XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. Xenopus Phenotype Ontology definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by 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 has_exact_synonym is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 external quality uberon 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 uberon 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 preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 is preceded by takes place after uberon preceded_by preceded_by preceded by preceded_by is preceded by SIO:000249 takes place after Allen:precedes precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 uberon precedes precedes precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in 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 BFO:0000067 uberon contains_process contains_process 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 contains process This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about 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 RO:0000053 uberon bearer_of bearer_of 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 X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately_preceded_by A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. SIO:000251 is immediately preceded by SIO:000251 David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes A overlaps B if they share some part in common. x overlaps y if and only if there exists some z such that x has part z and z part of y BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 uberon overlaps overlaps overlaps 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. RO:0002180 uberon has_component has_component has component has component RO:0002202 xenopus_anatomy develops_from develops_from develops from 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) RO:0002215 uberon capable_of capable_of capable of capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) RO:0002216 uberon capable_of_part_of capable_of_part_of capable of part of 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 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 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 p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. Chris Mungall results_in_developmental_progression_of results in developmental progression 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 RO:0002328 uberon functionally_related_to functionally_related_to functionally related to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false RO:0002329 uberon part_of_structure_that_is_capable_of part_of_structure_that_is_capable_of part of structure that is capable of part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p 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 RO:0002352 uberon input_of input_of input of input of 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. The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall Vasundra Touré molecularly controls activity directly regulates activity of 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. The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly inhibits inhibits molecularly decreases activity of activity directly negatively regulates activity of 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. The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall Vasundra Touré activates directly activates molecularly increases activity of activity directly positively regulates activity of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true Chris Mungall is kinase activity 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 q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. Chris Mungall towards The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities causal relation between material entities Chris Mungall causally influenced by (entity-centric) 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 p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall results in movement of 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 The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Chris Mungall Vasundra Touré causally influences (entity-centric) causally influences (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 Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. Vasundra Touré regulates activity of p has anatomical participant c iff p has participant c, and c is an anatomical entity cjm 2018-09-26T01:08:58Z has anatomical participant 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] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process 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] An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity immaterial entity anatomical entity connected anatomical structure material anatomical entity immaterial anatomical entity 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 An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain an additional tiers: the upstream MAP4K. The kinases in each tier phosphorylate and activate the kinase in the downstream tier to transmit a signal within a cell. Wikipedia:MAPK_cascade Wikipedia:Mitogen-activated_protein_kinase MAP kinase cascade MAP kinase kinase kinase cascade MAPK signal transduction MAPKKK cascade mitogen-activated protein kinase cascade ERK/MAPK cascade MAPKKK cascade during sporulation biological_process MAPK signaling MAPK signalling GO:0000165 MAPK cascades lie downstream of many cell surface receptors and cooperate in transmitting various extracellular signals to the nucleus. One way by which the specificity of each cascade is regulated is through the existence of several distinct components in each tier of the different cascades. The cascades are typically named according to the component in the MAPK tier. MAPK cascade An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain an additional tiers: the upstream MAP4K. The kinases in each tier phosphorylate and activate the kinase in the downstream tier to transmit a signal within a cell. GOC:bf GOC:mtg_signaling_feb11 PMID:20811974 PMID:9561267 MAPK signal transduction GOC:signaling mitogen-activated protein kinase cascade GOC:bf A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a meiotic cell cycle. GO:0043147 meiotic spindle organisation spindle organization during meiosis biological_process meiotic spindle organization and biogenesis meiotic spindle stabilization GO:0000212 meiotic spindle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a meiotic cell cycle. GOC:go_curators GOC:mah spindle organization during meiosis GOC:mah meiotic spindle 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 microtubules and their associated proteins. microtubule cytoskeleton organisation microtubule dynamics biological_process microtubule cytoskeleton organization and biogenesis GO:0000226 microtubule 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 microtubules and their associated proteins. GOC:mah microtubule cytoskeleton organisation GOC:mah microtubule dynamics GOC:dph GOC:tb microtubule cytoskeleton organization and biogenesis GOC:mah A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. nuclear interphase chromosome cellular_component GO:0000228 nuclear chromosome A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. GOC:dph GOC:mah A chromosome found in the cytoplasm. cytoplasmic interphase chromosome cellular_component GO:0000229 cytoplasmic chromosome A chromosome found in the cytoplasm. GOC:mah 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 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. 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 ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. GO:0005717 NIF_Subcellular:sao1615953555 cellular_component chromosome scaffold GO:0000785 Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromatin The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. GOC:elh PMID:20404130 The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the cytoplasm. cellular_component GO:0000789 cytoplasmic chromatin The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the cytoplasm. GOC:elh PMID:20404130 The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. cellular_component GO:0000790 nuclear chromatin The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. GOC:elh PMID:20404130 The developmental process in which the size or shape of a cell is generated and organized. GO:0007148 GO:0045790 GO:0045791 cellular morphogenesis biological_process GO:0000902 cell morphogenesis The developmental process in which the size or shape of a cell is generated and organized. GOC:clt GOC:dph GOC:go_curators GOC:tb The change in form (cell shape and size) that occurs when 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. biological_process GO:0000904 cell morphogenesis involved in differentiation The change in form (cell shape and size) that occurs when 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. GOC:go_curators 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 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 Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. krc 2010-09-23T03:44:23Z Reactome:R-HSA-6814549 Reactome:R-HSA-6814559 DNA-directed RNA polymerase activity involved in transcription from RNA polymerase II promoter molecular_function GO:0001055 RNA polymerase II activity Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. GOC:txnOH Reactome:R-HSA-6814549 Pre-snRNA transcript initiation, Integrator binding, LEC binding Reactome:R-HSA-6814559 Pre-snRNA is elongated and capped with 7-methylguanosine Any process that modulates the frequency, rate, extent or direction of cell growth. biological_process GO:0001558 regulation of cell growth Any process that modulates the frequency, rate, extent or direction of cell growth. GOC:go_curators A process that results in a parallel arrangement of microtubules. microtubule bundling biological_process GO:0001578 microtubule bundle formation A process that results in a parallel arrangement of microtubules. GOC:dph 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 Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates. establishment of planar cell polarity biological_process GO:0001736 establishment of planar polarity Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates. GOC:dph The morphogenetic process in which the anatomical structures of a polarized epithelium are generated and organized. A polarized epithelium is an epithelium where the epithelial sheet is oriented with respect to the planar axis. epithelial polarization biological_process GO:0001738 morphogenesis of a polarized epithelium The morphogenetic process in which the anatomical structures of a polarized epithelium are generated and organized. A polarized epithelium is an epithelium where the epithelial sheet is oriented with respect to the planar axis. GOC:dph epithelial polarization GOC:dph The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo. Wikipedia:Somitogenesis formation of mesodermal clusters biological_process GO:0001756 somitogenesis The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo. ISBN:0721662544 formation of mesodermal clusters The morphogenesis of an embryonic epithelium into a tube-shaped structure. biological_process GO:0001838 embryonic epithelial tube formation The morphogenesis of an embryonic epithelium into a tube-shaped structure. GOC:dph ISBN:0824072820 The process in which the anatomical structures of the neural plate are generated and organized. The neural plate is a specialized region of columnar epithelial cells in the dorsal ectoderm that will give rise to nervous system tissue. biological_process GO:0001839 neural plate morphogenesis The process in which the anatomical structures of the neural plate are generated and organized. The neural plate is a specialized region of columnar epithelial cells in the dorsal ectoderm that will give rise to nervous system tissue. GOC:dph ISBN:0878932437 The process whose specific outcome is the progression of the neural plate over time, from its formation to the mature structure. The neural plate is a flat, thickened layer of ectodermal cells. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system. biological_process GO:0001840 neural plate development The process whose specific outcome is the progression of the neural plate over time, from its formation to the mature structure. The neural plate is a flat, thickened layer of ectodermal cells. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system. GOC:dph GOC:ef ISBN:0878932437 ISBN:0878932585 The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. GO:0001679 Wikipedia:Neurulation neural tube morphogenesis neurulation biological_process GO:0001841 neural tube formation The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. GOC:dph ISBN:0878932437 neural tube morphogenesis GOC:dph The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline. biological_process GO:0001843 neural tube closure The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline. GOC:dph ISBN:0878932437 Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein. regulation of protein amino acid phosphorylation biological_process GO:0001932 regulation of protein phosphorylation Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein. GOC:hjd regulation of protein amino acid phosphorylation GOC:bf Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein. positive regulation of protein amino acid phosphorylation up regulation of protein amino acid phosphorylation up-regulation of protein amino acid phosphorylation upregulation of protein amino acid phosphorylation activation of protein amino acid phosphorylation stimulation of protein amino acid phosphorylation biological_process GO:0001934 positive regulation of protein phosphorylation Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein. GOC:hjd positive regulation of protein amino acid phosphorylation GOC:bf The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation. cardiac looping biological_process GO:0001947 heart looping The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation. GOC:dph PMID:12094232 The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube. epithelium morphogenesis biological_process GO:0002009 morphogenesis of an epithelium The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube. GOC:dph GOC:jl GOC:tb ISBN:0198506732 The process in which the anatomical structures of an epithelial sheet are generated and organized. An epithelial sheet is a flat surface consisting of closely packed epithelial cells. biological_process GO:0002011 morphogenesis of an epithelial sheet The process in which the anatomical structures of an epithelial sheet are generated and organized. An epithelial sheet is a flat surface consisting of closely packed epithelial cells. GOC:jl The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface. biological_process GO:0002064 epithelial cell development The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface. GOC:dph The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. biological_process GO:0002065 columnar/cuboidal epithelial cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. GOC:dph The process in which a relatively unspecialized cell acquires specialized features of a glandular epithelial cell. A glandular epithelial cell is a columnar/cuboidal epithelial cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland. biological_process GO:0002067 glandular epithelial cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a glandular epithelial cell. A glandular epithelial cell is a columnar/cuboidal epithelial cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland. GOC:dph 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 The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. biological_process cardiac morphogenesis GO:0003007 heart morphogenesis The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. GOC:dph GOC:isa_complete 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 A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. Wikipedia:Circulatory_system biological_process GO:0003013 circulatory system process A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. GOC:mtg_cardio A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. biological_process cardiac process GO:0003015 heart process A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. GOC:mtg_cardio The series of events by which an endogenous stimulus is received by a cilium on a cell and converted to a molecular signal contributing to left/right asymmetry. tb 2009-09-22T02:45:48Z biological_process GO:0003127 detection of nodal flow The series of events by which an endogenous stimulus is received by a cilium on a cell and converted to a molecular signal contributing to left/right asymmetry. GOC:mtg_heart The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart. tb 2009-09-22T04:21:17Z biological_process GO:0003143 embryonic heart tube morphogenesis The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart. GOC:mtg_heart A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the determination of left/right symmetry. tb 2009-09-24T05:34:57Z BMP signaling pathway involved in determination of left/right asymmetry BMP signalling pathway involved in determination of left/right symmetry biological_process GO:0003154 BMP signaling pathway involved in determination of left/right symmetry A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the determination of left/right symmetry. GOC:mtg_heart GOC:signaling BMP signaling pathway involved in determination of left/right asymmetry GOC:dph BMP signalling pathway involved in determination of left/right symmetry GOC:mah Developmental growth that contributes to the shaping of the heart. dph 2009-10-13T11:28:46Z biological_process GO:0003241 growth involved in heart morphogenesis Developmental growth that contributes to the shaping of the heart. GOC:mtg_heart Any apoptotic process that contributes to the shaping of the heart. dph 2009-10-20T09:40:22Z apoptosis involved in heart morphogenesis biological_process GO:0003278 apoptotic process involved in heart morphogenesis Any apoptotic process that contributes to the shaping of the heart. GOC:mtg_apoptosis GOC:mtg_heart The series of molecular signals initiated by binding of Wnt protein to a receptor on the surface of the target cell, resulting a change in cell state that contributes to the progression of the heart over time. dph 2009-10-22T12:26:07Z Wnt receptor signaling pathway involved in heart development Wnt receptor signalling pathway involved in heart development Wnt-activated signaling pathway involved in heart development biological_process GO:0003306 Wnt signaling pathway involved in heart development The series of molecular signals initiated by binding of Wnt protein to a receptor on the surface of the target cell, resulting a change in cell state that contributes to the progression of the heart over time. GOC:mtg_heart Wnt receptor signalling pathway involved in heart development GOC:mah Wnt-activated signaling pathway involved in heart development GOC:signaling Any process that modulates the rate, frequency, or extent of the series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell, resulting a change in cell state that contributes to the progression of the heart over time. dph 2009-10-22T12:32:10Z regulation of Wnt receptor signaling pathway involved in heart development regulation of Wnt receptor signalling pathway involved in heart development regulation of Wnt-activated signaling pathway involved in heart development biological_process GO:0003307 regulation of Wnt signaling pathway involved in heart development Any process that modulates the rate, frequency, or extent of the series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell, resulting a change in cell state that contributes to the progression of the heart over time. GOC:mtg_heart regulation of Wnt receptor signalling pathway involved in heart development GOC:mah regulation of Wnt-activated signaling pathway involved in heart development GOC:signaling The process in which relatively unspecialized cells acquire specialized structural and/or functional features of a type B pancreatic cell. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin. dph 2009-10-26T09:27:23Z pancreatic B cell differentiation pancreatic beta cell differentiation biological_process GO:0003309 type B pancreatic cell differentiation The process in which relatively unspecialized cells acquire specialized structural and/or functional features of a type B pancreatic cell. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin. CL:0000169 GOC:dph PMID:11076772 pancreatic B cell differentiation GOC:mah pancreatic beta cell differentiation GOC:dph The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell. dph 2009-12-08T04:50:41Z biological_process GO:0003365 establishment of cell polarity involved in ameboidal cell migration The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell. GOC:ascb_2009 GOC:dph GOC:tb The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell taking part in gastrulation. dph 2009-12-09T06:54:44Z biological_process GO:0003379 establishment of cell polarity involved in gastrulation cell migration The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell taking part in gastrulation. GOC:ascb_2009 GOC:dph GOC:tb The change in form that occurs when an epithelial cell progresses from it initial formation to its mature state, contributing to the process of gastrulation. dph 2009-12-09T07:18:53Z biological_process GO:0003381 epithelial cell morphogenesis involved in gastrulation The change in form that occurs when an epithelial cell progresses from it initial formation to its mature state, contributing to the process of gastrulation. GOC:ascb_2009 GOC:dph GOC:tb The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state. dph 2009-12-09T07:21:06Z biological_process GO:0003382 epithelial cell morphogenesis The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state. GOC:ascb_2009 GOC:dph GOC:tb The actin-mediated process that results in the contraction of the apical end of a polarized columnar epithelial cell. dph 2009-12-09T07:30:34Z biological_process GO:0003383 apical constriction The actin-mediated process that results in the contraction of the apical end of a polarized columnar epithelial cell. GOC:ascb_2009 GOC:dph GOC:tb The actin-mediated process that results in the contraction of the apical end of a polarized columnar epithelial cell, contributing to the process of gastrulation. dph 2009-12-09T07:35:38Z biological_process GO:0003384 apical constriction involved in gastrulation The actin-mediated process that results in the contraction of the apical end of a polarized columnar epithelial cell, contributing to the process of gastrulation. GOC:ascb_2009 GOC:dph GOC:tb 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 The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal to modulate cytoskeletal elements and control cell polarity that contributes to axis elongation. dph 2009-12-21T01:22:11Z biological_process GO:0003402 planar cell polarity pathway involved in axis elongation The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal to modulate cytoskeletal elements and control cell polarity that contributes to axis elongation. 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. 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 Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. GO:0000129 DNA-directed RNA polymerase activity transcriptase EC:2.7.7.6 MetaCyc:DNA-DIRECTED-RNA-POLYMERASE-RXN Reactome:R-HSA-111264 Reactome:R-HSA-167113 Reactome:R-HSA-167115 Reactome:R-HSA-167117 Reactome:R-HSA-167121 Reactome:R-HSA-167136 Reactome:R-HSA-174425 Reactome:R-HSA-203901 Reactome:R-HSA-427366 Reactome:R-HSA-5601926 Reactome:R-HSA-6781824 Reactome:R-HSA-68913 Reactome:R-HSA-74986 Reactome:R-HSA-75850 Reactome:R-HSA-75869 Reactome:R-HSA-75873 Reactome:R-HSA-76576 DNA-dependent RNA nucleotidyltransferase activity DNA-dependent RNA polymerase activity DNA-dependent ribonucleate nucleotidyltransferase activity RNA nucleotidyltransferase (DNA-directed) activity deoxyribonucleic acid-dependent ribonucleic acid polymerase activity nucleoside-triphosphate:RNA nucleotidyltransferase (DNA-directed) activity DNA-directed RNA polymerase I activity DNA-directed RNA polymerase II activity DNA-directed RNA polymerase III activity RNA polymerase I activity RNA polymerase II activity RNA polymerase III activity molecular_function C RNA formation factors C ribonucleic acid formation factors GO:0003899 DNA-directed 5'-3' RNA polymerase activity Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. EC:2.7.7.6 GOC:pf transcriptase EC:2.7.7.6 Reactome:R-HSA-111264 Addition of nucleotides between position +11 and +30 Reactome:R-HSA-167113 Addition of the fourth nucleotide on the nascent HIV-1 transcript: Second Transition Reactome:R-HSA-167115 Addition of nucleotides between position +11 and +30 on HIV-1 transcript Reactome:R-HSA-167117 Addition of nucleotides 10 and 11 on the growing HIV-1 transcript: Third Transition Reactome:R-HSA-167121 Addition of the third nucleotide on the nascent HIV-1 transcript Reactome:R-HSA-167136 Addition of nucleotides 5 through 9 on the growing HIV-1 transcript Reactome:R-HSA-174425 The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere Reactome:R-HSA-203901 Pol II mediated transcription of microRNA genes Reactome:R-HSA-427366 Transcription of intergenic spacer of the rRNA gene Reactome:R-HSA-5601926 RNA polymerase II polymerizes primary piRNA transcript Reactome:R-HSA-6781824 Active RNA Pol II complex transcribes lesion-containing DNA template Reactome:R-HSA-68913 The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer at the origin Reactome:R-HSA-74986 Elongation of pre-rRNA transcript Reactome:R-HSA-75850 Addition of the third nucleotide on the nascent transcript Reactome:R-HSA-75869 Addition of the fourth nucleotide on the Nascent Transcript: Second Transition Reactome:R-HSA-75873 Addition of Nucleotides 5 through 9 on the growing Transcript Reactome:R-HSA-76576 Addition of nucleotides 10 and 11 on the growing transcript: Third Transition DNA-dependent RNA nucleotidyltransferase activity EC:2.7.7.6 DNA-dependent RNA polymerase activity EC:2.7.7.6 DNA-dependent ribonucleate nucleotidyltransferase activity EC:2.7.7.6 RNA nucleotidyltransferase (DNA-directed) activity EC:2.7.7.6 deoxyribonucleic acid-dependent ribonucleic acid polymerase activity EC:2.7.7.6 nucleoside-triphosphate:RNA nucleotidyltransferase (DNA-directed) activity EC:2.7.7.6 RNA polymerase I activity EC:2.7.7.6 RNA polymerase II activity EC:2.7.7.6 RNA polymerase III activity EC:2.7.7.6 C RNA formation factors EC:2.7.7.6 C ribonucleic acid formation factors EC:2.7.7.6 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain. GO:0016809 MetaCyc:RXN0-5195 Reactome:R-HSA-1168640 Reactome:R-HSA-1234159 Reactome:R-HSA-1236935 Reactome:R-HSA-1236970 Reactome:R-HSA-1251997 Reactome:R-HSA-1433374 Reactome:R-HSA-1504193 Reactome:R-HSA-174058 Reactome:R-HSA-174105 Reactome:R-HSA-174202 Reactome:R-HSA-174203 Reactome:R-HSA-174255 Reactome:R-HSA-180573 Reactome:R-HSA-180603 Reactome:R-HSA-187574 Reactome:R-HSA-188191 Reactome:R-HSA-193682 Reactome:R-HSA-209061 Reactome:R-HSA-211715 Reactome:R-HSA-2130282 Reactome:R-HSA-2213200 Reactome:R-HSA-264458 Reactome:R-HSA-353125 Reactome:R-HSA-3640874 Reactome:R-HSA-3928656 Reactome:R-HSA-450466 Reactome:R-HSA-4608855 Reactome:R-HSA-4641256 Reactome:R-HSA-4641260 Reactome:R-HSA-5358340 Reactome:R-HSA-5358460 Reactome:R-HSA-5362448 Reactome:R-HSA-5387392 Reactome:R-HSA-5607724 Reactome:R-HSA-5607731 Reactome:R-HSA-5610754 Reactome:R-HSA-5610757 Reactome:R-HSA-5610758 Reactome:R-HSA-5610760 Reactome:R-HSA-5635854 Reactome:R-HSA-5635868 Reactome:R-HSA-5658430 Reactome:R-HSA-5668481 Reactome:R-HSA-5668520 Reactome:R-HSA-5687112 Reactome:R-HSA-5693081 Reactome:R-HSA-6784628 Reactome:R-HSA-6784676 Reactome:R-HSA-68825 Reactome:R-HSA-68948 Reactome:R-HSA-69016 Reactome:R-HSA-69600 Reactome:R-HSA-74730 Reactome:R-HSA-75825 Reactome:R-HSA-8849797 Reactome:R-HSA-8850992 Reactome:R-HSA-8852354 Reactome:R-HSA-8854044 Reactome:R-HSA-8854071 Reactome:R-HSA-8866553 Reactome:R-HSA-8866858 Reactome:R-HSA-8934819 Reactome:R-HSA-8939801 Reactome:R-HSA-8952408 Reactome:R-HSA-8957265 Reactome:R-HSA-9008110 Reactome:R-HSA-9008475 Reactome:R-HSA-9009362 Reactome:R-HSA-9010096 Reactome:R-HSA-9011313 Reactome:R-HSA-9604642 Reactome:R-HSA-983150 Reactome:R-HSA-983158 endoprotease activity proteasome endopeptidase activity proteinase molecular_function elastase activity GO:0004175 endopeptidase activity Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain. http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE Reactome:R-HSA-1168640 Ubiquitinated IkB is degraded Reactome:R-HSA-1234159 Proteasome proteolyzes ub-HIF-alpha Reactome:R-HSA-1236935 Proteasomal cleavage of substrate Reactome:R-HSA-1236970 Proteasomal clevage of exogenous antigen Reactome:R-HSA-1251997 Cleavage of ERBB4m80 by gamma-scretase complex Reactome:R-HSA-1433374 Processing of SCF isoform 1 Reactome:R-HSA-1504193 Ubiquitinated DVL is degraded by the proteasome Reactome:R-HSA-174058 Degradation of multiubiquitinated Cdh1 Reactome:R-HSA-174105 Degradation of multiubiquitinated cell cycle proteins Reactome:R-HSA-174202 Degradation of multiubiquitinated Securin Reactome:R-HSA-174203 SCF-mediated degradation of Emi1 Reactome:R-HSA-174255 Degradation multiubiquitinated Cyclin A Reactome:R-HSA-180573 Degradation of ubiquitinated CD4 Reactome:R-HSA-180603 Proteosome-mediated degradation of APOBEC3G Reactome:R-HSA-187574 Degradation of ubiquitinated p27/p21 by the 26S proteasome Reactome:R-HSA-188191 APC/C:Cdh1-mediated degradation of Skp2 Reactome:R-HSA-193682 gamma-secretase cleaves the p75NTR transmembrane domain Reactome:R-HSA-209061 Ubiquitinated and phosphorylated IKBA binds to and is degraded by the proteasome complex Reactome:R-HSA-211715 Proteasome mediated degradation of PAK-2p34 Reactome:R-HSA-2130282 Degradation of ubiquitinated beta catenin by the proteasome Reactome:R-HSA-2213200 Release of endostatin-like peptides Reactome:R-HSA-264458 Proteasome mediated degradation of COP1 Reactome:R-HSA-353125 26S proteosome degrades ODC holoenzyme complex Reactome:R-HSA-3640874 Ub-RibC-AXIN is degraded by the proteasome Reactome:R-HSA-3928656 gamma-secretase cleaves EPHB2 Reactome:R-HSA-450466 AUF1:mRNA complex is destroyed Reactome:R-HSA-4608855 PRICKLE1 is degraded by the proteasome Reactome:R-HSA-4641256 Ubiquitinated AXIN is degraded by the proteasome Reactome:R-HSA-4641260 Ubiquitinated DVL1 is degraded by the proteasome Reactome:R-HSA-5358340 Autoproteolytic cleavage of Hh precursors Reactome:R-HSA-5358460 HPE SHH variants don't undergo autoproteolytic cleavage Reactome:R-HSA-5362448 Hh C-terminal fragments are degraded by the proteasome Reactome:R-HSA-5387392 processing defective Hh variants are degraded by the proteasome Reactome:R-HSA-5607724 26S proteasome processes K48PolyUb-K21,22-p-S32,36-IkBA:NF-kB complex to form NF-kB complex Reactome:R-HSA-5607731 26S proteasome processes p-7S-p100:RELB to form p52:RELB Reactome:R-HSA-5610754 GLI3 is partially degraded by the proteasome to yield the GLI3 repressor Reactome:R-HSA-5610757 GLI2 is degraded by the proteasome Reactome:R-HSA-5610758 GLI1 is degraded by the proteasome after ubiquitination by beta-TrCP Reactome:R-HSA-5610760 GLI1 is degraded by the proteasome after ubiquitination by ITCH Reactome:R-HSA-5635854 GLI2,3 are degraded by the proteasome Reactome:R-HSA-5635868 ub-GLI is degraded by the proteasome Reactome:R-HSA-5658430 NF1 is degraded by the proteasome Reactome:R-HSA-5668481 Protesomal degradation of K48polyUb-TRAF3 Reactome:R-HSA-5668520 26Sproteasome degrades K48polyUb-NIK Reactome:R-HSA-5687112 MAPK6 is degraded by the 26S proteasome Reactome:R-HSA-5693081 FURIN cleaves 7K-BACE1 to 7K-BACE1(46-501) Reactome:R-HSA-6784628 PCSK6,FURIN mediate dissociation of 2 x LPL from GPIHBP1:HSPG:LPL dimer Reactome:R-HSA-6784676 PCSK5 mediates dissociation of 2 x LPL from GPIHBP1:HSPG:LPL dimer Reactome:R-HSA-68825 Ubiquitinated geminin is degraded by the proteasome Reactome:R-HSA-68948 Ubiquitinated Orc1 is degraded by the proteasome Reactome:R-HSA-69016 Ubiquitinated Cdc6 is degraded by the proteasome Reactome:R-HSA-69600 Proteolytic degradation of ubiquitinated-Cdc25A Reactome:R-HSA-74730 Insulin degradation Reactome:R-HSA-75825 Proteasome mediated degradation of Cyclin D1 Reactome:R-HSA-8849797 Membrane proteases cleave Profilaggrin producing Filaggrin Reactome:R-HSA-8850992 Proteasome degrades polyubiquitinated PTEN Reactome:R-HSA-8852354 GTSE1 facilitates proteasome-mediated degradation of TP53 Reactome:R-HSA-8854044 Proteasome degrades AURKA ubiquitinated by SCF-FBXL7 Reactome:R-HSA-8854071 Proteasome-mediated degradation of PolyUb-FBXL7 Reactome:R-HSA-8866553 misfolded CFTR is degraded by the 26S proteasome Reactome:R-HSA-8866858 CFTR F508del is degraded by the 26S proteasome Reactome:R-HSA-8934819 Cytoplasmic proteases cleave Profilaggrin producing Filaggrin Reactome:R-HSA-8939801 26S proteasome degrades PolyUb-RUNX2 Reactome:R-HSA-8952408 Polyubiquitinated RUNX3 is degraded by the proteasome Reactome:R-HSA-8957265 26S proteasome degrades TP73 polyubiquitinated by ITCH Reactome:R-HSA-9008110 Proteasome degrades polyubiquitinated RUNX2 Reactome:R-HSA-9008475 Proteasome degrades polyubiquitinated RUNX2 Reactome:R-HSA-9009362 Proteasome degrades PolyUb-RUNX2 Reactome:R-HSA-9010096 Gamma-secretase cleaves APP(672-770) to APP(672-711) and APP(672-713) Reactome:R-HSA-9011313 Proteasome degrades ubiquitinated ROBO3.1 Reactome:R-HSA-9604642 Proteasome degrades ubiquitinated NICD4 Reactome:R-HSA-983150 Proteasomal cleavage of substrate Reactome:R-HSA-983158 Trimming of peptides in ER elastase activity GOC:krc Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. EC:3.4.22 Reactome:R-HSA-114252 Reactome:R-HSA-114259 Reactome:R-HSA-114261 Reactome:R-HSA-1236948 Reactome:R-HSA-139898 Reactome:R-HSA-139952 Reactome:R-HSA-1678920 Reactome:R-HSA-1678981 Reactome:R-HSA-201595 Reactome:R-HSA-201603 Reactome:R-HSA-201608 Reactome:R-HSA-201611 Reactome:R-HSA-201622 Reactome:R-HSA-201628 Reactome:R-HSA-201629 Reactome:R-HSA-201630 Reactome:R-HSA-201631 Reactome:R-HSA-201634 Reactome:R-HSA-201636 Reactome:R-HSA-201637 Reactome:R-HSA-201639 Reactome:R-HSA-201640 Reactome:R-HSA-2028692 Reactome:R-HSA-2028697 Reactome:R-HSA-202917 Reactome:R-HSA-202939 Reactome:R-HSA-202947 Reactome:R-HSA-202960 Reactome:R-HSA-202966 Reactome:R-HSA-202967 Reactome:R-HSA-202969 Reactome:R-HSA-211186 Reactome:R-HSA-211190 Reactome:R-HSA-211651 Reactome:R-HSA-212552 Reactome:R-HSA-2130336 Reactome:R-HSA-2130349 Reactome:R-HSA-2130504 Reactome:R-HSA-2130706 Reactome:R-HSA-2562564 Reactome:R-HSA-264865 Reactome:R-HSA-264871 Reactome:R-HSA-3465448 Reactome:R-HSA-350158 Reactome:R-HSA-350318 Reactome:R-HSA-350319 Reactome:R-HSA-350651 Reactome:R-HSA-351849 Reactome:R-HSA-351871 Reactome:R-HSA-351876 Reactome:R-HSA-351877 Reactome:R-HSA-351894 Reactome:R-HSA-351901 Reactome:R-HSA-351913 Reactome:R-HSA-351936 Reactome:R-HSA-352268 Reactome:R-HSA-418845 Reactome:R-HSA-418846 Reactome:R-HSA-418852 Reactome:R-HSA-448703 Reactome:R-HSA-5357828 Reactome:R-HSA-5634228 Reactome:R-HSA-5660663 Reactome:R-HSA-5681987 Reactome:R-HSA-5682377 Reactome:R-HSA-6814387 Reactome:R-HSA-9012556 Reactome:R-HSA-9013895 Reactome:R-HSA-933532 Reactome:R-HSA-9603534 thiol endopeptidase activity caspase activity lysosomal cysteine-type endopeptidase metacaspase activity molecular_function GO:0004197 cysteine-type endopeptidase activity Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. GOC:mah http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE Reactome:R-HSA-114252 Cleavage of Procaspase-3 by the apoptosome Reactome:R-HSA-114259 Cleavage of Procaspase9 to caspase9 Reactome:R-HSA-114261 Cleavage of Procaspase-7 by the apoptosome Reactome:R-HSA-1236948 Antigen processing by cathepsin S in endosoytic vesicle Reactome:R-HSA-139898 Caspase-8 activates BID by cleavage Reactome:R-HSA-139952 Caspase-8 processing in the DISC Reactome:R-HSA-1678920 TLR processing at low pH Reactome:R-HSA-1678981 TLR9 processing at neutral pH Reactome:R-HSA-201595 Caspase-mediated cleavage of plakophilin-1 Reactome:R-HSA-201603 Caspase-mediated cleavage of PKC theta Reactome:R-HSA-201608 Caspase-mediated cleavage of alpha adducin Reactome:R-HSA-201611 Caspase-mediated cleavage of Rock-1 Reactome:R-HSA-201622 Caspase-mediated cleavage of gelsolin Reactome:R-HSA-201628 Caspase-mediated cleavage of vimentin at DSVD (85) Reactome:R-HSA-201629 Caspase-mediated cleavage of Tau Reactome:R-HSA-201630 Caspase-mediated cleavage of Acinus Reactome:R-HSA-201631 Caspase-mediated cleavage of Desmoglein 3 Reactome:R-HSA-201634 Caspase-mediated cleavage of FADK 1 Reactome:R-HSA-201636 Caspase-mediated cleavage of Desmoplakin Reactome:R-HSA-201637 Caspase-mediated cleavage of plectin-1 Reactome:R-HSA-201639 Caspase-mediated cleavage of GAS2 Reactome:R-HSA-201640 Caspase-mediated cleavage of farnesyltransferase/geranyl- geranyltransferase subunit alpha Reactome:R-HSA-2028692 Cleavage of p-STK4 (p-MST1) by caspase 3 Reactome:R-HSA-2028697 Cleavage of p-STK3 (p-MST2) by caspase 3 Reactome:R-HSA-202917 Caspase-mediated cleavage of Desmoglein 1 Reactome:R-HSA-202939 Caspase-mediated cleavage of E-Cadherin Reactome:R-HSA-202947 Caspase mediated cleavage of APC Reactome:R-HSA-202960 Caspase mediated cleavage of C-IAP1 Reactome:R-HSA-202966 Caspase mediated cleavage of HIP-55 Reactome:R-HSA-202967 Caspase mediated cleavage of alpha-II-Fodrin Reactome:R-HSA-202969 Caspase mediated cleavage of beta-catenin Reactome:R-HSA-211186 Cleavage of DFF45 (224) by caspase-3 Reactome:R-HSA-211190 Caspase 3-mediated cleavage of DFF45 (117) Reactome:R-HSA-211651 Cleavage of PAK-2 at 212 Reactome:R-HSA-212552 Caspase 3-mediated cleavage of PKC delta Reactome:R-HSA-2130336 Initial proteolyis of Ii by aspartic proteases to lip22 Reactome:R-HSA-2130349 Generation of CLIP from lip10 Reactome:R-HSA-2130504 Cleavage of lip22 to lip10 Reactome:R-HSA-2130706 MHC class II antigen processing Reactome:R-HSA-2562564 Caspase-8 processing within TLR4 complex Reactome:R-HSA-264865 Caspase-mediated cleavage of Lamin A Reactome:R-HSA-264871 Caspase-mediated cleavage of Lamin B1 Reactome:R-HSA-3465448 Caspase-8 and FLIP(L) processing at DISC Reactome:R-HSA-350158 LGMN degrades GC Reactome:R-HSA-350318 Caspase-mediated cleavage of vimentin at TNLD (429) Reactome:R-HSA-350319 Caspase mediated cleavage of vimentin at IDVD (259) Reactome:R-HSA-350651 Caspase-mediated cleavage of MASK Reactome:R-HSA-351849 Caspase-mediated cleavage of Etk Reactome:R-HSA-351871 Caspase-mediated cleavage of Z0-2 Reactome:R-HSA-351876 Caspase-mediated cleavage of occludin Reactome:R-HSA-351877 Caspase-mediated cleavage of Desmoglein 2 Reactome:R-HSA-351894 Caspase mediated cleavage of BAP31 Reactome:R-HSA-351901 Caspase-mediated cleavage of MST3 Reactome:R-HSA-351913 Caspase-mediated cleavage of TJP1 Reactome:R-HSA-351936 Caspase-mediated cleavage of claspin Reactome:R-HSA-352268 Cleavage of Satb1 Reactome:R-HSA-418845 Activation of caspase-3 Reactome:R-HSA-418846 Caspase cleavage of UNC5A Reactome:R-HSA-418852 Caspase cleavage of UNC5B Reactome:R-HSA-448703 Interleukin-1 family precursors are cleaved by caspase-1 Reactome:R-HSA-5357828 RIP1 is cleaved by CASP8 Reactome:R-HSA-5634228 TRAF1 is cleaved by caspases Reactome:R-HSA-5660663 Caspase-8 cleaves IL1B precursor Reactome:R-HSA-5681987 LC3 is cleaved by ATG4 Reactome:R-HSA-5682377 LC3 de-lipidation by ATG4 Reactome:R-HSA-6814387 CASP14 cleaves filaggrin Reactome:R-HSA-9012556 IL37:2x(CASP1(120-197):CASP1(317-404)) cleaves IL37 Reactome:R-HSA-9013895 Caspase-8 processing within TLR3 complex Reactome:R-HSA-933532 Processing of caspases Reactome:R-HSA-9603534 Unknown caspase cleaves NTRK3 caspase activity GOC:mtg_apoptosis metacaspase activity GOC:mtg_apoptosis Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. GO:0050222 MetaCyc:PROTEIN-KINASE-RXN Reactome:R-HSA-156832 Reactome:R-HSA-937034 Reactome:R-HSA-9604606 Reactome:R-HSA-975139 protamine kinase activity molecular_function GO:0004672 Note that triphosphate is used as a phosphate donor by at least one kinase. protein kinase activity Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. MetaCyc:PROTEIN-KINASE-RXN Reactome:R-HSA-156832 INF-gamma induced phosphorylation of L13a Reactome:R-HSA-937034 IRAK1 phosphorylates Pellino Reactome:R-HSA-9604606 Unknown kinase phosphorylates NICD4 Reactome:R-HSA-975139 IRAK1 phosphorylates Pellino upon TLR7/8 or 9 activation Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. GO:0004695 GO:0004696 GO:0004700 RHEA:17989 RHEA:46608 Reactome:R-HSA-109702 Reactome:R-HSA-109822 Reactome:R-HSA-109823 Reactome:R-HSA-109860 Reactome:R-HSA-109862 Reactome:R-HSA-111919 Reactome:R-HSA-111970 Reactome:R-HSA-112342 Reactome:R-HSA-112381 Reactome:R-HSA-1168635 Reactome:R-HSA-1168638 Reactome:R-HSA-1168641 Reactome:R-HSA-1181149 Reactome:R-HSA-1181156 Reactome:R-HSA-1181355 Reactome:R-HSA-1225894 Reactome:R-HSA-1358791 Reactome:R-HSA-1362270 Reactome:R-HSA-139908 Reactome:R-HSA-139918 Reactome:R-HSA-1445144 Reactome:R-HSA-1449597 Reactome:R-HSA-1454699 Reactome:R-HSA-1458463 Reactome:R-HSA-1549526 Reactome:R-HSA-156673 Reactome:R-HSA-156678 Reactome:R-HSA-156682 Reactome:R-HSA-156699 Reactome:R-HSA-156723 Reactome:R-HSA-1592233 Reactome:R-HSA-162363 Reactome:R-HSA-162657 Reactome:R-HSA-163010 Reactome:R-HSA-1632857 Reactome:R-HSA-163416 Reactome:R-HSA-163418 Reactome:R-HSA-1638803 Reactome:R-HSA-164151 Reactome:R-HSA-165162 Reactome:R-HSA-165182 Reactome:R-HSA-165692 Reactome:R-HSA-165718 Reactome:R-HSA-165726 Reactome:R-HSA-165758 Reactome:R-HSA-165766 Reactome:R-HSA-165777 Reactome:R-HSA-166119 Reactome:R-HSA-166245 Reactome:R-HSA-166284 Reactome:R-HSA-166286 Reactome:R-HSA-167084 Reactome:R-HSA-167098 Reactome:R-HSA-168053 Reactome:R-HSA-168140 Reactome:R-HSA-170055 Reactome:R-HSA-170076 Reactome:R-HSA-170087 Reactome:R-HSA-170116 Reactome:R-HSA-170126 Reactome:R-HSA-170977 Reactome:R-HSA-174119 Reactome:R-HSA-174174 Reactome:R-HSA-176116 Reactome:R-HSA-176298 Reactome:R-HSA-187688 Reactome:R-HSA-187949 Reactome:R-HSA-188350 Reactome:R-HSA-193647 Reactome:R-HSA-193705 Reactome:R-HSA-195275 Reactome:R-HSA-195283 Reactome:R-HSA-195287 Reactome:R-HSA-195300 Reactome:R-HSA-195318 Reactome:R-HSA-198270 Reactome:R-HSA-198347 Reactome:R-HSA-198371 Reactome:R-HSA-198599 Reactome:R-HSA-198609 Reactome:R-HSA-198611 Reactome:R-HSA-198613 Reactome:R-HSA-198621 Reactome:R-HSA-198640 Reactome:R-HSA-198669 Reactome:R-HSA-198731 Reactome:R-HSA-198746 Reactome:R-HSA-198756 Reactome:R-HSA-199298 Reactome:R-HSA-199299 Reactome:R-HSA-199839 Reactome:R-HSA-199863 Reactome:R-HSA-199895 Reactome:R-HSA-199910 Reactome:R-HSA-199917 Reactome:R-HSA-199929 Reactome:R-HSA-199935 Reactome:R-HSA-200143 Reactome:R-HSA-200421 Reactome:R-HSA-201677 Reactome:R-HSA-201691 Reactome:R-HSA-201717 Reactome:R-HSA-202222 Reactome:R-HSA-202437 Reactome:R-HSA-202459 Reactome:R-HSA-202500 Reactome:R-HSA-202510 Reactome:R-HSA-202541 Reactome:R-HSA-2028284 Reactome:R-HSA-2028555 Reactome:R-HSA-2028583 Reactome:R-HSA-2028589 Reactome:R-HSA-2028591 Reactome:R-HSA-2028598 Reactome:R-HSA-2028629 Reactome:R-HSA-2028635 Reactome:R-HSA-2028661 Reactome:R-HSA-2028670 Reactome:R-HSA-2028673 Reactome:R-HSA-2028675 Reactome:R-HSA-2028679 Reactome:R-HSA-2029454 Reactome:R-HSA-2029460 Reactome:R-HSA-2029469 Reactome:R-HSA-2060328 Reactome:R-HSA-209087 Reactome:R-HSA-211164 Reactome:R-HSA-211583 Reactome:R-HSA-211650 Reactome:R-HSA-2168079 Reactome:R-HSA-2176475 Reactome:R-HSA-2214351 Reactome:R-HSA-2243938 Reactome:R-HSA-2243942 Reactome:R-HSA-2294580 Reactome:R-HSA-2396007 Reactome:R-HSA-2399941 Reactome:R-HSA-2399966 Reactome:R-HSA-2399969 Reactome:R-HSA-2399977 Reactome:R-HSA-2399981 Reactome:R-HSA-2399982 Reactome:R-HSA-2399985 Reactome:R-HSA-2399988 Reactome:R-HSA-2399992 Reactome:R-HSA-2399996 Reactome:R-HSA-2399999 Reactome:R-HSA-2400001 Reactome:R-HSA-2422927 Reactome:R-HSA-2430535 Reactome:R-HSA-2466068 Reactome:R-HSA-2470508 Reactome:R-HSA-2529020 Reactome:R-HSA-2562526 Reactome:R-HSA-2574840 Reactome:R-HSA-2730856 Reactome:R-HSA-2730868 Reactome:R-HSA-2730876 Reactome:R-HSA-2730896 Reactome:R-HSA-2730900 Reactome:R-HSA-2984226 Reactome:R-HSA-2984258 Reactome:R-HSA-2990880 Reactome:R-HSA-2993898 Reactome:R-HSA-3000310 Reactome:R-HSA-3000327 Reactome:R-HSA-3132737 Reactome:R-HSA-3209160 Reactome:R-HSA-3222006 Reactome:R-HSA-3222020 Reactome:R-HSA-3228469 Reactome:R-HSA-3229102 Reactome:R-HSA-3229152 Reactome:R-HSA-3239014 Reactome:R-HSA-3239019 Reactome:R-HSA-3249371 Reactome:R-HSA-3371435 Reactome:R-HSA-3371531 Reactome:R-HSA-3371567 Reactome:R-HSA-349426 Reactome:R-HSA-349444 Reactome:R-HSA-349455 Reactome:R-HSA-374696 Reactome:R-HSA-3769394 Reactome:R-HSA-377186 Reactome:R-HSA-3772435 Reactome:R-HSA-380272 Reactome:R-HSA-381091 Reactome:R-HSA-381111 Reactome:R-HSA-3857328 Reactome:R-HSA-3857329 Reactome:R-HSA-3858480 Reactome:R-HSA-389756 Reactome:R-HSA-392752 Reactome:R-HSA-3928577 Reactome:R-HSA-3928608 Reactome:R-HSA-3928616 Reactome:R-HSA-3928620 Reactome:R-HSA-3928625 Reactome:R-HSA-3928640 Reactome:R-HSA-399939 Reactome:R-HSA-399944 Reactome:R-HSA-399950 Reactome:R-HSA-399951 Reactome:R-HSA-399952 Reactome:R-HSA-399978 Reactome:R-HSA-400382 Reactome:R-HSA-4088134 Reactome:R-HSA-419083 Reactome:R-HSA-419087 Reactome:R-HSA-419197 Reactome:R-HSA-419644 Reactome:R-HSA-428961 Reactome:R-HSA-429016 Reactome:R-HSA-429714 Reactome:R-HSA-432110 Reactome:R-HSA-4332358 Reactome:R-HSA-4332363 Reactome:R-HSA-4332388 Reactome:R-HSA-4411383 Reactome:R-HSA-4411402 Reactome:R-HSA-442724 Reactome:R-HSA-442739 Reactome:R-HSA-442832 Reactome:R-HSA-445072 Reactome:R-HSA-446694 Reactome:R-HSA-446701 Reactome:R-HSA-448948 Reactome:R-HSA-448955 Reactome:R-HSA-450222 Reactome:R-HSA-450325 Reactome:R-HSA-450463 Reactome:R-HSA-450474 Reactome:R-HSA-450490 Reactome:R-HSA-450499 Reactome:R-HSA-450827 Reactome:R-HSA-451152 Reactome:R-HSA-451347 Reactome:R-HSA-4551570 Reactome:R-HSA-4608825 Reactome:R-HSA-4793911 Reactome:R-HSA-5082387 Reactome:R-HSA-5082405 Reactome:R-HSA-5213464 Reactome:R-HSA-5213466 Reactome:R-HSA-5218814 Reactome:R-HSA-5218821 Reactome:R-HSA-5218826 Reactome:R-HSA-5218854 Reactome:R-HSA-5218906 Reactome:R-HSA-5218916 Reactome:R-HSA-5228811 Reactome:R-HSA-5229343 Reactome:R-HSA-5260201 Reactome:R-HSA-5357472 Reactome:R-HSA-5357477 Reactome:R-HSA-5357831 Reactome:R-HSA-5578777 Reactome:R-HSA-5607722 Reactome:R-HSA-5607726 Reactome:R-HSA-5607732 Reactome:R-HSA-5607742 Reactome:R-HSA-5610718 Reactome:R-HSA-5610722 Reactome:R-HSA-5610730 Reactome:R-HSA-5610732 Reactome:R-HSA-5624473 Reactome:R-HSA-5624492 Reactome:R-HSA-5627775 Reactome:R-HSA-5632670 Reactome:R-HSA-5632672 Reactome:R-HSA-5635841 Reactome:R-HSA-5635842 Reactome:R-HSA-5665868 Reactome:R-HSA-5666160 Reactome:R-HSA-5668545 Reactome:R-HSA-5668932 Reactome:R-HSA-5668947 Reactome:R-HSA-5668984 Reactome:R-HSA-5669250 Reactome:R-HSA-5671763 Reactome:R-HSA-5671919 Reactome:R-HSA-5672008 Reactome:R-HSA-5672010 Reactome:R-HSA-5672828 Reactome:R-HSA-5672948 Reactome:R-HSA-5672973 Reactome:R-HSA-5672978 Reactome:R-HSA-5674496 Reactome:R-HSA-5675194 Reactome:R-HSA-5675198 Reactome:R-HSA-5675868 Reactome:R-HSA-5679205 Reactome:R-HSA-5682026 Reactome:R-HSA-5682101 Reactome:R-HSA-5682598 Reactome:R-HSA-5682983 Reactome:R-HSA-5683425 Reactome:R-HSA-5683792 Reactome:R-HSA-5683801 Reactome:R-HSA-5683964 Reactome:R-HSA-5684096 Reactome:R-HSA-5684140 Reactome:R-HSA-5684887 Reactome:R-HSA-5685156 Reactome:R-HSA-5685230 Reactome:R-HSA-5685242 Reactome:R-HSA-5686578 Reactome:R-HSA-5686704 Reactome:R-HSA-5687086 Reactome:R-HSA-5687090 Reactome:R-HSA-5687094 Reactome:R-HSA-5687101 Reactome:R-HSA-5687121 Reactome:R-HSA-5687183 Reactome:R-HSA-5690250 Reactome:R-HSA-5692768 Reactome:R-HSA-5692775 Reactome:R-HSA-5692779 Reactome:R-HSA-5693536 Reactome:R-HSA-5693540 Reactome:R-HSA-5693549 Reactome:R-HSA-5693551 Reactome:R-HSA-5693575 Reactome:R-HSA-5693598 Reactome:R-HSA-5693609 Reactome:R-HSA-5694441 Reactome:R-HSA-6788392 Reactome:R-HSA-6795290 Reactome:R-HSA-6795460 Reactome:R-HSA-6795473 Reactome:R-HSA-6798372 Reactome:R-HSA-6798374 Reactome:R-HSA-6799097 Reactome:R-HSA-6799246 Reactome:R-HSA-6799332 Reactome:R-HSA-6799409 Reactome:R-HSA-6800490 Reactome:R-HSA-6801666 Reactome:R-HSA-6801675 Reactome:R-HSA-6802911 Reactome:R-HSA-6802919 Reactome:R-HSA-6802926 Reactome:R-HSA-6802933 Reactome:R-HSA-6802935 Reactome:R-HSA-6802943 Reactome:R-HSA-6802973 Reactome:R-HSA-6804266 Reactome:R-HSA-6804276 Reactome:R-HSA-6804955 Reactome:R-HSA-6805059 Reactome:R-HSA-6805103 Reactome:R-HSA-6805126 Reactome:R-HSA-6805276 Reactome:R-HSA-6805285 Reactome:R-HSA-6805399 Reactome:R-HSA-6805479 Reactome:R-HSA-6805640 Reactome:R-HSA-6805785 Reactome:R-HSA-6810233 Reactome:R-HSA-6811454 Reactome:R-HSA-6814409 Reactome:R-HSA-6814559 Reactome:R-HSA-69604 Reactome:R-HSA-69608 Reactome:R-HSA-69685 Reactome:R-HSA-69891 Reactome:R-HSA-75010 Reactome:R-HSA-75028 Reactome:R-HSA-75809 Reactome:R-HSA-75820 Reactome:R-HSA-77071 Reactome:R-HSA-8850945 Reactome:R-HSA-8852306 Reactome:R-HSA-8852317 Reactome:R-HSA-8853419 Reactome:R-HSA-8853444 Reactome:R-HSA-8854908 Reactome:R-HSA-8856813 Reactome:R-HSA-8863007 Reactome:R-HSA-8863011 Reactome:R-HSA-8863014 Reactome:R-HSA-8863895 Reactome:R-HSA-8868260 Reactome:R-HSA-8868340 Reactome:R-HSA-8868344 Reactome:R-HSA-8868567 Reactome:R-HSA-8868573 Reactome:R-HSA-8868666 Reactome:R-HSA-8870558 Reactome:R-HSA-8873929 Reactome:R-HSA-8876446 Reactome:R-HSA-8877691 Reactome:R-HSA-8878050 Reactome:R-HSA-8878054 Reactome:R-HSA-8933446 Reactome:R-HSA-8939963 Reactome:R-HSA-8940100 Reactome:R-HSA-8942836 Reactome:R-HSA-8944454 Reactome:R-HSA-8948039 Reactome:R-HSA-8948146 Reactome:R-HSA-8948757 Reactome:R-HSA-8952289 Reactome:R-HSA-9007539 Reactome:R-HSA-9008480 Reactome:R-HSA-9008822 Reactome:R-HSA-9009208 Reactome:R-HSA-9012319 Reactome:R-HSA-9013978 Reactome:R-HSA-9022314 Reactome:R-HSA-9023132 Reactome:R-HSA-9032751 Reactome:R-HSA-9032863 Reactome:R-HSA-912470 Reactome:R-HSA-913996 Reactome:R-HSA-918229 Reactome:R-HSA-933525 Reactome:R-HSA-934559 Reactome:R-HSA-936951 Reactome:R-HSA-937022 Reactome:R-HSA-937059 Reactome:R-HSA-9604328 Reactome:R-HSA-9612980 Reactome:R-HSA-9619515 Reactome:R-HSA-9619843 Reactome:R-HSA-9620004 Reactome:R-HSA-9624526 Reactome:R-HSA-9626880 Reactome:R-HSA-9627089 Reactome:R-HSA-9632868 Reactome:R-HSA-9634702 Reactome:R-HSA-975125 Reactome:R-HSA-975134 Reactome:R-HSA-975160 Reactome:R-HSA-975170 Reactome:R-HSA-975180 Reactome:R-HSA-975853 Reactome:R-HSA-975861 Reactome:R-HSA-975865 Reactome:R-HSA-975874 Reactome:R-HSA-975878 protein serine-threonine kinase activity serine(threonine) protein kinase activity serine/threonine protein kinase activity protein kinase (phosphorylating) activity protein phosphokinase activity protein serine kinase activity protein-serine kinase activity serine kinase activity serine protein kinase activity serine-specific protein kinase activity threonine-specific protein kinase activity molecular_function GO:0004674 protein serine/threonine kinase activity Reactome:R-HSA-9604328 AKT1 phosphorylates NOTCH4 Reactome:R-HSA-9612980 BRAF in Rap1-GTP complex:BRAF complex autophosphorylates Reactome:R-HSA-9619515 AMPK phosphorylates MAPT Reactome:R-HSA-9619843 ERKs phosphorylate RSKs Reactome:R-HSA-9620004 RSKs autophosphorylate Reactome:R-HSA-9624526 AKT phosphorylates FOXO3 downstream of ESR1 and EGFR Reactome:R-HSA-9626880 MAPK11 or MAPK14 phosphorylates NCF1 at Ser345 Reactome:R-HSA-9627089 CASP9 is phosphorylated at T125 Reactome:R-HSA-9632868 CDKN1B is phosphorylated in response to estrogen Reactome:R-HSA-9634702 LINC01139 promotes phosphorylation of HIF1A by LRRK2 Reactome:R-HSA-975125 Multiple IRAK1 autophosphorylation steps within the complex pIRAK4:MyD88:activated TLR7/8 or 9 Reactome:R-HSA-975134 Second phosphorylation of IRAK1 by IRAK4 bound to MyD88: activated TLR 7/8 or 9 Reactome:R-HSA-975160 Phosphorylation of IRAK2 bound to the activated IRAK4:MyD88 oligomer:activated TLR 7/8 or 9 Reactome:R-HSA-975170 IRAK4 autophosphorylation in the complex with MyD88:activated TLR 7/8 or 9 Reactome:R-HSA-975180 First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR 7/8 or 9 Reactome:R-HSA-975853 Multiple IRAK1 autophosphorylation within the complex p-IRAK4:oligo MyD88:activated TLR Reactome:R-HSA-975861 Phosphorylation of IRAK2 bound to the activated IRAK4:MyD88 oligomerl:activated TLR5 or 10 complex Reactome:R-HSA-975865 IRAK4 autophosphorylation within the complex activated TLR:MyD88 Reactome:R-HSA-975874 Second phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR complex Reactome:R-HSA-975878 First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR protein serine-threonine kinase activity EC:2.7.11.1 serine(threonine) protein kinase activity EC:2.7.11.1 serine/threonine protein kinase activity EC:2.7.11.1 protein kinase (phosphorylating) activity EC:2.7.11.1 protein phosphokinase activity EC:2.7.11.1 protein serine kinase activity EC:2.7.11.1 protein-serine kinase activity EC:2.7.11.1 serine kinase activity EC:2.7.11.1 serine protein kinase activity EC:2.7.11.1 serine-specific protein kinase activity EC:2.7.11.1 threonine-specific protein kinase activity EC:2.7.11.1 Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. GOC:bf RHEA:17989 RHEA:46608 Reactome:R-HSA-109702 PDPK1 phosphorylates AKT2 Reactome:R-HSA-109822 MAPK3,(MAPK1) phosphorylates GRB2-1:SOS1:p-Y427-SHC1 Reactome:R-HSA-109823 MAPK3,(MAPK1) phosphorylates GRB2-1:SOS1:p-Y-IRS1,p-Y-IRS2 Reactome:R-HSA-109860 MAP2K1 phosphorylates MAPK3 Reactome:R-HSA-109862 MAP2K2 phosphorylates MAPK1 Reactome:R-HSA-111919 PKA phosphorylates CREB1 Reactome:R-HSA-111970 PKC phosphorylates GRK2 Reactome:R-HSA-112342 Inactivation of MAP2K1 by CDK1 Reactome:R-HSA-112381 Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex Reactome:R-HSA-1168635 PRKCB (PKC-beta) phosphorylates CARMA1 Reactome:R-HSA-1168638 Activated IKK phosphorylates I-kappaB Reactome:R-HSA-1168641 TAK1 associated with the CBM complex phosphorylates IKKbeta Reactome:R-HSA-1181149 ACVR2A/B (ActRIIA/B) phosphorylates ACVR1B (ActRIB, ALK4) in response to Activin Reactome:R-HSA-1181156 Type II Activin Receptor (ActRII/ACVR2) phosphorylates Type I Activin Receptor (ActRIB/ACVR1B) in response to NODAL Reactome:R-HSA-1181355 Phosphorylation of R-SMAD2/3 by NODAL receptor Reactome:R-HSA-1225894 Type II Activin Receptor (ActRIIB/ACVR2B) phosphorylates Type I Activin Receptor (ActRIC/ACVR1C) in response to NODAL Reactome:R-HSA-1358791 Phosphorylation of USP8 by P-AKT Reactome:R-HSA-1362270 Phosphorylation of LIN52 component of MuvB by DYRK1A Reactome:R-HSA-139908 Phosphorylation of DLC2 by MAPK8 Reactome:R-HSA-139918 Phosphorylation of BIM by JNK Reactome:R-HSA-1445144 p-AKT1,p-AKT2 phosphorylates AS160 (TBC1D4) Reactome:R-HSA-1449597 p-AKT2 phosphorylates Myosin 5A Reactome:R-HSA-1454699 AMPK-alpha2 phosphorylates TBC1D1 Reactome:R-HSA-1458463 p-AKT2 phosphorylates RGC2 Reactome:R-HSA-1549526 Phosphorylation of SMAD2/3 by Activin:Activin Receptor Reactome:R-HSA-156673 Regulation of KIF23 (MKLP1) by phosphorylation Reactome:R-HSA-156678 Activation of Cdc25C Reactome:R-HSA-156682 Regulation of NUDC by phosphorylation Reactome:R-HSA-156699 Inactivation of Wee1 kinase Reactome:R-HSA-156723 Regulation of KIF20A (MKL2) by phosphorylation Reactome:R-HSA-1592233 p38 MAPK phosphorylates PPARGC1A Reactome:R-HSA-162363 p-T309,S474-AKT2:PIP3 phosphorylates PDE3B Reactome:R-HSA-162657 Inactivation of Myt1 kinase Reactome:R-HSA-163010 Down Regulation of Emi1 through Phosphorylation of Emi1 Reactome:R-HSA-1632857 ULK1 phosphorylates AMBRA1:Beclin-1 complex Reactome:R-HSA-163416 hormone-sensitive lipase (HSL) + 2 ATP -> phosphorylated HSL + 2 ADP Reactome:R-HSA-163418 perilipin + 2 ATP -> phosphorylated perilipin + 2 ADP Reactome:R-HSA-1638803 Phosphorylation of cohesin by PLK1 at centromeres Reactome:R-HSA-164151 LKB1 phosphorylates the alpha subunit of AMPK heterotrimer Reactome:R-HSA-165162 Phosphorylation of TSC2 by PKB Reactome:R-HSA-165182 Phosphorylation of complexed TSC2 by PKB Reactome:R-HSA-165692 Phosphorylation of 4E-BP1 by activated mTORC1 Reactome:R-HSA-165718 mTORC1 phosphorylation of RPS6KB1 (S6K) Reactome:R-HSA-165726 Phosphorylation of Ribosomal protein S6 by activated S6K1 Reactome:R-HSA-165758 Phosphorylation and inactivation of eEF2K by activated S6K1 Reactome:R-HSA-165766 Phosphorylation and activation of eIF4G by activated S6K1 Reactome:R-HSA-165777 Phosphorylation and activation of eIF4B by activated S6K1 Reactome:R-HSA-166119 First phosphorylation of IRAK1 by IRAK4 bound to activated TLR:MyD88:Mal Reactome:R-HSA-166245 Phosphorylation of IRF-3/IRF7 and their release from the activated TLR complex Reactome:R-HSA-166284 Second phosphorylation of IRAK1 by IRAK4 bound to activated TLR:MyD88:TIRAP Reactome:R-HSA-166286 Multiple IRAK1 autophosphorylation steps Reactome:R-HSA-167084 Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex Reactome:R-HSA-167098 Phosphorylation (Ser5) of RNA pol II CTD Reactome:R-HSA-168053 Phosphorylated MAPKs phosphorylate ATF-2 Reactome:R-HSA-168140 Phospho-IKK Complex phosphorylates NFkB inhibitor within the NFkB inhibitor:NFkB complex Reactome:R-HSA-170055 Myt-1 mediated phosphorylation of Cyclin B:Cdc2 complexes Reactome:R-HSA-170076 CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes Reactome:R-HSA-170087 CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes Reactome:R-HSA-170116 Myt-1 mediated phosphorylation of Cyclin A:Cdc2 Reactome:R-HSA-170126 Phosphorylation of Cyclin B1 in the CRS domain Reactome:R-HSA-170977 FRS2 is phosphorylated by active TrkA receptor Reactome:R-HSA-174119 Free APC/C phosphorylated by Plk1 Reactome:R-HSA-174174 Phosphorylation of the Emi1 DSGxxS degron by Plk1 Reactome:R-HSA-176116 Recruitment and activation of Chk1 Reactome:R-HSA-176298 Activation of claspin Reactome:R-HSA-187688 p38 MAPK phosphorylates MAPKAPK2, MAPKAPK3 Reactome:R-HSA-187949 CAK-mediated phosphorylation of Cyclin A:Cdk2 Reactome:R-HSA-188350 CAK-mediated phosphorylation of Cyclin E:Cdk2 Reactome:R-HSA-193647 IRAK is activated Reactome:R-HSA-193705 IKKbeta phosphorylates IkB causing NF-kB to dissociate Reactome:R-HSA-195275 Phosphorylation of APC component of the destruction complex Reactome:R-HSA-195283 Phosphorylation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3 Reactome:R-HSA-195287 Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3 Reactome:R-HSA-195300 Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3 Reactome:R-HSA-195318 Phosphorylation of beta-catenin at Ser45 by CK1 alpha Reactome:R-HSA-198270 PDPK1 phosphorylates AKT at T308 Reactome:R-HSA-198347 AKT phosphorylates BAD Reactome:R-HSA-198371 AKT phosphorylates GSK3 Reactome:R-HSA-198599 AKT phosphorylates MDM2 Reactome:R-HSA-198609 AKT phosphorylates TSC2, inhibiting it Reactome:R-HSA-198611 AKT phosphorylates IKKalpha Reactome:R-HSA-198613 AKT phosphorylates p21Cip1 and p27Kip1 Reactome:R-HSA-198621 AKT phosphorylates caspase-9 Reactome:R-HSA-198640 TORC2 (mTOR) phosphorylates AKT at S473 Reactome:R-HSA-198669 p38MAPK phosphorylates MSK1 Reactome:R-HSA-198731 ERK1/2 activates ELK1 Reactome:R-HSA-198746 ERK1/2/5 activate RSK1/2/3 Reactome:R-HSA-198756 ERK1/2 phosphorylates MSK1 Reactome:R-HSA-199298 AKT phosphorylates CREB1 Reactome:R-HSA-199299 AKT phosphorylates FOXO transcription factors Reactome:R-HSA-199839 AKT can phosphorylate RSK Reactome:R-HSA-199863 AKT can phosphorylate NR4A1 (NUR77) Reactome:R-HSA-199895 RSK1/2/3 phosphorylates CREB at Serine 133 Reactome:R-HSA-199910 MSK1 activates ATF1 Reactome:R-HSA-199917 MAPKAPK2 phosphorylates CREB at Serine 133 Reactome:R-HSA-199929 ERK5 activates the transcription factor MEF2 Reactome:R-HSA-199935 MSK1 activates CREB Reactome:R-HSA-200143 AKT phosphorylates AKT1S1 (PRAS40) Reactome:R-HSA-200421 Activation of cytosolic AMPK by phosphorylation Reactome:R-HSA-201677 Phosphorylation of LRP5/6 cytoplasmic domain by membrane-associated GSK3beta Reactome:R-HSA-201691 Phosphorylation of LRP5/6 cytoplasmic domain by CSNKI Reactome:R-HSA-201717 CSNK2-mediated phosphorylation of DVL Reactome:R-HSA-202222 Phosphorylation of PKC theta Reactome:R-HSA-202437 Phosphorylation of CARMA1 Reactome:R-HSA-202459 Phosphorylation of Bcl10 Reactome:R-HSA-202500 Activation of IKK complex Reactome:R-HSA-202510 Activation of TAK1-TAB2 complex Reactome:R-HSA-202541 p-S177,S181-IKKB:IKKA:pUb-NEMO phosphorylates IkB-alpha:NF-kB Reactome:R-HSA-2028284 Phosphorylation of STK4 (MST1) and SAV1 by STK4 Reactome:R-HSA-2028555 Phosphorylation of LATS1 and 2 by p-STK4 (p-MST1) Reactome:R-HSA-2028583 Phosphorylation of YAP by LATS2 Reactome:R-HSA-2028589 Phosphorylation of LATS1 and 2 by p-STK3 (p-MST2) Reactome:R-HSA-2028591 Phosphorylation of STK3 (MST2) and SAV1 by STK3 Reactome:R-HSA-2028598 Phosphorylation of YAP by LATS1 Reactome:R-HSA-2028629 Phosphorylation of MOB1A and B by p-STK4 (p-MST1) Reactome:R-HSA-2028635 Phosphorylation of MOB1A and B by p-STK3 (p-MST2) Reactome:R-HSA-2028661 Phosphorylation of WWTR1 (TAZ) by LATS2 Reactome:R-HSA-2028670 Phosphorylation of MOB1A and B by p-STK4(MST1)/N Reactome:R-HSA-2028673 Phosphorylation of LATS1 and 2 by p-STK3 (MST2)/N Reactome:R-HSA-2028675 Phosphorylation of MOB1A and B by p-STK3(MST2)/N Reactome:R-HSA-2028679 Phosphorylation of LATS1 and 2 by p-STK4(MST1)/N Reactome:R-HSA-2029454 Autophosphorylation of PAK1 Reactome:R-HSA-2029460 PAK1 phosphorylates LIMK1 Reactome:R-HSA-2029469 p-ERK phosphorylates WAVEs and ABI Reactome:R-HSA-2060328 Phosphorylation of WWTR1 (TAZ) by LATS1 Reactome:R-HSA-209087 IKBA is phosphorylated by Phospho IKKB kinase Reactome:R-HSA-211164 AKT phosphorylates FOXO1A Reactome:R-HSA-211583 Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197 Reactome:R-HSA-211650 Autophosphorylation of PAK-2p34 in the activation loop Reactome:R-HSA-2168079 MASTL (GWL) phosphorylates ARPP19 Reactome:R-HSA-2176475 Phosphorylation of SMAD2 and SMAD3 linker regions by CDK8 or CDK9 Reactome:R-HSA-2214351 PLK1 phosphorylates GORASP1 Reactome:R-HSA-2243938 AKT1 E17K mutant is phosphorylated by TORC2 complex Reactome:R-HSA-2243942 PDPK1 phosphorylates AKT1 E17K mutant Reactome:R-HSA-2294580 PLK1 hyperphosphorylates Condensin II complex Reactome:R-HSA-2396007 IRF3 is phosphorylated by TBK1 Reactome:R-HSA-2399941 AKT1 E17K mutant phosphorylates BAD Reactome:R-HSA-2399966 AKT1 E17K mutant phosphorylates GSK3 Reactome:R-HSA-2399969 AKT1 E17K mutant phosphorylates p21Cip1 and p27Kip1 Reactome:R-HSA-2399977 AKT1 E17K mutant phosphorylates AKT1S1 (PRAS40) Reactome:R-HSA-2399981 AKT1 E17K mutant phosphorylates MDM2 Reactome:R-HSA-2399982 AKT1 E17K mutant phosphorylates TSC2, inhibiting it Reactome:R-HSA-2399985 AKT1 E17K mutant phosphorylates caspase-9 Reactome:R-HSA-2399988 AKT1 E17K mutant phosphorylates NR4A1 (NUR77) Reactome:R-HSA-2399992 AKT1 E17K mutant phosphorylates forkhead box transcription factors Reactome:R-HSA-2399996 AKT1 E17K mutant phosphorylates CREB1 Reactome:R-HSA-2399999 AKT1 E17K mutant phosphorylates RSK Reactome:R-HSA-2400001 AKT1 E17K mutant phosphorylates CHUK (IKKalpha) Reactome:R-HSA-2422927 MAPK3-3 or MAPK1 phosphorylate GORASP2 Reactome:R-HSA-2430535 MASTL phosphorylates ENSA Reactome:R-HSA-2466068 Phosphorylation of cohesin by PLK1 at chromosomal arms Reactome:R-HSA-2470508 ACVR2A/B (ActRIIA/B) phosphorylates ACVR1C (ActRIC, ALK7) in response to Activin Reactome:R-HSA-2529020 CK2 phosphorylates condensin I subunits Reactome:R-HSA-2562526 PLK1 phosphorylates OPTN Reactome:R-HSA-2574840 AJUBA facilitates AURKA autophosphorylation Reactome:R-HSA-2730856 Autophosphorylation of PAK Reactome:R-HSA-2730868 Phosphorylation of MEK7 by MEKK1 Reactome:R-HSA-2730876 Phosphorylation of IKK-beta by TAK1 Reactome:R-HSA-2730896 Phosphorylation of MEK4 by MEKK1 Reactome:R-HSA-2730900 Activation of TAK1 complex bound to pUb-TRAF6 Reactome:R-HSA-2984226 PLK1 phosphorylates NEK9 Reactome:R-HSA-2984258 NEK9 phosphorylates NEK6/NEK7 Reactome:R-HSA-2990880 NEK6/NEK7 phosphorylates NUP98 Reactome:R-HSA-2993898 VRK1/VRK2 phosphorylate BANF1 Reactome:R-HSA-3000310 AURKA phosphorylates PLK1 Reactome:R-HSA-3000327 PLK1 phosphorylates BORA Reactome:R-HSA-3132737 MAPKs phosphorylate ETS1 and ETS2 Reactome:R-HSA-3209160 Activated ERKs phosphorylate ERF Reactome:R-HSA-3222006 STK11 (LKB1) phosphorylates NUAK1 Reactome:R-HSA-3222020 NUAK1 phosphorylates TP53 Reactome:R-HSA-3228469 MAP3K5 phosphorylates MKK3 and MKK6 Reactome:R-HSA-3229102 p-MAPKAPK3 phosphorylates BMI1 Reactome:R-HSA-3229152 MAP3K5 (ASK1) phosphorylates MAP2K4 (SEK1) Reactome:R-HSA-3239014 MAPKAPK5 phosphorylates TP53 Reactome:R-HSA-3239019 Active p38 MAPK phosphorylates MAPKAPK5 Reactome:R-HSA-3249371 TBK1 phosphorylates STAT6 at Ser407 Reactome:R-HSA-3371435 Constitutive phosphorylation by GSK3 Reactome:R-HSA-3371531 Constitutive phosphorylation by pERK1/2 Reactome:R-HSA-3371567 DBC1 is phosphorylated by ATM/ART Reactome:R-HSA-349426 Phosphorylation of MDM4 by CHEK2 Reactome:R-HSA-349444 Phosphorylation of COP1 at Ser-387 by ATM Reactome:R-HSA-349455 Phosphorylation of MDM4 by ATM Reactome:R-HSA-374696 Phosphorylation of L1 by p90rsk Reactome:R-HSA-3769394 AKT phosphorylates CBY1 Reactome:R-HSA-377186 Activated Akt1 phosphorylates AKT1S1 (PRAS40) Reactome:R-HSA-3772435 WNT signaling stimulates CSNK1-dependent phosphorylation of DVL Reactome:R-HSA-380272 Plk1-mediated phosphorylation of Nlp Reactome:R-HSA-381091 IRE1 dimer autophosphorylates Reactome:R-HSA-381111 EIF2AK3 (PERK) phosphorylates EIF2S1 (eIF2-alpha)Phosphorylation of eIF2-alpha by PERK Reactome:R-HSA-3857328 RPS6KA1/2/3 phosphorylates CEBPB on S321 Reactome:R-HSA-3857329 MAPK3 (ERK1) and MAPK1 (ERK2) phosphorylate CEBPB Reactome:R-HSA-3858480 WNT-dependent phosphorylation of DVL Reactome:R-HSA-389756 AKT interacts and phosphorylates Cot Reactome:R-HSA-392752 Phosphorylation of L1 by CK-II Reactome:R-HSA-3928577 ROCK phosphorylates LIMK1,2 Reactome:R-HSA-3928608 LIMK phosphorylates CFL1, inactivating it Reactome:R-HSA-3928616 Activated ROCK phosphorylates MRLCs Reactome:R-HSA-3928620 PAK1 autophosphorylates Reactome:R-HSA-3928625 PAKs autophosphorylate Reactome:R-HSA-3928640 PAKs phosphorylate MLC Reactome:R-HSA-399939 Autophosphorylation of PAK Reactome:R-HSA-399944 Phosphorylation of CRMPs by Cdk5 Reactome:R-HSA-399950 Phosphorylation of cofilin by LIMK-1 Reactome:R-HSA-399951 Phosphorylation of CRMPs by GSK3beta Reactome:R-HSA-399952 Phosphorylation of LIMK-1 by PAK Reactome:R-HSA-399978 Protein kinase C, alpha type phosphorylates MARCKS Reactome:R-HSA-400382 CSNK1E,CSNK1D phosphorylate CRY and PER proteins Reactome:R-HSA-4088134 PLK1 phosphorylates FOXM1 Reactome:R-HSA-419083 Myosin phosphatase inactivation by ROCK Reactome:R-HSA-419087 LIM kinase phosphorylation by ROCK Reactome:R-HSA-419197 Myosin regulatory light chain phosphorylation by ROCK Reactome:R-HSA-419644 Transphosphorylation of pLIMK1 Reactome:R-HSA-428961 Phosphorylation of cPLA2 by MAPK p38 alpha Reactome:R-HSA-429016 ALOX5 is phosphorylated by MAPKAP2 Reactome:R-HSA-429714 monophospho-CERT + 2 ATP => multiphospho-CERT + 2 ADP Reactome:R-HSA-432110 Integrin alpha IIb beta3 T779 phosphorylation blocks SHC binding Reactome:R-HSA-4332358 Dissociation of CaM and CAMK2 autophosphorylation Reactome:R-HSA-4332363 Autophosphorylation and activation of CAMK2 Reactome:R-HSA-4332388 Activation of MAP3K7 in response to WNT Reactome:R-HSA-4411383 NLK phosphorylates TCF/LEF Reactome:R-HSA-4411402 Activation of NLK Reactome:R-HSA-442724 Phosphorylation of CREB1 by ribosomal protein S6 kinases (RSKs) Reactome:R-HSA-442739 PDPK1 phosphorylates RSKs Reactome:R-HSA-442832 PAK phosphorylates cortactin Reactome:R-HSA-445072 Interaction of PAK1 with Rac1-GTP Reactome:R-HSA-446694 IRAK4 phosphorylates IRAK1 Reactome:R-HSA-446701 IRAK4-activated IRAK1 autophosphorylates Reactome:R-HSA-448948 Phosphorylation of E proteins by p38 MAPK Reactome:R-HSA-448955 Phosphorylation of MEF2 proteins by p38 Reactome:R-HSA-450222 Active p38 MAPK phosphorylates MAPKAPK2 or 3 Reactome:R-HSA-450325 c-FOS activation by phospho ERK1/2 Reactome:R-HSA-450463 MK2 phosphorylates ZFP36 (Tristetraproline, TTP) Reactome:R-HSA-450474 MK2 phosphorylates BRF1 Reactome:R-HSA-450490 Protein Kinase B/Akt phosphorylates BRF1 Reactome:R-HSA-450499 Protein Kinase B (AKT) phosphorylates KSRP Reactome:R-HSA-450827 hp-IRAK1, hp-IRAK4 4 phosphorylate Pellino-1 and 2. Reactome:R-HSA-451152 MAP kinase p38 phosphorylates KSRP Reactome:R-HSA-451347 Activation of JNK by DSCAM Reactome:R-HSA-4551570 VANGL2 is phosphorylated in response to WNT5A Reactome:R-HSA-4608825 DVL2 is phosphorylated after WNT5A binding to FZD Reactome:R-HSA-4793911 MAPKAPK2 phosphorylates HSF1 Reactome:R-HSA-5082387 Phosphorylation of HSF1 at Ser230 induces transactivation Reactome:R-HSA-5082405 Phosphorylation of HSF1 at Ser326 induces transactivation Reactome:R-HSA-5213464 RIPK1 is phosphorylated Reactome:R-HSA-5213466 RIPK3 is phosphorylated Reactome:R-HSA-5218814 PAK2 autophorylates Reactome:R-HSA-5218821 PDK1 phosphorylates PKC Reactome:R-HSA-5218826 Active ROCK1,ROCK2 phosphorylates p-5Y-PTK2 on S732 Reactome:R-HSA-5218854 p-Y420-FYN is phosphorylated on S21 Reactome:R-HSA-5218906 RIPK3 phosphorylates MLKL Reactome:R-HSA-5218916 p-MAPK2/3 phosphorylates HSP27 Reactome:R-HSA-5228811 NFKBIA variant is not phosphorylated within IkBA:NF-kappaB Reactome:R-HSA-5229343 AXIN is phosphorylated in the destruction complex Reactome:R-HSA-5260201 p-AKT2 phosphorylates C2CD5 Reactome:R-HSA-5357472 PAK1-3 autophosphorylates Reactome:R-HSA-5357477 PAK1-3 phosphorylates VE-cadherin Reactome:R-HSA-5357831 CYLD is phosphorylated by IKK Reactome:R-HSA-5578777 DMPK phosphorylates PLN Reactome:R-HSA-5607722 Active NIK phosphorylates IKKA dimer Reactome:R-HSA-5607726 Active NIK:p-S176,180-IKKA dimer phosphorylates p100:RELB Reactome:R-HSA-5607732 K63polyUb-TAK1 autophosphorylates Reactome:R-HSA-5607742 K63polyUb-p-3T,1S-TAK1 phosphorylates IKK-beta Reactome:R-HSA-5610718 CK1 phosphorylates p-GLI2 Reactome:R-HSA-5610722 CK1 phosphorylates p-GLI3 Reactome:R-HSA-5610730 GSK3 phosphorylates p-GLI2 Reactome:R-HSA-5610732 GSK3 phosphorylates p-GLI3 Reactome:R-HSA-5624473 Protein kinase A (PKA) and RPS6KA5 (MSK1) phosphorylates p65 (RELA) subunit Reactome:R-HSA-5624492 PAK phosphorylates p21 RAF1 on S338 Reactome:R-HSA-5627775 Autophosphorylation of PAK1,2,3 Reactome:R-HSA-5632670 CSNK1A1 phosphorylates SMO dimer Reactome:R-HSA-5632672 ADRBK1 phosphorylates SMO dimer Reactome:R-HSA-5635841 GLI proteins are phosphorylated Reactome:R-HSA-5635842 ULK3 phosphorylates GLI Reactome:R-HSA-5665868 AMPK (complex) phosphorylates ULK1 (complex) Reactome:R-HSA-5666160 AURKB phosphorylates DIAPH2-2 at kinetochores Reactome:R-HSA-5668545 NIK autophosphorylates on T559 Reactome:R-HSA-5668932 PAK2 phosphorylates myosin regulatory light chain (MRLC) Reactome:R-HSA-5668947 PAK1 phosphorylates myosin phosphatase Reactome:R-HSA-5668984 PAK1 or PAK2 phosphorylates MYLK Reactome:R-HSA-5669250 PAK1 phosphorylates FLNA Reactome:R-HSA-5671763 p-T774-PKN1 phosphorylates PPP1R14A Reactome:R-HSA-5671919 Activated CIT phosphorylates MRLCs Reactome:R-HSA-5672008 Thr-180 of ULK1 is phosphorylated Reactome:R-HSA-5672010 Active mTORC1 phosphorylates ULK1 Reactome:R-HSA-5672828 mTORC1 phosphorylates AKT1S1 Reactome:R-HSA-5672948 MARK3 phosphorylates KSR1 Reactome:R-HSA-5672973 MAP2Ks phosphorylate MAPKs Reactome:R-HSA-5672978 RAF phosphorylates MAP2K dimer Reactome:R-HSA-5674496 Activated MAPKs phosphorylate MAP2K1 Reactome:R-HSA-5675194 Activated MAPK phosphorylates RAF1 Reactome:R-HSA-5675198 Activated MAPKs phosphorylate BRAF Reactome:R-HSA-5675868 ULK1 phosphorylates ATG13 and RB1CC1 Reactome:R-HSA-5679205 ULK1 phosphorylates Beclin-1 Reactome:R-HSA-5682026 MRN bound to shortened telomeres activates ATM Reactome:R-HSA-5682101 PKA phosphorylates 4xPALM-C-p-2S-ABCA1 tetramer Reactome:R-HSA-5682598 ATM phosphorylates HERC2 Reactome:R-HSA-5682983 ATM phosphorylates WHSC1 Reactome:R-HSA-5683425 ATM phosphorylates TP53BP1 at DNA DSBs Reactome:R-HSA-5683792 p-T68-CHEK2 autophosphorylates Reactome:R-HSA-5683801 CHEK2 phosphorylates BRCA1 Reactome:R-HSA-5683964 ATM phosphorylates EYA1-4 Reactome:R-HSA-5684096 CDK2 phosphorylates RBBP8 Reactome:R-HSA-5684140 ATM phosphorylates RBBP8 Reactome:R-HSA-5684887 Activation of CHEK1 at resected DNA DSBs Reactome:R-HSA-5685156 ATR phosphorylates RPA2 Reactome:R-HSA-5685230 CHEK1 phosphorylates RAD51 Reactome:R-HSA-5685242 CHEK1 phosphorylates BRCA2 Reactome:R-HSA-5686578 Activated ATM phosphorylates ABL1 Reactome:R-HSA-5686704 Activated ATM phosphorylates DCLRE1C Reactome:R-HSA-5687086 PAK1,2,3 phosphorylates MAPK6,4 Reactome:R-HSA-5687090 p-S MAPK6 phosphorylates NCOA3 Reactome:R-HSA-5687094 p-S MAPK6,4 phosphorylate MAPKAPK5 Reactome:R-HSA-5687101 p-T182 MAPKAPK5 phosphorylates FOXO3 Reactome:R-HSA-5687121 p-S MAPKAPK5 phosphorylates HSPB1 Reactome:R-HSA-5687183 PRKDC phosphorylates DCLRE1C at DNA DSBs Reactome:R-HSA-5690250 p-T182-MAPKAPK5 phoshphorylates DNAJB1 Reactome:R-HSA-5692768 MAPKAPK5 phosphorylates KALRN Reactome:R-HSA-5692775 SEPT7:p-S189 MAPK6:p-T182 MAPKAPK5 phosphorylates CDC42EPs Reactome:R-HSA-5692779 p-S182 MAPKAPK5 phosphorylates FOXO1 Reactome:R-HSA-5693536 ATM phosphorylates MDC1 Reactome:R-HSA-5693540 MRN activates ATM Reactome:R-HSA-5693549 ATM phosphorylates histone H2AFX on S139 at DNA DSBs Reactome:R-HSA-5693551 Phosphorylation of BRCA1-A complex at multiple sites by ATM Reactome:R-HSA-5693575 DNA-PKcs autophosphorylates Reactome:R-HSA-5693598 ATM phosphorylates NBN Reactome:R-HSA-5693609 ATM phosphorylates TP53 at S15 Reactome:R-HSA-5694441 CSNK1D phosphorylates SEC23 Reactome:R-HSA-6788392 ATR phosphorylates RPA2, FANCI, FANCD2 and FANCM at ICL-DNA Reactome:R-HSA-6795290 TORC2 complex phosphorylates SGK1 Reactome:R-HSA-6795460 SGK1 phosphorylates MDM2 Reactome:R-HSA-6795473 PDPK1 phosphorylates SGK1 Reactome:R-HSA-6798372 ATM phosphorylates DYRK2 Reactome:R-HSA-6798374 DYRK2 phosphorylates TP53 Reactome:R-HSA-6799097 ATM phosphorylates ZNF420 Reactome:R-HSA-6799246 CHEK1 phosphorylates TP53 Reactome:R-HSA-6799332 ATR phosphorylates TP53 Reactome:R-HSA-6799409 HIPK2 phosphorylates TP53 Reactome:R-HSA-6800490 ATM phosphorylates PIDD1 Reactome:R-HSA-6801666 PLK2 phosphorylates CENPJ Reactome:R-HSA-6801675 PLK2 phosphorylates NPM1 Reactome:R-HSA-6802911 High kinase activity BRAF complexes phosphorylate MAP2Ks Reactome:R-HSA-6802919 RAS:GTP:moderate kinase activity p-RAF complexes phosphorylate MAP2Ks Reactome:R-HSA-6802926 Mutant RAS:p-RAF complexes phosphorylate MAP2Ks Reactome:R-HSA-6802933 p-BRAF and RAF fusion dimers phosphorylate MAP2Ks Reactome:R-HSA-6802935 MAPKs are phosphorylated downstream of BRAF and RAF fusion dimers Reactome:R-HSA-6802943 RAS:GTP:inactive p-RAF complexes phosphorylate MAP2Ks Reactome:R-HSA-6802973 PLK3 phosphorylates CDC25C Reactome:R-HSA-6804266 CHEK2 phosphorylates TTC5 Reactome:R-HSA-6804276 ATM phosphorylates TTC5 Reactome:R-HSA-6804955 ATM phosphorylates MDM2 Reactome:R-HSA-6805059 CK2:FACT phosphorylates TP53 Reactome:R-HSA-6805103 AURKA phosphorylates TP53 Reactome:R-HSA-6805126 AURKB phosphorylates TP53 Reactome:R-HSA-6805276 CDK5 phosphorylates TP53 Reactome:R-HSA-6805285 PLK3 phosphorylates TP53 Reactome:R-HSA-6805399 TAF1 phosphorylates TP53 Reactome:R-HSA-6805479 TP53RK phosphorylates TP53 Reactome:R-HSA-6805640 AKT phosphorylates KAT6A Reactome:R-HSA-6805785 AKT phosphorylates PHF20 Reactome:R-HSA-6810233 CDK7 phosphorylates serine-5 and serine-7 of heptad repeats in C-terminal domain of RNA polymerase II at snRNA promoter Reactome:R-HSA-6811454 MAPKs phosphorylate PP2A Reactome:R-HSA-6814409 CK2 phosphorylates PDCL Reactome:R-HSA-6814559 Pre-snRNA is elongated and capped with 7-methylguanosine Reactome:R-HSA-69604 Phosphorylation of Cdc25A at Ser-123 by Chk1 Reactome:R-HSA-69608 Phosphorylation of Cdc25A at Ser-123 by Chk2 Reactome:R-HSA-69685 CHEK2 phosphorylates TP53 Reactome:R-HSA-69891 Phosphorylation and activation of CHEK2 by ATM Reactome:R-HSA-75010 Phosphorylation of Cdc25C at Ser 216 by Chk1 Reactome:R-HSA-75028 Phosphorylation of Wee1 kinase by Chk1 Reactome:R-HSA-75809 Phosphorylation of Cdc25C at Ser216 by CHEK2 Reactome:R-HSA-75820 Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta Reactome:R-HSA-77071 Phosphorylation (Ser5) of RNA pol II CTD Reactome:R-HSA-8850945 Casein kinase II phosphorylates PTEN Reactome:R-HSA-8852306 Mitotic phosphorylation-induced dissociation of GTSE1 from microtubule plus ends Reactome:R-HSA-8852317 PLK1 phosphorylates GTSE1 Reactome:R-HSA-8853419 TPX2 promotes AURKA autophosphorylation Reactome:R-HSA-8853444 AURKA phosphorylates PHLDA1 Reactome:R-HSA-8854908 PKA phosphorylates RET:GDNF:GFRA dimer Reactome:R-HSA-8856813 AAK1 phosphorylates AP-2 mu subunit at T156 Reactome:R-HSA-8863007 p25-bound CDK5 phosphorylates CDC25B Reactome:R-HSA-8863011 p25-bound CDK5 phosphorylates CDC25C Reactome:R-HSA-8863014 p25-bound CDK5 phosphorylates CDC25A Reactome:R-HSA-8863895 IKKB phosphorylates SNAP23 Reactome:R-HSA-8868260 CDK5:p25 phosphorylates GOLGA2 Reactome:R-HSA-8868340 CDK5:p25 phosphorylates lamin B1 Reactome:R-HSA-8868344 CDK5:p25 phosphorylates lamin A Reactome:R-HSA-8868567 CDK5:p25 phosphorylates PRDX1 Reactome:R-HSA-8868573 CDK5:p25 phosphorylates PRDX2 Reactome:R-HSA-8868666 CDK5:p25 phosphorylates JUN Reactome:R-HSA-8870558 CDK5:p25 phosphorylates FOXO3 Reactome:R-HSA-8873929 Casein kinase II phosphorylates STARD10 Reactome:R-HSA-8876446 p-ULK1 phosphorylates DENND3 Reactome:R-HSA-8877691 MAP2K6 phosphorylates PIP4K2B Reactome:R-HSA-8878050 HIPK2 phosphorylates RUNX1 and EP300 Reactome:R-HSA-8878054 HIPK2 phosphorylates RUNX1 Reactome:R-HSA-8933446 Active AKT phosphorylates DENND1A and DENND1B in response to insulin signaling Reactome:R-HSA-8939963 Activated AKT phosphorylates RUNX2 Reactome:R-HSA-8940100 CDK1 phosphorylates VCPIP1 Reactome:R-HSA-8942836 CDK4/6:CCND complexes are activated by T-loop phosphorylation of CDK4/6 Reactome:R-HSA-8944454 mTORC1 phosphorylates MAF1 Reactome:R-HSA-8948039 FUNDC1 is phosphorylated by CK2 Reactome:R-HSA-8948146 FUNDC1 is phosphorylated by ULK1 at Ser17 Reactome:R-HSA-8948757 AKT phosphorylates MKRN1 Reactome:R-HSA-8952289 FAM20C phosphorylates FAM20C substrates Reactome:R-HSA-9007539 CHEK1 phosphorylates E2F6 Reactome:R-HSA-9008480 GSK3B phosphorylates RUNX2 Reactome:R-HSA-9008822 PPM1D dephosphorylates RUNX2 Reactome:R-HSA-9009208 Activated ERKs phosphorylate RUNX2 Reactome:R-HSA-9012319 p-TEFb phosphorylates serine 2 in RNA polymerase II CTD Reactome:R-HSA-9013978 Phosphorylation of IRF-3/IRF7 and their release from the activated TLR3 complex Reactome:R-HSA-9022314 HIPK2 phosphorylates MECP2 Reactome:R-HSA-9023132 AURKB phosphorylates MECP2 at S423 Reactome:R-HSA-9032751 Estrogen-independent phosphorylation of ESR1 S118 by MAPK1 and MAPK3 Reactome:R-HSA-9032863 CDK5 phosphorylates NTRK2 Reactome:R-HSA-912470 ATR phosphorylates Histone H2A.X at unsynapsed regions Reactome:R-HSA-913996 PKA/PKG phosphorylate Rap1GAP2 Reactome:R-HSA-918229 Phosphorylation and release of IRF3/IRF7 Reactome:R-HSA-933525 Phosphorylation and release of IRF7 Reactome:R-HSA-934559 SPRY2 is phosphorylated by phosphorylated MNK1 Reactome:R-HSA-936951 Activation of TAK1 complex bound to activated TLR4 complex Reactome:R-HSA-937022 IRAK4 autophosphorylation in the complex with activated TLR:MyD88:TIRAP Reactome:R-HSA-937059 Phosphorylation of IRAK2 bound to the activated IRAK4:MyD88 oligomer:TIRAP:activated TLR complex Catalysis of the reaction: protein + ATP = protein phosphate + ADP. This reaction is the phosphorylation of proteins. Mitogen-activated protein kinase; a family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. They are activated by a wide range of proliferation- or differentiation-inducing signals; activation is strong with agonists such as polypeptide growth factors and tumor-promoting phorbol esters, but weak (in most cell backgrounds) by stress stimuli. GO:0008338 GO:0008339 GO:0016908 GO:0016909 EC:2.7.11.24 KEGG_REACTION:R00162 MetaCyc:2.7.11.24-RXN Reactome:R-HSA-111898 Reactome:R-HSA-198733 Reactome:R-HSA-445079 Reactome:R-HSA-451366 Reactome:R-HSA-5654560 Reactome:R-HSA-5654562 Reactome:R-HSA-5654565 Reactome:R-HSA-5654566 Reactome:R-HSA-73722 Reactome:R-HSA-9626832 ATP:protein phosphotransferase (MAPKK-activated) activity ERK1 mitogen activated kinase activity mitogen-activated protein kinase activity MAP kinase 1 activity MAP kinase 2 activity MBP kinase I activity MBP kinase II activity SAP kinase activity SAPK extracellular signal-regulated kinase activity myelin basic protein kinase activity stress-activated kinase activity stress-activated protein kinase activity molecular_function ERK ERK2 MAPK GO:0004707 MAP kinase activity Catalysis of the reaction: protein + ATP = protein phosphate + ADP. This reaction is the phosphorylation of proteins. Mitogen-activated protein kinase; a family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. They are activated by a wide range of proliferation- or differentiation-inducing signals; activation is strong with agonists such as polypeptide growth factors and tumor-promoting phorbol esters, but weak (in most cell backgrounds) by stress stimuli. GOC:ma ISBN:0198547684 Reactome:R-HSA-111898 Phosphorylation of cPLA2 by ERK-2 Reactome:R-HSA-198733 ERK5 is activated Reactome:R-HSA-445079 Phosphorylation of L1 by ERK Reactome:R-HSA-451366 Activation of p38MAPK by DSCAM Reactome:R-HSA-5654560 Activated ERK1/2 threonine-phosphorylates FGFR1-associated FRS2. Reactome:R-HSA-5654562 Activated ERK1/2 threonine-phosphorylates FGFR2-associated FRS2 Reactome:R-HSA-5654565 Activated ERK1/2 threonine-phosphorylates FGFR3-associated FRS2. Reactome:R-HSA-5654566 Activated ERK1/2 threonine-phosphorylates FGFR4-associated FRS2. Reactome:R-HSA-73722 Phosphorylation of UBF-1:rDNA Promoter Reactome:R-HSA-9626832 MAPK1 or MAPK3 phosphorylates NCF1 at Ser345 ATP:protein phosphotransferase (MAPKK-activated) activity EC:2.7.11.24 mitogen-activated protein kinase activity EC:2.7.11.24 MBP kinase I activity EC:2.7.11.24 MBP kinase II activity EC:2.7.11.24 extracellular signal-regulated kinase activity EC:2.7.11.24 myelin basic protein kinase activity EC:2.7.11.24 ERK EC:2.7.11.24 MAPK EC:2.7.11.24 PMID:20811974 Catalysis of the reaction: ribosomal protein S6 + ATP = ribosomal protein S6 phosphate + ATP. molecular_function GO:0004711 ribosomal protein S6 kinase activity Catalysis of the reaction: ribosomal protein S6 + ATP = ribosomal protein S6 phosphate + ATP. GOC:mah PMID:9822608 Catalysis of the reaction: retinol + NAD+ = retinal + NADH + H+. all-trans retinol dehydrogenase activity microsomal retinol dehydrogenase activity retinal reductase activity retinene reductase activity retinol (vitamin A1) dehydrogenase activity EC:1.1.1.105 MetaCyc:RETINOL-DEHYDROGENASE-RXN RHEA:21284 Reactome:R-HSA-2454081 Reactome:R-HSA-2466832 Reactome:R-HSA-5362518 Reactome:R-HSA-5362564 Reactome:R-HSA-5362721 retinol:NAD+ oxidoreductase activity molecular_function MDR GO:0004745 retinol dehydrogenase activity Catalysis of the reaction: retinol + NAD+ = retinal + NADH + H+. EC:1.1.1.105 all-trans retinol dehydrogenase activity EC:1.1.1.105 microsomal retinol dehydrogenase activity EC:1.1.1.105 retinal reductase activity GOC:ecd PMID:12036956 retinene reductase activity EC:1.1.1.105 retinol (vitamin A1) dehydrogenase activity EC:1.1.1.105 Reactome:R-HSA-2454081 RDH5 oxidises 11cROL to 11cRAL Reactome:R-HSA-2466832 Defective RDH5 does not oxidise 11cROL to 11cRAL and causes RPA Reactome:R-HSA-5362518 RDH10,16,DHRS9,RDHE2 oxidise atROL to atRAL Reactome:R-HSA-5362564 ADH1A,1C,4 oxidise atROL to atRAL in vitro Reactome:R-HSA-5362721 RDH5,RDH11 oxidise 11cROL to 11cRAL retinol:NAD+ oxidoreductase activity EC:1.1.1.105 MDR EC:1.1.1.105 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: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. 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:sao1337158144 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 A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus cellular_component GO:0005634 nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. GOC:go_curators horsetail nucleus GOC:al GOC:mah GOC:vw PMID:15030757 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. Wikipedia:Chromosome interphase chromosome prophase chromosome cellular_component chromatid GO:0005694 Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromosome A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. ISBN:0198547684 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. 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. Wikipedia:Vacuole cellular_component vacuolar carboxypeptidase Y GO:0005773 vacuole A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. GOC:mtg_sensu ISBN:0198506732 The volume enclosed within the vacuolar membrane. cellular_component GO:0005775 vacuolar lumen The volume enclosed within the vacuolar membrane. ISBN:0198506732 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. 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 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 A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GO:0072372 FMA:67181 NIF_Subcellular:sao787716553 Wikipedia:Cilium eukaryotic flagellum microtubule-based flagellum primary cilium cellular_component flagellum GO:0005929 Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms. cilium A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GOC:cilia GOC:curators GOC:kmv GOC:vw ISBN:0198547684 PMID:16824949 PMID:17009929 PMID:20144998 The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. Wikipedia:Cell_cortex cellular_component cell periphery peripheral cytoplasm GO:0005938 cell cortex The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. GOC:mah ISBN:0815316194 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GO:0055134 cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process nucleobase, nucleoside and nucleotide metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0006139 nucleobase-containing compound metabolic process Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:ai nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin. GO:0016568 chromatin organisation establishment or maintenance of chromatin architecture biological_process chromatin modification GO:0006325 chromatin organization Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin. GOC:mah GOC:vw PMID:20404130 chromatin organisation GOC:mah establishment or maintenance of chromatin architecture GOC:mah The cellular synthesis of RNA on a template of DNA. GO:0006350 GO:0061018 GO:0061022 cellular transcription transcription Wikipedia:Transcription_(genetics) DNA-dependent transcription cellular transcription, DNA-dependent transcription, DNA-dependent biological_process transcription regulator activity GO:0006351 transcription, DNA-templated The cellular synthesis of RNA on a template of DNA. GOC:jl GOC:txnOH transcription, DNA-dependent GOC:txnOH Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0032583 GO:0045449 GO:0061019 transcriptional control regulation of cellular transcription, DNA-dependent regulation of transcription, DNA-dependent biological_process regulation of gene-specific transcription GO:0006355 regulation of transcription, DNA-templated Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GOC:go_curators GOC:txnOH regulation of transcription, DNA-dependent GOC:txnOH Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II. GO:0006358 GO:0010551 regulation of transcription from Pol II promoter regulation of transcription from RNA polymerase II promoter biological_process global transcription regulation from Pol II promoter regulation of gene-specific transcription from RNA polymerase II promoter regulation of global transcription from Pol II promoter regulation of transcription from RNA polymerase II promoter, global GO:0006357 regulation of transcription by RNA polymerase II Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II. GOC:go_curators GOC:txnOH The synthesis of RNA from a DNA template by RNA polymerase II (RNAP II), originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs). https://github.com/geneontology/go-ontology/issues/14854 GO:0032568 GO:0032569 transcription from Pol II promoter transcription from RNA polymerase II promoter biological_process RNA polymerase II transcription factor activity gene-specific transcription from RNA polymerase II promoter general transcription from RNA polymerase II promoter specific transcription from RNA polymerase II promoter GO:0006366 transcription by RNA polymerase II The synthesis of RNA from a DNA template by RNA polymerase II (RNAP II), originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs). GOC:jl GOC:txnOH ISBN:0321000382 specific transcription from RNA polymerase II promoter GOC:mah The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure. GO:0007022 GO:0007024 GO:0007025 Wikipedia:Protein_folding alpha-tubulin folding beta-tubulin folding chaperonin-mediated tubulin folding biological_process chaperone activity chaperonin ATPase activity co-chaperone activity co-chaperonin activity glycoprotein-specific chaperone activity non-chaperonin molecular chaperone ATPase activity protein complex assembly, multichaperone pathway GO:0006457 protein folding The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure. GOC:go_curators GOC:rb alpha-tubulin folding GOC:mah beta-tubulin folding GOC:mah chaperonin-mediated tubulin folding GOC:mah The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). protein modification process biological_process process resulting in protein modification protein tagging activity GO:0006464 cellular protein modification process The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). GOC:go_curators protein modification process GOC:bf GOC:jl The process of introducing a phosphate group on to a protein. protein amino acid phosphorylation biological_process GO:0006468 protein phosphorylation The process of introducing a phosphate group on to a protein. GOC:hb protein amino acid phosphorylation GOC:bf The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. protein amino acid acetylation biological_process GO:0006473 protein acetylation The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. GOC:ai protein amino acid acetylation GOC:bf The addition of an acetyl group to a non-terminal amino acid in a protein. biological_process GO:0006475 internal protein amino acid acetylation The addition of an acetyl group to a non-terminal amino acid in a protein. GOC:mah The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom. protein amino acid methylation biological_process GO:0006479 protein methylation The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom. GOC:ai protein amino acid methylation GOC:bf The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. Wikipedia:Proteolysis peptidolysis ATP-dependent proteolysis biological_process GO:0006508 This term was intentionally placed under 'protein metabolic process ; GO:0019538' rather than 'protein catabolic process ; GO:0030163' to cover all processes centered on breaking peptide bonds, including those involved in protein processing. proteolysis The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. GOC:bf GOC:mah ATP-dependent proteolysis GOC:mah The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents. amino acid derivative metabolic process cellular amino acid derivative metabolic process cellular amino acid derivative metabolism cellular modified amino acid metabolism modified amino acid metabolic process modified amino acid metabolism biological_process GO:0006575 cellular modified amino acid metabolic process The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents. GOC:ai cellular modified amino acid metabolism GOC:mah modified amino acid metabolic process GOC:mah modified amino acid metabolism GOC:mah The formation of either of the compounds secreted by the thyroid gland, mainly thyroxine and triiodothyronine. This is achieved by the iodination and joining of tyrosine molecules to form the precursor thyroglobin, proteolysis of this precursor gives rise to the thyroid hormones. biological_process GO:0006590 Note that this term does not fall under the general GO definition for biosynthetic processes, which is 'The chemical reactions and pathways resulting in the formation of... ', because thyroid hormones can only be formed by the proteolysis of a larger molecule (see term definition). The word 'generation' is therefore used in place of biosynthesis. thyroid hormone generation The formation of either of the compounds secreted by the thyroid gland, mainly thyroxine and triiodothyronine. This is achieved by the iodination and joining of tyrosine molecules to form the precursor thyroglobin, proteolysis of this precursor gives rise to the thyroid hormones. GOC:jl ISBN:0716720094 The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. aromatic compound metabolism aromatic hydrocarbon metabolic process aromatic hydrocarbon metabolism biological_process GO:0006725 cellular aromatic compound metabolic process The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. GOC:ai ISBN:0198506732 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 chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. nitrogen compound metabolism biological_process GO:0006807 nitrogen compound metabolic process The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. GOC:jl ISBN:0198506732 The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. jl 2012-12-13T16:25:32Z GO:0015457 GO:0015460 GO:0044765 small molecule transport solute:solute exchange biological_process single-organism transport GO:0006810 Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. transport The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. GOC:dos GOC:dph GOC:jl GOC:mah The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0006811 ion transport The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0006819 GO:0015674 di-, tri-valent inorganic cation transport biological_process GO:0006812 cation transport The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai di-, tri-valent inorganic cation transport GOC:mah The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. calcium transport mitochondrial sodium/calcium ion exchange sodium:calcium exchange biological_process GO:0006816 calcium ion transport The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GO:0032779 biological_process copper-induced intracellular protein transport GO:0006886 intracellular protein transport The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GOC:mah copper-induced intracellular protein transport GOC:al The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. biological_process GO:0006903 vesicle targeting The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. GOC:mah PMID:17335816 A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GO:0006917 GO:0008632 cell suicide cellular suicide Wikipedia:Apoptosis apoptotic cell death apoptotic programmed cell death programmed cell death by apoptosis activation of apoptosis apoptosis apoptosis signaling apoptotic program type I programmed cell death biological_process apoptosis activator activity caspase-dependent programmed cell death commitment to apoptosis induction of apoptosis induction of apoptosis by p53 signaling (initiator) caspase activity GO:0006915 apoptotic process A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GOC:cjm GOC:dhl GOC:ecd GOC:go_curators GOC:mtg_apoptosis GOC:tb ISBN:0198506732 PMID:18846107 PMID:21494263 apoptotic cell death GOC:sl apoptotic program GOC:add 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. 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 The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). Wikipedia:Chemotaxis taxis in response to chemical stimulus biological_process GO:0006935 chemotaxis The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). ISBN:0198506732 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). 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 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. 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 cytoskeletal organization and biogenesis GOC:mah cytoskeleton organization and biogenesis GOC:mah Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. biological_process GO:0007017 microtubule-based process Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. GOC:mah A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. biological_process GO:0007018 microtubule-based movement A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. GOC:cjm ISBN:0815316194 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. 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 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart. GO:0043146 spindle organisation biological_process spindle organization and biogenesis spindle stabilization GO:0007051 spindle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart. GOC:go_curators GOC:mah spindle 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 the microtubule spindle during a mitotic cell cycle. https://github.com/geneontology/go-ontology/issues/15341 GO:0000071 GO:0030472 GO:0043148 mitotic spindle organisation spindle organization and biogenesis during mitosis mitotic spindle organisation in nucleus mitotic spindle organization and biogenesis in cell nucleus mitotic spindle organization and biogenesis in nucleus mitotic spindle organization in nucleus spindle organization and biogenesis in nucleus during mitosis biological_process mitotic spindle organization and biogenesis mitotic spindle stabilization GO:0007052 In fission yeast most mitotic spindle organization occurs in the nucleus. mitotic spindle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle. GOC:go_curators GOC:mah mitotic spindle organization and biogenesis GOC:mah The aggregation, arrangement and bonding together of a set of components to form the spindle during a meiotic cell cycle in males. An example of this is found in Drosophila melanogaster. biological_process GO:0007053 spindle assembly involved in male meiosis The aggregation, arrangement and bonding together of a set of components to form the spindle during a meiotic cell cycle in males. An example of this is found in Drosophila melanogaster. GOC:mah 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 A cell cycle process that occurs as part of the male meiotic cell cycle and results in the division of the cytoplasm of a cell to produce two daughter cells. cytokinesis after male meiosis cytokinesis involved in male meiotic cell cycle biological_process GO:0007112 male meiosis cytokinesis A cell cycle process that occurs as part of the male meiotic cell cycle and results in the division of the cytoplasm of a cell to produce two daughter cells. GOC:ai cytokinesis after male meiosis GOC:dph GOC:tb cytokinesis involved in male meiotic cell cycle GOC:dph GOC:tb A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline. male nuclear division biological_process male meiosis GO:0007140 male meiotic nuclear division A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline. GOC:dph GOC:mah GOC:vw 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 attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. dos 2014-04-15T15:59:10Z GO:0098602 Wikipedia:Cell_adhesion biological_process cell adhesion molecule activity single organism cell adhesion GO:0007155 cell adhesion The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. GOC:hb GOC:pf Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns. GO:0030012 GO:0030467 biological_process cell polarity establishment and/or maintenance of cell polarity establishment and/or maintenance of cell polarization GO:0007163 establishment or maintenance of cell polarity Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns. GOC:mah cell polarity GOC:mah GOC:vw Coordinated organization of groups of cells in a tissue, such that they all orient to similar coordinates. biological_process GO:0007164 establishment of tissue polarity Coordinated organization of groups of cells in a tissue, such that they all orient to similar coordinates. GOC:jid 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 A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. cell surface receptor linked signal transduction cell surface receptor linked signaling pathway cell surface receptor linked signalling pathway biological_process GO:0007166 cell surface receptor signaling pathway A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. GOC:bf GOC:mah GOC:pr GOC:signaling cell surface receptor linked signaling pathway GOC:bf cell surface receptor linked signalling pathway GOC:mah Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription. enzyme linked receptor protein signalling pathway biological_process GO:0007167 enzyme linked receptor protein signaling pathway Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription. GOC:mah GOC:signaling ISBN:0815316194 A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription. transmembrane receptor protein tyrosine kinase signalling pathway biological_process GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription. GOC:ceb GOC:signaling A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses serine/threonine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription. transmembrane receptor protein serine/threonine kinase signalling pathway biological_process GO:0007178 transmembrane receptor protein serine/threonine kinase signaling pathway A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses serine/threonine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription. GOC:mah GOC:signaling An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (a MAP3K). The cascade can also contain an additional tier: the upstream MAP4K. The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell. SAPK cascade stress-activated protein kinase cascade c-Jun N-terminal kinase cascade JNK1 cascade JNK2 cascade JNK3 cascade MAPK10 cascade MAPK8 cascade MAPK9 cascade biological_process GO:0007254 JNK cascade An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (a MAP3K). The cascade can also contain an additional tier: the upstream MAP4K. The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell. GOC:bf GOC:signaling PMID:11790549 PMID:20811974 c-Jun N-terminal kinase cascade PMID:20811974 JNK1 cascade GOC:add JNK2 cascade GOC:add JNK3 cascade GOC:add MAPK10 cascade GOC:add MAPK8 cascade GOC:add MAPK9 cascade GOC:add 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 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). 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 The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. GO:0009552 biological_process gametogenesis GO:0007276 gamete generation The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. GOC:ems GOC:mtg_sensu The developmental process by which male germ line stem cells self renew or give rise to successive cell types resulting in the development of a spermatozoa. Wikipedia:Spermatogenesis generation of spermatozoa biological_process GO:0007283 spermatogenesis The developmental process by which male germ line stem cells self renew or give rise to successive cell types resulting in the development of a spermatozoa. GOC:jid ISBN:9780878933846 PMID:28073824 PMID:30990821 generation of spermatozoa The mitotic divisions of the primary spermatogonial cell (a primordial male germ cell) to form secondary spermatogonia (primary spermatocytes). spermatogonium division biological_process GO:0007284 See also the Cell Ontology terms 'spermatogonium ; CL:0000020' and 'primary spermatocyte ; CL:0000656'. spermatogonial cell division The mitotic divisions of the primary spermatogonial cell (a primordial male germ cell) to form secondary spermatogonia (primary spermatocytes). GOC:bf GOC:pr ISBN:0879694238 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 The establishment of an organism's body plan or part of an organism with respect to the left and right halves. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry. determination of left/right asymmetry biological_process GO:0007368 determination of left/right symmetry The establishment of an organism's body plan or part of an organism with respect to the left and right halves. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry. GOC:dph GOC:jid determination of left/right asymmetry GOC:dph 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. 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. 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. 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 De novo generation of a long process of a neuron, including the terminal branched region. Refers to the morphogenesis or creation of shape or form of the developing axon, which carries efferent (outgoing) action potentials from the cell body towards target cells. GO:0007410 axon morphogenesis neuron long process generation axon growth biological_process GO:0007409 Note that 'axonogenesis' differs from 'axon development' in that the latter also covers other processes, such as axon regeneration (regrowth after loss or damage, not necessarily of the whole axon). axonogenesis De novo generation of a long process of a neuron, including the terminal branched region. Refers to the morphogenesis or creation of shape or form of the developing axon, which carries efferent (outgoing) action potentials from the cell body towards target cells. GOC:dph GOC:jid GOC:pg GOC:pr ISBN:0198506732 axon morphogenesis GOC:bf PMID:23517308 neuron long process generation The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues. GO:0008040 Wikipedia:Axon_guidance axon pathfinding axon growth cone guidance biological_process axon chemotaxis GO:0007411 axon guidance The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues. ISBN:0878932437 axon pathfinding GOC:mah 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 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 establishment of the sex of an organism by physical differentiation. 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 jl 2012-09-20T14:06:08Z GO:0023032 GO:0044708 GO:0044709 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 The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes. Wikipedia:Mating_behaviour mating behaviour biological_process GO:0007617 mating behavior The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes. GOC:ai GOC:dph The pairwise union of individuals for the purpose of sexual reproduction, ultimately resulting in the formation of zygotes. biological_process GO:0007618 mating The pairwise union of individuals for the purpose of sexual reproduction, ultimately resulting in the formation of zygotes. GOC:jl ISBN:0387520546 The behavior of an organism for the purpose of attracting sexual partners. courtship behaviour biological_process GO:0007619 courtship behavior The behavior of an organism for the purpose of attracting sexual partners. GOC:ai GOC:dph The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. behavior via locomotion locomotion in response to stimulus locomotory behavioral response to stimulus locomotory behaviour locomotory behavioural response to stimulus biological_process GO:0007626 locomotory behavior The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. GOC:dph Behavior associated with the intake of food. https://github.com/geneontology/go-ontology/issues/18547 jl 2011-10-27T03:53:33Z GO:0044366 GO:0044367 GO:0044368 GO:0044369 GO:0044370 GO:0044371 GO:0044372 MIPS_funcat:36.03 Wikipedia:List_of_feeding_behaviours behavioral response to food behavioural response to food feeding behaviour drinking eating feeding from phloem of other organism feeding from plant phloem feeding from tissue of other organism feeding from vascular tissue of another organism feeding from xylem of other organism feeding on blood of other organism feeding on or from other organism feeding on plant sap hematophagy injection of substance into other organism during feeding on blood of other organism taking of blood meal biological_process GO:0007631 See also the biological process term 'behavior ; GO:0007610'. feeding behavior Behavior associated with the intake of food. GOC:mah The behavior of an organism in response to a visual stimulus. behavioral response to visual stimulus behavioural response to visual stimulus visual behaviour biological_process GO:0007632 visual behavior The behavior of an organism in response to a visual stimulus. GOC:jid GOC:pr The behavior of an organism pertaining to movement of the eyes and of objects in the visual field, as in nystagmus. optokinetic behaviour biological_process GO:0007634 optokinetic behavior The behavior of an organism pertaining to movement of the eyes and of objects in the visual field, as in nystagmus. GOC:jid GOC:pr http://www.mercksource.com Behavior that is dependent upon the sensation of chemicals. behavioral response to chemical stimulus behavioural response to chemical stimulus chemosensory behaviour biological_process GO:0007635 chemosensory behavior Behavior that is dependent upon the sensation of chemicals. GOC:go_curators Behavior that is dependent upon the sensation of a mechanical stimulus. behavioral response to mechanical stimulus behavioural response to mechanical stimulus mechanosensory behaviour biological_process GO:0007638 mechanosensory behavior Behavior that is dependent upon the sensation of a mechanical stimulus. GOC:go_curators The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. GO:0070261 biological_process hemolymph circulation GO:0008015 blood circulation The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. GOC:mtg_heart ISBN:0192800825 Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body. regulation of cardiac contraction biological_process GO:0008016 regulation of heart contraction Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body. GOC:dph GOC:go_curators GOC:tb Any process in which a protein is transported to, or maintained in, a specific location. GO:0008105 protein localisation biological_process asymmetric protein localisation asymmetric protein localization establishment and maintenance of asymmetric protein localization establishment and maintenance of protein localization GO:0008104 protein localization Any process in which a protein is transported to, or maintained in, a specific location. GOC:ai protein localisation GOC:mah asymmetric protein localisation GOC:mah 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 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 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. 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 jl 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 addition of an alkyl group to a protein amino acid. An alkyl group is any group derived from an alkane by removal of one hydrogen atom. protein amino acid alkylation biological_process GO:0008213 protein alkylation The addition of an alkyl group to a protein amino acid. An alkyl group is any group derived from an alkane by removal of one hydrogen atom. GOC:ma protein amino acid alkylation GOC:bf Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). biological_process accidental cell death necrosis GO:0008219 This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term. cell death Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). GOC:mah GOC:mtg_apoptosis PMID:25236395 Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. EC:3.4 Reactome:R-HSA-205112 Reactome:R-HSA-3000243 Reactome:R-HSA-3139027 Reactome:R-HSA-376149 Reactome:R-HSA-448678 Reactome:R-HSA-5655483 Reactome:R-HSA-5684864 Reactome:R-HSA-5685902 Reactome:R-HSA-5693319 hydrolase, acting on peptide bonds peptide hydrolase activity protease activity proteinase activity molecular_function GO:0008233 peptidase activity Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. GOC:jl ISBN:0815332181 Reactome:R-HSA-205112 gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6 Reactome:R-HSA-3000243 Unknown protease degrades GIF:Cbl to release Cbl Reactome:R-HSA-3139027 Maturation of HIV Virion Reactome:R-HSA-376149 Proteolytic processing of SLIT Reactome:R-HSA-448678 CTSG cleaves CASP1(1-404) Reactome:R-HSA-5655483 USP1 autocleavage Reactome:R-HSA-5684864 NAPSA, CTSH, PGA3-5 cleave pro-SFTPB Reactome:R-HSA-5685902 NAPSA, CTSH, PGA3-5 cleave pro-SFTPC Reactome:R-HSA-5693319 CTRC hydrolyses PRSS1 Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. GO:0004220 Reactome:R-HSA-2022381 Reactome:R-HSA-2467775 Reactome:R-HSA-2467809 Reactome:R-HSA-5660752 cysteine protease activity thiol protease activity molecular_function GO:0008234 cysteine-type peptidase activity Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. GOC:mah http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE Reactome:R-HSA-2022381 Cathepsin Z (Cathepsin X) hydrolyzes Angiotensin-(1-10) to Angiotensin-(1-8) Reactome:R-HSA-2467775 Autocleavage of ESPL1 (Separase) Reactome:R-HSA-2467809 ESPL1 (Separase) cleaves centromeric cohesin Reactome:R-HSA-5660752 USP9X deubiquitinates Ub-SNCA 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 The series of molecular signals generated as a consequence of the insulin receptor binding to insulin. insulin receptor signalling pathway daf-2 receptor signaling pathway biological_process GO:0008286 insulin receptor signaling pathway The series of molecular signals generated as a consequence of the insulin receptor binding to insulin. GOC:ceb Any process that modulates the size of a cell. cell size control biological_process GO:0008361 regulation of cell size Any process that modulates the size of a cell. GOC:go_curators The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands. FGF receptor signaling pathway FGF receptor signalling pathway FGFR signaling pathway fibroblast growth factor receptor signalling pathway biological_process GO:0008543 fibroblast growth factor receptor signaling pathway The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands. GOC:ceb The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. jl 2012-10-17T15:52:18Z GO:0044274 GO:0044711 formation Wikipedia:Anabolism anabolism biosynthesis synthesis multicellular organismal biosynthetic process biological_process single-organism biosynthetic process GO:0009058 biosynthetic process The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis macromolecule formation macromolecule synthesis biological_process GO:0009059 macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:mah biopolymer biosynthetic process GOC:mtg_chebi_dec09 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 electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation. MIPS_funcat:32.01.13 response to electromagnetic radiation stimulus response to radiation stimulus biological_process GO:0009314 Note that 'radiation' refers to electromagnetic radiation of any wavelength. response to radiation 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 electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation. GOC:jl Wikipedia:Electromagnetic_radiation 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 light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light. MIPS_funcat:34.11.01 MIPS_funcat:34.11.01.01 MIPS_funcat:36.20.35.11 biological_process GO:0009416 response to light 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 a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light. GOC:go_curators ISBN:0582227089 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 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 mechanical stimulus. MIPS_funcat:34.11.05 MIPS_funcat:36.20.35.15 mechanical stimulus response biological_process chemi-mechanical coupling GO:0009612 response to mechanical 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 a mechanical 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 an abiotic (not derived from living organisms) stimulus. https://github.com/geneontology/go-ontology/issues/16572 response to abiotic stress biological_process GO:0009628 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. 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. Changed definition as requested in https://github.com/geneontology/go-ontology/issues/16572. response to abiotic 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 abiotic (not derived from living organisms) stimulus. GOC:hb 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 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 arising within the organism. biological_process GO:0009719 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 endogenous 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 a stimulus arising within the organism. GOC:sm 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 hormone stimulus. response to hormone stimulus biological_process growth regulator GO:0009725 response to hormone 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 hormone stimulus. GOC:jl response to hormone stimulus GOC:dos The series of events in which an endogenous stimulus is received by a cell and converted into a molecular signal. biological_process perception of endogenous stimulus GO:0009726 detection of endogenous stimulus The series of events in which an endogenous stimulus is received by a cell and converted into a molecular signal. GOC:sm 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 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. 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 establishment of an organism's body plan or part of an organism such that a similar arrangement in form and relationship of parts around a common axis, or around each side of a plane is created. determination of symmetry biological_process GO:0009799 specification of symmetry The establishment of an organism's body plan or part of an organism such that a similar arrangement in form and relationship of parts around a common axis, or around each side of a plane is created. GOC:go_curators determination of symmetry GOC:dph The establishment of an organism's body plan or part of an organism with respect to a single longitudinal plane. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry. determination of bilateral asymmetry biological_process GO:0009855 determination of bilateral symmetry The establishment of an organism's body plan or part of an organism with respect to a single longitudinal plane. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry. GOC:go_curators determination of bilateral asymmetry GOC:dph Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. histogenesis and organogenesis biological_process GO:0009887 animal organ morphogenesis Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GOC:dgh GOC:go_curators ISBN:0471245208 ISBN:0721662544 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 modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. regulation of anabolism regulation of biosynthesis regulation of formation regulation of synthesis biological_process GO:0009889 regulation of biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. positive regulation of anabolism positive regulation of biosynthesis positive regulation of formation positive regulation of synthesis up regulation of biosynthetic process up-regulation of biosynthetic process upregulation of biosynthetic process activation of biosynthetic process stimulation of biosynthetic process biological_process GO:0009891 positive regulation of biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators 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. 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. 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 jl 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 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 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 organic substance stimulus. GO:1990367 process resulting in tolerance to organic substance biological_process GO:0010033 response to organic substance 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 organic substance stimulus. GOC:sm PMID:23356676 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 organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond. response to organic nitrogen biological_process GO:0010243 response to organonitrogen compound 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 organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond. PMID:9869419 The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. Wikipedia:Gene_expression biological_process GO:0010467 gene expression The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. Wikipedia:Regulation_of_gene_expression regulation of protein expression biological_process regulation of gene product expression GO:0010468 This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation. regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. 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 modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010556 regulation of macromolecule biosynthetic process Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010557 positive regulation of macromolecule biosynthetic process Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. 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 the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010604 positive regulation of macromolecule metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb The activation of endogenous cellular processes that result in the death of a cell as part of its development. developmental programmed cell death programmed cell death involved in development biological_process GO:0010623 This process is part of the natural developmental program of some cell types, but it does not always happen as part of the development or shaping of a gross anatomical structure. programmed cell death involved in cell development The activation of endogenous cellular processes that result in the death of a cell as part of its development. GOC:dph GOC:mtg_apoptosis GOC:tb Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. biological_process GO:0010628 positive regulation of gene expression Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. 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 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