Ontology about Xenopus. Xenopus Phenotype Ontology CC-BY Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition definition textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by term replaced by An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime defined by inverse logical macro assertion on an annotation property relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' Chris Mungall is direct form of 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 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). RO:0002604 quality is_opposite_of true true is_opposite_of is opposite of cjm 2018-03-14T00:03:16Z is positive form of cjm 2018-03-14T00:03:24Z is negative form of part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. cjm 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for Manually annotated by ChEBI Team Term not to be used for direct annotation Term not to be used for direct manual annotation AGR slim Aspergillus GO slim Candida GO slim ChEMBL protein targets summary FlyBase Drosophila GO ribbon slim Generic GO slim Metagenomics GO slim Mouse GO slim PIR GO slim Plant GO slim Fission yeast GO slim synapse GO slim Yeast GO slim label approved by the SynGO project Systematic synonym Abnormal/normal slim Absent/present slim Attribute slim cell_quality Disposition slim Human phenotype slim Pathology slim Relational slim: types of quality that require an additional entity in order to exist Scalar slim Value slim eco subset PLURAL Anatomical Site slim Frequently Used Anatomy slim Organism View slim Sectional Anatomy Item slim consider has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym has_scope has_synonym_type in_subset shorthand label label is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 external quality xenopus_anatomy part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 chebi_ontology external quality has_part false has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part has part has_part Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. PATOC:CJM 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 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. precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in BFO:0000066 external occurs_in occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence 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 bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. dos 2017-07-19T17:30:36Z has ligand dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps true w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan RO:0002202 xenopus_anatomy develops_from develops_from This is the transitive form of the develops from relation develops from develops from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan develops into Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. Chris Mungall David Osumi-Sutherland has developmental precursor FBbt TODO - add child relations from DOS directly develops from inverse of directly develops from developmental precursor of directly develops into process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 external regulates regulates regulates regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) RO:0002212 external negatively_regulates negatively_regulates negatively regulates negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) RO:0002213 external positively_regulates positively_regulates 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. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of true x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in actively participates in 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent obsolete has active participant true Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to x develops from part of y if and only if there exists some z such that x develops from z and z is part of y Chris Mungall develops from part of p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall has developmental contribution from inverse of has developmental contribution from Chris Mungall developmentally contributes to Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within Inverse of developmentally preceded by Chris Mungall developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue Chris Mungall part of developmental precursor of cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect q inheres in 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 inheres in part of Chris Mungall inheres in part of true A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of involved in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by inverse of has input Chris Mungall input of x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y Chris Mungall 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 Chris Mungall has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y Chris Mungall has potential to directly develop into inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. Chris Mungall molecularly controls activity directly regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall inhibits molecularly decreases activity of activity directly negatively regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall activates molecularly increases activity of activity directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true Chris Mungall is kinase activity x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships Chris Mungall transformation of x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t Chris Mungall immediate transformation of A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall 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 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entities Chris Mungall causally influenced by (material entity to material entity) causally influenced by Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall causally influences (material entity to material entity) causally influences A relation that holds between an attribute or a qualifier and another attribute. Chris Mungall This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. has modifier Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. obsolete related via dependence to true Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect quality correlates_with correlates_with q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. quality has_cross_section Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has_cross_section s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. PATOC:CJM q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased_in_magnitude_relative_to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. quality reciprocal_of There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal_of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. PATOC:CJM quality towards Relation binding a relational quality or disposition to the relevant type of entity. towards Anatomical structure/expression stops being viable, obvious or of utility during this developmental stage. xenopus_anatomy end_stage ends during Anatomical structure/expression stops being viable, obvious or of utility during this developmental stage. XAO:curators xenopus_anatomy preceded_by preceded by Anatomical structure/expression begins being viable, obvious or of utility during this developmental stage. xenopus_anatomy start_stage starts during Anatomical structure/expression begins being viable, obvious or of utility during this developmental stage. XAO:curators 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. 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 A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] 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. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. 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] 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] 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 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 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. 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] specifically dependent continuant 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] 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. 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. 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] 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] 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] anatomical entity connected anatomical structure material anatomical entity cell part (CARO) cell part multicellular anatomical structure biological entity A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology CHEBI:24431 chemical entity chemical entity UniProt cell neuron The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GO:0019952 GO:0050876 Wikipedia:Reproduction reproductive physiological process biological_process GO:0000003 reproduction The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GOC:go_curators GOC:isa_complete GOC:jl ISBN:0198506732 Any of the spindle microtubules that radiate in all directions from the spindle poles and are thought to contribute to the forces that separate the poles and position them in relation to the rest of the cell. cellular_component GO:0000235 astral microtubule Any of the spindle microtubules that radiate in all directions from the spindle poles and are thought to contribute to the forces that separate the poles and position them in relation to the rest of the cell. ISBN:0815316194 Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GO:0007067 MIPS_funcat:10.03.01 MIPS_funcat:10.03.01.01 Wikipedia:Mitosis biological_process mitosis GO:0000278 mitotic cell cycle Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 Reactome:69278 The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. MIPS_funcat:10.03.04 MIPS_funcat:10.03.04.07 biological_process karyokinesis GO:0000280 nuclear division The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. GOC:mah A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells. cytokinesis after mitosis biological_process GO:0000281 mitotic cytokinesis A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells. GOC:mtg_cell_cycle The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells. GO:0007104 GO:0016288 GO:0033205 MIPS_funcat:10.03.03 Wikipedia:Cytokinesis cell cycle cytokinesis cytokinesis involved in cell cycle biological_process GO:0000910 Note that this term should not be used for direct annotation. When annotating eukaryotic species, mitotic or meiotic cytokinesis should always be specified for manual annotation and for prokaryotic species use 'FtsZ-dependent cytokinesis ; GO:0043093' or Cdv-dependent cytokinesis ; GO:0061639. Also, note that cytokinesis does not necessarily result in physical separation and detachment of the two daughter cells from each other. cytokinesis The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells. GOC:mtg_cell_cycle cytokinesis involved in cell cycle GOC:dph GOC:tb A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities. MIPS_funcat:34.03.03 biological_process GO:0001508 Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. action potential A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities. GOC:dph GOC:go_curators GOC:tb ISBN:978-0-07-139011-8 The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight. GO:0042460 MIPS_funcat:47.03.02.02 Wikipedia:Eye_development biological_process GO:0001654 eye development The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight. GOC:jid GOC:jl The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure. biological_process GO:0001655 urogenital system development The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure. GOC:go_curators Cell migration that is accomplished by extension and retraction of a pseudopodium. ameboid cell migration amoeboid cell migration amoeboidal cell migration biological_process GO:0001667 Note that this term refers to a mode of migration rather than to any particular cell type. ameboidal-type cell migration Cell migration that is accomplished by extension and retraction of a pseudopodium. GOC:dph The formation of the ectoderm, mesoderm and endoderm during gastrulation. biological_process GO:0001704 formation of primary germ layer The formation of the ectoderm, mesoderm and endoderm during gastrulation. GOC:go_curators The formation of ectoderm during gastrulation. biological_process GO:0001705 ectoderm formation The formation of ectoderm during gastrulation. GOC:go_curators The formation of the endoderm during gastrulation. endoblast formation biological_process GO:0001706 endoderm formation The formation of the endoderm during gastrulation. GOC:go_curators endoblast formation GOC:dph GOC:sdb_2009 GOC:tb The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts. biological_process GO:0001707 mesoderm formation The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts. GOC:go_curators The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine. MIPS_funcat:47.03.07.01 Wikipedia:Kidney_development biological_process nephrogenesis GO:0001822 kidney development The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine. GOC:dph GOC:mtg_kidney_jan10 ISBN:0124020607 ISBN:0721662544 nephrogenesis GOC:rph The process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the mesonephros will form the mature kidney. Wolffian body development biological_process GO:0001823 mesonephros development The process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the mesonephros will form the mature kidney. GOC:dph ISBN:0124020607 ISBN:0721662544 PMID:10535314 Wolffian body development GOC:dph The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes. MIPS_funcat:47.03.11.07 biological_process GO:0001889 liver development The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes. GOC:add ISBN:068340007X Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. Wikipedia:Immune_system biological_process GO:0002376 Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022. immune system process Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. GOC:add GOC:mtg_15nov05 GO_REF:0000022 The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. biological_process GO:0002520 immune system development The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. GOC:add GOC:dph Any process that modulates the frequency, rate, or extent of an immune system process. biological_process GO:0002682 regulation of immune system process Any process that modulates the frequency, rate, or extent of an immune system process. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process. down regulation of immune system process down-regulation of immune system process downregulation of immune system process inhibition of immune system process biological_process GO:0002683 negative regulation of immune system process Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process. GOC:add Any process that activates or increases the frequency, rate, or extent of an immune system process. up regulation of immune system process up-regulation of immune system process upregulation of immune system process activation of immune system process stimulation of immune system process biological_process GO:0002684 positive regulation of immune system process Any process that activates or increases the frequency, rate, or extent of an immune system process. GOC:add The pattern specification process that results in the subdivision of an axis or axes in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment. biological_process pattern formation GO:0003002 regionalization The pattern specification process that results in the subdivision of an axis or axes in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment. GOC:dph GOC:isa_complete pattern formation GOC:dph A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring. puberty biological_process reproductive developmental process GO:0003006 developmental process involved in reproduction A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring. GOC:dph GOC:isa_complete puberty GOC:dph reproductive developmental process GOC:dph GOC:tb A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. organ system process biological_process GO:0003008 system process A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. GOC:mtg_cardio The progression of a cardiac chamber over time, from its formation to the mature structure. A cardiac chamber is an enclosed cavity within the heart. dph 2009-10-13T09:11:18Z biological_process GO:0003205 cardiac chamber development The progression of a cardiac chamber over time, from its formation to the mature structure. A cardiac chamber is an enclosed cavity within the heart. GOC:mtg_heart The process whose specific outcome is the progression of a cardiac ventricle over time, from its formation to the mature structure. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart. dph 2009-10-13T11:03:16Z biological_process GO:0003231 cardiac ventricle development The process whose specific outcome is the progression of a cardiac ventricle over time, from its formation to the mature structure. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart. GOC:mtg_heart The developmental growth that results in the elongation of a line that defines polarity or symmetry in an anatomical structure. dph 2009-12-21T01:12:15Z biological_process elongation of an axis GO:0003401 axis elongation The developmental growth that results in the elongation of a line that defines polarity or symmetry in an anatomical structure. GOC:ascb_2009 GOC:dph GOC:tb elongation of an axis GOC:ascb_2009 GOC:dph GOC:tb 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. molecular process 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 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. 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. 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 OBSOLETE. Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. GO:0005062 GO:0009369 GO:0009370 hematopoietin/interferon-class (D200-domain) cytokine receptor signal transducer activity quorum sensing response regulator activity quorum sensing signal generator activity molecular_function GO:0004871 This term was obsoleted because it was not clearly defined and is not a useful grouping term, see https://github.com/geneontology/go-ontology/issues/14232. obsolete signal transducer activity true OBSOLETE. Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. GOC:go_curators true Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. receptor binding Wikipedia:Ligand_(biochemistry) receptor ligand molecular_function receptor-associated protein activity GO:0005102 Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'. signaling receptor binding Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. GOC:bf GOC:ceb ISBN:0198506732 The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. Wikipedia:Binding_(molecular) ligand molecular_function GO:0005488 Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. binding The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. GOC:ceb GOC:mah ISBN:0198506732 Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). GO:0001948 GO:0045308 MIPS_funcat:16.01 MIPS_funcat:18.01.07 Reactome:R-HSA-170835 Reactome:R-HSA-170846 protein amino acid binding glycoprotein binding molecular_function GO:0005515 protein binding Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). GOC:go_curators Reactome:R-HSA-170835 An anchoring protein, ZFYVE9 (SARA), recruits SMAD2/3 Reactome:R-HSA-170846 TGFBR2 recruits TGFBR1 A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). GO:0008372 NIF_Subcellular:sao-1337158144 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 use 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 when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). GOC:pdt NIF_Subcellular:sao-1337158144 subcellular entity NIF_Subcellular:nlx_subcell_100315 The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. Wikipedia:Intracellular internal to cell protoplasm cellular_component nucleocytoplasm protoplast GO:0005622 intracellular The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. ISBN:0198506732 nucleocytoplasm GOC:mah protoplast GOC:mah The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. cell and encapsulating structures NIF_Subcellular:sao1813327414 Wikipedia:Cell_(biology) cellular_component GO:0005623 cell The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:go_curators 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. MIPS_funcat:70.10 NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus cellular_component GO:0005634 nucleus 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 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. MIPS_funcat:70.03 Wikipedia:Cytoplasm cellular_component GO:0005737 cytoplasm All of 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. MIPS_funcat:70.25 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 An array of microtubules emanating from a spindle pole MTOC that do not connect to kinetochores. cellular_component GO:0005818 aster An array of microtubules emanating from a spindle pole MTOC that do not connect to kinetochores. GOC:clt The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart. Wikipedia:Spindle_apparatus cellular_component GO:0005819 spindle The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart. ISBN:0198547684 Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. MIPS_funcat:70.04 Wikipedia:Cytoskeleton cellular_component GO:0005856 cytoskeleton Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. GOC:mah ISBN:0198547684 PMID:16959967 Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. NIF_Subcellular:sao1846835077 Wikipedia:Microtubule microtubuli microtubulus neurotubule cellular_component GO:0005874 microtubule Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. ISBN:0879693568 neurotubule NIF_Subcellular:sao248349196 Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole. cellular_component GO:0005876 spindle microtubule Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole. ISBN:0815316194 Any microtubule in the nucleus of a cell. cellular_component GO:0005880 nuclear microtubule Any microtubule in the nucleus of a cell. GOC:mah Any microtubule in the cytoplasm of a cell. non-spindle-associated astral microtubule cellular_component GO:0005881 cytoplasmic microtubule Any microtubule in the cytoplasm of a cell. GOC:mah A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. FMA:63850 NIF_Subcellular:sao1588493326 Wikipedia:Actin microfilament cellular_component GO:0005884 actin filament A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. GOC:mah ISBN:0198506732 PMID:10666339 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane cell membrane cellular membrane cytoplasmic membrane plasmalemma bacterial inner membrane inner endospore 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 chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). phosphorus metabolism biological_process GO:0006793 phosphorus metabolic process The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). GOC:ai The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. MIPS_funcat:01.04 phosphate metabolism biological_process phosphate metabolic process GO:0006796 phosphate-containing compound metabolic process The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. GOC:ai The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore. MIPS_funcat:02.45.11 MIPS_funcat:34.05 cellular component motion cellular component movement biological_process cell movement GO:0006928 Note that in GO cellular components include whole cells (cell is_a cellular component). movement of cell or subcellular component The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore. GOC:dgh GOC:dph GOC:jl GOC:mlg cellular component motion GOC:dph GOC:jl Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). MIPS_funcat:32.01 biological_process response to abiotic stress response to biotic stress GO:0006950 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stress Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. jl 2013-12-19T15:25:51Z GO:1902589 organelle organisation single organism organelle organization biological_process organelle organization and biogenesis single-organism organelle organization GO:0006996 organelle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:mah organelle organisation GOC:curators single organism organelle organization GOC:TermGenie organelle organization and biogenesis GOC:dph GOC:jl GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. MIPS_funcat:42.04 cytoskeleton organisation biological_process cytoskeletal organization and biogenesis cytoskeletal regulator activity cytoskeleton organization and biogenesis GO:0007010 cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:dph GOC:jl GOC:mah cytoskeleton organisation GOC:curators cytoskeletal organization and biogenesis GOC:mah cytoskeleton organization and biogenesis GOC:mah The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. MIPS_funcat:10 MIPS_funcat:10.03 Wikipedia:Cell_cycle cell-division cycle biological_process GO:0007049 cell cycle The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. GOC:go_curators GOC:mtg_cell_cycle Any process that modulates the frequency, rate or extent of mitosis. regulation of mitosis biological_process GO:0007088 regulation of mitotic nuclear division Any process that modulates the frequency, rate or extent of mitosis. GOC:go_curators Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. Wikipedia:Cell_signaling biological_process GO:0007154 cell communication Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:mah The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GO:0023033 MIPS_funcat:30 Wikipedia:Signal_transduction signaling cascade signalling cascade biological_process signaling pathway signalling pathway GO:0007165 Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. signal transduction The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GOC:go_curators GOC:mtg_signaling_feb11 signalling pathway GOC:mah Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. cell-cell signalling biological_process GO:0007267 cell-cell signaling Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. GOC:dos GOC:mah The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. signal transmission across a synapse synaptic transmission MIPS_funcat:34.03.01 Wikipedia:Neurotransmission biological_process neurotransmission GO:0007268 chemical synaptic transmission The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. GOC:jl MeSH:D009435 neurotransmission GOC:dph 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). MIPS_funcat:41 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 Any process that modulates the rate or extent of progress through the mitotic cell cycle. mitotic cell cycle modulation mitotic cell cycle regulation modulation of mitotic cell cycle progression regulation of mitotic cell cycle progression regulation of progression through mitotic cell cycle biological_process mitotic cell cycle regulator GO:0007346 regulation of mitotic cell cycle Any process that modulates the rate or extent of progress through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb regulation of progression through mitotic cell cycle GOC:dph GOC:tb A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. MIPS_funcat:41.05.09 Wikipedia:Gastrulation biological_process GO:0007369 gastrulation A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. GOC:curators ISBN:9780878933846 Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate. MIPS_funcat:41.01.03 biological_process pattern biosynthesis pattern formation GO:0007389 pattern specification process Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate. GOC:go_curators GOC:isa_complete ISBN:0521436125 The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation. biological_process GO:0007398 ectoderm development The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation. GOC:dph GOC:tb The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. MIPS_funcat:45.03.17 MIPS_funcat:47.03.01 biological_process pan-neural process GO:0007399 nervous system development The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. GOC:dgh The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. MIPS_funcat:47.03.01.01 Wikipedia:Neural_development CNS development biological_process GO:0007417 central nervous system development The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. GOC:bf GOC:jid ISBN:0582227089 The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). MIPS_funcat:47.03.01.01.01 biological_process GO:0007420 brain development The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). GOC:dph GOC:jid GOC:tb UBERON:0000955 The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure. sense organ development biological_process GO:0007423 sensory organ development The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure. GOC:go_curators sense organ development GOC:dph The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues. biological_process GO:0007492 endoderm development The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues. GOC:dph GOC:tb The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue. biological_process GO:0007498 mesoderm development The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue. GOC:dph GOC:tb The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. GO:0007511 MIPS_funcat:47.03.03.01 Wikipedia:Heart_development dorsal vessel development biological_process cardiac development GO:0007507 heart development The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. GOC:jid UBERON:0000948 The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work. MIPS_funcat:45.03.12 biological_process GO:0007517 muscle organ development The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work. GOC:jid ISBN:0198506732 The establishment of the sex of an organism by physical differentiation. MIPS_funcat:41.05.23 Wikipedia:Sexual_differentiation biological_process GO:0007548 sex differentiation The establishment of the sex of an organism by physical differentiation. GOC:ai The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. janelomax 2012-09-20T14:06:08Z GO:0044708 Wikipedia:Behavior behavioral response to stimulus behaviour behavioural response to stimulus biological_process single-organism behavior GO:0007610 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). behavior The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. GOC:ems GOC:jl ISBN:0395448956 PMID:20160973 A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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. janelomax 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 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 A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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 chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. janelomax 2012-10-17T15:46:40Z GO:0044236 GO:0044710 MIPS_funcat:01 Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth multicellular organism metabolic process biological_process single-organism metabolic process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. GOC:go_curators ISBN:0198547684 The multiplication or reproduction of cells, resulting in the expansion of a cell population. biological_process cell proliferation GO:0008283 This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms. cell population proliferation The multiplication or reproduction of cells, resulting in the expansion of a cell population. GOC:mah GOC:mb Any process that activates or increases the rate or extent of cell proliferation. up regulation of cell proliferation up-regulation of cell proliferation upregulation of cell proliferation activation of cell proliferation stimulation of cell proliferation biological_process positive regulation of cell proliferation GO:0008284 positive regulation of cell population proliferation Any process that activates or increases the rate or extent of cell proliferation. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of cell proliferation. down regulation of cell proliferation down-regulation of cell proliferation downregulation of cell proliferation inhibition of cell proliferation biological_process negative regulation of cell proliferation GO:0008285 negative regulation of cell population proliferation Any process that stops, prevents or reduces the rate or extent of cell proliferation. GOC:go_curators The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones. gonadogenesis biological_process GO:0008406 gonad development The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones. GOC:ems ISBN:0198506732 gonadogenesis GOC:cjm The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species. biological_process hypodermis development GO:0008544 epidermis development The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species. GOC:go_curators UBERON:0001003 hypodermis development GOC:kmv GOC:rk Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus. MIPS_funcat:36.20.35 response to environmental stimulus biological_process GO:0009605 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to external stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus. GOC:hb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism. GO:0002245 physiological response to wounding biological_process GO:0009611 response to wounding Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism. GOC:go_curators The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. embryogenesis and morphogenesis Wikipedia:Morphogenesis anatomical structure organization morphogenesis biological_process GO:0009653 anatomical structure morphogenesis The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. GOC:go_curators ISBN:0521436125 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 an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell. embryogenesis MIPS_funcat:41.05.03 biological_process GO:0009792 embryo development ending in birth or egg hatching The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell. GOC:go_curators GOC:isa_complete GOC:mtg_sensu The establishment, maintenance and elaboration of a pattern along a line or around a point. MIPS_funcat:41.05.19 biological_process axis determination GO:0009798 axis specification The establishment, maintenance and elaboration of a pattern along a line or around a point. GOC:dph GOC:go_curators GOC:isa_complete The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure. histogenesis and organogenesis Wikipedia:Histogenesis histogenesis biological_process GO:0009888 tissue development The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure. ISBN:0471245208 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044252 down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process negative regulation of metabolism negative regulation of organismal metabolism inhibition of metabolic process inhibition of organismal metabolic process negative regulation of multicellular organismal metabolic process biological_process GO:0009892 negative regulation of metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044253 positive regulation of metabolism up regulation of metabolic process up-regulation of metabolic process upregulation of metabolic process activation of metabolic process positive regulation of multicellular organismal metabolic process positive regulation of organismal metabolism stimulation of metabolic process stimulation of organismal metabolic process up-regulation of organismal metabolic process biological_process GO:0009893 positive regulation of metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators The establishment, maintenance and elaboration of the proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end). proximodistal axis specification biological_process proximal/distal axis determination GO:0009946 proximal/distal axis specification The establishment, maintenance and elaboration of the proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end). GOC:dph GOC:go_curators GOC:tb proximal/distal axis determination GOC:dph The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism. MIPS_funcat:41.05.19.05 biological_process anterior/posterior axis determination GO:0009948 anterior/posterior axis specification The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism. GOC:dph GOC:go_curators GOC:tb anterior/posterior axis determination GOC:dph The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism. MIPS_funcat:41.05.19.07 dorsal-ventral axis specification dorsoventral axis specification biological_process dorsal/ventral axis determination GO:0009950 dorsal/ventral axis specification The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism. GOC:dph GOC:go_curators GOC:tb dorsal-ventral axis specification GOC:mah dorsoventral axis specification GOC:mah dorsal/ventral axis determination GOC:dph The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism. biological_process anterior/posterior pattern formation GO:0009952 anterior/posterior pattern specification The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism. GOC:dph GOC:go_curators GOC:isa_complete GOC:tb The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism. dorsal-ventral pattern formation dorsoventral pattern formation dorsal/ventral pattern specification biological_process GO:0009953 dorsal/ventral pattern formation The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism. GOC:dph GOC:go_curators GOC:isa_complete GOC:tb dorsal-ventral pattern formation GOC:mah dorsoventral pattern formation GOC:mah The regionalization process in which specific areas of cell differentiation are determined along a proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end). proximal/distal pattern specification biological_process GO:0009954 proximal/distal pattern formation The regionalization process in which specific areas of cell differentiation are determined along a proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end). GOC:dph GOC:go_curators GOC:isa_complete Any process that modulates the frequency, rate or extent of signal transduction. GO:0035466 biological_process regulation of signaling pathway regulation of signalling pathway GO:0009966 regulation of signal transduction Any process that modulates the frequency, rate or extent of signal transduction. GOC:sm regulation of signalling pathway GOC:mah Any process that activates or increases the frequency, rate or extent of signal transduction. GO:0035468 up regulation of signal transduction up-regulation of signal transduction upregulation of signal transduction activation of signal transduction stimulation of signal transduction biological_process positive regulation of signaling pathway positive regulation of signalling pathway GO:0009967 positive regulation of signal transduction Any process that activates or increases the frequency, rate or extent of signal transduction. GOC:sm positive regulation of signalling pathway GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GO:0035467 down regulation of signal transduction down-regulation of signal transduction downregulation of signal transduction inhibition of signal transduction biological_process negative regulation of signaling pathway negative regulation of signalling pathway GO:0009968 negative regulation of signal transduction Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GOC:sm negative regulation of signalling pathway GOC:mah 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. janelomax 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 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 Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity. regulation of receptor activity biological_process GO:0010469 regulation of signaling receptor activity Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity. GOC:dph GOC:tb Any process that modulates the rate or extent of gastrulation. Gastrulation is the complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. biological_process GO:0010470 regulation of gastrulation Any process that modulates the rate or extent of gastrulation. Gastrulation is the complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. biological_process GO:0010562 positive regulation of phosphorus metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. biological_process GO:0010563 negative regulation of phosphorus metabolic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:dph GOC:tb Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. biological_process GO:0010564 regulation of cell cycle process Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. positive regulation of organelle organisation biological_process positive regulation of organelle organization and biogenesis GO:0010638 positive regulation of organelle organization Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:dph GOC:tb positive regulation of organelle organisation GOC:mah positive regulation of organelle organization and biogenesis GOC:mah Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. negative regulation of organelle organisation biological_process negative regulation of organelle organization and biogenesis GO:0010639 negative regulation of organelle organization Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:dph GOC:tb negative regulation of organelle organisation GOC:mah negative regulation of organelle organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010646 regulation of cell communication Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010647 positive regulation of cell communication Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010648 negative regulation of cell communication Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process GO:0010720 positive regulation of cell development Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:BHF GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process GO:0010721 negative regulation of cell development Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:BHF GOC:dph GOC:tb The cellular component assembly that is part of the initial shaping of the component during its developmental progression. biological_process GO:0010927 cellular component assembly involved in morphogenesis The cellular component assembly that is part of the initial shaping of the component during its developmental progression. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. tanyaberardini 2009-04-27T09:53:22Z biological_process GO:0010948 negative regulation of cell cycle process Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). tanyaberardini 2009-06-01T10:44:45Z regulation of neurite biosynthesis regulation of neurite development regulation of neurite formation regulation of neurite growth biological_process GO:0010975 regulation of neuron projection development Any process that modulates the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). GOC:dph GOC:tb regulation of neurite biosynthesis GOC:mah regulation of neurite development GOC:mah regulation of neurite formation GOC:mah regulation of neurite growth GOC:mah Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). tanyaberardini 2009-06-01T10:46:44Z positive regulation of neurite biosynthesis positive regulation of neurite development positive regulation of neurite formation positive regulation of neurite growth biological_process GO:0010976 positive regulation of neuron projection development Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). GOC:dph GOC:tb positive regulation of neurite biosynthesis GOC:mah positive regulation of neurite development GOC:mah positive regulation of neurite formation GOC:mah positive regulation of neurite growth GOC:mah Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). tanyaberardini 2009-06-01T10:47:42Z negative regulation of neurite biosynthesis negative regulation of neurite development negative regulation of neurite formation negative regulation of neurite growth biological_process growth cone collapse GO:0010977 negative regulation of neuron projection development Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). GOC:dph GOC:tb negative regulation of neurite biosynthesis GOC:mah negative regulation of neurite development GOC:mah negative regulation of neurite formation GOC:mah negative regulation of neurite growth GOC:mah growth cone collapse GOC:pr 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 The process aimed at the progression of a mesenchymal cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. biological_process GO:0014031 mesenchymal cell development The process aimed at the progression of a mesenchymal cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. GOC:dh GOC:ef The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. biological_process GO:0014032 neural crest cell development The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. GOC:dh GOC:ef The process in which a relatively unspecialized cell acquires specialized features of a neural crest cell. biological_process GO:0014033 neural crest cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a neural crest cell. GOC:dh GOC:ef The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. MIPS_funcat:70.04.03 cellular_component GO:0015629 actin cytoskeleton The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. GOC:jl ISBN:0395825172 ISBN:0815316194 The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. MIPS_funcat:70.04.05 cellular_component GO:0015630 microtubule cytoskeleton The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. GOC:jl ISBN:0395825172 A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. Wikipedia:Biological_membrane cellular_component GO:0016020 membrane membrane A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. GOC:dos GOC:mah ISBN:0815316194 A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0044235 GO:0071842 MIPS_funcat:42 cell organisation cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism biological_process cell organization and biogenesis GO:0016043 cellular component organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:ai GOC:jl GOC:mah cellular component organisation at cellular level GOC:mah cellular component organisation in other organism GOC:mah cell organization and biogenesis 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 The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. Wikipedia:Phosphorylation biological_process GO:0016310 phosphorylation The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. ISBN:0198506732 The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. MIPS_funcat:34.05.01 Wikipedia:Cell_migration biological_process GO:0016477 cell migration The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. GOC:cjm GOC:dph GOC:ems GOC:pf http://en.wikipedia.org/wiki/Cell_migration 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-6787403 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-6787403 GTPBP3 and MTO1 transform uridine-34 yielding 5-taurinomethyluridine-34 in tRNA 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 self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. stem cell renewal biological_process GO:0017145 stem cell division The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. GOC:jid ISBN:0582227089 The specific behavior of an organism that is associated with reproduction. janelomax 2012-09-19T16:01:37Z GO:0033057 GO:0044704 reproductive behavior in a multicellular organism reproductive behaviour multicellular organism reproductive behavior biological_process single-organism reproductive behavior GO:0019098 reproductive behavior The specific behavior of an organism that is associated with reproduction. GOC:jl GOC:pr reproductive behavior in a multicellular organism GOC:curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. regulation of phosphate metabolism biological_process GO:0019220 regulation of phosphate metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044246 regulation of metabolism regulation of multicellular organismal metabolic process regulation of organismal metabolic process biological_process GO:0019222 regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators regulation of organismal metabolic process GOC:tb The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission. conduction of nerve impulse signal transmission along a neuron biological_process GO:0019226 transmission of nerve impulse The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission. GOC:curators ISBN:0815316194 conduction of nerve impulse GOC:dph The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues. biological_process GO:0021510 This term was added by GO_REF:0000021. spinal cord development The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues. GOC:cls GOC:dgh GOC:dph GOC:jid GOC:mtg_15jun06 GO_REF:0000021 Generation of cells within the nervous system. Wikipedia:Neurogenesis nervous system cell generation biological_process neural cell differentiation GO:0022008 This term was added by GO_REF:0000021. neurogenesis Generation of cells within the nervous system. GOC:cls GOC:curators GOC:dgh GOC:dph GOC:jid GOC:mtg_15jun06 GO_REF:0000021 nervous system cell generation neural cell differentiation GOC:BHF GOC:dph The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. biological_process GO:0022402 cell cycle process The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. GOC:isa_complete GOC:mtg_cell_cycle A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism. reproductive cellular process in multicellular organism biological_process GO:0022412 cellular process involved in reproduction in multicellular organism A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism. GOC:isa_complete reproductive cellular process in multicellular organism GOC:curators A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. janelomax 2012-09-19T15:56:06Z GO:0044702 biological_process single organism reproductive process GO:0022414 reproductive process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:dph GOC:isa_complete Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis. regulation of morphogenesis biological_process GO:0022603 regulation of anatomical structure morphogenesis Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis. GOC:mah The aggregation, arrangement and bonding together of a cellular component. GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process GO:0022607 cellular component assembly The aggregation, arrangement and bonding together of a cellular component. GOC:isa_complete Any process that modulates the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process regulation of signaling process regulation of signalling process GO:0023051 regulation of signaling Any process that modulates the frequency, rate or extent of a signaling process. GOC:mtg_signal regulation of signaling process GOC:bf regulation of signalling process GOC:mah The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. janelomax 2010-02-16T09:30:50Z GO:0023046 GO:0044700 biological signaling signaling process signalling biological_process signalling process single organism signaling GO:0023052 Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. signaling The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. GOC:mtg_signal GOC:mtg_signaling_feb11 GOC:signaling signalling process GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z positive regulation of signalling process biological_process positive regulation of signaling process GO:0023056 positive regulation of signaling Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. GOC:mtg_signal positive regulation of signalling process GOC:mah positive regulation of signaling process GOC:bf Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process negative regulation of signaling process negative regulation of signalling process GO:0023057 negative regulation of signaling Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. GOC:mtg_signal negative regulation of signaling process GOC:bf negative regulation of signalling process GOC:mah The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism. Wikipedia:Myofibril cellular_component striated muscle fiber striated muscle fibre GO:0030016 myofibril The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism. ISBN:0815316194 The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. Wikipedia:Sarcomere cellular_component GO:0030017 sarcomere The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. ISBN:0815316194 Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins. biological_process microfilament-based process GO:0030029 actin filament-based process Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. cell projection organisation biological_process cell projection organization and biogenesis cell surface structure organization and biogenesis GO:0030030 cell projection organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah http://www.cogsci.princeton.edu/~wn/ cell projection organisation GOC:curators cell projection organization and biogenesis GOC:mah cell surface structure organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. MIPS_funcat:42.04.03 actin cytoskeleton organisation biological_process actin cytoskeleton organization and biogenesis actin modulating activity GO:0030036 actin cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. GOC:dph GOC:jl GOC:mah actin cytoskeleton organisation GOC:curators actin cytoskeleton organization and biogenesis GOC:mah A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. secretory vesicle cellular_component GO:0030141 Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'transport vesicle ; GO:0030133'. secretory granule A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. GOC:mah ISBN:0198506732 The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. MIPS_funcat:40.02 Wikipedia:Cellular_differentiation biological_process GO:0030154 cell differentiation The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. ISBN:0198506732 The process in which a relatively unspecialized cell acquires specialized features of a neuron. MIPS_funcat:43.03.13 biological_process GO:0030182 neuron differentiation The process in which a relatively unspecialized cell acquires specialized features of a neuron. GOC:mah Formation of myofibrils, the repeating units of striated muscle. biological_process GO:0030239 myofibril assembly Formation of myofibrils, the repeating units of striated muscle. GOC:mah The process whose specific outcome is the progression of the respiratory tube over time, from its formation to the mature structure. The respiratory tube is assumed to mean any tube in the respiratory tract. biological_process GO:0030323 respiratory tube development The process whose specific outcome is the progression of the respiratory tube over time, from its formation to the mature structure. The respiratory tube is assumed to mean any tube in the respiratory tract. GOC:jid The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. MIPS_funcat:47.03.09.01 biological_process GO:0030324 lung development The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. GOC:jid UBERON:0002048 The process whose specific outcome is the progression of the adrenal gland over time, from its formation to the mature structure. This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells. MIPS_funcat:47.03.21.03.01 biological_process interrenal gland GO:0030325 adrenal gland development The process whose specific outcome is the progression of the adrenal gland over time, from its formation to the mature structure. This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells. GOC:dgh Any process that modulates the frequency, rate or extent of cell migration. biological_process GO:0030334 regulation of cell migration Any process that modulates the frequency, rate or extent of cell migration. GOC:go_curators Any process that activates or increases the frequency, rate or extent of cell migration. up regulation of cell migration up-regulation of cell migration upregulation of cell migration activation of cell migration stimulation of cell migration biological_process GO:0030335 positive regulation of cell migration Any process that activates or increases the frequency, rate or extent of cell migration. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. down regulation of cell migration down-regulation of cell migration downregulation of cell migration inhibition of cell migration biological_process GO:0030336 negative regulation of cell migration Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. GOC:go_curators The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. MIPS_funcat:18.02.07 molecular_function GO:0030545 receptor regulator activity The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. GOC:ceb The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. receptor activator activity molecular_function GO:0030546 signaling receptor activator activity The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. GOC:ceb The process whose specific outcome is the progression of the thyroid gland over time, from its formation to the mature structure. The thyroid gland is an endoderm-derived gland that produces thyroid hormone. MIPS_funcat:47.03.21.03.06 biological_process GO:0030878 thyroid gland development The process whose specific outcome is the progression of the thyroid gland over time, from its formation to the mature structure. The thyroid gland is an endoderm-derived gland that produces thyroid hormone. GOC:dgh The process whose specific outcome is the progression of the notochord over time, from its formation to the mature structure. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column. biological_process GO:0030903 notochord development The process whose specific outcome is the progression of the notochord over time, from its formation to the mature structure. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column. GOC:dgh The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes. MIPS_funcat:47.03.11.09 Wikipedia:Pancreas biological_process GO:0031016 pancreas development The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes. GOC:cvs A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin. The myosin may be organized into filaments. actomyosin organization actomyosin structure organisation biological_process actomyosin structure organization and biogenesis GO:0031032 Note that this term is a child of 'actin cytoskeleton organization and biogenesis ; GO:0030036' because the actin cytoskeleton is defined as actin filaments and associated proteins. actomyosin structure organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin. The myosin may be organized into filaments. GOC:dph GOC:jl GOC:mah actomyosin structure organisation GOC:curators actomyosin structure organization and biogenesis GOC:mah Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted. NIF_Subcellular:sao772007592 dense core vesicle cellular_component GO:0031045 dense core granule Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted. NIF_Subcellular:sao772007592 PMID:14690495 dense core vesicle GOC:kmv The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass). Wikipedia:Regeneration_(biology) biological_process GO:0031099 regeneration The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass). GOC:mah GOC:pr The regrowth of neuronal processes such as axons or dendrites in response to their loss or damage. neurite regeneration biological_process GO:0031102 neuron projection regeneration The regrowth of neuronal processes such as axons or dendrites in response to their loss or damage. GOC:dgh GOC:dph GOC:tb neurite regeneration GOC:mah The regrowth of axons following their loss or damage. biological_process GO:0031103 axon regeneration The regrowth of axons following their loss or damage. GOC:dgh GOC:dph GOC:tb The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). neurite biosynthesis neurite development neurite formation neurite growth neurite outgrowth biological_process GO:0031175 neuron projection development The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). GOC:mah neurite development GOC:dph Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. regulation of cellular metabolism biological_process GO:0031323 regulation of cellular metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. down regulation of cellular metabolic process down-regulation of cellular metabolic process downregulation of cellular metabolic process negative regulation of cellular metabolism inhibition of cellular metabolic process biological_process GO:0031324 negative regulation of cellular metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. positive regulation of cellular metabolism up regulation of cellular metabolic process up-regulation of cellular metabolic process upregulation of cellular metabolic process activation of cellular metabolic process stimulation of cellular metabolic process biological_process GO:0031325 positive regulation of cellular metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. regulation of cell projection organisation biological_process regulation of cell projection organization and biogenesis GO:0031344 regulation of cell projection organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. GOC:mah regulation of cell projection organisation GOC:curators regulation of cell projection organization and biogenesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. down regulation of cell projection organization down-regulation of cell projection organization downregulation of cell projection organization negative regulation of cell projection organisation inhibition of cell projection organization biological_process negative regulation of cell projection organization and biogenesis GO:0031345 negative regulation of cell projection organization Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. GOC:mah down regulation of cell projection organization GOC:mah negative regulation of cell projection organisation GOC:curators negative regulation of cell projection organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. positive regulation of cell projection organisation up regulation of cell projection organization up-regulation of cell projection organization upregulation of cell projection organization activation of cell projection organization stimulation of cell projection organization biological_process positive regulation of cell projection organization and biogenesis GO:0031346 positive regulation of cell projection organization Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. GOC:mah positive regulation of cell projection organisation GOC:curators positive regulation of cell projection organization and biogenesis GOC:mah A vesicle found in the cytoplasm of a cell. GO:0016023 NIF_Subcellular:sao180601769 cellular_component cytoplasmic membrane bounded vesicle cytoplasmic membrane-enclosed vesicle cytoplasmic, membrane-bounded vesicle GO:0031410 cytoplasmic vesicle A vesicle found in the cytoplasm of a cell. GOC:ai GOC:mah GOC:vesicles Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system. regulation of neurological process regulation of neurological system process regulation of neurophysiological process biological_process GO:0031644 regulation of nervous system process Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system. GOC:dph GOC:mah GOC:tb regulation of neurological process GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process. down regulation of neurological process down-regulation of neurological process downregulation of neurological process negative regulation of neurological process negative regulation of neurological system process negative regulation of neurophysiological process inhibition of neurological process biological_process GO:0031645 negative regulation of nervous system process Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process. GOC:dph GOC:mah GOC:tb negative regulation of neurological process GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of a neurophysiological process. positive regulation of neurological process positive regulation of neurological system process positive regulation of neurophysiological process up regulation of neurological process up-regulation of neurological process upregulation of neurological process activation of neurological process stimulation of neurological process biological_process GO:0031646 positive regulation of nervous system process Any process that activates or increases the frequency, rate or extent of a neurophysiological process. GOC:dph GOC:mah GOC:tb positive regulation of neurological process GOC:dph GOC:tb A two-stranded helical polymer of the protein actin. Wikipedia:Actin F-actin cellular_component GO:0031941 Note that this term refers only to the actin portion of a microfilament, and does not encompass associated proteins. See also the cellular component term 'actin filament ; GO:0005884'. filamentous actin A two-stranded helical polymer of the protein actin. GOC:mah Any small, fluid-filled, spherical organelle enclosed by membrane. GO:0031988 NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component membrane-bounded vesicle membrane-enclosed vesicle GO:0031982 vesicle Any small, fluid-filled, spherical organelle enclosed by membrane. GOC:mah GOC:pz GOC:vesicles Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. down regulation of protein binding down-regulation of protein binding downregulation of protein binding inhibition of protein binding biological_process GO:0032091 negative regulation of protein binding Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. GOC:mah Any process that activates or increases the frequency, rate or extent of protein binding. up regulation of protein binding up-regulation of protein binding upregulation of protein binding activation of protein binding stimulation of protein binding biological_process GO:0032092 positive regulation of protein binding Any process that activates or increases the frequency, rate or extent of protein binding. GOC:mah Any process that modulates the frequency, rate or extent of a response to an external stimulus. biological_process GO:0032101 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to external stimulus Any process that modulates the frequency, rate or extent of a response to an external stimulus. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus. down regulation of response to external stimulus down-regulation of response to external stimulus downregulation of response to external stimulus inhibition of response to external stimulus biological_process GO:0032102 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. negative regulation of response to external stimulus Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus. GOC:mah Any process that activates, maintains or increases the rate of a response to an external stimulus. up regulation of response to external stimulus up-regulation of response to external stimulus upregulation of response to external stimulus activation of response to external stimulus stimulation of response to external stimulus biological_process GO:0032103 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. positive regulation of response to external stimulus Any process that activates, maintains or increases the rate of a response to an external stimulus. GOC:mah Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells. GO:0071775 regulation of cell cycle cytokinesis biological_process GO:0032465 regulation of cytokinesis Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the division of the cytoplasm of a cell, and its separation into two daughter cells. GO:0071776 down regulation of cytokinesis down-regulation of cytokinesis downregulation of cytokinesis inhibition of cytokinesis biological_process negative regulation of cell cycle cytokinesis GO:0032466 negative regulation of cytokinesis Any process that stops, prevents, or reduces the frequency, rate or extent of the division of the cytoplasm of a cell, and its separation into two daughter cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the division of the cytoplasm of a cell, and its separation into two daughter cells. GO:0071777 up regulation of cytokinesis up-regulation of cytokinesis upregulation of cytokinesis activation of cytokinesis stimulation of cytokinesis biological_process positive regulation of cell cycle cytokinesis GO:0032467 positive regulation of cytokinesis Any process that activates or increases the frequency, rate or extent of the division of the cytoplasm of a cell, and its separation into two daughter cells. GOC:mah Any biological process, occurring at the level of a multicellular organism, pertinent to its function. janelomax 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. janelomax 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 The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. biological_process GO:0032504 multicellular organism reproduction The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:isa_complete GOC:jid Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. regulation of localisation biological_process GO:0032879 regulation of localization Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. GOC:mah regulation of localisation GOC:mah Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. regulation of actin cytoskeleton organisation biological_process regulation of actin cytoskeleton organization and biogenesis GO:0032956 regulation of actin cytoskeleton organization Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. GOC:mah regulation of actin cytoskeleton organisation GOC:mah regulation of actin cytoskeleton organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the actin cytoskeleton. biological_process GO:0032970 regulation of actin filament-based process Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the actin cytoskeleton. GOC:mah The process in which cellular structures, including whole cells or cell parts, are generated and organized. cellular structure morphogenesis biological_process GO:0032989 cellular component morphogenesis The process in which cellular structures, including whole cells or cell parts, are generated and organized. GOC:dph GOC:mah GOC:tb cellular structure morphogenesis GOC:dph GOC:tb A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 macromolecular complex macromolecule complex protein containing complex protein complex protein-protein complex cellular_component GO:0032991 A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. protein-containing complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GOC:dos GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. regulation of organelle organisation biological_process regulation of organelle organization and biogenesis GO:0033043 regulation of organelle organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:mah regulation of organelle organisation GOC:mah regulation of organelle organization and biogenesis GOC:mah The process whose specific outcome is the progression of a fin over time, from its formation to the mature structure. biological_process GO:0033333 fin development The process whose specific outcome is the progression of a fin over time, from its formation to the mature structure. GOC:dgh Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). biological_process GO:0033554 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to stress Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. down regulation of kinase activity down-regulation of kinase activity downregulation of kinase activity inhibition of kinase activity kinase inhibitor biological_process GO:0033673 negative regulation of kinase activity Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:mah Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. up regulation of kinase activity up-regulation of kinase activity upregulation of kinase activity kinase activator stimulation of kinase activity biological_process GO:0033674 positive regulation of kinase activity Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:mah The developmental process that results in the creation of defined areas or spaces within the pronephros along the anterior/posterior axis to which cells respond and eventually are instructed to differentiate. anterior/posterior pattern specification involved in pronephric kidney development biological_process GO:0034672 anterior/posterior pattern specification involved in pronephros development The developmental process that results in the creation of defined areas or spaces within the pronephros along the anterior/posterior axis to which cells respond and eventually are instructed to differentiate. GOC:mah anterior/posterior pattern specification involved in pronephric kidney development GOC:mtg_kidney_jan10 The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell that will form part of the cardiac organ of an individual. cardiac cell differentiation heart cell differentiation biological_process GO:0035051 cardiocyte differentiation The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell that will form part of the cardiac organ of an individual. GOC:bf The specific behavior of an organism during the emergence from an egg shell. In Drosophila for example, the larva swings its head reiteratively through a semicircular arc, using its mouth hooks to tear apart the chorion in front of it and thus free itself from within the egg shell. hatching behaviour biological_process GO:0035187 hatching behavior The specific behavior of an organism during the emergence from an egg shell. In Drosophila for example, the larva swings its head reiteratively through a semicircular arc, using its mouth hooks to tear apart the chorion in front of it and thus free itself from within the egg shell. GOC:pr PMID:10436051 The emergence of an immature organism from a protective structure. biological_process GO:0035188 hatching The emergence of an immature organism from a protective structure. GOC:dgh GOC:isa_complete ISBN:0198612001 The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. biological_process GO:0035239 tube morphogenesis The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. GOC:bf PMID:14624839 Progression of the endocrine system over time, from its formation to a mature structure. The endocrine system is a system of hormones and ductless glands, where the glands release hormones directly into the blood, lymph or other intercellular fluid, and the hormones circulate within the body to affect distant organs. The major glands that make up the human endocrine system are the hypothalamus, pituitary, thyroid, parathryoids, adrenals, pineal body, and the reproductive glands which include the ovaries and testes. biological_process GO:0035270 endocrine system development Progression of the endocrine system over time, from its formation to a mature structure. The endocrine system is a system of hormones and ductless glands, where the glands release hormones directly into the blood, lymph or other intercellular fluid, and the hormones circulate within the body to affect distant organs. The major glands that make up the human endocrine system are the hypothalamus, pituitary, thyroid, parathryoids, adrenals, pineal body, and the reproductive glands which include the ovaries and testes. GOC:bf ISBN:0198506732 http://encyclopedia.thefreedictionary.com/Endocrine+sytem The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts. biological_process GO:0035295 tube development The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts. PMID:12526790 The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. rfoulger 2010-05-14T01:14:37Z GO:0007242 GO:0007243 GO:0023013 GO:0023034 intracellular signaling chain intracellular protein kinase cascade intracellular signal transduction pathway protein kinase cascade signal transmission via intracellular cascade biological_process intracellular signaling cascade intracellular signaling pathway signal transduction via intracellular signaling cascade GO:0035556 intracellular signal transduction The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. GOC:bf GOC:jl GOC:signaling ISBN:3527303782 intracellular signaling chain ISBN:3527303782 intracellular protein kinase cascade GOC:signaling protein kinase cascade GOC:signaling intracellular signaling cascade GOC:signaling The transfer of information occurring at the level of a multicellular organism. rfoulger 2011-01-14T10:13:50Z multicellular organismal signalling biological_process GO:0035637 multicellular organismal signaling The transfer of information occurring at the level of a multicellular organism. GOC:go_curators multicellular organismal signalling GOC:bf The orderly movement of a cell from one site to another that will contribute to the progression of the kidney over time, from its formation to the mature organ. rfoulger 2011-04-06T10:39:52Z biological_process GO:0035787 cell migration involved in kidney development The orderly movement of a cell from one site to another that will contribute to the progression of the kidney over time, from its formation to the mature organ. GOC:bf GOC:mtg_kidney_jan10 GOC:yaf The process whose specific outcome is the progression of the cloaca over time, from it's formation to the mature structure. The cloaca is the common chamber into which intestinal, genital and urinary canals open in vertebrates. rfoulger 2011-05-06T01:54:35Z cloacal development biological_process GO:0035844 cloaca development The process whose specific outcome is the progression of the cloaca over time, from it's formation to the mature structure. The cloaca is the common chamber into which intestinal, genital and urinary canals open in vertebrates. GOC:dgh ISBN:0582227089 cloacal development GOC:bf Self-propelled movement of an organism from one location to another through water, often by means of active fin movement. rfoulger 2012-07-04T10:12:24Z biological_process GO:0036268 For behavioral aspects of swimming, consider instead annotating to 'swimming behavior ; GO:0036269'. swimming Self-propelled movement of an organism from one location to another through water, often by means of active fin movement. GOC:cvs PMID:22459995 The process in which a post-anal tail is generated and organized. A post-anal tail is a muscular region of the body that extends posterior to the anus. The post-anal tail may aid locomotion and balance. rfoulger 2012-09-11T13:54:49Z biological_process GO:0036342 post-anal tail morphogenesis The process in which a post-anal tail is generated and organized. A post-anal tail is a muscular region of the body that extends posterior to the anus. The post-anal tail may aid locomotion and balance. GOC:bf GOC:kmv Wikipedia:Chordate Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. rfoulger 2011-08-01T02:45:27Z GO:0004872 GO:0019041 receptor activity receptor activity involved in signal transduction molecular_function GO:0038023 signaling receptor activity Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. GOC:bf GOC:signaling receptor activity involved in signal transduction GOC:bf The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the pronephros as it progresses from its formation to the mature state. rfoulger 2010-07-02T09:59:25Z cell differentiation involved in pronephric kidney development biological_process GO:0039014 cell differentiation involved in pronephros development The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the pronephros as it progresses from its formation to the mature state. GOC:mtg_kidney_jan10 cell differentiation involved in pronephric kidney development GOC:mtg_kidney_jan10 The multiplication or reproduction of cells, resulting in the expansion of the population in the pronephros. rfoulger 2010-07-02T10:01:49Z cell proliferation involved in pronephric kidney development biological_process GO:0039015 cell proliferation involved in pronephros development The multiplication or reproduction of cells, resulting in the expansion of the population in the pronephros. GOC:mtg_kidney_jan10 cell proliferation involved in pronephric kidney development GOC:mtg_kidney_jan10 Any process that mediates the transfer of information from one cell to another and contributes to the progression of the pronephros over time, from its formation to the mature organ. rfoulger 2010-07-02T10:03:16Z cell-cell signaling involved in pronephric kidney development cell-cell signalling involved in pronephros development biological_process GO:0039016 cell-cell signaling involved in pronephros development Any process that mediates the transfer of information from one cell to another and contributes to the progression of the pronephros over time, from its formation to the mature organ. GOC:mtg_kidney_jan10 cell-cell signaling involved in pronephric kidney development GOC:mtg_kidney_jan10 cell-cell signalling involved in pronephros development GOC:mah Any developmental process that results in the creation of defined areas or spaces within the pronephros to which cells respond and eventually are instructed to differentiate. rfoulger 2010-07-02T10:04:39Z pattern specification involved in pronephric kidney development biological_process GO:0039017 pattern specification involved in pronephros development Any developmental process that results in the creation of defined areas or spaces within the pronephros to which cells respond and eventually are instructed to differentiate. GOC:mtg_kidney_jan10 pattern specification involved in pronephric kidney development GOC:mtg_kidney_jan10 The increase in size or mass of an entire organism, a part of an organism or a cell. GO:0048590 biological_process growth pattern non-developmental growth GO:0040007 See also the biological process term 'cell growth ; GO:0016049'. growth The increase in size or mass of an entire organism, a part of an organism or a cell. GOC:bf GOC:ma non-developmental growth GOC:mah Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. biological_process GO:0040008 regulation of growth Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. GOC:ems GOC:mah Self-propelled movement of a cell or organism from one location to another. MIPS_funcat:02.45.11 biological_process GO:0040011 locomotion Self-propelled movement of a cell or organism from one location to another. GOC:dgh Any process that modulates the frequency, rate or extent of locomotion of a cell or organism. biological_process GO:0040012 regulation of locomotion Any process that modulates the frequency, rate or extent of locomotion of a cell or organism. GOC:ems Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism. down regulation of locomotion down-regulation of locomotion downregulation of locomotion inhibition of locomotion biological_process GO:0040013 negative regulation of locomotion Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism. up regulation of locomotion up-regulation of locomotion upregulation of locomotion activation of locomotion stimulation of locomotion biological_process GO:0040017 positive regulation of locomotion Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of embryonic development. up regulation of embryonic development up-regulation of embryonic development upregulation of embryonic development activation of embryonic development stimulation of embryonic development biological_process GO:0040019 positive regulation of embryonic development Any process that activates or increases the frequency, rate or extent of embryonic development. GOC:go_curators The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression). biological_process GO:0042074 cell migration involved in gastrulation The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression). GOC:jl ISBN:0878932437 http://www.cellmigration.org/ Any process that modulates the frequency, rate or extent of cell proliferation. biological_process regulation of cell proliferation GO:0042127 regulation of cell population proliferation Any process that modulates the frequency, rate or extent of cell proliferation. GOC:jl Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. biological_process GO:0042325 regulation of phosphorylation Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. GOC:jl Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. down regulation of phosphorylation down-regulation of phosphorylation downregulation of phosphorylation inhibition of phosphorylation biological_process GO:0042326 negative regulation of phosphorylation Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. GOC:jl Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. up regulation of phosphorylation up-regulation of phosphorylation upregulation of phosphorylation activation of phosphorylation stimulation of phosphorylation biological_process GO:0042327 positive regulation of phosphorylation Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. GOC:jl Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. biological_process GO:0042391 regulation of membrane potential Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. GOC:jl GOC:mtg_cardio GOC:tb ISBN:0198506732 The process in which a relatively unspecialized cell acquires specialized features of a muscle cell. biological_process myogenesis GO:0042692 muscle cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a muscle cell. CL:0000187 GOC:go_curators The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching. biological_process GO:0043009 chordate embryonic development The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching. GOC:mtg_sensu The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field. GO:0001747 GO:0031075 biological_process GO:0043010 camera-type eye development The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field. GOC:go_curators GOC:mtg_sensu Any process that activates or increases the activity of an enzyme. GO:0048554 MIPS_funcat:18.02.01.01 positive regulation of enzyme activity up regulation of enzyme activity up-regulation of enzyme activity upregulation of enzyme activity activation of enzyme activity activation of metalloenzyme activity positive regulation of metalloenzyme activity stimulation of enzyme activity stimulation of metalloenzyme activity up regulation of metalloenzyme activity up-regulation of metalloenzyme activity upregulation of metalloenzyme activity biological_process GO:0043085 positive regulation of catalytic activity Any process that activates or increases the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw positive regulation of enzyme activity GOC:tb Any process that stops or reduces the activity of an enzyme. GO:0048553 down regulation of enzyme activity down-regulation of enzyme activity down-regulation of metalloenzyme activity downregulation of enzyme activity negative regulation of enzyme activity down regulation of metalloenzyme activity downregulation of metalloenzyme activity inhibition of enzyme activity inhibition of metalloenzyme activity negative regulation of metalloenzyme activity biological_process GO:0043086 negative regulation of catalytic activity Any process that stops or reduces the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw negative regulation of enzyme activity GOC:tb 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, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component GO:0043228 non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. 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 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. intracellular non-membrane-enclosed organelle cellular_component GO:0043232 intracellular non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. GOC:go_curators Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. muscle fiber muscle fibre contractile fibre cellular_component GO:0043292 contractile fiber Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. GOC:go_curators ISBN:0815316194 Any process that modulates the frequency, rate or extent of protein binding. biological_process GO:0043393 regulation of protein binding Any process that modulates the frequency, rate or extent of protein binding. GOC:go_curators Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. biological_process GO:0043549 regulation of kinase activity Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:bf The process whose specific outcome is the progression of the ear over time, from its formation to the mature structure. The ear is the sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. MIPS_funcat:47.03.02.01 hearing organ development biological_process GO:0043583 ear development The process whose specific outcome is the progression of the ear over time, from its formation to the mature structure. The ear is the sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. GOC:jl ISBN:0192801023 The process whose specific outcome is the progression of the nose over time, from its formation to the mature structure. The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity). MIPS_funcat:47.03.02.03 nasus development biological_process GO:0043584 nose development The process whose specific outcome is the progression of the nose over time, from its formation to the mature structure. The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity). GOC:jl http://www.mercksource.com/ Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system. biological_process GO:0044057 regulation of system process Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system. GOC:jl A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 cellular component biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. GOC:jl GOC:mah Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. biological_process GO:0044087 regulation of cellular component biogenesis Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. GOC:jl Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. biological_process GO:0044089 positive regulation of cellular component biogenesis Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. GOC:jl Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jane 2009-04-21T04:07:27Z biological_process GO:0044092 negative regulation of molecular function Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jane 2009-04-21T04:11:06Z biological_process GO:0044093 positive regulation of molecular function Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism biological_process intermediary metabolism GO:0044237 cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. GOC:go_curators intermediary metabolism GOC:mah Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane. cellular_component GO:0044422 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. organelle part Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane. GOC:jl Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. cellular_component GO:0044424 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. intracellular part Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. GOC:jl Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. cellular_component GO:0044425 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. membrane part Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. GOC:jl Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. NIF_Subcellular:sao1499850686 nuclear subcomponent nucleus component cellular_component GO:0044428 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. nuclear part Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. GOC:jl nuclear subcomponent NIF_Subcellular:sao1499850686 Any constituent part of the cytoskeleton, a cellular scaffolding or skeleton that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (e.g. the movement of vesicles and organelles) and cellular division. Includes constituent parts of intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice. NIF_Subcellular:sao1635329413 cytoskeletal element cytoskeleton component cellular_component GO:0044430 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cytoskeletal part Any constituent part of the cytoskeleton, a cellular scaffolding or skeleton that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (e.g. the movement of vesicles and organelles) and cellular division. Includes constituent parts of intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice. GOC:jl cytoskeletal element NIF_Subcellular:sao1635329413 Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell. cellular_component GO:0044433 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cytoplasmic vesicle part Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell. GOC:jl Any constituent part of a vacuole, a closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. vacuole component cellular_component GO:0044437 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. vacuolar part Any constituent part of a vacuole, a closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. GOC:jl Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. cytoplasm component cellular_component GO:0044444 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cytoplasmic part Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GOC:jl A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane. cellular_component GO:0044446 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. intracellular organelle part A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane. GOC:jl Any constituent part of a contractile fiber, a fiber composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. muscle fiber component muscle fibre component contractile fibre component cellular_component GO:0044449 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. contractile fiber part Any constituent part of a contractile fiber, a fiber composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. GOC:jl Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. cellular_component GO:0044459 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. plasma membrane part Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GOC:jl Any constituent part of a cell, the basic structural and functional unit of all organisms. NIF_Subcellular:sao628508602 cellular subcomponent cellular_component protoplast GO:0044464 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cell part cell part Any constituent part of a cell, the basic structural and functional unit of all organisms. GOC:jl cellular subcomponent NIF_Subcellular:sao628508602 protoplast GOC:mah The process whose specific outcome is the progression of the primary sexual characteristics over time, from their formation to the mature structures. The primary sexual characteristics are the testes in males and the ovaries in females and they develop in response to sex hormone secretion. biological_process GO:0045137 development of primary sexual characteristics The process whose specific outcome is the progression of the primary sexual characteristics over time, from their formation to the mature structures. The primary sexual characteristics are the testes in males and the ovaries in females and they develop in response to sex hormone secretion. GOC:ai The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. GO:0006938 sarcomere alignment sarcomere organisation biological_process GO:0045214 sarcomere organization The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. GOC:bf sarcomere organisation GOC:curators