XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.
Xenopus Phenotype Ontology
2021-03-05
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
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
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
dos
2017-09-17T13:52:24Z
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
directly regulated by
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
GOC:dos
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
dos
2017-09-17T13:52:38Z
directly negatively regulated by
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
GOC:dos
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
dos
2017-09-17T13:52:47Z
directly positively regulated by
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
GOC:dos
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
dos
2017-09-22T14:14:36Z
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
GOC:dos
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
David Osumi-Sutherland
starts_at_end_of
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
RO:0002087
directly preceded by
is directly preceded by
is immediately preceded by
starts_at_end_of
uberon
immediately_preceded_by
immediately_preceded_by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
immediately_preceded_by
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
SIO:000251
is immediately preceded by
SIO:000251
David Osumi-Sutherland
ends_at_start_of
meets
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
true
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
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)
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
Chris Mungall
has function in
RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
capable of part of
true
Chris Mungall
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
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
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
Chris Mungall
false
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
Chris Mungall
actively involved in
enables part of
involved in
inverse of enables
Chris Mungall
enabled by
inverse of regulates
Chris Mungall
regulated by (processual)
regulated by
inverse of negatively regulates
Chris Mungall
negatively regulated by
inverse of positively regulates
Chris Mungall
positively regulated by
inverse of has input
Chris Mungall
input of
inverse of upstream of
Chris Mungall
causally downstream of
Chris Mungall
immediately causally downstream of
This relation groups causal relations between material entities and causal relations between processes
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
Chris Mungall
immediately causally upstream of
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
affects
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
Chris Mungall
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
Chris Mungall
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
Chris Mungall
involved in negative regulation of
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
Chris Mungall
involved in or reguates
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
Chris Mungall
executes activity in
enables activity in
is active in
true
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
GOC:cjm
GOC:dos
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Chris Mungall
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/MI_0914
https://github.com/oborel/obo-relations/wiki/InteractionRelations
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
Chris Mungall
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
Axiomatization to GO to be added later
Chris Mungall
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
Chris Mungall
Vasundra Touré
molecularly controls
directly regulates activity of
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly inhibits
molecularly decreases activity of
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly activates
molecularly increases activity of
directly positively regulates activity of
Chris Mungall
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
Chris Mungall
has part that occurs in
true
Chris Mungall
is kinase activity
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
Chris Mungall
causally influenced by (entity-centric)
causally influenced by
Chris Mungall
interaction relation helper property
https://github.com/oborel/obo-relations/wiki/InteractionRelations
Chris Mungall
molecular interaction relation helper property
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
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
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
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II.
GO:0010553
GO:0045816
down regulation of transcription from RNA polymerase II promoter
down-regulation of transcription from RNA polymerase II promoter
downregulation of transcription from RNA polymerase II promoter
inhibition of transcription from RNA polymerase II promoter
negative regulation of transcription from Pol II promoter
negative regulation of transcription from RNA polymerase II promoter
biological_process
down regulation of global transcription from RNA polymerase II promoter
down-regulation of global transcription from RNA polymerase II promoter
downregulation of global transcription from RNA polymerase II promoter
inhibition of global transcription from RNA polymerase II promoter
negative regulation of gene-specific transcription from RNA polymerase II promoter
negative regulation of global transcription from Pol II promoter
negative regulation of transcription from RNA polymerase II promoter, global
GO:0000122
negative regulation of transcription by RNA polymerase II
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II.
GOC:go_curators
GOC:txnOH
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 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
Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.
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:0000789
GO:0000790
GO:0005717
NIF_Subcellular:sao1615953555
cytoplasmic chromatin
nuclear chromatin
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 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
A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
biological_process
GO:0001775
cell activation
A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
GOC:mgi_curators
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 stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
down regulation of protein amino acid phosphorylation
down-regulation of protein amino acid phosphorylation
downregulation of protein amino acid phosphorylation
negative regulation of protein amino acid phosphorylation
inhibition of protein amino acid phosphorylation
biological_process
GO:0001933
negative regulation of protein phosphorylation
Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
GOC:hjd
negative 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
Any process that decreases 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
2009-10-22T12:36:11Z
negative regulation of Wnt receptor signaling pathway involved in heart development
negative regulation of Wnt receptor signalling pathway involved in heart development
negative regulation of Wnt-activated signaling pathway involved in heart development
biological_process
GO:0003308
negative regulation of Wnt signaling pathway involved in heart development
Any process that decreases 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
negative regulation of Wnt receptor signalling pathway involved in heart development
GOC:mah
negative 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.
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
Reactome:R-HSA-9670149
Reactome:R-HSA-9697084
Reactome:R-HSA-9697085
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
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
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
Reactome:R-HSA-9670149
TERRA transcription
Reactome:R-HSA-9697084
Defective rpoB in Mtb RNAP transcribes RNA polyanion
Reactome:R-HSA-9697085
RNAP transcribes Mtb RNA polyanion
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
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
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
GO:0016809
EC:3.4.99.-
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-9614271
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-9614271
Autocleavage of ADGRG6
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.-
EC:3.4.22.1
EC:3.4.22.14
EC:3.4.22.15
EC:3.4.22.16
EC:3.4.22.27
EC:3.4.22.28
EC:3.4.22.34
EC:3.4.22.38
EC:3.4.22.40
EC:3.4.22.41
EC:3.4.22.8
MetaCyc:3.4.22.1-RXN
MetaCyc:3.4.22.14-RXN
MetaCyc:3.4.22.15-RXN
MetaCyc:3.4.22.16-RXN
MetaCyc:3.4.22.27-RXN
MetaCyc:3.4.22.34-RXN
MetaCyc:3.4.22.38-RXN
MetaCyc:3.4.22.40-RXN
MetaCyc:3.4.22.41-RXN
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
Reactome:R-HSA-9647999
Reactome:R-HSA-9684273
Reactome:R-HSA-9684309
Reactome:R-HSA-9684321
Reactome:R-HSA-9684336
Reactome:R-HSA-9684340
Reactome:R-HSA-9684351
Reactome:R-HSA-9684352
Reactome:R-HSA-9686930
Reactome:R-HSA-9693929
Reactome:R-HSA-9694338
Reactome:R-HSA-9694377
Reactome:R-HSA-9694441
Reactome:R-HSA-9694551
Reactome:R-HSA-9694601
Reactome:R-HSA-9694625
Reactome:R-HSA-9694732
Reactome:R-HSA-9697750
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
https://www.ebi.ac.uk/merops/about/glossary.shtml#CATTYPE
https://www.ebi.ac.uk/merops/about/glossary.shtml#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
RIPK1 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
Reactome:R-HSA-9647999
RCE1 cleaves S-Farn proRAS proteins
Reactome:R-HSA-9684273
3CLp cleaves pp1a
Reactome:R-HSA-9684309
3CLp cleaves nsp6-11
Reactome:R-HSA-9684321
nsp3 cleaves nsp1-4
Reactome:R-HSA-9684336
nsp1-4 cleaves itself
Reactome:R-HSA-9684340
3CLp cleaves pp1ab
Reactome:R-HSA-9684351
pp1a cleaves itself
Reactome:R-HSA-9684352
nsp3-4 cleaves itself
Reactome:R-HSA-9686930
RIPK3 is cleaved by CASP8
Reactome:R-HSA-9693929
RIPK1 variant is not cleaved by CASP8
Reactome:R-HSA-9694338
nsp1-4 cleaves itself
Reactome:R-HSA-9694377
pp1a cleaves itself
Reactome:R-HSA-9694441
3CLp cleaves pp1a
Reactome:R-HSA-9694551
3CLp cleaves nsp6-11
Reactome:R-HSA-9694601
nsp3-4 cleaves itself
Reactome:R-HSA-9694625
nsp3 cleaves nsp1-4
Reactome:R-HSA-9694732
3CLp cleaves pp1ab
Reactome:R-HSA-9697750
RIPK1 is cleaved by CASP8:FLIP(L)
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-9673284
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-9673284
GTP-bound RAC1 contributes to MAPK8 activation
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
EC:2.7.11.-
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-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-8868118
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-9610153
Reactome:R-HSA-9610156
Reactome:R-HSA-9610163
Reactome:R-HSA-9612501
Reactome:R-HSA-9612509
Reactome:R-HSA-9612980
Reactome:R-HSA-9613530
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-9633008
Reactome:R-HSA-9633742
Reactome:R-HSA-9634702
Reactome:R-HSA-9645535
Reactome:R-HSA-9648089
Reactome:R-HSA-9648883
Reactome:R-HSA-9648888
Reactome:R-HSA-9652165
Reactome:R-HSA-9653503
Reactome:R-HSA-9656214
Reactome:R-HSA-9656215
Reactome:R-HSA-9662823
Reactome:R-HSA-9673346
Reactome:R-HSA-9681627
Reactome:R-HSA-9683664
Reactome:R-HSA-9694293
Reactome:R-HSA-9694620
Reactome:R-HSA-9699579
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 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
protein serine-threonine kinase activity
serine(threonine) protein kinase activity
serine/threonine protein kinase activity
GO:0004674
protein serine/threonine kinase activity
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
Reactome:R-HSA-9604328
AKT1 phosphorylates NOTCH4
Reactome:R-HSA-9610153
Activated BRAF phosphorylates MAP2K dimers downstream of RAP1 and NGF
Reactome:R-HSA-9610156
MAP2Ks phosphorylate MAPKs downstream of BRAF and NGF
Reactome:R-HSA-9610163
BRAF autophosphorylates downstream of RAP1 and NGF
Reactome:R-HSA-9612501
SGK phosphorylates CREB1
Reactome:R-HSA-9612509
SGK phosphorylates SRF
Reactome:R-HSA-9612980
BRAF in Rap1-GTP complex:BRAF complex autophosphorylates
Reactome:R-HSA-9613530
PRKAA2 phosphorylates PLINs
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-9633008
p-T899-EIF2AK4 (GCN2) phosphorylates EIF2AS1
Reactome:R-HSA-9633742
EIF2AK4 (GCN2) dimer autophosphorylates
Reactome:R-HSA-9634702
LINC01139 promotes phosphorylation of HIF1A by LRRK2
Reactome:R-HSA-9645535
ALPK1 phosphorylates TIFA
Reactome:R-HSA-9648089
NEK6 and NEK7 phosphorylate EML4
Reactome:R-HSA-9648883
p-T-EIF2AK1:ferriheme dimer autophosphorylates
Reactome:R-HSA-9648888
p-T,T486,T488-EIF2AK1 phosphorylates EIF2S1 (eIF2-alpha)
Reactome:R-HSA-9652165
MAP2K mutants constitutively phosphorylate MAPKs
Reactome:R-HSA-9653503
KRAS4B is phosphorylated on serine 181
Reactome:R-HSA-9656214
MAP2Ks phosphorylate MAPKs downstream of RAF1 mutants
Reactome:R-HSA-9656215
RAF1 mutant complexes phosphorylate MAP2K dimer
Reactome:R-HSA-9662823
PLK2, MAPK14 phosphorylate ADAM17
Reactome:R-HSA-9673346
Unknown kinase phosphorylates p-DVL
Reactome:R-HSA-9681627
GSK3 phosphorylates N
Reactome:R-HSA-9683664
GSK3B phosphorylates Ncap
Reactome:R-HSA-9694293
GSK3B phosphorylates Ncap
Reactome:R-HSA-9694620
GSK3 phosphorylates N
Reactome:R-HSA-9699579
AKT phosphorylates FOXO3 downstream of FLT3
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 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
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
Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
GOC:bf
PMID:2956925
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
PLK1 phosphorylates NUDC
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:BECN1 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-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-8868118
MAPK12 phosphorylates PTPN3
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
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
ERK1
mitogen activated 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
ATP:protein phosphotransferase (MAPKK-activated) activity
ERK
ERK2
MAPK
mitogen-activated protein kinase activity
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
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
ATP:protein phosphotransferase (MAPKK-activated) activity
EC:2.7.11.24
ERK
EC:2.7.11.24
MAPK
EC:2.7.11.24
PMID:20811974
mitogen-activated protein kinase activity
EC:2.7.11.24
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
molecular_function
MDR
retinol:NAD+ oxidoreductase activity
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
MDR
EC:1.1.1.105
retinol:NAD+ oxidoreductase activity
EC:1.1.1.105
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.
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
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.
https://github.com/geneontology/go-ontology/issues/17776
Wikipedia:Intracellular
internal to cell
intracellular
protoplasm
cellular_component
nucleocytoplasm
protoplast
GO:0005622
intracellular anatomical structure
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.
ISBN:0198506732
nucleocytoplasm
GOC:mah
protoplast
GOC:mah
A 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
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
Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
down regulation of protein kinase activity
down-regulation of protein kinase activity
downregulation of protein kinase activity
inhibition of protein kinase activity
biological_process
GO:0006469
negative regulation of protein kinase activity
Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
GOC:go_curators
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.
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
GO:0072512
di-, tri-valent inorganic cation transport
trivalent 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 anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GO:0006822
biological_process
GO:0006820
anion transport
The directed movement of anions, atoms or small molecules with a net negative charge, 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 process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
down regulation of cell adhesion
down-regulation of cell adhesion
downregulation of cell adhesion
inhibition of cell adhesion
biological_process
cell adhesion receptor inhibitor activity
GO:0007162
negative regulation of cell adhesion
Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
GOC:go_curators
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:0023014
GO:0023015
GO:0023016
GO:0023033
GO:0023045
Wikipedia:Signal_transduction
signal transduction by cis-phosphorylation
signal transduction by conformational transition
signal transduction by protein phosphorylation
signal transduction by trans-phosphorylation
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
The union of male and female gametes to form a zygote.
biological_process
zygote biosynthesis
zygote formation
GO:0007338
single fertilization
The union of male and female gametes to form a zygote.
GOC:ems
GOC:mtg_sensu
The process in which the egg becomes metabolically active, initiates protein and DNA synthesis and undergoes structural changes to its cortex and/or cytoplasm.
Wikipedia:Egg_activation
biological_process
GO:0007343
egg activation
The process in which the egg becomes metabolically active, initiates protein and DNA synthesis and undergoes structural changes to its cortex and/or cytoplasm.
GOC:bf
PMID:9630751
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
A biological process in which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's form or structure. Examples include the change from tadpole to frog, and the change from larva to adult. An example of this is found in Drosophila melanogaster.
GO:0046698
GO:0046699
Wikipedia:Metamorphosis
biological_process
GO:0007552
metamorphosis
A biological process in which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's form or structure. Examples include the change from tadpole to frog, and the change from larva to adult. An example of this is found in Drosophila melanogaster.
GOC:sensu
ISBN:0198506732
ISBN:0721662544
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.
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
Wikipedia:List_of_feeding_behaviours
behavioral response to food
behavioural response to food
feeding behaviour
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
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.
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.
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.
jl
2012-10-17T15:46:40Z
GO:0044236
GO:0044710
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.
GO:0070010
GO:0070011
EC:3.4.-.-
Reactome:R-HSA-205112
Reactome:R-HSA-3000243
Reactome:R-HSA-3065958
Reactome:R-HSA-3065959
Reactome:R-HSA-3139027
Reactome:R-HSA-376149
Reactome:R-HSA-4167501
Reactome:R-HSA-448678
Reactome:R-HSA-5655483
Reactome:R-HSA-5684864
Reactome:R-HSA-5685902
Reactome:R-HSA-5693319
Reactome:R-HSA-6803060
hydrolase, acting on peptide bonds
peptide hydrolase activity
protease activity
peptidase activity, acting on D-amino acid peptides
peptidase activity, acting on L-amino acid peptides
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-3065958
An unknown protease degrades ACACA
Reactome:R-HSA-3065959
An unknown protease degrades hCBXs
Reactome:R-HSA-3139027
Maturation of HIV Virion
Reactome:R-HSA-376149
Proteolytic processing of SLIT
Reactome:R-HSA-4167501
An unknown protease degrades ACACB
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
Reactome:R-HSA-6803060
DCD(63-110) is processed to DCD(63-109)
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
https://www.ebi.ac.uk/merops/about/glossary.shtml#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
Any process that stops, prevents or reduces the rate or extent of cell proliferation.
down regulation of cell proliferation
down-regulation of cell proliferation
downregulation of cell proliferation
inhibition of cell proliferation
biological_process
negative regulation of cell proliferation
GO:0008285
negative regulation of cell population proliferation
Any process that stops, prevents or reduces the rate or extent of cell proliferation.
GOC:go_curators
The 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.
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.
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
The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
https://github.com/geneontology/go-ontology/issues/20176
Wikipedia:Fertilisation
syngamy
biological_process
GO:0009566
fertilization
The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
GOC:tb
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 an external stimulus.
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.
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.
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 stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances.
down regulation of biosynthetic process
down-regulation of biosynthetic process
downregulation of biosynthetic process
negative regulation of anabolism
negative regulation of biosynthesis
negative regulation of formation
negative regulation of synthesis
inhibition of biosynthetic process
biological_process
GO:0009890
negative regulation of biosynthetic process
Any process that stops, prevents, or reduces the rate 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.
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
Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
biological_process
GO:0010466
negative regulation of peptidase activity
Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
GOC:dph
GOC:tb
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 p