multi-cellular organism uberon Koerper body whole body whole organism UBERON:0000468 multicellular organism Anatomical structure that is an individual member of a species and consists of more than one cell. CARO:0000012 Wikipedia:Multi-cellular_organism http://orcid.org/0000-0001-9114-8737 organism FBbt:00000001 VHOG:0000671 WBbt:0007833 FBbt:00000001 multi-cellular organism CARO:0000012 Koerper BTO:0001489 body AEO:0000103 BIRNLEX:18 FMA:256135 NCIT:C13041 whole body BTO:0001489 whole organism FBbt:00000001 Anatomical entity that comprises the organism 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. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. embryonic Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 BSA:0000039 BTO:0000379 CALOHA:TS-0229 EFO:0001367 EHDAA2:0000002 EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 FBbt:00000052 FMA:69068 GAID:963 IDOMAL:0000646 MAT:0000226 MESH:D004622 MIAA:0000019 NCIT:C28147 OGEM:000001 SCTID:57991002 UMLS:C0013935 VHOG:0001766 Wikipedia:Embryo XAO:0000113 ZFA:0000103 http://neurolex.org/wiki/Category:Embryonic_organism embryonic organism uberon developing organism developmental tissue UBERON:0000922 embryo https://github.com/obophenotype/uberon/issues/503 https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg Anatomical entity that comprises the organism 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. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. BTO:0000379 FB:FBrf0039741 FB:FBrf0041814 GO:0009790 Wikipedia:Embryo Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo ZFA FBbt:00000052 IDOMAL:0000646 https://github.com/biopragmatics/biomappings UMLS:C0013935 ncithesaurus:Embryo embryonic organism BILA:0000056 developing organism BILA:0000056 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 BFO:0000004 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 FBbt:10000000 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 http://orcid.org/0000-0001-9114-8737 FBbt:10000000 UMLS:C1515976 ncithesaurus:Anatomic_Structure_System_or_Substance A multicellular organism that existence_starts_with a post-embryonic stage. MA:0002405 postnatal organism TS28 mouse post-hatching organism post-natal organism postnatal mouse uberon UBERON:0009953 post-embryonic organism https://github.com/obophenotype/uberon/issues/667 A multicellular organism that existence_starts_with a post-embryonic stage. OBOL:automatic TS28 mouse MA:0002405 post-hatching organism https://orcid.org/0000-0002-6601-2165 post-natal organism https://orcid.org/0000-0002-6601-2165 postnatal mouse MA:0002405 An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 multicellular anatomical structure An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure FBbt:00100313 Any structure that is placed on one side of the left-right axis of a bilaterian. This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 lateral structure Any structure that is placed on one side of the left-right axis of a bilaterian. http://orcid.org/0000-0002-6601-2165 example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope 2 2 1 2 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 can't be added as a property chain because it causes a circularity violation for 'part of'. This can't be added as a property chain because it causes a circularity violation for 'part of'. This can't be added as a property chain because it causes a circularity violation for 'part of'. 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).