None
Pattern Test Ontology - Matching Pipeline
2022-11-18
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
description
license
title
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
BFO:0000050
external
quality
uberon
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)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
BFO:0000051
external
quality
uberon
has_part
has_part
has part
has part
has_part
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
BFO:0000062
external
uberon
preceded_by
preceded_by
preceded by
preceded by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
BFO:0000063
external
uberon
precedes
precedes
precedes
precedes
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
RO:0000053
external
bearer_of
bearer_of
bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
RO:0000056
external
uberon
participates_in
participates_in
participates in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
RO:0000057
external
has_participant
has_participant
has participant
has participant
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
RO:0000086
uberon
has_quality
has_quality
has quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
disposition of
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
dos
2017-05-24T09:30:46Z
RO:0002013
external
has_regulatory_component_activity
has_regulatory_component_activity
has regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
dos
2017-05-24T09:31:01Z
RO:0002014
external
has_negative_regulatory_component_activity
has_negative_regulatory_component_activity
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
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
David Osumi-Sutherland
starts_at_end_of
RO:0002087
external
uberon
immediately_preceded_by
immediately_preceded_by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
immediately preceded by
David Osumi-Sutherland
ends_at_start_of
meets
RO:0002090
external
immediately_precedes
immediately_precedes
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
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)
RO:0002131
external
uberon
overlaps
overlaps
overlaps
overlaps
true
lactation SubClassOf 'only in taxon' some 'Mammalia'
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.
'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
Chris Mungall
RO:0002160
uberon
only_in_taxon
only_in_taxon
only in taxon
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Chris Mungall
Jennifer Deegan
RO:0002162
uberon
in_taxon
in_taxon
Connects a biological entity to its taxon of origin.
in taxon
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO:0002180
external
uberon
has_component
has_component
has component
has component
p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
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
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
Chris Mungall
negatively regulates (process to process)
RO:0002212
external
negatively_regulates
negatively_regulates
negatively regulates
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
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:0002215
external
uberon
capable_of
capable_of
capable of
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
Chris Mungall
has function in
RO:0002216
external
uberon
capable_of_part_of
capable_of_part_of
capable of part of
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
inverse of starts with
Chris Mungall
Allen
RO:0002223
uberon
starts
starts
starts
starts
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Chris Mungall
started by
RO:0002224
external
uberon
starts_with
starts_with
starts with
starts with
inverse of ends with
Chris Mungall
RO:0002229
uberon
ends
ends
ends
ends
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Chris Mungall
finished by
RO:0002230
external
uberon
ends_with
ends_with
ends with
ends with
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
Chris Mungall
consumes
RO:0002233
external
has_input
has_input
has input
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
Chris Mungall
produces
RO:0002234
external
has_output
has_output
has output
has output
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
RO:0002295
external
results_in_developmental_progression_of
results_in_developmental_progression_of
results in developmental progression of
results in developmental progression of
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
Chris Mungall
GOC:mtg_berkeley_2013
RO:0002297
external
results_in_formation_of
results_in_formation_of
results in formation of
results in formation of
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
cjm
RO:0002304
external
causally_upstream_of,_positive_effect
causally_upstream_of,_positive_effect
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
causally upstream of, positive effect
p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
cjm
RO:0002305
external
causally_upstream_of,_negative_effect
causally_upstream_of,_negative_effect
causally upstream of, negative effect
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
Chris Mungall
inheres in part of
characteristic of part of
true
A relationship that holds via some environmental process
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
evolutionarily related to
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
c enables p iff c is capable of p and c acts to execute p.
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.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
RO:0002328
uberon
functionally_related_to
functionally_related_to
functionally related to
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
Chris Mungall
false
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)
RO:0002334
external
regulated_by
regulated_by
regulated by
regulated by
inverse of negatively regulates
Chris Mungall
RO:0002335
external
negatively_regulated_by
negatively_regulated_by
negatively regulated by
negatively regulated by
inverse of positively regulates
Chris Mungall
RO:0002336
external
positively_regulated_by
positively_regulated_by
positively regulated by
positively regulated by
inverse of has input
Chris Mungall
RO:0002352
uberon
input_of
input_of
input of
input of
inverse of has output
Chris Mungall
RO:0002353
external
uberon
output_of
output_of
output of
output of
Chris Mungall
formed as result of
inverse of upstream of
Chris Mungall
RO:0002404
external
causally_downstream_of
causally_downstream_of
causally downstream of
causally downstream of
Chris Mungall
RO:0002405
external
immediately_causally_downstream_of
immediately_causally_downstream_of
immediately causally downstream of
immediately causally downstream of
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
Chris Mungall
indirectly activates
indirectly positively regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
Chris Mungall
indirectly inhibits
indirectly negatively regulates
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative?
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
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
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
https://en.wikipedia.org/wiki/Causality
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
Chris Mungall
RO:0002411
external
causally_upstream_of
causally_upstream_of
causally upstream of
causally upstream of
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
Chris Mungall
RO:0002412
external
immediately_causally_upstream_of
immediately_causally_upstream_of
immediately causally upstream of
immediately causally upstream of
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
RO:0002418
external
affects
causally_upstream_of_or_within
causally_upstream_of_or_within
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
RO:0002427
external
causally_downstream_of_or_within
causally_downstream_of_or_within
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
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 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/ro/docs/interaction-relations/
http://purl.obolibrary.org/obo/MI_0914
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
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)
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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
Chris Mungall
depends on
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between entities
Chris Mungall
causally influenced by (entity-centric)
causally influenced by
Chris Mungall
interaction relation helper property
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
Chris Mungall
molecular interaction relation helper property
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
Chris Mungall
Vasundra Touré
causally influences (entity-centric)
causally influences
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
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
p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p
results in breakdown of
RO:0002588
external
results_in_assembly_of
results_in_assembly_of
results in assembly of
RO:0002590
external
results_in_disassembly_of
results_in_disassembly_of
results in disassembly of
p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
RO:0002592
external
results_in_organization_of
results_in_organization_of
results in organization 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'
RO:0002608
external
process_has_causal_agent
process_has_causal_agent
process has causal agent
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
directly positively regulates
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
directly negatively regulates
p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
cjm
2018-12-13T11:26:17Z
RO:0004007
external
has_primary_input_or_output
has_primary_input_or_output
has primary input or output
p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
cjm
2018-12-13T11:26:32Z
RO:0004008
external
has_primary_output
has_primary_output
has primary output
p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
GOC:cjm
GOC:dph
GOC:kva
GOC:pt
PMID:27812932
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 is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
pg
2022-09-26T06:07:17Z
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
pg
2022-09-26T06:08:01Z
indirectly regulates
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
https://orcid.org/0000-0001-9625-1899
https://orcid.org/0000-0003-2620-0345
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
2021-11-08T12:00:00Z
utilizes
device utilizes material
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
RO:0019000
gene_ontology
regulates_characteristic
regulates_characteristic
regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
RO:0019001
gene_ontology
positively_regulates_characteristic
positively_regulates_characteristic
positively regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
RO:0019002
gene_ontology
negatively_regulates_characteristic
negatively_regulates_characteristic
negatively regulates characteristic
p has anatomical participant c iff p has participant c, and c is an anatomical entity
cjm
2018-09-26T01:08:58Z
RO:0040036
external
results_in_changes_to_anatomical_or_cellular_structure
results_in_changes_to_anatomical_or_cellular_structure
results in changes to anatomical or cellular structure
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.
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
disposition
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
realizable entity
quality
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.
specifically dependent continuant
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
role
function
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.
-1
0.000548579903
0.0
KEGG:C05359
PMID:21614077
Wikipedia:Electron
electron
chebi_ontology
Elektron
beta
beta(-)
beta-particle
e
e(-)
e-
negatron
CHEBI:10545
electron
PMID:21614077
Europe PMC
electron
ChEBI
electron
IUPAC
electron
KEGG_COMPOUND
Elektron
ChEBI
beta
IUPAC
beta(-)
ChEBI
beta-particle
IUPAC
e
IUPAC
e(-)
UniProt
e-
KEGG_COMPOUND
negatron
IUPAC
Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).
Wikipedia:https://en.wikipedia.org/wiki/Gas
chebi_ontology
gas molecular entities
gaseous molecular entities
gaseous molecular entity
CHEBI:138675
gas molecular entity
gas molecular entities
ChEBI
gaseous molecular entities
ChEBI
gaseous molecular entity
ChEBI
-1
CH2NO2
InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1
KXDHJXZQYSOELW-UHFFFAOYSA-M
60.03212
60.00910
NC([O-])=O
Beilstein:3903503
CAS:302-11-4
Gmelin:239604
carbamate
chebi_ontology
Carbamat
Karbamat
carbamate ion
carbamic acid, ion(1-)
CHEBI:13941
carbamate
Beilstein:3903503
Beilstein
CAS:302-11-4
ChemIDplus
Gmelin:239604
Gmelin
carbamate
IUPAC
carbamate
UniProt
Carbamat
ChEBI
Karbamat
ChEBI
carbamate ion
ChemIDplus
carbamic acid, ion(1-)
ChemIDplus
A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
CHEBI:13699
CHEBI:2377
KEGG:C00028
KEGG:C16722
Acceptor
chebi_ontology
A
Akzeptor
Hydrogen-acceptor
Oxidized donor
accepteur
CHEBI:15339
acceptor
Acceptor
KEGG_COMPOUND
A
KEGG_COMPOUND
Akzeptor
ChEBI
Hydrogen-acceptor
KEGG_COMPOUND
Oxidized donor
KEGG_COMPOUND
accepteur
ChEBI
A peptide containing ten or more amino acid residues.
C4H6N2O3R2(C2H2NOR)n
CHEBI:14860
CHEBI:8314
KEGG:C00403
Polypeptide
polypeptides
chebi_ontology
Polypeptid
polipeptido
CHEBI:15841
polypeptide
Polypeptide
KEGG_COMPOUND
polypeptides
IUPAC
Polypeptid
ChEBI
polipeptido
ChEBI
A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues.
0
(C5H8O6PR)n.C10H17O10PR2
CHEBI:13672
CHEBI:14859
CHEBI:8312
KEGG:C00419
Polynucleotide
chebi_ontology
polynucleotides
CHEBI:15986
polynucleotide
Polynucleotide
KEGG_COMPOUND
polynucleotides
ChEBI
An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.
0
H3N
InChI=1S/H3N/h1H3
QGZKDVFQNNGYKY-UHFFFAOYSA-N
17.03056
17.02655
[H]N([H])[H]
CHEBI:13405
CHEBI:13406
CHEBI:13407
CHEBI:13771
CHEBI:22533
CHEBI:44269
CHEBI:44284
CHEBI:44404
CHEBI:7434
Beilstein:3587154
CAS:7664-41-7
Drug_Central:4625
Gmelin:79
HMDB:HMDB0000051
KEGG:C00014
KEGG:D02916
KNApSAcK:C00007267
MetaCyc:AMMONIA
MolBase:930
PDBeChem:NH3
PMID:110589
PMID:11139349
PMID:11540049
PMID:11746427
PMID:11783653
PMID:13753780
PMID:14663195
PMID:15092448
PMID:15094021
PMID:15554424
PMID:15969015
PMID:16008360
PMID:16050680
PMID:16348008
PMID:16349403
PMID:16614889
PMID:16664306
PMID:16842901
PMID:17025297
PMID:17439666
PMID:17569513
PMID:17737668
PMID:18670398
PMID:22002069
PMID:22081570
PMID:22088435
PMID:22100291
PMID:22130175
PMID:22150211
PMID:22240068
PMID:22290316
PMID:22342082
PMID:22385337
PMID:22443779
PMID:22560242
Reaxys:3587154
Wikipedia:Ammonia
AMMONIA
Ammonia
ammonia
azane
chebi_ontology
Ammoniak
NH3
R-717
[NH3]
ammoniac
amoniaco
spirit of hartshorn
CHEBI:16134
ammonia
Beilstein:3587154
Beilstein
CAS:7664-41-7
ChemIDplus
CAS:7664-41-7
KEGG COMPOUND
CAS:7664-41-7
NIST Chemistry WebBook
Drug_Central:4625
DrugCentral
Gmelin:79
Gmelin
PMID:110589
Europe PMC
PMID:11139349
Europe PMC
PMID:11540049
Europe PMC
PMID:11746427
Europe PMC
PMID:11783653
Europe PMC
PMID:13753780
Europe PMC
PMID:14663195
Europe PMC
PMID:15092448
Europe PMC
PMID:15094021
Europe PMC
PMID:15554424
Europe PMC
PMID:15969015
Europe PMC
PMID:16008360
Europe PMC
PMID:16050680
Europe PMC
PMID:16348008
Europe PMC
PMID:16349403
Europe PMC
PMID:16614889
Europe PMC
PMID:16664306
Europe PMC
PMID:16842901
Europe PMC
PMID:17025297
Europe PMC
PMID:17439666
Europe PMC
PMID:17569513
Europe PMC
PMID:17737668
Europe PMC
PMID:18670398
Europe PMC
PMID:22002069
Europe PMC
PMID:22081570
Europe PMC
PMID:22088435
Europe PMC
PMID:22100291
Europe PMC
PMID:22130175
Europe PMC
PMID:22150211
Europe PMC
PMID:22240068
Europe PMC
PMID:22290316
Europe PMC
PMID:22342082
Europe PMC
PMID:22385337
Europe PMC
PMID:22443779
Europe PMC
PMID:22560242
Europe PMC
Reaxys:3587154
Reaxys
AMMONIA
PDBeChem
Ammonia
KEGG_COMPOUND
ammonia
IUPAC
azane
IUPAC
Ammoniak
ChemIDplus
NH3
IUPAC
NH3
KEGG_COMPOUND
NH3
UniProt
R-717
ChEBI
[NH3]
MolBase
ammoniac
ChEBI
amoniaco
ChEBI
spirit of hartshorn
ChemIDplus
A naturally occurring polypeptide synthesized at the ribosome.
CHEBI:8526
KEGG:C00017
chebi_ontology
Protein
a protein
polypeptide chain
protein polypeptide chains
CHEBI:16541
protein polypeptide chain
Protein
KEGG_COMPOUND
a protein
UniProt
polypeptide chain
ChEBI
protein polypeptide chains
ChEBI
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
0
(C2H2NOR)nC2H3NOR
CHEBI:14753
CHEBI:25906
CHEBI:7990
KEGG:C00012
Peptide
peptides
chebi_ontology
Peptid
peptido
peptidos
CHEBI:16670
peptide
Peptide
KEGG_COMPOUND
peptides
IUPAC
Peptid
ChEBI
peptido
ChEBI
peptidos
ChEBI
A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
CHEBI:14202
CHEBI:4697
KEGG:C01351
Donor
chebi_ontology
Donator
donneur
CHEBI:17891
donor
Donor
KEGG_COMPOUND
Donator
ChEBI
donneur
ChEBI
That part of DNA or RNA that may be involved in pairing.
CHEBI:13873
CHEBI:25598
CHEBI:2995
KEGG:C00701
Wikipedia:Nucleobase
chebi_ontology
Base
nucleobases
CHEBI:18282
nucleobase
Base
KEGG_COMPOUND
nucleobases
ChEBI
An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids.
acyl group
alkanoyl
chebi_ontology
acyl groups
alkanoyl group
groupe acyle
CHEBI:22221
acyl group
acyl group
IUPAC
alkanoyl
IUPAC
acyl groups
ChEBI
alkanoyl group
ChEBI
groupe acyle
IUPAC
A monoatomic or polyatomic species having one or more elementary charges of the electron.
Anion
anion
chebi_ontology
Anionen
aniones
anions
CHEBI:22563
anion
Anion
ChEBI
anion
ChEBI
anion
IUPAC
Anionen
ChEBI
aniones
ChEBI
anions
IUPAC
A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base).
KEGG:C00701
Base
base
chebi_ontology
Base1
Base2
Basen
Nucleobase
bases
CHEBI:22695
base
Base
ChEBI
base
ChEBI
base
IUPAC
Base1
KEGG_COMPOUND
Base2
KEGG_COMPOUND
Basen
ChEBI
Nucleobase
KEGG_COMPOUND
bases
ChEBI
The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid.
0
CH2NO
44.03272
44.01364
*C(N)=O
PMID:24168430
carbamoyl
chebi_ontology
-C(O)NH2
-CONH2
aminocarbonyl
carbamyl
carbamyl group
carboxamide
CHEBI:23004
carbamoyl group
PMID:24168430
Europe PMC
carbamoyl
IUPAC
-C(O)NH2
ChEBI
-CONH2
IUPAC
aminocarbonyl
IUPAC
carbamyl
ChEBI
carbamyl group
ChEBI
carboxamide
IUPAC
0
CO
28.01010
27.99491
O=C(*)*
carbonyl
carbonyl group
chebi_ontology
>C=O
CHEBI:23019
carbonyl group
carbonyl
IUPAC
carbonyl group
ChEBI
carbonyl group
UniProt
>C=O
IUPAC
An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).
Wikipedia:Cofactor_(biochemistry)
cofactor
cofactors
chebi_ontology
CHEBI:23357
cofactor
cofactor
IUPAC
cofactors
IUPAC
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
molecular entity
chebi_ontology
entidad molecular
entidades moleculares
entite moleculaire
molecular entities
molekulare Entitaet
CHEBI:23367
molecular entity
molecular entity
IUPAC
entidad molecular
IUPAC
entidades moleculares
IUPAC
entite moleculaire
IUPAC
molecular entities
IUPAC
molekulare Entitaet
ChEBI
A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.
enzyme inhibitor
chebi_ontology
enzyme inhibitors
inhibidor enzimatico
inhibidores enzimaticos
inhibiteur enzymatique
inhibiteurs enzymatiques
CHEBI:23924
enzyme inhibitor
enzyme inhibitor
IUPAC
enzyme inhibitors
ChEBI
inhibidor enzimatico
ChEBI
inhibidores enzimaticos
ChEBI
inhibiteur enzymatique
ChEBI
inhibiteurs enzymatiques
ChEBI
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
A role played by the molecular entity or part thereof within a biological context.
chebi_ontology
biological function
CHEBI:24432
biological role
biological function
ChEBI
A defined linked collection of atoms or a single atom within a molecular entity.
group
chebi_ontology
Gruppe
Rest
groupe
grupo
grupos
CHEBI:24433
group
group
IUPAC
Gruppe
ChEBI
Rest
ChEBI
groupe
IUPAC
grupo
IUPAC
grupos
IUPAC
A cyclic compound having as ring members atoms of carbon and at least of one other element.
chebi_ontology
organic heterocycle
organic heterocyclic compounds
CHEBI:24532
organic heterocyclic compound
organic heterocycle
ChEBI
organic heterocyclic compounds
ChEBI
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
chebi_ontology
CHEBI:24651
hydroxides
A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
oxoacid
oxoacids
chebi_ontology
oxacids
oxiacids
oxo acid
oxy-acids
oxyacids
CHEBI:24833
oxoacid
oxoacid
IUPAC
oxoacids
IUPAC
oxacids
ChEBI
oxiacids
ChEBI
oxo acid
ChEBI
oxy-acids
ChEBI
oxyacids
ChEBI
chebi_ontology
inorganic anions
CHEBI:24834
inorganic anion
inorganic anions
ChEBI
A molecular entity that contains no carbon.
chebi_ontology
anorganische Verbindungen
inorganic compounds
inorganic entity
inorganic molecular entities
inorganics
CHEBI:24835
inorganic molecular entity
anorganische Verbindungen
ChEBI
inorganic compounds
ChEBI
inorganic entity
ChEBI
inorganic molecular entities
ChEBI
inorganics
ChEBI
A molecular entity having a net electric charge.
Ion
ion
chebi_ontology
Ionen
iones
ions
CHEBI:24870
ion
Ion
ChEBI
ion
ChEBI
ion
IUPAC
Ionen
ChEBI
iones
ChEBI
ions
ChEBI
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
CHEBI:26619
CHEBI:35220
metabolite
chebi_ontology
metabolites
primary metabolites
secondary metabolites
CHEBI:25212
metabolite
metabolite
IUPAC
metabolites
ChEBI
primary metabolites
ChEBI
secondary metabolites
ChEBI
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
molecule
chebi_ontology
Molekuel
molecula
molecules
neutral molecular compounds
CHEBI:25367
molecule
molecule
IUPAC
Molekuel
ChEBI
molecula
IUPAC
molecules
IUPAC
neutral molecular compounds
IUPAC
0
N
14.007
14.00307
WebElements:N
nitrogen
chebi_ontology
7N
N
Stickstoff
azote
nitrogen
nitrogeno
CHEBI:25555
nitrogen atom
nitrogen
IUPAC
7N
IUPAC
N
IUPAC
Stickstoff
ChEBI
azote
IUPAC
nitrogen
ChEBI
nitrogeno
ChEBI
nonmetal
chebi_ontology
Nichtmetall
Nichtmetalle
no metal
no metales
non-metal
non-metaux
nonmetal
nonmetals
CHEBI:25585
nonmetal atom
nonmetal
IUPAC
Nichtmetall
ChEBI
Nichtmetalle
ChEBI
no metal
ChEBI
no metales
ChEBI
non-metal
ChEBI
non-metaux
ChEBI
nonmetal
ChEBI
nonmetals
ChEBI
Any organic ion with a net negative charge.
chebi_ontology
organic anions
CHEBI:25696
organic anion
organic anions
ChEBI
chebi_ontology
organic ions
CHEBI:25699
organic ion
organic ions
ChEBI
An oxide is a chemical compound of oxygen with other chemical elements.
oxide
chebi_ontology
oxides
CHEBI:25741
oxide
oxide
ChEBI
oxides
ChEBI
0
O
InChI=1S/O
QVGXLLKOCUKJST-UHFFFAOYSA-N
15.99940
15.99491
[O]
KEGG:C00007
WebElements:O
oxygen
chebi_ontology
8O
O
Sauerstoff
oxigeno
oxygen
oxygene
CHEBI:25805
oxygen atom
oxygen
IUPAC
8O
IUPAC
O
IUPAC
Sauerstoff
ChEBI
oxigeno
ChEBI
oxygen
ChEBI
oxygene
ChEBI
oxygen molecular entity
chebi_ontology
oxygen molecular entities
CHEBI:25806
oxygen molecular entity
oxygen molecular entity
ChEBI
oxygen molecular entities
ChEBI
A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid.
chebi_ontology
univalent acyl group
univalent carboacyl groups
univalent carboxylic acyl groups
CHEBI:27207
univalent carboacyl group
univalent acyl group
ChEBI
univalent carboacyl groups
ChEBI
univalent carboxylic acyl groups
ChEBI
A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer).
zwitterion
zwitterions
chebi_ontology
compose zwitterionique
compuestos zwitterionicos
zwitteriones
zwitterionic compounds
CHEBI:27369
zwitterion
zwitterion
IUPAC
zwitterions
IUPAC
compose zwitterionique
IUPAC
compuestos zwitterionicos
IUPAC
zwitteriones
IUPAC
zwitterionic compounds
IUPAC
0
C
InChI=1S/C
OKTJSMMVPCPJKN-UHFFFAOYSA-N
12.01070
12.00000
[C]
CHEBI:23009
CHEBI:3399
CAS:7440-44-0
KEGG:C06265
WebElements:C
carbon
chebi_ontology
6C
C
Carbon
Kohlenstoff
carbon
carbone
carbonium
carbono
CHEBI:27594
carbon atom
CAS:7440-44-0
ChemIDplus
CAS:7440-44-0
KEGG COMPOUND
carbon
IUPAC
6C
IUPAC
C
IUPAC
C
KEGG_COMPOUND
Carbon
KEGG_COMPOUND
Kohlenstoff
ChEBI
carbon
ChEBI
carbone
ChEBI
carbonium
ChEBI
carbono
ChEBI
A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised.
0
CH3NO2
InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)
KXDHJXZQYSOELW-UHFFFAOYSA-N
61.04006
61.01638
NC(O)=O
CHEBI:22504
CHEBI:23002
CHEBI:3386
CHEBI:44573
Beilstein:1734754
CAS:463-77-4
DrugBank:DB04261
Gmelin:130345
KEGG:C01563
PDBeChem:OUT
Wikipedia:Carbamic_acid
CARBAMIC ACID
Carbamic acid
carbamic acid
chebi_ontology
Aminoameisensaeure
Aminoformic acid
Carbamate
Carbamidsaeure
CHEBI:28616
carbamic acid
Beilstein:1734754
Beilstein
CAS:463-77-4
ChemIDplus
CAS:463-77-4
KEGG COMPOUND
Gmelin:130345
Gmelin
CARBAMIC ACID
PDBeChem
Carbamic acid
KEGG_COMPOUND
carbamic acid
IUPAC
Aminoameisensaeure
ChEBI
Aminoformic acid
KEGG_COMPOUND
Carbamate
KEGG_COMPOUND
Carbamidsaeure
ChEBI
An onium cation obtained by protonation of ammonia.
+1
H4N
InChI=1S/H3N/h1H3/p+1
QGZKDVFQNNGYKY-UHFFFAOYSA-O
18.03850
18.03383
[H][N+]([H])([H])[H]
CHEBI:22534
CHEBI:49783
CHEBI:7435
CAS:14798-03-9
Gmelin:84
KEGG:C01342
MetaCyc:AMMONIUM
MolBase:929
PDBeChem:NH4
PMID:11319011
PMID:11341317
PMID:12096804
PMID:14512268
PMID:14879753
PMID:16345391
PMID:16903292
PMID:17392693
PMID:18515490
PMID:19199063
PMID:19596600
PMID:19682559
PMID:19716251
PMID:21993530
PMID:22265469
PMID:22524020
PMID:22562341
PMID:22631217
Reaxys:16093784
Wikipedia:Ammonium
ammonium
azanium
chebi_ontology
Ammonium(1+)
NH4(+)
NH4+
[NH4](+)
ammonium cation
ammonium ion
CHEBI:28938
ammonium
CAS:14798-03-9
ChemIDplus
CAS:14798-03-9
NIST Chemistry WebBook
Gmelin:84
Gmelin
PMID:11319011
Europe PMC
PMID:11341317
Europe PMC
PMID:12096804
Europe PMC
PMID:14512268
Europe PMC
PMID:14879753
Europe PMC
PMID:16345391
Europe PMC
PMID:16903292
Europe PMC
PMID:17392693
Europe PMC
PMID:18515490
Europe PMC
PMID:19199063
Europe PMC
PMID:19596600
Europe PMC
PMID:19682559
Europe PMC
PMID:19716251
Europe PMC
PMID:21993530
Europe PMC
PMID:22265469
Europe PMC
PMID:22524020
Europe PMC
PMID:22562341
Europe PMC
PMID:22631217
Europe PMC
Reaxys:16093784
Reaxys
ammonium
ChEBI
ammonium
IUPAC
azanium
IUPAC
Ammonium(1+)
ChemIDplus
NH4(+)
IUPAC
NH4(+)
UniProt
NH4+
KEGG_COMPOUND
[NH4](+)
MolBase
ammonium cation
ChemIDplus
ammonium ion
PDBeChem
The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.
-1
CO2R
44.00950
43.98983
[O-]C([*])=O
CHEBI:13626
CHEBI:13945
CHEBI:23026
CHEBI:58657
chebi_ontology
a carboxylate
carboxylic acid anions
carboxylic anions
CHEBI:29067
carboxylic acid anion
a carboxylate
UniProt
carboxylic acid anions
ChEBI
carboxylic anions
ChEBI
-1
H2N
InChI=1S/H2N/h1H2/q-1
HYGWNUKOUCZBND-UHFFFAOYSA-N
16.02262
16.01927
[H][N-][H]
amide
azanide
dihydridonitrate(1-)
chebi_ontology
NH2(-)
CHEBI:29337
azanide
amide
IUPAC
azanide
IUPAC
dihydridonitrate(1-)
IUPAC
NH2(-)
IUPAC
A divalent inorganic anion resulting from the removal of two protons from ammonia.
-2
HN
InChI=1S/HN/h1H/q-2
DZQYTNGKSBCIOE-UHFFFAOYSA-N
15.01468
15.01200
[N--][H]
azanediide
hydridonitrate(2-)
chebi_ontology
NH(2-)
imide
CHEBI:29340
hydridonitrate(2-)
azanediide
IUPAC
hydridonitrate(2-)
IUPAC
NH(2-)
IUPAC
imide
IUPAC
An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
CHEBI:22473
CHEBI:2633
KEGG:C00241
Amide
amides
chebi_ontology
CHEBI:32988
amide
Amide
KEGG_COMPOUND
amides
IUPAC
Intended use of the molecular entity or part thereof by humans.
chebi_ontology
CHEBI:33232
application
A particle not known to have substructure.
elementary particle
chebi_ontology
elementary particles
CHEBI:33233
fundamental particle
elementary particle
IUPAC
elementary particles
ChEBI
chebi_ontology
inorganic hydrides
CHEBI:33242
inorganic hydride
inorganic hydrides
ChEBI
Any substituent group which does not contain carbon.
chebi_ontology
inorganic groups
CHEBI:33246
inorganic group
inorganic groups
ChEBI
Any substituent group or skeleton containing carbon.
chebi_ontology
organic groups
CHEBI:33247
organic group
organic groups
ChEBI
Any organic substituent group, regardless of functional type, having one free valence at a carbon atom.
organyl group
organyl groups
chebi_ontology
groupe organyle
grupo organilo
grupos organilo
CHEBI:33249
organyl group
organyl group
IUPAC
organyl groups
IUPAC
groupe organyle
IUPAC
grupo organilo
IUPAC
grupos organilo
IUPAC
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
CHEBI:22671
CHEBI:23907
atom
chebi_ontology
atome
atomo
atoms
atomus
element
elements
CHEBI:33250
atom
atom
IUPAC
atome
IUPAC
atomo
IUPAC
atoms
ChEBI
atomus
ChEBI
element
ChEBI
elements
ChEBI
A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
nucleus
chebi_ontology
Atomkern
Kern
noyau
noyau atomique
nuclei
nucleo
nucleo atomico
nucleus atomi
CHEBI:33252
atomic nucleus
nucleus
IUPAC
Atomkern
ChEBI
Kern
ChEBI
noyau
IUPAC
noyau atomique
ChEBI
nuclei
ChEBI
nucleo
IUPAC
nucleo atomico
ChEBI
nucleus atomi
ChEBI
Heavy nuclear particle: proton or neutron.
nucleon
chebi_ontology
Nukleon
Nukleonen
nucleons
CHEBI:33253
nucleon
nucleon
IUPAC
nucleon
IUPAC
Nukleon
ChEBI
Nukleonen
ChEBI
nucleons
ChEBI
A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
primary amide
primary amides
chebi_ontology
CHEBI:33256
primary amide
primary amide
IUPAC
primary amides
IUPAC
An anion consisting of more than one atom.
chebi_ontology
polyatomic anions
CHEBI:33273
polyatomic anion
polyatomic anions
ChEBI
A nutrient is a food component that an organism uses to survive and grow.
chebi_ontology
nutrients
CHEBI:33284
nutrient
nutrients
ChEBI
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
chebi_ontology
heteroorganic entities
organoelement compounds
CHEBI:33285
heteroorganic entity
heteroorganic entities
ChEBI
organoelement compounds
ChEBI
Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
pnictogens
chebi_ontology
group 15 elements
group V elements
nitrogenoideos
nitrogenoides
pnictogene
pnictogenes
CHEBI:33300
pnictogen
pnictogens
IUPAC
group 15 elements
ChEBI
group V elements
ChEBI
nitrogenoideos
ChEBI
nitrogenoides
ChEBI
pnictogene
ChEBI
pnictogenes
ChEBI
A p-block molecular entity containing any pnictogen.
pnictogen molecular entity
chebi_ontology
pnictogen molecular entities
CHEBI:33302
pnictogen molecular entity
pnictogen molecular entity
ChEBI
pnictogen molecular entities
ChEBI
Any p-block element belonging to the group 16 family of the periodic table.
PMID:17084588
chalcogen
chalcogens
chebi_ontology
Chalkogen
Chalkogene
anfigeno
anfigenos
calcogeno
calcogenos
chalcogene
chalcogenes
group 16 elements
group VI elements
CHEBI:33303
chalcogen
PMID:17084588
Europe PMC
chalcogen
IUPAC
chalcogens
IUPAC
Chalkogen
ChEBI
Chalkogene
ChEBI
anfigeno
ChEBI
anfigenos
ChEBI
calcogeno
ChEBI
calcogenos
ChEBI
chalcogene
ChEBI
chalcogenes
ChEBI
group 16 elements
ChEBI
group VI elements
ChEBI
Any p-block molecular entity containing a chalcogen.
chalcogen molecular entity
chebi_ontology
chalcogen compounds
chalcogen molecular entities
CHEBI:33304
chalcogen molecular entity
chalcogen molecular entity
ChEBI
chalcogen compounds
ChEBI
chalcogen molecular entities
ChEBI
group 14 elements
chebi_ontology
carbon group element
carbon group elements
carbonoides
cristallogene
cristallogenes
group IV elements
CHEBI:33306
carbon group element atom
group 14 elements
IUPAC
carbon group element
ChEBI
carbon group elements
ChEBI
carbonoides
ChEBI
cristallogene
ChEBI
cristallogenes
ChEBI
group IV elements
ChEBI
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
main group elements
chebi_ontology
Hauptgruppenelement
Hauptgruppenelemente
main group element
CHEBI:33318
main group element atom
main group elements
IUPAC
Hauptgruppenelement
ChEBI
Hauptgruppenelemente
ChEBI
main group element
ChEBI
An amino-acid anion obtained by deprotonation of any alpha-amino acid.
alpha-amino-acid anion
chebi_ontology
alpha-amino acid anions
alpha-amino-acid anions
CHEBI:33558
alpha-amino-acid anion
alpha-amino-acid anion
ChEBI
alpha-amino acid anions
ChEBI
alpha-amino-acid anions
ChEBI
chebi_ontology
s-block element
s-block elements
CHEBI:33559
s-block element atom
s-block element
ChEBI
s-block elements
ChEBI
Any main group element atom belonging to the p-block of the periodic table.
chebi_ontology
p-block element
p-block elements
CHEBI:33560
p-block element atom
p-block element
ChEBI
p-block elements
ChEBI
A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
0
CHO2R
45.01740
44.99765
OC([*])=O
CHEBI:13428
CHEBI:13627
CHEBI:23027
PMID:17147560
PMID:18433345
Wikipedia:Carboxylic_acid
carboxylic acid
carboxylic acids
chebi_ontology
Carbonsaeure
Carbonsaeuren
Karbonsaeure
RC(=O)OH
acide carboxylique
acides carboxyliques
acido carboxilico
acidos carboxilicos
CHEBI:33575
carboxylic acid
PMID:17147560
Europe PMC
PMID:18433345
Europe PMC
carboxylic acid
IUPAC
carboxylic acids
IUPAC
Carbonsaeure
ChEBI
Carbonsaeuren
ChEBI
Karbonsaeure
ChEBI
RC(=O)OH
IUPAC
acide carboxylique
IUPAC
acides carboxyliques
IUPAC
acido carboxilico
IUPAC
acidos carboxilicos
IUPAC
A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
chebi_ontology
main group compounds
main group molecular entities
CHEBI:33579
main group molecular entity
main group compounds
ChEBI
main group molecular entities
ChEBI
carbon group molecular entity
chebi_ontology
carbon group molecular entities
CHEBI:33582
carbon group molecular entity
carbon group molecular entity
ChEBI
carbon group molecular entities
ChEBI
Any molecule that consists of a series of atoms joined together to form a ring.
Wikipedia:Cyclic_compound
chebi_ontology
cyclic compounds
CHEBI:33595
cyclic compound
cyclic compounds
ChEBI
chebi_ontology
hydrogen compounds
hydrogen molecular entities
CHEBI:33608
hydrogen molecular entity
hydrogen compounds
ChEBI
hydrogen molecular entities
ChEBI
A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character.
aromatic compounds
aromatic molecular entity
chebi_ontology
aromatics
aromatische Verbindungen
CHEBI:33655
aromatic compound
aromatic compounds
IUPAC
aromatic molecular entity
IUPAC
aromatics
ChEBI
aromatische Verbindungen
ChEBI
chebi_ontology
organic aromatic compounds
CHEBI:33659
organic aromatic compound
organic aromatic compounds
ChEBI
An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.
s-block molecular entity
chebi_ontology
s-block compounds
s-block molecular entities
CHEBI:33674
s-block molecular entity
s-block molecular entity
ChEBI
s-block compounds
ChEBI
s-block molecular entities
ChEBI
A main group molecular entity that contains one or more atoms of a p-block element.
chebi_ontology
p-block compounds
p-block molecular entities
p-block molecular entitiy
CHEBI:33675
p-block molecular entity
p-block compounds
ChEBI
p-block molecular entities
ChEBI
p-block molecular entitiy
ChEBI
Hydrides are chemical compounds of hydrogen with other chemical elements.
chebi_ontology
CHEBI:33692
hydrides
A macromolecule formed by a living organism.
biopolymer
chebi_ontology
Biopolymere
biomacromolecules
biopolymers
CHEBI:33694
biomacromolecule
biopolymer
IUPAC
Biopolymere
ChEBI
biomacromolecules
ChEBI
biopolymers
ChEBI
chebi_ontology
genetically encoded biomacromolecules
genetically encoded biopolymers
information biomacromolecules
information biopolymers
information macromolecule
information macromolecules
CHEBI:33695
information biomacromolecule
genetically encoded biomacromolecules
ChEBI
genetically encoded biopolymers
ChEBI
information biomacromolecules
ChEBI
information biopolymers
ChEBI
information macromolecule
ChEBI
information macromolecules
ChEBI
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
nucleic acids
chebi_ontology
NA
Nukleinsaeure
Nukleinsaeuren
acide nucleique
acides nucleiques
acido nucleico
acidos nucleicos
CHEBI:33696
nucleic acid
nucleic acids
IUPAC
NA
ChEBI
Nukleinsaeure
ChEBI
Nukleinsaeuren
ChEBI
acide nucleique
ChEBI
acides nucleiques
ChEBI
acido nucleico
ChEBI
acidos nucleicos
ChEBI
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
CAS:63231-63-0
ribonucleic acid
ribonucleic acids
chebi_ontology
RNA
RNS
Ribonukleinsaeure
pentosenucleic acids
ribonucleic acids
ribose nucleic acid
yeast nucleic acid
CHEBI:33697
ribonucleic acid
CAS:63231-63-0
ChemIDplus
ribonucleic acid
IUPAC
ribonucleic acids
IUPAC
RNA
IUPAC
RNA
UniProt
RNS
ChEBI
Ribonukleinsaeure
ChEBI
pentosenucleic acids
ChemIDplus
ribonucleic acids
ChEBI
ribose nucleic acid
ChEBI
yeast nucleic acid
ChEBI
chebi_ontology
canonical amino-acid residue
canonical amino-acid residues
common amino acid residues
proteinogenic amino-acid residues
standard amino acid residues
standard amino-acid residues
CHEBI:33700
proteinogenic amino-acid residue
canonical amino-acid residue
ChEBI
canonical amino-acid residues
ChEBI
common amino acid residues
ChEBI
proteinogenic amino-acid residues
ChEBI
standard amino acid residues
ChEBI
standard amino-acid residues
ChEBI
An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group.
0
C2H4NO2R
74.05870
74.02420
NC([*])C(O)=O
CHEBI:10208
CHEBI:13779
CHEBI:22442
CHEBI:2642
KEGG:C00045
KEGG:C05167
alpha-amino acid
chebi_ontology
Amino acid
Amino acids
alpha-amino acids
alpha-amino carboxylic acids
CHEBI:33704
alpha-amino acid
alpha-amino acid
IUPAC
Amino acid
KEGG_COMPOUND
Amino acids
KEGG_COMPOUND
alpha-amino acids
ChEBI
alpha-amino acids
JCBN
alpha-amino carboxylic acids
IUPAC
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
amino-acid residue
chebi_ontology
amino acid residue
amino-acid residues
CHEBI:33708
amino-acid residue
amino-acid residue
IUPAC
amino acid residue
ChEBI
amino-acid residues
JCBN
A carboxylic acid containing one or more amino groups.
CHEBI:13815
CHEBI:22477
Wikipedia:Amino_acid
chebi_ontology
Aminocarbonsaeure
Aminokarbonsaeure
Aminosaeure
amino acids
CHEBI:33709
amino acid
Aminocarbonsaeure
ChEBI
Aminokarbonsaeure
ChEBI
Aminosaeure
ChEBI
amino acids
ChEBI
chebi_ontology
alpha-amino-acid residues
CHEBI:33710
alpha-amino-acid residue
alpha-amino-acid residues
ChEBI
chebi_ontology
canonical nucleoside residues
common nucleoside residues
nucleoside residue
standard nucleoside residues
CHEBI:33791
canonical nucleoside residue
canonical nucleoside residues
ChEBI
common nucleoside residues
CBN
nucleoside residue
CBN
standard nucleoside residues
ChEBI
chebi_ontology
N
Nuc
canonical ribonucleoside residues
common ribonucleoside residue
common ribonucleoside residues
standard ribonucleoside residues
CHEBI:33792
canonical ribonucleoside residue
N
CBN
Nuc
CBN
canonical ribonucleoside residues
ChEBI
common ribonucleoside residue
CBN
common ribonucleoside residues
CBN
standard ribonucleoside residues
ChEBI
Any organic molecule that consists of atoms connected in the form of a ring.
chebi_ontology
organic cyclic compounds
CHEBI:33832
organic cyclic compound
organic cyclic compounds
ChEBI
A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2).
heteroarenes
chebi_ontology
hetarenes
CHEBI:33833
heteroarene
heteroarenes
IUPAC
hetarenes
IUPAC
A macromolecule is a 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.
Wikipedia:Macromolecule
macromolecule
chebi_ontology
macromolecules
polymer
polymer molecule
polymers
CHEBI:33839
macromolecule
macromolecule
IUPAC
macromolecules
ChEBI
polymer
ChEBI
polymer molecule
IUPAC
polymers
ChEBI
A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
reagent
chebi_ontology
reactif
reactivo
reagents
CHEBI:33893
reagent
reagent
IUPAC
reactif
IUPAC
reactivo
IUPAC
reagents
ChEBI
Any nutrient required in large quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Macronutrients are usually chemical elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur) that humans consume in the largest quantities. Calcium, sodium, magnesium and potassium are sometimes included as macronutrients because they are required in relatively large quantities compared with other vitamins and minerals.
chebi_ontology
macronutrients
CHEBI:33937
macronutrient
macronutrients
ChEBI
chebi_ontology
nitrogen hydrides
CHEBI:35106
nitrogen hydride
nitrogen hydrides
ChEBI
Saturated acyclic nitrogen hydrides having the general formula NnHn+2.
chebi_ontology
azanes
CHEBI:35107
azane
azanes
ChEBI
A substance that diminishes the rate of a chemical reaction.
inhibitor
chebi_ontology
inhibidor
inhibiteur
inhibitors
CHEBI:35222
inhibitor
inhibitor
IUPAC
inhibidor
ChEBI
inhibiteur
ChEBI
inhibitors
ChEBI
The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group.
amino acid zwitterion
chebi_ontology
CHEBI:35238
amino acid zwitterion
amino acid zwitterion
ChEBI
Any heteroorganic entity containing at least one carbon-nitrogen bond.
organonitrogen compounds
chebi_ontology
organonitrogens
CHEBI:35352
organonitrogen compound
organonitrogen compounds
IUPAC
organonitrogens
ChEBI
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
CHEBI:33274
CHEBI:33436
oxoanion
chebi_ontology
oxoacid anions
oxoanions
CHEBI:35406
oxoanion
oxoanion
ChEBI
oxoacid anions
ChEBI
oxoanions
ChEBI
chebi_ontology
carbon oxoacids
oxoacids of carbon
CHEBI:35605
carbon oxoacid
carbon oxoacids
ChEBI
oxoacids of carbon
ChEBI
pnictogen hydride
chebi_ontology
pnictogen hydrides
CHEBI:35881
pnictogen hydride
pnictogen hydride
ChEBI
pnictogen hydrides
ChEBI
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
CHEBI:13677
CHEBI:14911
proteins
chebi_ontology
CHEBI:36080
protein
proteins
IUPAC
Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).
chebi_ontology
leptons
CHEBI:36338
lepton
leptons
ChEBI
Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).
chebi_ontology
baryons
CHEBI:36339
baryon
baryons
ChEBI
Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.
fermion
chebi_ontology
fermions
CHEBI:36340
fermion
fermion
IUPAC
fermions
ChEBI
A particle smaller than an atom.
Wikipedia:Subatomic_particle
chebi_ontology
subatomic particles
CHEBI:36342
subatomic particle
subatomic particles
ChEBI
A subatomic particle known to have substructure (i.e. consisting of smaller particles).
chebi_ontology
composite particles
CHEBI:36343
composite particle
composite particles
ChEBI
Hadron is a subatomic particle which experiences the strong force.
chebi_ontology
hadrons
CHEBI:36344
hadron
hadrons
ChEBI
A nucleus or any of its constituents in any of their energy states.
nuclear particle
chebi_ontology
CHEBI:36347
nuclear particle
nuclear particle
IUPAC
Any molecular entity consisting of more than one atom.
chebi_ontology
polyatomic entities
CHEBI:36357
polyatomic entity
polyatomic entities
ChEBI
An ion consisting of more than one atom.
chebi_ontology
polyatomic ions
CHEBI:36358
polyatomic ion
polyatomic ions
ChEBI
Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.
carbonyl compounds
chebi_ontology
CHEBI:36586
carbonyl compound
carbonyl compounds
IUPAC
Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element.
oxo compounds
chebi_ontology
organic oxo compounds
CHEBI:36587
organic oxo compound
oxo compounds
IUPAC
organic oxo compounds
ChEBI
chebi_ontology
inorganic ions
CHEBI:36914
inorganic ion
inorganic ions
ChEBI
chebi_ontology
inorganic cations
CHEBI:36915
inorganic cation
inorganic cations
ChEBI
A monoatomic or polyatomic species having one or more elementary charges of the proton.
CHEBI:23058
CHEBI:3473
KEGG:C01373
Cation
cation
chebi_ontology
Kation
Kationen
cationes
cations
CHEBI:36916
cation
Cation
KEGG_COMPOUND
cation
ChEBI
cation
IUPAC
Kation
ChEBI
Kationen
ChEBI
cationes
ChEBI
cations
ChEBI
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
organochalcogen compound
chebi_ontology
organochalcogen compounds
CHEBI:36962
organochalcogen compound
organochalcogen compound
ChEBI
organochalcogen compounds
ChEBI
An organochalcogen compound containing at least one carbon-oxygen bond.
PMID:17586126
organooxygen compound
chebi_ontology
organooxygen compounds
CHEBI:36963
organooxygen compound
PMID:17586126
Europe PMC
organooxygen compound
ChEBI
organooxygen compounds
ChEBI
amino-acid anion
chebi_ontology
amino acid anions
amino-acid anions
CHEBI:37022
amino-acid anion
amino-acid anion
ChEBI
amino acid anions
ChEBI
amino-acid anions
ChEBI
mononuclear parent hydrides
chebi_ontology
mononuclear hydride
mononuclear hydrides
CHEBI:37176
mononuclear parent hydride
mononuclear parent hydrides
IUPAC
mononuclear hydride
ChEBI
mononuclear hydrides
IUPAC
An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid).
CHEBI:13800
CHEBI:13801
CHEBI:22209
CHEBI:2426
KEGG:C00174
Acid
acid
chebi_ontology
Saeure
Saeuren
acide
acido
acids
CHEBI:37527
acid
Acid
KEGG_COMPOUND
acid
IUPAC
Saeure
ChEBI
Saeuren
ChEBI
acide
IUPAC
acido
ChEBI
acids
ChEBI
A molecular entity consisting of two or more chemical elements.
chebi_ontology
chemical compound
heteroatomic molecular entities
CHEBI:37577
heteroatomic molecular entity
chemical compound
ChEBI
heteroatomic molecular entities
ChEBI
An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
0
CNOR3
42.01680
41.99799
[*]C(=O)N([*])[*]
CHEBI:35354
CHEBI:35355
carboxamides
chebi_ontology
carboxamides
primary carboxamide
CHEBI:37622
carboxamide
carboxamides
IUPAC
carboxamides
ChEBI
primary carboxamide
ChEBI
A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid.
carboacyl groups
carboxylic acyl group
chebi_ontology
carboxylic acyl groups
CHEBI:37838
carboacyl group
carboacyl groups
IUPAC
carboxylic acyl group
IUPAC
carboxylic acyl groups
IUPAC
Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.
chebi_ontology
heterocyclic organonitrogen compounds
organonitrogen heterocyclic compounds
CHEBI:38101
organonitrogen heterocyclic compound
heterocyclic organonitrogen compounds
ChEBI
organonitrogen heterocyclic compounds
ChEBI
A molecular entity capable of donating a hydron to an acceptor (Bronsted base).
Bronsted acid
chebi_ontology
Bronsted-Saeure
acide de Bronsted
donneur d'hydron
hydron donor
CHEBI:39141
Bronsted acid
Bronsted acid
IUPAC
Bronsted-Saeure
ChEBI
acide de Bronsted
IUPAC
donneur d'hydron
IUPAC
hydron donor
IUPAC
A molecular entity capable of accepting a hydron from a donor (Bronsted acid).
Bronsted base
chebi_ontology
Bronsted-Base
accepteur d'hydron
base de Bronsted
hydron acceptor
CHEBI:39142
Bronsted base
Bronsted base
IUPAC
Bronsted-Base
ChEBI
accepteur d'hydron
IUPAC
base de Bronsted
IUPAC
hydron acceptor
IUPAC
A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct.
Lewis base
chebi_ontology
Lewis-Base
base de Lewis
donneur d'une paire d'electrons
electron donor
CHEBI:39144
Lewis base
Lewis base
IUPAC
Lewis-Base
ChEBI
base de Lewis
IUPAC
donneur d'une paire d'electrons
ChEBI
electron donor
ChEBI
0
HO
17.00734
17.00274
*O[H]
CHEBI:24706
CHEBI:43171
PDBeChem:OH
HYDROXY GROUP
hydroxy
hydroxy group
chebi_ontology
-OH
hydroxyl
hydroxyl group
CHEBI:43176
hydroxy group
HYDROXY GROUP
PDBeChem
hydroxy
IUPAC
hydroxy group
UniProt
-OH
IUPAC
hydroxyl
ChEBI
hydroxyl group
ChEBI
0
O
15.99940
15.99491
O=*
CHEBI:29353
CHEBI:44607
PDBeChem:O
OXO GROUP
oxo
chebi_ontology
=O
CHEBI:46629
oxo group
OXO GROUP
PDBeChem
oxo
IUPAC
=O
IUPAC
0
CHO2
45.01744
44.99765
*C(=O)O
CHEBI:23025
CHEBI:41420
PDBeChem:FMT
CARBOXY GROUP
carboxy
chebi_ontology
-C(O)OH
-CO2H
-COOH
carboxyl group
CHEBI:46883
carboxy group
CARBOXY GROUP
PDBeChem
carboxy
IUPAC
-C(O)OH
IUPAC
-CO2H
ChEBI
-COOH
IUPAC
carboxyl group
ChEBI
0
H
InChI=1S/H
YZCKVEUIGOORGS-UHFFFAOYSA-N
1.00794
1.00783
[H]
CHEBI:24634
CHEBI:49636
WebElements:H
hydrogen
chebi_ontology
1H
H
Wasserstoff
hidrogeno
hydrogen
hydrogene
CHEBI:49637
hydrogen atom
hydrogen
IUPAC
1H
IUPAC
H
IUPAC
Wasserstoff
ChEBI
hidrogeno
ChEBI
hydrogen
ChEBI
hydrogene
ChEBI
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
chebi_ontology
organic amino compounds
CHEBI:50047
organic amino compound
organic amino compounds
ChEBI
chebi_ontology
canonical nucleotide residues
CHEBI:50297
canonical nucleotide residue
canonical nucleotide residues
ChEBI
chebi_ontology
canonical ribonucleotide residues
CHEBI:50299
canonical ribonucleotide residue
canonical ribonucleotide residues
ChEBI
chebi_ontology
CHEBI:50312
onium compound
Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families.
onium cations
chebi_ontology
onium cations
onium ion
onium ions
CHEBI:50313
onium cation
onium cations
IUPAC
onium cations
ChEBI
onium ion
ChEBI
onium ions
ChEBI
chebi_ontology
nucleotide residues
CHEBI:50319
nucleotide residue
nucleotide residues
ChEBI
chebi_ontology
nucleoside residues
CHEBI:50320
nucleoside residue
nucleoside residues
ChEBI
Any molecular entity that contains carbon.
CHEBI:25700
CHEBI:33244
chebi_ontology
organic compounds
organic entity
organic molecular entities
CHEBI:50860
organic molecular entity
organic compounds
ChEBI
organic entity
ChEBI
organic molecular entities
ChEBI
A role is particular behaviour which a material entity may exhibit.
chebi_ontology
CHEBI:50906
role
A poison that interferes with the functions of the nervous system.
CHEBI:50911
Wikipedia:Neurotoxin
chebi_ontology
agente neurotoxico
nerve poison
nerve poisons
neurotoxic agent
neurotoxic agents
neurotoxicant
neurotoxins
CHEBI:50910
neurotoxin
agente neurotoxico
ChEBI
nerve poison
ChEBI
nerve poisons
ChEBI
neurotoxic agent
ChEBI
neurotoxic agents
ChEBI
neurotoxicant
ChEBI
neurotoxins
ChEBI
A role played by the molecular entity or part thereof within a chemical context.
chebi_ontology
CHEBI:51086
chemical role
CHEBI:25556
CHEBI:7594
KEGG:C06061
chebi_ontology
Nitrogenous compounds
nitrogen compounds
nitrogen molecular entities
CHEBI:51143
nitrogen molecular entity
Nitrogenous compounds
KEGG_COMPOUND
nitrogen compounds
ChEBI
nitrogen molecular entities
ChEBI
An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case.
chebi_ontology
dipolar compounds
CHEBI:51151
dipolar compound
dipolar compounds
ChEBI
Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s).
chebi_ontology
organodiyl groups
CHEBI:51422
organodiyl group
organodiyl groups
ChEBI
chebi_ontology
CHEBI:51446
organic divalent group
chebi_ontology
CHEBI:51447
organic univalent group
A biological role played by the molecular entity or part thereof within a biochemical context.
chebi_ontology
CHEBI:52206
biochemical role
A role played by the molecular entity or part thereof which causes the development of a pathological process.
chebi_ontology
etiopathogenetic agent
etiopathogenetic role
CHEBI:52209
aetiopathogenetic role
etiopathogenetic agent
ChEBI
etiopathogenetic role
ChEBI
chebi_ontology
CHEBI:52211
physiological role
A cyclic compound having as ring members atoms of at least two different elements.
Heterocyclic compound
chebi_ontology
compuesto heterociclico
compuestos heterociclicos
heterocycle
heterocyclic compounds
CHEBI:5686
heterocyclic compound
Heterocyclic compound
KEGG_COMPOUND
compuesto heterociclico
IUPAC
compuestos heterociclicos
IUPAC
heterocycle
ChEBI
heterocyclic compounds
ChEBI
A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons.
chebi_ontology
nucleophile
nucleophiles
nucleophilic reagents
CHEBI:59740
nucleophilic reagent
nucleophile
ChEBI
nucleophiles
ChEBI
nucleophilic reagents
ChEBI
An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one.
chebi_ontology
a monovalent cation
CHEBI:60242
monovalent inorganic cation
a monovalent cation
UniProt
Zwitterionic form of any peptide where, in general, the amino terminus is positively charged and the carboxy terminus is negatively charged.
0
C2H4NO2R(C2H2NOR)n
chebi_ontology
a peptide
peptide zwitterions
CHEBI:60466
peptide zwitterion
a peptide
UniProt
peptide zwitterions
ChEBI
Any compound that has a nucleobase as a part.
chebi_ontology
nucleobase-containing compound
nucleobase-containing compounds
nucleobase-containing molecular entities
CHEBI:61120
nucleobase-containing molecular entity
nucleobase-containing compound
SUBMITTER
nucleobase-containing compounds
ChEBI
nucleobase-containing molecular entities
ChEBI
An organic molecular entity containing a single carbon atom (C1).
chebi_ontology
one-carbon compounds
CHEBI:64708
one-carbon compound
one-carbon compounds
ChEBI
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
chebi_ontology
organic acids
CHEBI:64709
organic acid
organic acids
ChEBI
Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism.
Wikipedia:Poison
chebi_ontology
poisonous agent
poisonous agents
poisonous substance
poisonous substances
poisons
toxic agent
toxic agents
toxic substance
toxic substances
CHEBI:64909
poison
poisonous agent
ChEBI
poisonous agents
ChEBI
poisonous substance
ChEBI
poisonous substances
ChEBI
poisons
ChEBI
toxic agent
ChEBI
toxic agents
ChEBI
toxic substance
ChEBI
toxic substances
ChEBI
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
chebi_ontology
organic compound
organic compounds
organic molecules
CHEBI:72695
organic molecule
organic compound
ChEBI
organic compounds
ChEBI
organic molecules
ChEBI
Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms.
chebi_ontology
eukaryotic metabolites
CHEBI:75763
eukaryotic metabolite
eukaryotic metabolites
ChEBI
Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals.
CHEBI:77721
CHEBI:77743
chebi_ontology
animal metabolites
CHEBI:75767
animal metabolite
animal metabolites
ChEBI
Any animal metabolite produced during a metabolic reaction in mammals.
CHEBI:77464
CHEBI:77744
chebi_ontology
mammalian metabolites
CHEBI:75768
mammalian metabolite
mammalian metabolites
ChEBI
Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus).
chebi_ontology
Mus musculus metabolite
Mus musculus metabolites
mouse metabolites
CHEBI:75771
mouse metabolite
Mus musculus metabolite
ChEBI
Mus musculus metabolites
ChEBI
mouse metabolites
ChEBI
Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae).
CHEBI:76949
CHEBI:76951
chebi_ontology
S. cerevisiae metabolite
S. cerevisiae metabolites
S. cerevisiae secondary metabolite
S. cerevisiae secondary metabolites
Saccharomyces cerevisiae metabolites
Saccharomyces cerevisiae secondary metabolites
baker's yeast metabolite
baker's yeast metabolites
baker's yeast secondary metabolite
baker's yeast secondary metabolites
CHEBI:75772
Saccharomyces cerevisiae metabolite
S. cerevisiae metabolite
ChEBI
S. cerevisiae metabolites
ChEBI
S. cerevisiae secondary metabolite
ChEBI
S. cerevisiae secondary metabolites
ChEBI
Saccharomyces cerevisiae metabolites
ChEBI
Saccharomyces cerevisiae secondary metabolites
ChEBI
baker's yeast metabolite
ChEBI
baker's yeast metabolites
ChEBI
baker's yeast secondary metabolite
ChEBI
baker's yeast secondary metabolites
ChEBI
Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea.
chebi_ontology
prokaryotic metabolites
CHEBI:75787
prokaryotic metabolite
prokaryotic metabolites
ChEBI
Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*).
Wikipedia:Hydrolase
chebi_ontology
EC 3.* (hydrolase) inhibitors
EC 3.* inhibitor
EC 3.* inhibitors
EC 3.*.*.* inhibitor
EC 3.*.*.* inhibitors
hydrolase (EC 3.*) inhibitor
hydrolase (EC 3.*) inhibitors
hydrolase inhibitor
hydrolase inhibitors
CHEBI:76759
EC 3.* (hydrolase) inhibitor
EC 3.* (hydrolase) inhibitors
ChEBI
EC 3.* inhibitor
ChEBI
EC 3.* inhibitors
ChEBI
EC 3.*.*.* inhibitor
ChEBI
EC 3.*.*.* inhibitors
ChEBI
hydrolase (EC 3.*) inhibitor
ChEBI
hydrolase (EC 3.*) inhibitors
ChEBI
hydrolase inhibitor
ChEBI
hydrolase inhibitors
ChEBI
Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*).
chebi_ontology
EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor
EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors
EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor
EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors
EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors
EC 3.5.* inhibitor
EC 3.5.* inhibitors
CHEBI:76764
EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor
EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor
ChEBI
EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors
ChEBI
EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor
ChEBI
EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors
ChEBI
EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors
ChEBI
EC 3.5.* inhibitor
ChEBI
EC 3.5.* inhibitors
ChEBI
An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*).
chebi_ontology
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors
EC 3.5.1.* inhibitor
EC 3.5.1.* inhibitors
non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor
non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors
CHEBI:76807
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors
ChEBI
EC 3.5.1.* inhibitor
ChEBI
EC 3.5.1.* inhibitors
ChEBI
non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor
ChEBI
non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors
ChEBI
Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds.
CHEBI:75765
CHEBI:76947
chebi_ontology
fungal metabolites
CHEBI:76946
fungal metabolite
fungal metabolites
ChEBI
Any prokaryotic metabolite produced during a metabolic reaction in bacteria.
CHEBI:75760
CHEBI:76970
chebi_ontology
CHEBI:76969
bacterial metabolite
Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.
chebi_ontology
E.coli metabolite
E.coli metabolites
Escherichia coli metabolites
CHEBI:76971
Escherichia coli metabolite
E.coli metabolite
ChEBI
E.coli metabolites
ChEBI
Escherichia coli metabolites
ChEBI
Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).
CHEBI:75770
CHEBI:77123
chebi_ontology
H. sapiens metabolite
H. sapiens metabolites
Homo sapiens metabolite
Homo sapiens metabolites
CHEBI:77746
human metabolite
H. sapiens metabolite
ChEBI
H. sapiens metabolites
ChEBI
Homo sapiens metabolite
ChEBI
Homo sapiens metabolites
ChEBI
An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4).
Wikipedia:Amidase
chebi_ontology
EC 3.5.1.4 (amidase) inhibitors
EC 3.5.1.4 inhibitor
EC 3.5.1.4 inhibitors
N-acetylaminohydrolase inhibitor
N-acetylaminohydrolase inhibitors
acylamidase inhibitor
acylamidase inhibitors
acylamide amidohydrolase inhibitor
acylamide amidohydrolase inhibitors
amidase (EC 3.5.1.4) inhibitor
amidase (EC 3.5.1.4) inhibitors
amidase inhibitor
amidase inhibitors
amidohydrolase inhibitor
amidohydrolase inhibitors
deaminase inhibitor
deaminase inhibitors
fatty acylamidase inhibitor
fatty acylamidase inhibitors
CHEBI:77941
EC 3.5.1.4 (amidase) inhibitor
EC 3.5.1.4 (amidase) inhibitors
ChEBI
EC 3.5.1.4 inhibitor
ChEBI
EC 3.5.1.4 inhibitors
ChEBI
N-acetylaminohydrolase inhibitor
ChEBI
N-acetylaminohydrolase inhibitors
ChEBI
acylamidase inhibitor
ChEBI
acylamidase inhibitors
ChEBI
acylamide amidohydrolase inhibitor
ChEBI
acylamide amidohydrolase inhibitors
ChEBI
amidase (EC 3.5.1.4) inhibitor
ChEBI
amidase (EC 3.5.1.4) inhibitors
ChEBI
amidase inhibitor
ChEBI
amidase inhibitors
ChEBI
amidohydrolase inhibitor
ChEBI
amidohydrolase inhibitors
ChEBI
deaminase inhibitor
ChEBI
deaminase inhibitors
ChEBI
fatty acylamidase inhibitor
ChEBI
fatty acylamidase inhibitors
ChEBI
A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants.
chebi_ontology
dietary component
dietary components
food components
CHEBI:78295
food component
dietary component
ChEBI
dietary components
ChEBI
food components
ChEBI
A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a "R" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure.
Wikipedia:Refrigerant
chebi_ontology
refrigerants
CHEBI:78433
refrigerant
refrigerants
ChEBI
An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3.
0
C2H4NO2R
74.059
74.02420
[NH3+]C([*])C([O-])=O
CHEBI:83409
MetaCyc:Alpha-Amino-Acids
chebi_ontology
an alpha-amino acid
CHEBI:78608
alpha-amino acid zwitterion
MetaCyc:Alpha-Amino-Acids
SUBMITTER
an alpha-amino acid
UniProt
Any inorganic anion with a valency of two.
chebi_ontology
divalent inorganic anions
CHEBI:79388
divalent inorganic anion
divalent inorganic anions
ChEBI
Any inorganic anion with a valency of one.
chebi_ontology
monovalent inorganic anions
CHEBI:79389
monovalent inorganic anion
monovalent inorganic anions
ChEBI
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CALOHA:TS-2035
FBbt:00007002
FMA:68646
GO:0005623
KUPO:0000002
MESH:D002477
VHOG:0001533
WBbt:0004017
XAO:0003012
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
cell
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CARO:mah
Binding to an acyl group, any group formally derived by removal of the hydroxyl group from the acid function of a carboxylic acid.
acyl-CoA or acyl binding
molecular_function
GO:0000035
acyl binding
Binding to an acyl group, any group formally derived by removal of the hydroxyl group from the acid function of a carboxylic acid.
GOC:curators
ISBN:0198506732
Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).
translation initiation ternary complex assembly
biological_process
GO:0001677
formation of translation initiation ternary complex
Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).
GOC:hjd
Binding to a nucleobase, any of a class of pyrmidines or purines, organic nitrogenous bases.
molecular_function
GO:0002054
nucleobase binding
Binding to a nucleobase, any of a class of pyrmidines or purines, organic nitrogenous bases.
GOC:hjd
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
Binding to a nucleic acid.
GO:0000496
base pairing
molecular_function
GO:0003676
nucleic acid binding
Binding to a nucleic acid.
GOC:jl
Binding to an RNA molecule or a portion thereof.
GO:0000498
GO:0044822
Reactome:R-HSA-203922
base pairing with RNA
molecular_function
poly(A) RNA binding
poly(A)-RNA binding
poly-A RNA binding
GO:0003723
RNA binding
Binding to an RNA molecule or a portion thereof.
GOC:jl
GOC:mah
Reactome:R-HSA-203922
Exportin-5 recognizes 3' overhang of pre-miRNA
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
Binds to and stops, prevents or reduces the activity of an enzyme.
GO:0048551
metalloenzyme inhibitor activity
molecular_function
GO:0004857
This term should only be used in cases when the regulator directly interacts with the enzyme.
enzyme inhibitor activity
Binds to and stops, prevents or reduces the activity of an enzyme.
GOC:ai
GOC:ebc
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
Wikipedia:Binding_(molecular)
ligand
molecular_function
GO:0005488
Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
binding
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
GOC:ceb
GOC:mah
ISBN:0198506732
Binding to a protein.
GO:0001948
GO:0045308
protein amino acid binding
glycoprotein binding
molecular_function
GO:0005515
protein binding
Binding to a protein.
GOC:go_curators
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 membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
NIF_Subcellular:sao1702920020
Wikipedia:Cell_nucleus
cell nucleus
horsetail nucleus
cellular_component
GO:0005634
nucleus
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
GOC:go_curators
horsetail nucleus
GOC:al
GOC:mah
GOC:vw
PMID:15030757
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
GO:0005636
Wikipedia:Nuclear_envelope
cellular_component
GO:0005635
nuclear envelope
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
ISBN:0198547684
The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
https://github.com/geneontology/go-ontology/issues/23023
Wikipedia:Cytoplasm
cellular_component
GO:0005737
cytoplasm
The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
ISBN:0198547684
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
Wikipedia:Vacuole
cellular_component
vacuolar carboxypeptidase Y
GO:0005773
vacuole
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
GOC:mtg_sensu
ISBN:0198506732
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0005887
GO:0005904
juxtamembrane
NIF_Subcellular:sao1663586795
Wikipedia:Cell_membrane
cell membrane
cellular membrane
cytoplasmic membrane
plasmalemma
bacterial inner membrane
inner endospore membrane
integral component of plasma membrane
integral to plasma membrane
plasma membrane lipid bilayer
cellular_component
GO:0005886
plasma membrane
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
ISBN:0716731363
cellular membrane
NIF_Subcellular:sao6433132645
plasma membrane lipid bilayer
GOC:mah
The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
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
The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.
organic acid metabolism
biological_process
GO:0006082
organic acid metabolic process
The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.
ISBN:0198506732
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
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
GO:0006416
GO:0006453
GO:0043037
Wikipedia:Translation_(genetics)
protein anabolism
protein biosynthesis
protein biosynthetic process
protein formation
protein synthesis
protein translation
biological_process
GO:0006412
translation
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
GOC:go_curators
The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
GO:0006440
GO:0006454
biopolymerisation
biopolymerization
protein synthesis initiation
translation initiation
biological_process
GO:0006413
translational initiation
The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
ISBN:019879276X
The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
GO:0006442
GO:0006455
protein synthesis elongation
translation elongation
biological_process
GO:0006414
translational elongation
The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
GOC:ems
The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
GO:0006443
GO:0006456
protein synthesis termination
translation termination
translational complex disassembly
biological_process
GO:0006415
translational termination
The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
GOC:hjd
ISBN:019879276X
The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
peptide metabolism
biological_process
GO:0006518
peptide metabolic process
The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
GOC:go_curators
The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
https://github.com/geneontology/go-ontology/issues/17904
GO:0006519
cellular amino acid metabolic process
cellular amino acid metabolism
biological_process
amino acid and derivative metabolism
cellular amino acid and derivative metabolic process
GO:0006520
amino acid metabolic process
The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
ISBN:0198506732
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 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
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 the nucleus.
GO:0048287
nuclear organisation
nuclear organization
biological_process
nuclear morphology
nuclear organization and biogenesis
nucleus organization and biogenesis
GO:0006997
nucleus organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
GOC:dph
GOC:ems
GOC:jl
GOC:mah
nuclear organization and biogenesis
GOC:mah
nucleus 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 nuclear envelope.
nuclear envelope organisation
biological_process
nuclear envelope organization and biogenesis
GO:0006998
nuclear envelope organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope.
GOC:dph
GOC:ems
GOC:jl
GOC:mah
nuclear envelope organisation
GOC:mah
nuclear envelope 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 plasma membrane.
plasma membrane organisation
biological_process
plasma membrane organization and biogenesis
GO:0007009
plasma membrane organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane.
GOC:dph
GOC:jl
GOC:mah
plasma membrane 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 cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
cytoplasm organisation
biological_process
cytoplasm organization and biogenesis
GO:0007028
cytoplasm organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GOC:curators
GOC:dph
GOC:jl
GOC:mah
cytoplasm 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 a vacuole.
GO:0044086
vacuole organisation
vacuolar assembly
biological_process
vacuole biogenesis
vacuole organization and biogenesis
GO:0007033
vacuole organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole.
GOC:mah
vacuolar assembly
GOC:mah
vacuole biogenesis
GOC:mah
vacuole organization and biogenesis
GOC:mah
Binds to and increases the activity of an enzyme.
GO:0010577
metalloenzyme activator activity
molecular_function
GO:0008047
This term should only be used in cases when the regulator directly interacts with the enzyme.
enzyme activator activity
Binds to and increases the activity of an enzyme.
GOC:dph
GOC:mah
GOC:tb
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 chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
https://github.com/geneontology/go-ontology/issues/17904
Wikipedia:Amino_acid_synthesis
amino acid anabolism
amino acid biosynthesis
amino acid formation
amino acid synthesis
cellular amino acid biosynthetic process
biological_process
GO:0008652
amino acid biosynthetic process
The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
ISBN:0198506732
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
The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine.
nucleobase metabolism
biological_process
GO:0009112
nucleobase metabolic process
The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine.
GOC:ma
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
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system.
endomembrane organization
endomembrane system organisation
biological_process
GO:0010256
endomembrane system organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system.
GOC:mah
GOC:sm
endomembrane system organisation
GOC:mah
The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.
https://github.com/geneontology/go-ontology/issues/22557
Wikipedia:Gene_expression
biological_process
GO:0010467
gene expression
The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.
GOC:txnOH-2018
PMID:25934543
PMID:31580950
A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
Wikipedia:Endomembrane_system
cellular_component
GO:0012505
endomembrane system
A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
GOC:lh
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
2014-03-06T11:37:54Z
GO:0016021
GO:0098589
GO:0098805
Wikipedia:Biological_membrane
Wikipedia:Transmembrane_protein
integral component of membrane
integral to membrane
membrane region
region of membrane
whole membrane
cellular_component
transmembrane
GO:0016020
membrane
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
GOC:dos
GOC:mah
ISBN:0815316194
transmembrane
GOC:mah
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
GO:0044235
GO:0071842
cell organisation
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
biological_process
cell organization and biogenesis
GO:0016043
cellular component organization
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
GOC:ai
GOC:jl
GOC:mah
cellular component organisation at cellular level
GOC:mah
cellular component organisation in other organism
GOC:mah
cell organization and biogenesis
GOC:mah
The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage.
organic acid anabolism
organic acid biosynthesis
organic acid formation
organic acid synthesis
biological_process
GO:0016053
organic acid biosynthetic process
The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage.
ISBN:0198506732
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
RNA metabolism
biological_process
GO:0016070
RNA metabolic process
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
ISBN:0198506732
true
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Reactome:R-HSA-6788855
Reactome:R-HSA-6788867
phosphokinase activity
molecular_function
GO:0016301
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
kinase activity
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
ISBN:0198506732
Reactome:R-HSA-6788855
FN3KRP phosphorylates PsiAm, RibAm
Reactome:R-HSA-6788867
FN3K phosphorylates ketosamines
Binding to an amino acid, organic acids containing one or more amino substituents.
molecular_function
GO:0016597
amino acid binding
Binding to an amino acid, organic acids containing one or more amino substituents.
GOC:ai
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
EC:2.-.-.-
Reactome:R-HSA-1483089
Reactome:R-HSA-1483186
Reactome:R-HSA-5668414
Reactome:R-HSA-8868783
molecular_function
GO:0016740
transferase activity
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
ISBN:0198506732
Reactome:R-HSA-1483089
PE is converted to PS by PTDSS2
Reactome:R-HSA-1483186
PC is converted to PS by PTDSS1
Reactome:R-HSA-5668414
TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK
Reactome:R-HSA-8868783
TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
EC:2.7.-.-
molecular_function
GO:0016772
Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
transferase activity, transferring phosphorus-containing groups
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
GOC:jl
ISBN:0198506732
The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
heterocycle anabolism
heterocycle biosynthesis
heterocycle formation
heterocycle synthesis
biological_process
GO:0018130
heterocycle biosynthetic process
The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
ISBN:0198547684
Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
molecular_function
GO:0019207
kinase regulator activity
Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GOC:ai
Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
molecular_function
GO:0019209
kinase activator activity
Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GOC:ai
Binds to and stops, prevents or reduces the activity of a kinase.
molecular_function
GO:0019210
kinase inhibitor activity
Binds to and stops, prevents or reduces the activity of a kinase.
GOC:mah
The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.
aromatic compound anabolism
aromatic compound biosynthesis
aromatic compound formation
aromatic compound synthesis
aromatic hydrocarbon biosynthesis
aromatic hydrocarbon biosynthetic process
biological_process
GO:0019438
aromatic compound biosynthetic process
The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.
GOC:ai
The chemical reactions and pathways involving a protein. Includes protein modification.
https://github.com/geneontology/go-ontology/issues/23112
GO:0006411
GO:0044267
GO:0044268
Wikipedia:Protein_metabolism
cellular protein metabolic process
cellular protein metabolism
protein metabolic process and modification
protein metabolism
protein metabolism and modification
multicellular organismal protein metabolic process
biological_process
GO:0019538
protein metabolic process
The chemical reactions and pathways involving a protein. Includes protein modification.
GOC:ma
The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
carboxylic acid metabolism
biological_process
GO:0019752
carboxylic acid metabolic process
The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
ISBN:0198506732
A cellular process that results in the breakdown of a cellular component.
GO:0071845
cell structure disassembly
cellular component disassembly at cellular level
biological_process
GO:0022411
cellular component disassembly
A cellular process that results in the breakdown of a cellular component.
GOC:isa_complete
The aggregation, arrangement and bonding together of a cellular component.
GO:0071844
cell structure assembly
cellular component assembly at cellular level
biological_process
GO:0022607
cellular component assembly
The aggregation, arrangement and bonding together of a cellular component.
GOC:isa_complete
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex.
RNA-protein complex biogenesis
ribonucleoprotein complex biogenesis and assembly
biological_process
GO:0022613
ribonucleoprotein complex biogenesis
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex.
GOC:isa_complete
GOC:mah
RNA-protein complex biogenesis
GOC:mah
ribonucleoprotein complex biogenesis and assembly
GOC:mah
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.
RNA-protein complex assembly
RNP complex assembly
protein-RNA complex assembly
biological_process
GO:0022618
ribonucleoprotein complex assembly
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.
GOC:jl
Binds to and modulates the activity of an enzyme.
GO:0010576
catalytic regulator activity
enzyme modulator
metalloenzyme regulator activity
molecular_function
GO:0030234
This term should only be used in cases when the regulator directly interacts with the enzyme.
enzyme regulator activity
Binds to and modulates the activity of an enzyme.
GOC:dph
GOC:mah
GOC:tb
catalytic regulator activity
GOC:dph
The controlled breakdown of any cell membrane in the context of a normal process such as autophagy.
membrane breakdown
membrane catabolism
membrane degradation
biological_process
GO:0030397
membrane disassembly
The controlled breakdown of any cell membrane in the context of a normal process such as autophagy.
GOC:mah
A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
NIF_Subcellular:sao830981606
cellular_component
intracellular membrane
GO:0031090
organelle membrane
A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
GOC:dos
GOC:mah
intracellular membrane
NIF_Subcellular:sao830981606
Binding to a carboxylic acid, an organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
molecular_function
GO:0031406
carboxylic acid binding
Binding to a carboxylic acid, an organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
GOC:mah
ISBN:0198506732
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
NIF_Subcellular:sao1687101204
cellular_component
GO:0031965
nuclear membrane
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
GOC:mah
GOC:pz
A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes.
cellular_component
GO:0031967
organelle envelope
A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes.
GOC:mah
GOC:pz
A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers.
cellular_component
GO:0031975
envelope
A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers.
GOC:mah
GOC:pz
The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication.
GO:0062103
RNA anabolism
RNA biosynthesis
RNA formation
RNA synthesis
double-stranded RNA biosynthesis
double-stranded RNA biosynthetic process
dsRNA biosynthesis
dsRNA biosynthetic process
biological_process
GO:0032774
Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study.
RNA biosynthetic process
The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication.
GOC:mah
GOC:txnOH
dsRNA biosynthetic process
GOC:BHF
GOC:BHF_telomere
GOC:nc
GOC:rl
The disaggregation of a protein-containing macromolecular complex into its constituent components.
https://github.com/geneontology/go-ontology/issues/22580
GO:0034623
GO:0043241
GO:0043624
protein complex disassembly
biological_process
cellular macromolecule complex disassembly
cellular protein complex disassembly
macromolecule complex disassembly
GO:0032984
protein-containing complex disassembly
The disaggregation of a protein-containing macromolecular complex into its constituent components.
GOC:mah
The disaggregation of a protein-RNA complex into its constituent components.
RNA-protein complex disassembly
RNP complex disassembly
protein-RNA complex disassembly
biological_process
GO:0032988
ribonucleoprotein complex disassembly
The disaggregation of a protein-RNA complex into its constituent components.
GOC:mah
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
GO:0043234
macromolecular complex
macromolecule complex
protein containing complex
protein complex
protein-protein complex
cellular_component
GO:0032991
A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
protein-containing complex
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
GOC:dos
GOC:mah
Binding to an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
molecular_function
GO:0033218
amide binding
Binding to an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
GOC:mah
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
cellular nitrogen compound metabolism
biological_process
GO:0034641
cellular nitrogen compound metabolic process
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
GOC:mah
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, carried out by individual cells.
GO:0034961
cellular biopolymer biosynthetic process
cellular macromolecule anabolism
cellular macromolecule biosynthesis
cellular macromolecule formation
cellular macromolecule synthesis
biological_process
GO:0034645
cellular 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, carried out by individual cells.
GOC:mah
cellular biopolymer biosynthetic process
GOC:mtg_chebi_dec09
cellular macromolecule anabolism
GOC:mah
cellular macromolecule biosynthesis
GOC:mah
cellular macromolecule formation
GOC:mah
cellular macromolecule synthesis
GOC:mah
The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase, nucleoside, nucleotide and nucleic acid anabolism
nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis
nucleobase, nucleoside, nucleotide and nucleic acid formation
nucleobase, nucleoside, nucleotide and nucleic acid synthesis
biological_process
GO:0034654
nucleobase-containing compound biosynthetic process
The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids.
GOC:mah
Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule.
bf
2012-01-17T04:20:34Z
molecular_function
GO:0036094
Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
small molecule binding
Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule.
GOC:curators
GOC:pde
GOC:pm
Binding to a peptide, an organic compound comprising two or more amino acids linked by peptide bonds.
molecular_function
GO:0042277
peptide binding
Binding to a peptide, an organic compound comprising two or more amino acids linked by peptide bonds.
GOC:jl
Binding to a complex of RNA and protein.
RNP binding
protein-RNA complex binding
ribonucleoprotein binding
molecular_function
GO:0043021
ribonucleoprotein complex binding
Binding to a complex of RNA and protein.
GOC:bf
GOC:go_curators
GOC:vk
protein-RNA complex binding
GOC:bf
GOC:vk
ribonucleoprotein binding
GOC:bf
GOC:vk
The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide.
peptide anabolism
peptide biosynthesis
peptide formation
peptide synthesis
biological_process
GO:0043043
peptide biosynthetic process
The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide.
GOC:dph
GOC:jl
Binding to an ion, a charged atoms or groups of atoms.
molecular_function
atom binding
GO:0043167
ion binding
Binding to an ion, a charged atoms or groups of atoms.
GOC:jl
Binding to an anion, a charged atom or group of atoms with a net negative charge.
molecular_function
GO:0043168
anion binding
Binding to an anion, a charged atom or group of atoms with a net negative charge.
GOC:jl
Binding to a cation, a charged atom or group of atoms with a net positive charge.
molecular_function
GO:0043169
cation binding
Binding to a cation, a charged atom or group of atoms with a net positive charge.
GOC:jl
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GO:0043283
GO:0044259
biopolymer metabolic process
macromolecule metabolism
organismal macromolecule metabolism
multicellular organismal macromolecule metabolic process
biological_process
GO:0043170
macromolecule metabolic process
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GOC:mah
biopolymer metabolic process
GOC:mtg_chebi_dec09
Binding to an organic acid, any acidic compound containing carbon in covalent linkage.
molecular_function
GO:0043177
organic acid binding
Binding to an organic acid, any acidic compound containing carbon in covalent linkage.
GOC:jl
ISBN:0198506732
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
NIF_Subcellular:sao1539965131
Wikipedia:Organelle
cellular_component
GO:0043226
organelle
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
NIF_Subcellular:sao414196390
membrane-enclosed organelle
cellular_component
GO:0043227
membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
cellular_component
GO:0043229
intracellular organelle
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
intracellular membrane-enclosed organelle
cellular_component
GO:0043231
intracellular membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
GOC:go_curators
The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
keto acid metabolic process
keto acid metabolism
ketoacid metabolic process
ketoacid metabolism
oxo acid metabolic process
oxo acid metabolism
oxoacid metabolism
biological_process
GO:0043436
oxoacid metabolic process
The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
Wikipedia:Oxyacid
The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells.
amide metabolism
cellular amide metabolic process
biological_process
GO:0043603
amide metabolic process
The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells.
GOC:curators
The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
biological_process
GO:0043604
amide biosynthetic process
The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
GOC:curators
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.
https://github.com/geneontology/go-ontology/issues/22580
mah
2010-09-08T10:01:42Z
GO:0034600
GO:0034621
GO:0071822
protein complex subunit organisation
protein complex subunit organization
biological_process
cellular macromolecular complex organization
cellular macromolecular complex subunit organisation
cellular macromolecular complex subunit organization
macromolecular complex organization
macromolecular complex subunit organisation
macromolecular complex subunit organization
protein-containing complex subunit organization
GO:0043933
protein-containing complex organization
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.
GOC:mah
protein complex subunit organisation
GOC:mah
A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.
GO:0071843
cellular component biogenesis at cellular level
biological_process
GO:0044085
cellular component biogenesis
A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.
GOC:jl
GOC:mah
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a membrane.
biological_process
GO:0044091
membrane biogenesis
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a membrane.
GOC:jl
A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).
jl
2009-10-22T02:38:55Z
translation initiation (ternary) complex
Met-tRNA/eIF2.GTP ternary complex
cellular_component
GO:0044207
translation initiation ternary complex
A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).
GOC:jl
The chemical reactions and pathways by which individual cells transform chemical substances.
cellular metabolism
biological_process
intermediary metabolism
GO:0044237
cellular metabolic process
The chemical reactions and pathways by which individual cells transform chemical substances.
GOC:go_curators
intermediary metabolism
GOC:mah
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
primary metabolism
biological_process
GO:0044238
primary metabolic process
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
GOC:go_curators
http://www.metacyc.org
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
cellular anabolism
cellular biosynthesis
cellular formation
cellular synthesis
biological_process
GO:0044249
cellular biosynthetic process
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
GOC:jl
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
GO:0034960
cellular biopolymer metabolic process
cellular macromolecule metabolism
biological_process
GO:0044260
cellular macromolecule metabolic process
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
GOC:mah
cellular biopolymer metabolic process
GOC:mtg_chebi_dec09
The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.
nitrogen compound anabolism
nitrogen compound biosynthesis
nitrogen compound formation
nitrogen compound synthesis
biological_process
GO:0044271
cellular nitrogen compound biosynthetic process
The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.
GOC:jl
ISBN:0198506732
The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
jl
2010-01-26T12:05:20Z
small molecule metabolism
biological_process
GO:0044281
Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
small molecule metabolic process
The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
GOC:curators
GOC:pde
GOC:vw
The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.
jl
2010-01-26T12:06:49Z
small molecule biosynthesis
biological_process
GO:0044283
Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
small molecule biosynthetic process
The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.
GOC:curators
GOC:pde
GOC:vw
Binding to a macromolecular complex.
jl
2014-12-16T11:38:58Z
GO:0032403
protein complex binding
molecular_function
macromolecular complex binding
GO:0044877
protein-containing complex binding
Binding to a macromolecular complex.
GOC:jl
The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.
nucleobase anabolism
nucleobase biosynthesis
nucleobase formation
nucleobase synthesis
biological_process
GO:0046112
nucleobase biosynthetic process
The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.
GOC:ai
The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups.
carboxylic acid anabolism
carboxylic acid biosynthesis
carboxylic acid formation
carboxylic acid synthesis
biological_process
GO:0046394
carboxylic acid biosynthetic process
The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups.
ISBN:0198506732
The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
heterocycle metabolism
biological_process
GO:0046483
heterocycle metabolic process
The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
ISBN:0198506732
The controlled breakdown of the nuclear membranes, for example during cellular division.
biological_process
nuclear envelope breakdown
nuclear envelope catabolism
nuclear envelope degradation
nuclear envelope disassembly
GO:0051081
nuclear membrane disassembly
The controlled breakdown of the nuclear membranes, for example during cellular division.
GOC:ai
The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
nucleobase, nucleoside and nucleotide metabolism
biological_process
nucleobase, nucleoside and nucleotide metabolic process
GO:0055086
nucleobase-containing small molecule metabolic process
The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
GOC:vw
A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
jl
2010-02-08T02:43:11Z
GO:0016044
GO:0044802
cellular membrane organisation
cellular membrane organization
membrane organisation
biological_process
membrane organization and biogenesis
single-organism membrane organization
GO:0061024
membrane organization
A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
GOC:dph
GOC:tb
membrane organisation
GOC:mah
membrane organization and biogenesis
GOC:mah
A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
dph
2015-05-06T11:22:38Z
cellular_component
GO:0061695
transferase complex, transferring phosphorus-containing groups
A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
GOC:bhm
GOC:dph
The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.
https://github.com/geneontology/go-ontology/issues/22580
GO:0006461
GO:0034622
GO:0043623
cellular protein complex assembly
biological_process
cellular macromolecule complex assembly
cellular protein-containing complex assembly
chaperone activity
macromolecular complex assembly
macromolecule complex assembly
protein complex assembly
protein complex formation
GO:0065003
protein-containing complex assembly
The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.
GOC:jl
Binding to ammonium ions (NH4+).
molecular_function
ammonium binding
GO:0070405
ammonium ion binding
Binding to ammonium ions (NH4+).
CHEBI:28938
GOC:ecd
The aggregation, arrangement and bonding together of a set of components to form an organelle. 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.
mah
2009-09-15T03:00:51Z
biological_process
GO:0070925
organelle assembly
The aggregation, arrangement and bonding together of a set of components to form an organelle. 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
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
mah
2010-03-08T03:32:18Z
organic molecular entity metabolic process
organic molecular entity metabolism
organic substance metabolism
biological_process
GO:0071704
organic substance metabolic process
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
GOC:mah
The aggregation, arrangement and bonding together of a set of components to form a membrane.
mah
2010-03-10T11:19:17Z
biological_process
GO:0071709
membrane assembly
The aggregation, arrangement and bonding together of a set of components to form a membrane.
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 nuclear inner or outer membrane.
mah
2010-03-29T03:59:35Z
nuclear membrane organisation
biological_process
nuclear membrane organization and biogenesis
GO:0071763
nuclear membrane organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear inner or outer membrane.
GOC:mah
nuclear membrane organisation
GOC:mah
nuclear membrane organization and biogenesis
GOC:mah
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex.
mah
2010-09-08T10:10:35Z
RNA-protein complex subunit organization
protein-RNA complex subunit organization
ribonucleoprotein complex subunit organisation
biological_process
GO:0071826
ribonucleoprotein complex subunit organization
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex.
GOC:mah
RNA-protein complex subunit organization
GOC:mah
protein-RNA complex subunit organization
GOC:mah
ribonucleoprotein complex subunit organisation
GOC:mah
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
mah
2010-09-10T01:39:16Z
GO:0071841
cellular component organisation or biogenesis
cellular component organisation or biogenesis at cellular level
cellular component organization or biogenesis at cellular level
biological_process
GO:0071840
cellular component organization or biogenesis
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
GOC:mah
cellular component organisation or biogenesis
GOC:mah
cellular component organisation or biogenesis at cellular level
GOC:mah
The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
mah
2010-10-04T01:51:47Z
cellular_component
GO:0071944
cell periphery
The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
GOC:mah
Any cellular metabolic process involving nucleic acids.
tb
2010-04-07T10:18:47Z
biological_process
GO:0090304
nucleic acid metabolic process
Any cellular metabolic process involving nucleic acids.
GOC:dph
GOC:tb
Binding to an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure.
pr
2011-09-23T02:31:01Z
molecular_function
GO:0097159
organic cyclic compound binding
Binding to an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure.
GOC:sjw
PMID:7583672
The chemical reactions and pathways involving the ammonium ion.
pr
2011-09-28T04:21:30Z
ammonium ion metabolism
biological_process
ammonium metabolic process
GO:0097164
ammonium ion metabolic process
The chemical reactions and pathways involving the ammonium ion.
GOC:dhl
GOC:tb
PMID:14671018
A membrane that is a (regional) part of the plasma membrane.
dos
2014-03-06T11:55:32Z
region of plasma membrane
cellular_component
GO:0098590
Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass.
plasma membrane region
A membrane that is a (regional) part of the plasma membrane.
GOC:dos
A molecular function regulator regulates the activity of its target via non-covalent binding that does not result in covalent modification to the target. Examples of molecular function regulators include regulatory subunits of multimeric enzymes and channels. Mechanisms of regulation include allosteric changes in the target and competitive inhibition.
https://github.com/geneontology/go-ontology/issues/20854
https://github.com/geneontology/go-ontology/issues/20862
molecular function regulator
molecular_function
GO:0098772
molecular function regulator activity
A molecular function regulator regulates the activity of its target via non-covalent binding that does not result in covalent modification to the target. Examples of molecular function regulators include regulatory subunits of multimeric enzymes and channels. Mechanisms of regulation include allosteric changes in the target and competitive inhibition.
GOC:dos
GOC:pt
Any protein complex that is part of a membrane.
cellular_component
GO:0098796
membrane protein complex
Any protein complex that is part of a membrane.
GOC:dos
Any protein complex that is part of the plasma membrane.
cellular_component
GO:0098797
plasma membrane protein complex
Any protein complex that is part of the plasma membrane.
GOC:dos
Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.
cellular_component
GO:0099568
cytoplasmic region
Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.
GOC:dos
The complete extent of cell cortex that underlies some some region of the plasma membrane.
perimembrane region
cellular_component
GO:0099738
cell cortex region
The complete extent of cell cortex that underlies some some region of the plasma membrane.
GOC:dos
The process in which a nuclear membrane is synthesized, aggregates, and bonds together.
biological_process
GO:0101025
nuclear membrane biogenesis
The process in which a nuclear membrane is synthesized, aggregates, and bonds together.
GOC:vw
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
kmv
2019-08-12T18:01:37Z
cellular_component
GO:0110165
cellular anatomical entity
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
GOC:kmv
Catalytic activity that acts to modify a protein.
https://github.com/geneontology/go-ontology/issues/14225
pg
2017-09-14T10:32:59Z
molecular_function
GO:0140096
catalytic activity, acting on a protein
Catalytic activity that acts to modify a protein.
GOC:molecular_function_refactoring
GOC:pdt
Catalytic activity that acts to modify RNA, driven by ATP hydrolysis.
https://github.com/geneontology/go-ontology/issues/14225
https://github.com/geneontology/go-ontology/issues/21612
pg
2017-09-14T12:05:21Z
molecular_function
GO:0140098
catalytic activity, acting on RNA
Catalytic activity that acts to modify RNA, driven by ATP hydrolysis.
GOC:molecular_function_refactoring
GOC:pdt
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus.
pg
2020-09-09T05:12:38Z
nuclear complex
cellular_component
GO:0140513
nuclear protein-containing complex
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus.
GOC:pg
Catalytic activity that acts to modify a nucleic acid.
https://github.com/geneontology/go-ontology/issues/21402
pg
2021-05-11T06:31:07Z
molecular_function
GO:0140640
catalytic activity, acting on a nucleic acid
Catalytic activity that acts to modify a nucleic acid.
GOC:pg
A molecular function regulator that activates or increases the activity of its target via non-covalent binding that does not result in covalent modification to the target.
https://github.com/geneontology/go-ontology/issues/21782
pg
2021-07-07T07:24:16Z
molecular_function
GO:0140677
molecular function activator activity
A molecular function regulator that activates or increases the activity of its target via non-covalent binding that does not result in covalent modification to the target.
GOC:curators
A molecular function regulator that inhibits or decreases the activity of its target via non-covalent binding that does not result in covalent modification to the target.
https://github.com/geneontology/go-ontology/issues/21782
pg
2021-07-07T07:24:32Z
molecular_function
GO:0140678
molecular function inhibitor activity
A molecular function regulator that inhibits or decreases the activity of its target via non-covalent binding that does not result in covalent modification to the target.
GOC:curators
A protein complex capable of activating an enzyme. Activating subunits may dissociate from the catalytic unit before the enzyme is active.
cellular_component
GO:0150005
enzyme activator complex
A protein complex capable of activating an enzyme. Activating subunits may dissociate from the catalytic unit before the enzyme is active.
GOC:bhm
PMID:16244137
PMID:28710280
The chemical reactions and pathways involving organic cyclic compound.
bf
2012-09-14T09:03:51Z
organic cyclic compound metabolism
biological_process
GO:1901360
organic cyclic compound metabolic process
The chemical reactions and pathways involving organic cyclic compound.
GOC:TermGenie
organic cyclic compound metabolism
GOC:TermGenie
The chemical reactions and pathways resulting in the formation of organic cyclic compound.
bf
2012-09-14T09:05:22Z
organic cyclic compound anabolism
organic cyclic compound biosynthesis
organic cyclic compound formation
organic cyclic compound synthesis
biological_process
GO:1901362
organic cyclic compound biosynthetic process
The chemical reactions and pathways resulting in the formation of organic cyclic compound.
GOC:TermGenie
organic cyclic compound anabolism
GOC:TermGenie
organic cyclic compound biosynthesis
GOC:TermGenie
organic cyclic compound formation
GOC:TermGenie
organic cyclic compound synthesis
GOC:TermGenie
Binding to heterocyclic compound.
bf
2012-09-14T13:53:50Z
molecular_function
GO:1901363
heterocyclic compound binding
Binding to heterocyclic compound.
GOC:TermGenie
The chemical reactions and pathways involving organonitrogen compound.
pr
2012-11-04T15:17:52Z
organonitrogen compound metabolism
biological_process
GO:1901564
organonitrogen compound metabolic process
The chemical reactions and pathways involving organonitrogen compound.
GOC:TermGenie
GOC:pr
organonitrogen compound metabolism
GOC:TermGenie
The chemical reactions and pathways resulting in the formation of organonitrogen compound.
pr
2012-11-04T15:18:00Z
organonitrogen compound anabolism
organonitrogen compound biosynthesis
organonitrogen compound formation
organonitrogen compound synthesis
biological_process
GO:1901566
organonitrogen compound biosynthetic process
The chemical reactions and pathways resulting in the formation of organonitrogen compound.
GOC:TermGenie
GOC:pr
organonitrogen compound anabolism
GOC:TermGenie
organonitrogen compound biosynthesis
GOC:TermGenie
organonitrogen compound formation
GOC:TermGenie
organonitrogen compound synthesis
GOC:TermGenie
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
pr
2012-11-05T11:04:40Z
organic molecular entity anabolism
organic molecular entity biosynthesis
organic molecular entity biosynthetic process
organic molecular entity formation
organic molecular entity synthesis
organic substance anabolism
organic substance biosynthesis
organic substance formation
organic substance synthesis
biological_process
GO:1901576
organic substance biosynthetic process
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
GOC:TermGenie
GOC:pr
organic molecular entity anabolism
GOC:TermGenie
organic molecular entity biosynthesis
GOC:TermGenie
organic molecular entity formation
GOC:TermGenie
organic molecular entity synthesis
GOC:TermGenie
The chemical reactions and pathways involving an alpha-amino acid.
tb
2012-11-08T17:39:50Z
alpha-amino acid metabolism
biological_process
GO:1901605
alpha-amino acid metabolic process
The chemical reactions and pathways involving an alpha-amino acid.
GOC:TermGenie
alpha-amino acid metabolism
GOC:TermGenie
The chemical reactions and pathways resulting in the formation of an alpha-amino acid.
tb
2012-11-08T17:39:58Z
alpha-amino acid anabolism
alpha-amino acid biosynthesis
alpha-amino acid formation
alpha-amino acid synthesis
biological_process
GO:1901607
alpha-amino acid biosynthetic process
The chemical reactions and pathways resulting in the formation of an alpha-amino acid.
GOC:TermGenie
alpha-amino acid anabolism
GOC:TermGenie
alpha-amino acid biosynthesis
GOC:TermGenie
alpha-amino acid formation
GOC:TermGenie
alpha-amino acid synthesis
GOC:TermGenie
A protein complex which is capable of catalytic activity.
https://github.com/geneontology/go-ontology/issues/19980
bhm
2013-11-13T16:18:47Z
enzyme complex
cellular_component
GO:1902494
catalytic complex
A protein complex which is capable of catalytic activity.
GOC:TermGenie
GOC:bhm
PMID:8077207
enzyme complex
GOC:bhm
GOC:jl
The disaggregation of an organelle into its constituent components.
jl
2014-05-13T12:36:03Z
organelle degradation
biological_process
GO:1903008
organelle disassembly
The disaggregation of an organelle into its constituent components.
GOC:TermGenie
GO_REF:0000079
The disaggregation of a nucleus into its constituent components.
pr
2016-11-14T13:38:57Z
cell nucleus disassembly
biological_process
GO:1905690
nucleus disassembly
The disaggregation of a nucleus into its constituent components.
GOC:TermGenie
GOC:autophagy
GOC:pr
GO_REF:0000079
cell nucleus disassembly
GOC:TermGenie
A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor).
bhm
2013-11-12T13:20:12Z
cellular_component
GO:1990234
transferase complex
A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor).
GOC:bhm
PMID:16540464
A macromolecular complex that contains both RNA and protein molecules.
pr
2015-11-19T12:26:37Z
GO:0030529
GO:1990903
Wikipedia:Ribonucleoprotein
RNA-protein complex
RNP
protein-RNA complex
extracellular ribonucleoprotein complex
intracellular ribonucleoprotein complex
cellular_component
GO:1990904
ribonucleoprotein complex
A macromolecular complex that contains both RNA and protein molecules.
GOC:krc
GOC:vesicles
GC_ID:1
ncbi_taxonomy
all
NCBITaxon:1
root
all
GC_ID:1
ncbi_taxonomy
biota
NCBITaxon:131567
cellular organisms
biota
GC_ID:1
PMID:23020233
PMID:30257078
eucaryotes
eukaryotes
ncbi_taxonomy
Eucarya
Eucaryotae
Eukarya
Eukaryotae
eukaryotes
NCBITaxon:2759
Eukaryota
eucaryotes
eukaryotes
Eucarya
Eucaryotae
Eukarya
Eukaryotae
eukaryotes
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
quality (PATO)
PATO:0000072
quality
PATO:0000001
quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATOC:GVG
A quality which inheres in a continuant.
PATO:0001237
PATO:0001238
snap:Quality
monadic quality of a continuant
multiply inhering quality of a physical entity
quality of a continuant
quality of a single physical entity
quality of an object
quality of continuant
monadic quality of an object
monadic quality of continuant
quality
PATO:0001241
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
physical object quality
A quality which inheres in a continuant.
PATOC:GVG
A monadic quality of continuant that exists at the cellular level of organisation.
quality
PATO:0001396
cellular quality
A monadic quality of continuant that exists at the cellular level of organisation.
PATOC:GVG
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
quality
PATO:0001404
nucleate quality
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
PATOC:GVG
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
quality
PATO:0001405
anucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
Biology-online:Biology-online
A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.
quality
PATO:0001406
binucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.
Biology-online:Biology-online
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
quality
PATO:0001407
mononucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
Biology-online:Biology-online
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
quality
PATO:0001908
multinucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
PATOC:GVG
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
2013-10-21T05:44:34Z
quality
PATO:0002505
nucleated
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
PATOC:GVG
A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components.
http://orcid.org/0000-0001-7258-9596
quality
PATO:0070044
anatomical structure quality
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
natural protein
native protein
protein
PR:000000001
The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].
protein
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
PRO:DAN
PRO:WCB
natural protein
PRO:DAN
native protein
IEDB:BP
An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
peptide
polypeptide
protein
PR:000018263
Category=external.
amino acid chain
An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
PRO:DAN
PRO:JSG
peptide
PRO:DAN
polypeptide
PRO:DAN
A protein that is encoded in the genome of some Eukaryota.
Eukaryota protein
protein
PR:000036194
eukaryotic protein
A protein that is encoded in the genome of some Eukaryota.
PRO:DAN
Eukaryota protein
PRO:DAN
root node
2
1
2
true
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
infer input from direct reg
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
enabling an MF enables its parts
true
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
involved in BP
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).