http://orcid.org/0000-0002-1373-1705
http://orcid.org/0000-0002-7073-9172
https://orcid.org/0000-0001-5948-3092
https://orcid.org/0000-0002-0027-0858
An ontology of Drosophila melanogaster developmental stages.
FlyBase Developmental Ontology (FBdv)
https://creativecommons.org/licenses/by/3.0/
* FBdv:$sequence(8,7000,10000)$
25:03:2020 09:10
FlyBase_development_CV
1.2
editor preferred term
example of usage
has curation status
definition
editor note
term editor
alternative term
definition source
curator note
imported from
expand expression to
OBO foundry unique label
elucidation
term replaced by
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
https://github.com/oborel/obo-relations/wiki/ROAndTime
defined by inverse
logical macro assertion on an annotation property
relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
The general property hierarchy is:
"directly P" SubPropertyOf "P"
Transitive(P)
Where we have an annotation assertion
"directly P" "is direct form of" "P"
If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
Chris Mungall
is direct form of
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
is a defining property chain axiom
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
cjm
2018-03-14T00:03:16Z
is positive form of
cjm
2018-03-14T00:03:24Z
is negative form of
part-of is homeomorphic for independent continuants.
R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
cjm
2018-10-21T19:46:34Z
R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
is homeomorphic for
Term not to be used for direct annotation
Term not to be used for direct manual annotation
ChEMBL GO slim
Aspergillus GO slim
Candida GO slim
ChEMBL GO slim
Generic GO slim
Metagenomics GO slim
PIR GO slim
Plant GO slim
Fission yeast GO slim
Yeast GO slim
Prokaryotic GO subset
Systematic synonym
Term not to be used for direct annotation
Term not to be used for direct manual annotation
AGR slim
Aspergillus GO slim
Candida GO slim
ChEMBL protein targets summary
Drosophila GO slim
FlyBase Drosophila GO ribbon slim
Generic GO slim
Metagenomics GO slim
Mouse GO slim
PIR GO slim
Plant GO slim
Fission yeast GO slim
Yeast GO slim
eco subset
namespace-id-rule
subset_property
synonym_type_property
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
has_scope
in_subset
shorthand
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
BFO:0000050
external
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
BFO:0000051
OBO_REL:has_part
external
relationship
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
OBO_REL:preceded_by
relationship
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.
precedes
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
BFO:0000066
external
occurs_in
occurs_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
occurs in
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
FBdv:00018001
relationship
substage_of
substage_of
Creating this relation as a temporary fix, pending adding the axiom occurent_part_of subpropertyof happens_during to RO
substage_of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
A part of relation that applies only between occurents.
RO:0002012
FlyBase_development_CV
occurent_part_of
occurent_part_of
occurent part of
occurent_part_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
has regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
dos
2017-05-24T09:31:01Z
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
dos
2017-05-24T09:31:17Z
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
dos
2017-05-24T09:44:33Z
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
dos
2017-05-24T09:49:21Z
has component process
A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
dos
2017-07-19T17:30:36Z
has ligand
dos
2017-09-17T13:52:24Z
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
directly regulated by
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
GOC:dos
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
dos
2017-09-17T13:52:38Z
directly negatively regulated by
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
GOC:dos
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
dos
2017-09-17T13:52:47Z
directly positively regulated by
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
GOC:dos
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
dos
2017-09-22T14:14:36Z
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
GOC:dos
David Osumi-Sutherland
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which ends
David Osumi-Sutherland
di
Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
encompasses
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
FlyBase_development_CV
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
Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which starts
David Osumi-Sutherland
ends_at_start_of
meets
RO:0002090
FlyBase_development_CV
ends_at_start_of
ends_at_start_of
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
ends_at_start_of
immediately precedes
David Osumi-Sutherland
io
RO:0002091
external
starts_during
starts_during
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
starts_during
David Osumi-Sutherland
d
during
RO:0002092
external
happens_during
happens_during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
happens during
David Osumi-Sutherland
o
overlaps
RO:0002093
external
ends_during
ends_during
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
ends_during
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
FlyBase_development_CV
overlaps
overlaps
overlaps
overlaps
true
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
Terry Meehan
This is the transitive form of the develops from relation
develops from
inverse of develops from
Chris Mungall
David Osumi-Sutherland
Terry Meehan
develops into
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
RO:0002211
external
regulates
regulates
regulates
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
negatively regulates (process to process)
RO:0002212
external
negatively_regulates
negatively_regulates
negatively regulates
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
positively regulates (process to process)
RO:0002213
external
positively_regulates
positively_regulates
positively regulates
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
Chris Mungall
has function realized in
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
RO_0000053 some (RO_0000054 only ?Y)
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
Chris Mungall
has function in
RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
capable of part of
true
OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role
Chris Mungall
agent in
Obsoleted as the inverse property was obsoleted.
obsolete actively participates in
true
'heart development' has active participant some Shh protein
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
Chris Mungall
has agent
obsolete has active participant
true
Chris Mungall
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
Chris Mungall
consumes
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
Chris Mungall
produces
has output
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
Chris Mungall
has developmental contribution from
inverse of has developmental contribution from
Chris Mungall
developmentally contributes to
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
false
Chris Mungall
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
acts upstream of
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
affects
acts upstream of or within
Inverse of developmentally preceded by
Chris Mungall
developmentally succeeded by
cjm
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
causally upstream of, positive effect
cjm
holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
causally upstream of, negative effect
A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
ecologically 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
Chris Mungall
catalyzes
executes
has
is catalyzing
is executing
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
Chris Mungall
false
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
Chris Mungall
actively involved in
enables part of
involved in
inverse of enables
Chris Mungall
enabled by
inverse of regulates
Chris Mungall
regulated by (processual)
regulated by
inverse of negatively regulates
Chris Mungall
negatively regulated by
inverse of positively regulates
Chris Mungall
positively regulated by
inverse of has input
Chris Mungall
input of
inverse of has output
Chris Mungall
output of
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
Chris Mungall
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
Chris Mungall
has potential to developmentally contribute to
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
Chris Mungall
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
Chris Mungall
has potential to directly develop into
inverse of upstream of
Chris Mungall
causally downstream of
Chris Mungall
immediately causally downstream of
This relation groups causal relations between material entities and causal relations between processes
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
Chris Mungall
immediately causally upstream of
transitive form of directly_provides_input_for
Chris Mungall
This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
transitively provides input for (process to process)
transitively provides input for
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
affects
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
Chris Mungall
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
Chris Mungall
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
Chris Mungall
involved in negative regulation of
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
Chris Mungall
involved in or reguates
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
Chris Mungall
executes activity in
enables activity in
is active in
true
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
GOC:cjm
GOC:dos
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Chris Mungall
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/MI_0914
https://github.com/oborel/obo-relations/wiki/InteractionRelations
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
Chris Mungall
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
Axiomatization to GO to be added later
Chris Mungall
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
Chris Mungall
Vasundra Touré
molecularly controls
directly regulates activity of
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly inhibits
molecularly decreases activity of
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly activates
molecularly increases activity of
directly positively regulates activity of
Chris Mungall
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
Chris Mungall
has part that occurs in
true
Chris Mungall
is kinase activity
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
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
A relation that holds between two entities that have the property of being sequences or having sequences.
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene.
sequentially related to
The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y
Chris Mungall
bounds sequence of
inverse of bounds sequence of
Chris Mungall
is bound by sequence of
x has subsequence y iff all of the sequence parts of x are sequence parts of y
Chris Mungall
contains
http://www.ncbi.nlm.nih.gov/pubmed/20226267
has subsequence
inverse of has subsequence
Chris Mungall
contained by
is subsequence of
x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.
Chris Mungall
overlaps sequence of
Chris Mungall
causally influenced by (entity-centric)
causally influenced by
Chris Mungall
interaction relation helper property
https://github.com/oborel/obo-relations/wiki/InteractionRelations
Chris Mungall
molecular interaction relation helper property
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
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Chris Mungall
directly regulates (processual)
directly regulates
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
Chris Mungall
has part structure that is capable of
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
capable of positively regulating
Inverse of 'causal agent in process'
process has causal agent
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
directly positively regulates (process to process)
directly positively regulates
Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
directly negatively regulates (process to process)
directly negatively regulates
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Melissa Haendel
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
a produced_by b iff some process that occurs_in b has_output a.
Melissa Haendel
produced by
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
has primary input or output
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
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
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 continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
generically dependent continuant
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
anatomical entity
biological entity
The life of an individual of the species Drosophila melanogaster, from fertilization to death.
FBdv_root:00000000
Drosophila life cycle
FlyBase_development_CV
FBdv:00000000
Drosophila life
The life of an individual of the species Drosophila melanogaster, from fertilization to death.
FBC:DOS
A collective term for stages 1-4.
FlyBase_development_CV
FBdv:00000054
Temporal ordering number - 25.
cleavage stage
A collective term for stages 1-4.
FBC:DOS
A collective term for stages 11 and 12.
FlyBase_development_CV
FBdv:00004450
Temporal ordering number - 300.
late extended germ band stage
A collective term for stages 11 and 12.
FBC:DOS
GO:0048477
oogenesis stage
FlyBase_development_CV
FBdv:00004886
Temporal ordering number - 10000.
oogenesis
A temporal subdivision of a developmental process.
djs93
2009-10-01T05:56:56Z
FBdv:00007010
FlyBase_development_CV
FBdv:00005259
developmental stage
A temporal subdivision of a developmental process.
FBC:DOS
Earliest stage of ovarian cyst development - lasts while the 16 cell cyst is within the germarium (region 3).
FlyBase_development_CV
FBdv:00005261
Temporal ordering number - 10010.
oogenesis stage S1
Earliest stage of ovarian cyst development - lasts while the 16 cell cyst is within the germarium (region 3).
FlyBase:FBrf0021038
FlyBase:FBrf0034074
FlyBase:FBrf0064777
Oogenesis stage that begins when the cyst leaves the germarium (from this point the cyst is referred to as an egg chamber). During this stage, polyploidation of the nurse cells begins, they reach a ploidy of 8C, and follicle cells start to divide.
FlyBase_development_CV
FBdv:00005262
Temporal ordering number - 10020.
oogenesis stage S2
Oogenesis stage that begins when the cyst leaves the germarium (from this point the cyst is referred to as an egg chamber). During this stage, polyploidation of the nurse cells begins, they reach a ploidy of 8C, and follicle cells start to divide.
FlyBase:FBrf0021038
FlyBase:FBrf0034074
FlyBase:FBrf0064777
Oogenesis stage that begins when the oocyte chromosomes condense into a karyosome attached to a distinctive spherical structure known as an endobody. The oocyte nucleolus disappears completely. During this stage, nurse cell ploidy reaches 16C.
FlyBase_development_CV
FBdv:00005263
Temporal ordering number - 10030.
oogenesis stage S3
Oogenesis stage that begins when the oocyte chromosomes condense into a karyosome attached to a distinctive spherical structure known as an endobody. The oocyte nucleolus disappears completely. During this stage, nurse cell ploidy reaches 16C.
FlyBase:FBrf0021038
FlyBase:FBrf0034074
FlyBase:FBrf0064777
Oogenesis stage that begins when the nurse cells chromosomes become bulbous. Nurse cell chromosomes during this stage are polytene and reach a ploidy of 32C. The egg chamber is oval shaped.
FlyBase_development_CV
FBdv:00005264
Temporal ordering number - 10040.
oogenesis stage S4
Oogenesis stage that begins when the nurse cells chromosomes become bulbous. Nurse cell chromosomes during this stage are polytene and reach a ploidy of 32C. The egg chamber is oval shaped.
FlyBase:FBrf0021038
FlyBase:FBrf0034074
FlyBase:FBrf0064777
Oogenesis stage that begins when nurse cell chromosomes are no longer bulbous - the association between homologs weakens so that these chromosomes no longer have a polytene structure. During this stage, posterior nurse cell nuclei have a higher ploidy (64C) than anterior ones.
FlyBase_development_CV
FBdv:00005265
Temporal ordering number - 10050.
oogenesis stage S5
Oogenesis stage that begins when nurse cell chromosomes are no longer bulbous - the association between homologs weakens so that these chromosomes no longer have a polytene structure. During this stage, posterior nurse cell nuclei have a higher ploidy (64C) than anterior ones.
FlyBase:FBrf0021038
FlyBase:FBrf0034074
FlyBase:FBrf0064777
Oogenesis stage during which follicle cell division ceases.
FlyBase_development_CV
FBdv:00005266
Temporal ordering number - 10060.
oogenesis stage S6
Oogenesis stage during which follicle cell division ceases.
FlyBase:FBrf0021038
FlyBase:FBrf0034074
FlyBase:FBrf0064777
Oogenesis stage during which polyploidation and enlargement of follicle cells begins. Nurse cell ploidy ranges from 256C (anterior) to 512C (posterior) and the egg chamber gains an elongated shape.
FlyBase_development_CV
FBdv:00005267
Temporal ordering number - 10070.
oogenesis stage S7
Oogenesis stage during which polyploidation and enlargement of follicle cells begins. Nurse cell ploidy ranges from 256C (anterior) to 512C (posterior) and the egg chamber gains an elongated shape.
FlyBase:FBrf0021038
FlyBase:FBrf0034074
FlyBase:FBrf0064777
Oogenesis stage which begins when yolk first appears in the oocyte. Follicle cell migration over the oocyte begins during this stage (although mostly occurs during stage 9).
FlyBase_development_CV
FBdv:00005268
Temporal ordering number - 10080.
oogenesis stage S8
Oogenesis stage which begins when yolk first appears in the oocyte. Follicle cell migration over the oocyte begins during this stage (although mostly occurs during stage 9).
FlyBase:FBrf0021038
FlyBase:FBrf0034074
FlyBase:FBrf0064777
Oogenesis stage that begins when the border cells begin to migrate. During this stage: the oocyte is about 1/3 the length of the egg chamber with its nucleus located antero-dorsally; follicle cell migration results in an anterior to posterior gradient of follicle cell thickness with posterior cells being thicker (-> columnar) and posterior cells thinner ( -> squamous); border cell migration begins and ends; secretion of vitelline membrane begins.
FlyBase_development_CV
FBdv:00005269
Temporal ordering number - 10090.
oogenesis stage S9
Oogenesis stage that begins when the border cells begin to migrate. During this stage: the oocyte is about 1/3 the length of the egg chamber with its nucleus located antero-dorsally; follicle cell migration results in an anterior to posterior gradient of follicle cell thickness with posterior cells being thicker (-> columnar) and posterior cells thinner ( -> squamous); border cell migration begins and ends; secretion of vitelline membrane begins.
FlyBase:FBrf0021038
FlyBase:FBrf0034074
FlyBase:FBrf0064777
Oogenesis stage that begins when all the oocyte associated follicular epithelium is columnar and all of the nurse cell associated follicular epithelium is completely squamous and ends with the beginning of nurse cell dumping.
FlyBase_development_CV
FBdv:00005270
Temporal ordering number - 10100.
oogenesis stage S10
Oogenesis stage that begins when all the oocyte associated follicular epithelium is columnar and all of the nurse cell associated follicular epithelium is completely squamous and ends with the beginning of nurse cell dumping.
FlyBase:FBrf0021038
FlyBase:FBrf0034074
FlyBase:FBrf0064777
Oogenesis stage which begins when all the oocyte associated follicular epithelium is columnar and all of the nurse cell associated follicular epithelium is completely squamous and ends when centripetal follicle migration begins. During this stage, the migrating border cells reach the oocyte. The oocyte is about 50% egg chamber length.
FlyBase_development_CV
FBdv:00005271
Temporal ordering number - 10110.
oogenesis stage S10A
Oogenesis stage which begins when all the oocyte associated follicular epithelium is columnar and all of the nurse cell associated follicular epithelium is completely squamous and ends when centripetal follicle migration begins. During this stage, the migrating border cells reach the oocyte. The oocyte is about 50% egg chamber length.
FlyBase:FBrf0021038
FlyBase:FBrf0034074
Oogenesis stage that begins when the centripetal follicle cells begin to migrate. As a result, the vitelline membrane extends into the opercular region. This stage ends when nurse cell dumping begins.
FlyBase_development_CV
FBdv:00005272
Temporal ordering number - 10120.
oogenesis stage S10B
Oogenesis stage that begins when the centripetal follicle cells begin to migrate. As a result, the vitelline membrane extends into the opercular region. This stage ends when nurse cell dumping begins.
FlyBase:FBrf0021038
FlyBase:FBrf0034074
FlyBase:FBrf0064777
Oogenesis stage that begins when nurse cell dumping begins and development of the wax layer begins. The dorsal appendages begin to form during this stage. This stage ends when dying nurse cells form an anterior cap to the oocyte.
FlyBase_development_CV
FBdv:00005273
Temporal ordering number - 10130.
oogenesis stage S11
Oogenesis stage that begins when nurse cell dumping begins and development of the wax layer begins. The dorsal appendages begin to form during this stage. This stage ends when dying nurse cells form an anterior cap to the oocyte.
FlyBase:FBrf0021038
FlyBase:FBrf0034074
FlyBase:FBrf0043885
FlyBase:FBrf0064777
Oogenesis stage that begins when dying nurse cells form an anterior cap to the oocyte. Shortly after this, nurse cell dumping and growth of the oocyte are complete. Elongation of the dorsal appendages and formation of the innermost chorionic layer and endochorion begins during this stage.
FlyBase_development_CV
FBdv:00005274
Temporal ordering number - 10160.
oogenesis stage S12
Oogenesis stage that begins when dying nurse cells form an anterior cap to the oocyte. Shortly after this, nurse cell dumping and growth of the oocyte are complete. Elongation of the dorsal appendages and formation of the innermost chorionic layer and endochorion begins during this stage.
FlyBase:FBrf0021038
FlyBase:FBrf0034074
FlyBase:FBrf0043885
FlyBase:FBrf0064777
Innermost chorionic layer and endochorion begin to form in the anterior of the follicle.
FlyBase_development_CV
FBdv:00005275
Temporal ordering number - 10170.
oogenesis stage S12A
Innermost chorionic layer and endochorion begin to form in the anterior of the follicle.
FlyBase:FBrf0043885
Secretion of innermost chorionic layer and endochorion begins in the main follicle cells.
FlyBase_development_CV
FBdv:00005276
Temporal ordering number - 10180.
oogenesis stage S12B
Secretion of innermost chorionic layer and endochorion begins in the main follicle cells.
FlyBase:FBrf0043885
Formation of specialized endochorion structures in the anterior of the follicle: branches in the developing dorsal appendages; compact endochorion lacking the pillars seen in the rest of the follicle.
FlyBase_development_CV
FBdv:00005277
Temporal ordering number - 10190.
oogenesis stage S12C
Formation of specialized endochorion structures in the anterior of the follicle: branches in the developing dorsal appendages; compact endochorion lacking the pillars seen in the rest of the follicle.
FlyBase:FBrf0021038
Oogenesis stage that begins when the micropyle begins to form. At the beginning of this stage, about 12-15 nurse cell nuclei remain at the anterior of the oocyte. By the end of this stage, none of these nuclei remain. Oocyte meiosis up to arrest at full metaphase I occurs during this stage.
FlyBase_development_CV
FBdv:00005278
Temporal ordering number - 10200.
oogenesis stage S13
Oogenesis stage that begins when the micropyle begins to form. At the beginning of this stage, about 12-15 nurse cell nuclei remain at the anterior of the oocyte. By the end of this stage, none of these nuclei remain. Oocyte meiosis up to arrest at full metaphase I occurs during this stage.
FlyBase:FBrf0021038
FlyBase:FBrf0029744
FlyBase:FBrf0034074
FlyBase:FBrf0064777
Oogenesis stage during which 12-15 nurse cell nuclei remain at the anterior of the oocyte. At this stage, the oocyte nucleus has reached its maximum volume and its chromosomes are compressed into a 5-7 micrometer karyosome.
FlyBase_development_CV
FBdv:00005279
Temporal ordering number - 10210. An alternative division of stage 13 into two sub-stages, A and B, has been defined on the basis of chorion development (see FBrf0043885). This ontology uses an alternative subdivision based on nurse cell nucleus number and oocyte meiosis, as the former at least, is easier to score than chorion ultrastructure.
oogenesis stage S13A
Oogenesis stage during which 12-15 nurse cell nuclei remain at the anterior of the oocyte. At this stage, the oocyte nucleus has reached its maximum volume and its chromosomes are compressed into a 5-7 micrometer karyosome.
FlyBase:FBrf0029744
Oogenesis stage during which 9-11 nurse cell nuclei remain at the anterior of the oocyte. During this stage, the nuclear membrane of the oocyte nucleus disappears, indicating the start of meiotic pro-metaphase.
FlyBase_development_CV
FBdv:00005280
Temporal ordering number - 10220. An alternative division of stage 13 into two sub-stages, A and B, has been defined on the basis of chorion development (see FBrf0043885). This ontology uses an alternative subdivision based on nurse cell nucleus number and oocyte meiosis, as the former at least, is easier to score than chorion ultrastructure.
oogenesis stage S13B
Oogenesis stage during which 9-11 nurse cell nuclei remain at the anterior of the oocyte. During this stage, the nuclear membrane of the oocyte nucleus disappears, indicating the start of meiotic pro-metaphase.
FlyBase:FBrf0029744
Oogenesis stage during which only 7-8 nurse cell nuclei remain at the anterior of the oocyte. At the beginning of this stage, oocyte chromosome bivalents separate from each other - indicating mid-prometaphase of oocyte meiosis.
FlyBase_development_CV
FBdv:00005281
Temporal ordering number - 10230.
oogenesis stage S13C
Oogenesis stage during which only 7-8 nurse cell nuclei remain at the anterior of the oocyte. At the beginning of this stage, oocyte chromosome bivalents separate from each other - indicating mid-prometaphase of oocyte meiosis.
FlyBase:FBrf0029744
Oogenesis stage during which only 5-6 nurse cell nuclei remain at the anterior of the oocyte. The oocyte nucleus is in late prometaphase:the bivalents arrange themselves in on the equatorial plane of the spindle; homologous centromeres are pulled towards the poles.
FlyBase_development_CV
FBdv:00005282
Temporal ordering number - 10240.
oogenesis stage S13D
Oogenesis stage during which only 5-6 nurse cell nuclei remain at the anterior of the oocyte. The oocyte nucleus is in late prometaphase:the bivalents arrange themselves in on the equatorial plane of the spindle; homologous centromeres are pulled towards the poles.
FlyBase:FBrf0029744
The last stage of oogenesis. This stage begins when no nurse cell nuclei remain at the anterior of the egg (chamber). Exochorion formation and secretion occurs during this stage. The dorsal appendages complete their elongation and the follicle cells die.
FlyBase_development_CV
FBdv:00005283
Temporal ordering number - 10260.
oogenesis stage S14
The last stage of oogenesis. This stage begins when no nurse cell nuclei remain at the anterior of the egg (chamber). Exochorion formation and secretion occurs during this stage. The dorsal appendages complete their elongation and the follicle cells die.
FlyBase:FBrf0043885
Secretion and formation of the outer endochorionic network by throughout the follicle. Crystallization of the innermost chorionic layer of the main body follicle cells.
FlyBase_development_CV
FBdv:00005284
Temporal ordering number - 10270.
oogenesis stage S14A
Secretion and formation of the outer endochorionic network by throughout the follicle. Crystallization of the innermost chorionic layer of the main body follicle cells.
FlyBase:FBrf0021038
FlyBase:FBrf0043885
Secretion of the exochorion begins and ends.
FlyBase_development_CV
FBdv:00005285
Temporal ordering number - 10280.
oogenesis stage S14B
Secretion of the exochorion begins and ends.
FlyBase:FBrf0021038
FlyBase:FBrf0043885
The stage of the Drosophila life-cycle from maturation of an egg to the end of fertilization. At the beginning of this stage, the nucleus is arrested in meiotic metaphase I. The completion of meiosis and the start of protein synthesis are triggered by ovulation. If the female has already mated, fertilization begins during meiosis.
FlyBase_development_CV
FBdv:00005286
Temporal ordering number - 10290.
egg stage
The stage of the Drosophila life-cycle from maturation of an egg to the end of fertilization. At the beginning of this stage, the nucleus is arrested in meiotic metaphase I. The completion of meiosis and the start of protein synthesis are triggered by ovulation. If the female has already mated, fertilization begins during meiosis.
FlyBase:FBrf0064779
FlyBase_development_CV
FBdv:00005287
Temporal ordering number - 10300.
unfertilized egg stage
FlyBase_development_CV
FBdv:00005288
Temporal ordering number - 10.
fertilized egg stage
The stage of the Drosophila life-cycle from fertilization to hatching.
FlyBase_development_CV
FBdv:00005289
Temporal ordering number - 20.
embryonic stage
The stage of the Drosophila life-cycle from fertilization to hatching.
FBC:DOS
Embryonic stage 1-3.
pre-blastoderm
FlyBase_development_CV
FBdv:00005290
Temporal ordering number - 30.
pre-blastoderm stage
Embryonic stage 1-3.
FBC:DOS
The embryonic stage that lasts from the end of fertilization to the end of the second nuclear division. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying).
FlyBase_development_CV
FBdv:00005291
Temporal ordering number - 40.
embryonic stage 1
The embryonic stage that lasts from the end of fertilization to the end of the second nuclear division. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying).
FlyBase:FBrf0064779
FlyBase:FBrf0089570
The first mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase_development_CV
FBdv:00005292
Temporal ordering number - 50.
embryonic cycle 1
The first mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase:FBrf0049535
Nuclear divisions 3-8. The egg cytoplasm contracts producing a clear separation from the vitelline membrane and empty spaces at the anterior and posterior. The cleavage nuclei migrate towards the periphery. Duration at 25 degrees C approximately 40 minutes (25-65 minutes AEL).
FlyBase_development_CV
FBdv:00005293
Temporal ordering number - 70.
embryonic stage 2
Nuclear divisions 3-8. The egg cytoplasm contracts producing a clear separation from the vitelline membrane and empty spaces at the anterior and posterior. The cleavage nuclei migrate towards the periphery. Duration at 25 degrees C approximately 40 minutes (25-65 minutes AEL).
FlyBase:FBrf0089570
The second mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase_development_CV
FBdv:00005294
Temporal ordering number - 60.
embryonic cycle 2
The second mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase:FBrf0049535
The third mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase_development_CV
FBdv:00005295
Temporal ordering number - 80.
embryonic cycle 3
The third mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase:FBrf0049535
The fourth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase_development_CV
FBdv:00005296
Temporal ordering number - 90.
embryonic cycle 4
The fourth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase:FBrf0049535
The fifth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase_development_CV
FBdv:00005297
Temporal ordering number - 100.
embryonic cycle 5
The fifth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase:FBrf0049535
The sixth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase_development_CV
FBdv:00005298
Temporal ordering number - 110.
embryonic cycle 6
The sixth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase:FBrf0049535
The seventh mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase_development_CV
FBdv:00005299
Temporal ordering number - 120.
embryonic cycle 7
The seventh mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase:FBrf0049535
The eighth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase_development_CV
FBdv:00005300
Temporal ordering number - 130.
embryonic cycle 8
The eighth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase:FBrf0049535
Nuclear division 9. The cleavage nuclei complete their migration to the periphery. Polar buds form at the posterior pole and divide once. Duration at 25 degrees C: approximately 15 minutes (65-80 minutes after egg laying).
FlyBase_development_CV
FBdv:00005301
Temporal ordering number - 140.
embryonic stage 3
Nuclear division 9. The cleavage nuclei complete their migration to the periphery. Polar buds form at the posterior pole and divide once. Duration at 25 degrees C: approximately 15 minutes (65-80 minutes after egg laying).
FlyBase:FBrf0089570
The ninth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase_development_CV
FBdv:00005302
Temporal ordering number - 150.
embryonic cycle 9
The ninth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase:FBrf0049535
The tenth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase_development_CV
FBdv:00005303
Temporal ordering number - 180.
embryonic cycle 10
The tenth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase:FBrf0049535
Embryonic stages 4 and 5.
blastoderm
FlyBase_development_CV
FBdv:00005304
Temporal ordering number - 160.
blastoderm stage
Embryonic stages 4 and 5.
FBC:DOS
FlyBase_development_CV
FBdv:00005305
syncytial blastoderm stage
true
Nuclear division 10-13. Polar buds divide twice and become tightly grouped at the posterior pole by the end of this stage. Nuclei visible at the rim of the embryo. Stage 4 ends with the beginning of cellularization. Duration at 25 degrees C: approximately 50 minutes (80-130 minutes after egg laying).
syncytial blastoderm
syncytial blastoderm stage
FlyBase_development_CV
FBdv:00005306
Temporal ordering number - 170.
embryonic stage 4
Nuclear division 10-13. Polar buds divide twice and become tightly grouped at the posterior pole by the end of this stage. Nuclei visible at the rim of the embryo. Stage 4 ends with the beginning of cellularization. Duration at 25 degrees C: approximately 50 minutes (80-130 minutes after egg laying).
FlyBase:FBrf0089570
The 11th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase_development_CV
FBdv:00005307
Temporal ordering number - 185.
embryonic cycle 11
The 11th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase:FBrf0049535
The 12th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase_development_CV
FBdv:00005308
Temporal ordering number - 190.
embryonic cycle 12
The 12th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase:FBrf0049535
The 13th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase_development_CV
FBdv:00005309
Temporal ordering number - 200.
embryonic cycle 13
The 13th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo.
FlyBase:FBrf0049535
FlyBase_development_CV
FBdv:00005310
cellular blastoderm stage
true
Cellularization. Stage 5 begins when cellularization starts. Near the end of this stage the pole cells begin to migrate dorsally and ventral midline cells acquire an irregular, wavy appearance. Stage 5 ends when ventral furrow formation becomes apparent. Duration at 25 degrees: approximately 40 minutes (130-170 minutes after egg laying).
cellular blastoderm
cellular blastoderm stage
FlyBase_development_CV
FBdv:00005311
Temporal ordering number - 210.
embryonic stage 5
Cellularization. Stage 5 begins when cellularization starts. Near the end of this stage the pole cells begin to migrate dorsally and ventral midline cells acquire an irregular, wavy appearance. Stage 5 ends when ventral furrow formation becomes apparent. Duration at 25 degrees: approximately 40 minutes (130-170 minutes after egg laying).
FlyBase:FBrf0089570
The 14th mitotic cell cycle of embryogenesis. This is the first round of nuclear division to occur in a cellularized embryo, so this is the first round of cell division. Embryonic cycle 14 mitosis is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains.
first blastoderm mitosis
FlyBase_development_CV
FBdv:00005312
Temporal ordering number - 255. The asynchronous nature of cycle 14 divisions means that this is not very useful for annotating stage. If possible a standard embryonic stage should be used instead.
embryonic cycle 14
The 14th mitotic cell cycle of embryogenesis. This is the first round of nuclear division to occur in a cellularized embryo, so this is the first round of cell division. Embryonic cycle 14 mitosis is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains.
FlyBase:FBrf0049535
FlyBase:FBrf0089570
first blastoderm mitosis
FlyBase:FBrf0089570
The interphase of embryonic cycle 14. This begins at the same time as cellularization and is of variable length depending on cell identity: embryonic cycle 14 M phase (14B) is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains.
embryonic cycle 14 interphase
FlyBase_development_CV
FBdv:00005313
Temporal ordering number - 256.
embryonic cycle 14A
The interphase of embryonic cycle 14. This begins at the same time as cellularization and is of variable length depending on cell identity: embryonic cycle 14 M phase (14B) is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains.
[FlyBase:FBrf0039741
embryonic cycle 14 interphase
FBC:DOS
The M-phase of embryonic cycle 14. This is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains.
embryonic cycle 14 M-phase
FlyBase_development_CV
FBdv:00005314
Temporal ordering number - 257. Not to be confused with mitotic domain 14B, which is a domain of cells in the dorsal midline of the head that don't undergo a 14th division (Foe, 1989). The asynchronous nature of cycle 14 divisions means that this is not very useful for annotating stage. If possible a standard embryonic stage should be used instead.
embryonic cycle 14B
The M-phase of embryonic cycle 14. This is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains.
FlyBase:FBrf0039741
embryonic cycle 14 M-phase
FBC:DOS
The 15th cell cycle of embryogenesis. Asynchronous.
second blastoderm mitosis
FlyBase_development_CV
FBdv:00005315
Temporal ordering number - 285. The asynchronous nature of cycle 15 divisions means that this is not very useful for annotating stage. If possible a standard embryonic stage should be used instead.
embryonic cycle 15
The 15th cell cycle of embryogenesis. Asynchronous.
FlyBase:FBrf0089570
second blastoderm mitosis
FlyBase:FBrf0089570
The 16th cell cycle division of embryogenesis. Asynchronous.
third blastoderm mitosis
FlyBase_development_CV
FBdv:00005316
Temporal ordering number - 295. The asynchronous nature of cycle 16 divisions means that this is not very useful for annotating stage. If possible a standard embryonic stage should be used instead.
embryonic cycle 16
The 16th cell cycle division of embryogenesis. Asynchronous.
FlyBase:FBrf0089570
third blastoderm mitosis
FlyBase:FBrf0089570
Stages during which gastrulation occurs. 6-8.
gastrula
FlyBase_development_CV
FBdv:00005317
Temporal ordering number - 220.
gastrula stage
Stages during which gastrulation occurs. 6-8.
FBC:DOS
Stage 6 begins when the ventral furrow becomes apparent, an event which is followed rapidly by the formation of the cephalic furrow. Stage 6 ends when the pole cells have adopted a dorsal (horizontal) position at the posterior. Duration at 25 degrees C: approximately 10 minutes (170-180 minutes after egg laying).
FlyBase_development_CV
FBdv:00005318
Temporal ordering number - 230.
embryonic stage 6
Stage 6 begins when the ventral furrow becomes apparent, an event which is followed rapidly by the formation of the cephalic furrow. Stage 6 ends when the pole cells have adopted a dorsal (horizontal) position at the posterior. Duration at 25 degrees C: approximately 10 minutes (170-180 minutes after egg laying).
FlyBase:FBrf0089570
Stage 7 begins when the pole cells have adopted a dorsal (horizontal) position at the posterior. Invagination of the anterior and posterior midgut and hindgut follows. The 'discoid plate' that carries the pole cells forms a pocket. Transverse furrows (dorsal folds) form on the dorsal surface. This stage ends when the anterior wall of the amnioproctodeal invagination starts moving anteriorly and the pole cells are no longer visible externally. Duration at 25 degrees C: approximately 10 minutes (180-190 minutes after egg laying).
FlyBase_development_CV
FBdv:00005319
Temporal ordering number - 240.
embryonic stage 7
Stage 7 begins when the pole cells have adopted a dorsal (horizontal) position at the posterior. Invagination of the anterior and posterior midgut and hindgut follows. The 'discoid plate' that carries the pole cells forms a pocket. Transverse furrows (dorsal folds) form on the dorsal surface. This stage ends when the anterior wall of the amnioproctodeal invagination starts moving anteriorly and the pole cells are no longer visible externally. Duration at 25 degrees C: approximately 10 minutes (180-190 minutes after egg laying).
FlyBase:FBrf0089570
FlyBase_development_CV
FBdv:00005320
germ band stage
true
Stages during which the germ band is extended - 9-12.
FlyBase_development_CV
FBdv:00005321
Temporal ordering number - 260.
extended germ band stage
Stages during which the germ band is extended - 9-12.
FBC:DOS
Stage 8 starts with the rapid phase of germ band extension and ends with the beginning of mesodermal segmentation. By the end of this stage germ band extension has progressed to the point where the proctodeal opening is at about 60% egg length and the dorsal folds (transverse furrows) are no longer visible. Duration at 25 degrees C: approximately 30 minutes (190-220 minutes after egg laying).
rapidly extending germ band stage
FlyBase_development_CV
FBdv:00005322
Temporal ordering number - 250.
embryonic stage 8
Stage 8 starts with the rapid phase of germ band extension and ends with the beginning of mesodermal segmentation. By the end of this stage germ band extension has progressed to the point where the proctodeal opening is at about 60% egg length and the dorsal folds (transverse furrows) are no longer visible. Duration at 25 degrees C: approximately 30 minutes (190-220 minutes after egg laying).
FlyBase:FBrf0089570
Stage 9 begins when mesodermal segmentation becomes (transiently) visible\, and ends with the appearance of the stomodeal invagination slightly ventral to the anterior pole. Duration at 25 degrees C: approximately 40 minutes (220-260 minutes after egg laying).
FlyBase_development_CV
FBdv:00005323
Temporal ordering number - 280.
embryonic stage 9
Stage 9 begins when mesodermal segmentation becomes (transiently) visible\, and ends with the appearance of the stomodeal invagination slightly ventral to the anterior pole. Duration at 25 degrees C: approximately 40 minutes (220-260 minutes after egg laying).
FlyBase:FBrf0089570
Stage 10 begins with the appearance of the stomodeal invagination, slightly ventral to the anterior pole. Periodic furrows appear in the embryonic epidermis around the middle of the stage. The germ band continues to extend, reaching its maximum extent of 75% egg length towards the end of the stage. The end of the stage is marked by the beginning of invagination of the tracheal placodes. Duration at 25 degrees : approximately 60 minutes (260-320 minutes after egg laying).
FlyBase_development_CV
FBdv:00005324
Temporal ordering number - 290.
embryonic stage 10
Stage 10 begins with the appearance of the stomodeal invagination, slightly ventral to the anterior pole. Periodic furrows appear in the embryonic epidermis around the middle of the stage. The germ band continues to extend, reaching its maximum extent of 75% egg length towards the end of the stage. The end of the stage is marked by the beginning of invagination of the tracheal placodes. Duration at 25 degrees : approximately 60 minutes (260-320 minutes after egg laying).
FlyBase:FBrf0089570
Stage 11 begins with the invagination of the tracheal placodes. Para-segmental furrow form and segment boundary furrows become deep folds. Within the head, gnathal protuberances become apparent. The end of this stage is signaled by the appearance of a distinct cleft at the posterior pole of the embryo, which becomes detached from the vitelline membrane. This marks the beginning of germ-band retraction. Duration at 25 degrees C: approximately 120 minutes (320-440 minutes after egg laying).
FlyBase_development_CV
FBdv:00005325
Temporal ordering number - 310.
embryonic stage 11
Stage 11 begins with the invagination of the tracheal placodes. Para-segmental furrow form and segment boundary furrows become deep folds. Within the head, gnathal protuberances become apparent. The end of this stage is signaled by the appearance of a distinct cleft at the posterior pole of the embryo, which becomes detached from the vitelline membrane. This marks the beginning of germ-band retraction. Duration at 25 degrees C: approximately 120 minutes (320-440 minutes after egg laying).
FlyBase:FBrf0089570
FlyBase_development_CV
FBdv:00005326
contracted germ band stage
true
Germ band retraction. Stage 12 begins when germ-band retraction starts and ends when this process is complete so that the prospective anal plate occupies the posterior pole. During this stage the posterior and anterior midgut primordia meet and fuse and the tracheal pits fuse to form the tracheal tree. Duration at 25 degrees C: approximately 120 minutes (440-560 minutes after egg laying).
retracting germ band stage
FlyBase_development_CV
FBdv:00005327
Temporal ordering number - 320.
embryonic stage 12
Germ band retraction. Stage 12 begins when germ-band retraction starts and ends when this process is complete so that the prospective anal plate occupies the posterior pole. During this stage the posterior and anterior midgut primordia meet and fuse and the tracheal pits fuse to form the tracheal tree. Duration at 25 degrees C: approximately 120 minutes (440-560 minutes after egg laying).
FlyBase:FBrf0089570
Stage 13 begins at the completion of germ-band retraction, when the prospective anal plate occupy the posterior pole. The dorsal ridge becomes apparent externally; the clypeolabrum retracts, leaving a triangular shaped gap at the anterior pole; the labium moves to the ventral midline. This stage ends when head involution begins. Duration at 25 degrees C: Approximately 60 minutes (560-620 minutes after egg laying).
contracted germ band stage
FlyBase_development_CV
FBdv:00005328
Temporal ordering number - 340.
embryonic stage 13
Stage 13 begins at the completion of germ-band retraction, when the prospective anal plate occupy the posterior pole. The dorsal ridge becomes apparent externally; the clypeolabrum retracts, leaving a triangular shaped gap at the anterior pole; the labium moves to the ventral midline. This stage ends when head involution begins. Duration at 25 degrees C: Approximately 60 minutes (560-620 minutes after egg laying).
FlyBase:FBrf0089570
FBdv:00005330
FlyBase_development_CV
FBdv:00005329
head involution stage
true
Stage 14 begins with the initiation of head involution. Closure of the midgut around the yolk and dorsal closure continue. Dorsal closure is 80% complete by the end of this stage. This stage ends with the appearance of the second midgut constriction. Duration at 25 degrees C: approximately 60 minutes (620-680 minutes after egg laying).
head involution stage
FlyBase_development_CV
FBdv:00005330
Temporal ordering number - 350.
embryonic stage 14
Stage 14 begins with the initiation of head involution. Closure of the midgut around the yolk and dorsal closure continue. Dorsal closure is 80% complete by the end of this stage. This stage ends with the appearance of the second midgut constriction. Duration at 25 degrees C: approximately 60 minutes (620-680 minutes after egg laying).
FlyBase:FBrf0089570
A collective term for stages 13-15.
FlyBase_development_CV
FBdv:00005331
Temporal ordering number - 330.
dorsal closure stage
A collective term for stages 13-15.
FBC:DOS
Stage 15 begins with the appearance of the second midgut constriction. During this stage the 1st and 3rd midgut constrictions form, dorsal closure is completed, and epidermal segmentation is accomplished. This stage ends when the intersegmental grooves can be distinguished at mid-dorsal level. Duration at 25 degrees C: approximately 100 minutes (680-780 minutes after egg laying).
FlyBase_development_CV
FBdv:00005332
Temporal ordering number - 360.
embryonic stage 15
Stage 15 begins with the appearance of the second midgut constriction. During this stage the 1st and 3rd midgut constrictions form, dorsal closure is completed, and epidermal segmentation is accomplished. This stage ends when the intersegmental grooves can be distinguished at mid-dorsal level. Duration at 25 degrees C: approximately 100 minutes (680-780 minutes after egg laying).
FlyBase:FBrf0089570
Embryonic stages 16-17.
FlyBase_development_CV
FBdv:00005333
Temporal ordering number - 370.
late embryonic stage
Embryonic stages 16-17.
FBC:DOS
Stage 16 begins when the intersegmental grooves can be distinguished at mid-dorsal level, and ends when the dorsal ridge (frontal sac) has overgrown the tip of the clypeolabrum, which is thereby enclosed in the atrium. During this stage the ventral cord retracts to about 60% egg length. Duration at 25 degrees C: approximately 180 minutes (780-960 minutes after egg laying).
FlyBase_development_CV
FBdv:00005334
Temporal ordering number - 380.
embryonic stage 16
Stage 16 begins when the intersegmental grooves can be distinguished at mid-dorsal level, and ends when the dorsal ridge (frontal sac) has overgrown the tip of the clypeolabrum, which is thereby enclosed in the atrium. During this stage the ventral cord retracts to about 60% egg length. Duration at 25 degrees C: approximately 180 minutes (780-960 minutes after egg laying).
FlyBase:FBrf0089570
Stage 17 begins when the dorsal ridge (frontal sac) has overgrown the tip of the clypeolabrum, which is thereby enclosed in the atrium. It lasts until hatching of the embryo (approximately 24 hours after egg laying), during which time much terminal differentiation occurs, the tracheal tree fills with air, so becoming completely visible, and the ventral cord continues to retract. Duration at 25 degrees C: approximately 8 hours (16-24 hours after egg laying).
FlyBase_development_CV
FBdv:00005335
Temporal ordering number - 390.
embryonic stage 17
Stage 17 begins when the dorsal ridge (frontal sac) has overgrown the tip of the clypeolabrum, which is thereby enclosed in the atrium. It lasts until hatching of the embryo (approximately 24 hours after egg laying), during which time much terminal differentiation occurs, the tracheal tree fills with air, so becoming completely visible, and the ventral cord continues to retract. Duration at 25 degrees C: approximately 8 hours (16-24 hours after egg laying).
FlyBase:FBrf0089570
The stage of the Drosophila life-cycle from hatching to the beginning of puparium formation.
FlyBase_development_CV
FBdv:00005336
Temporal ordering number - 400.
larval stage
The stage of the Drosophila life-cycle from hatching to the beginning of puparium formation.
FBC:DOS
The first larval instar begins at hatching and ends at the first larval molt. Anterior spiracles are not yet present; posterior spiracles have two openings each. Salivary glands are very small and all cells are uniform in size. Mouth hooks typically have one tooth. Duration at 25 degrees C: approximately 25 hours (24-49 hours after egg laying; 0-25 hours after hatching).
L1
first instar larva
FlyBase_development_CV
FBdv:00005337
Temporal ordering number - 410.
first instar larval stage
The first larval instar begins at hatching and ends at the first larval molt. Anterior spiracles are not yet present; posterior spiracles have two openings each. Salivary glands are very small and all cells are uniform in size. Mouth hooks typically have one tooth. Duration at 25 degrees C: approximately 25 hours (24-49 hours after egg laying; 0-25 hours after hatching).
FlyBase:FBrf0007733
The second larval instar begins at the first larval molt and ends at the second larval molt. Larvae are actively feeding and crawling in the food. Distinct anterior spiracles are present as enlargements at the end of the tracheal trunk, but not open to the outside; posterior spiracles have three openings each, and four groups of small unbranched hairs. The salivary glands extend to the first abdominal segment, and have cells that are uniform in size. Mouth hooks typically have two or three teeth. Duration at 25 degrees C: approximately 23 hours (49-72 hours after egg laying; 25-48 hours after hatching).
L2
second instar larva
FlyBase_development_CV
FBdv:00005338
Temporal ordering number - 420.
second instar larval stage
The second larval instar begins at the first larval molt and ends at the second larval molt. Larvae are actively feeding and crawling in the food. Distinct anterior spiracles are present as enlargements at the end of the tracheal trunk, but not open to the outside; posterior spiracles have three openings each, and four groups of small unbranched hairs. The salivary glands extend to the first abdominal segment, and have cells that are uniform in size. Mouth hooks typically have two or three teeth. Duration at 25 degrees C: approximately 23 hours (49-72 hours after egg laying; 25-48 hours after hatching).
FlyBase:FBrf0007733
The third larval instar begins at the second larval molt and ends at puparium formation. Anterior spiracles are open to the outside; posterior spiracles have three openings each, and four groups of large branched hairs. The salivary glands extend to the second abdominal segment, with cells larger in the posterior than in the anterior of the gland. Mouth hooks typically have 9-12 teeth. About 24 hours before pupariation (at 25 degree C), larvae stop feeding and climb away from their food. Duration at 25 degrees C: approximately 48 hours (72-120 hours after egg laying; 48-96 hours after hatching).
L3
FlyBase_development_CV
third instar larva
FBdv:00005339
Temporal ordering number - 430.
third instar larval stage
The third larval instar begins at the second larval molt and ends at puparium formation. Anterior spiracles are open to the outside; posterior spiracles have three openings each, and four groups of large branched hairs. The salivary glands extend to the second abdominal segment, with cells larger in the posterior than in the anterior of the gland. Mouth hooks typically have 9-12 teeth. About 24 hours before pupariation (at 25 degree C), larvae stop feeding and climb away from their food. Duration at 25 degrees C: approximately 48 hours (72-120 hours after egg laying; 48-96 hours after hatching).
FlyBase:FBrf0007733
Third instar larva prior to the wandering stage (approximately the first 24 hours of the third instar larval stage under standard conditions at 25'C.).
david
2008-11-13T11:51:56Z
FlyBase_development_CV
FBdv:00005340
Temporal ordering number - 440.
early third instar larval stage
Third instar larva prior to the wandering stage (approximately the first 24 hours of the third instar larval stage under standard conditions at 25'C.).
FlyBase:FBrf0049147
Stage of the third larval instar during which the larva wanders out of the food and climbs. Under optimum conditions at 25'C, this occurs approximately 24 hours after the start of the third instar larval stage.
david
2008-11-13T11:55:46Z
late third instar
post-feeding larva
FlyBase_development_CV
FBdv:00005341
Temporal ordering number - 460.
wandering third instar larval stage
Stage of the third larval instar during which the larva wanders out of the food and climbs. Under optimum conditions at 25'C, this occurs approximately 24 hours after the start of the third instar larval stage.
FlyBase:FBrf0049147
The prepupal stage begins at puparium formation and ends when larval/pupal apolysis is complete, as indicated by the completion of imaginal head sac eversion and the expulsion of the oral armature of the larva. Duration at 25 degrees C: approximately 12 hours. (120-132.2 hours after egg laying; 0-12.2 hours after puparium formation).
FlyBase_development_CV
FBdv:00005342
Temporal ordering number - 500.
prepupal stage
The prepupal stage begins at puparium formation and ends when larval/pupal apolysis is complete, as indicated by the completion of imaginal head sac eversion and the expulsion of the oral armature of the larva. Duration at 25 degrees C: approximately 12 hours. (120-132.2 hours after egg laying; 0-12.2 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
Extends from puparium formation through tanning of the pupal cuticle. Posterior spiracles and ridge between anterior spiracles tan orange. Wriggling stops completely. Puparium becomes brown to the unaided eye. Duration at 25 degrees C: approximately 20 minutes. (120-120.3 hours after egg laying; 0-0.3 hours after puparium formation).
pupal stage P1
puparium formation
white puparium stage
pupal stage P0
white prepupa
FlyBase_development_CV
FBdv:00005343
Temporal ordering number - 510.
prepupal stage P1
Extends from puparium formation through tanning of the pupal cuticle. Posterior spiracles and ridge between anterior spiracles tan orange. Wriggling stops completely. Puparium becomes brown to the unaided eye. Duration at 25 degrees C: approximately 20 minutes. (120-120.3 hours after egg laying; 0-0.3 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
puparium formation
FlyBase:FBrf0036849
white puparium stage
FlyBase:FBrf0036849
pupal stage P0
FlyBase:FBrf0036849
white prepupa
FlyBase:FBrf0036849
Male gonads become less distinct. Oral armature stops moving permanently. Dorsal medial abdominal contractions stop. Gas bubble becomes visible within abdomen. Duration at 25 degrees C: approximately 100 minutes. (120.3-122 hours after egg laying; 0.3-2 hours after puparium formation).
brown puparium stage
pupal stage P2
FlyBase_development_CV
FBdv:00005344
Temporal ordering number - 520.
prepupal stage P2
Male gonads become less distinct. Oral armature stops moving permanently. Dorsal medial abdominal contractions stop. Gas bubble becomes visible within abdomen. Duration at 25 degrees C: approximately 100 minutes. (120.3-122 hours after egg laying; 0.3-2 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
brown puparium stage
FlyBase:FBrf0036849
Ridge of the operculum becomes distinct. Puparium begins to separate from underlying epidermis. Becomes positively buoyant. Duration at 25 degrees C: approximately 4 hours, 45 minutes. (122-126.75 hours after egg laying; 2-6.75 hours after puparium formation).
bubble prepupa stage
pupal stage P3
FlyBase_development_CV
FBdv:00005345
Temporal ordering number - 530.
prepupal stage P3
Ridge of the operculum becomes distinct. Puparium begins to separate from underlying epidermis. Becomes positively buoyant. Duration at 25 degrees C: approximately 4 hours, 45 minutes. (122-126.75 hours after egg laying; 2-6.75 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
bubble prepupa stage
FlyBase:FBrf0036849
Prepupal stage P4 begins as the lateral trunk trachea become obscured and ends when the imaginal head sac is everted and the oral armature of the larva is expelled. Duration at 25 degrees C: approximately 5 hours, 30 minutes. (126.75-132.2 hours after egg laying; 6.75-12.2 hours after puparium formation).
cryptocephalic pupa
pupal stage P4
FlyBase_development_CV
FBdv:00005346
Temporal ordering number - 540.
prepupal stage P4
Prepupal stage P4 begins as the lateral trunk trachea become obscured and ends when the imaginal head sac is everted and the oral armature of the larva is expelled. Duration at 25 degrees C: approximately 5 hours, 30 minutes. (126.75-132.2 hours after egg laying; 6.75-12.2 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
cryptocephalic pupa
FlyBase:FBrf0036849
Lateral trunk tracheae become obscured. Dorsal medial abdominal contractions occur. Everted leg and wing discs become visible. Bubble appears in posterior of puparium, displacing the pupa anteriorly; abdominal bubble disappears. Duration at 25 degrees C: approximately 5 hours, 15 minutes. (126.75-132 hours after egg laying; 6.75-12 hours after puparium formation).
buoyant stage
pupal stage P4(i)
FlyBase_development_CV
FBdv:00005347
Temporal ordering number - 550.
prepupal stage P4(i)
Lateral trunk tracheae become obscured. Dorsal medial abdominal contractions occur. Everted leg and wing discs become visible. Bubble appears in posterior of puparium, displacing the pupa anteriorly; abdominal bubble disappears. Duration at 25 degrees C: approximately 5 hours, 15 minutes. (126.75-132 hours after egg laying; 6.75-12 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
buoyant stage
FlyBase:FBrf0036849
Bubble is displaced to anterior end of the puparium, and pupa withdraws to the posterior end. Imaginal head sac is everted and the oral armature of the larva is expelled. Duration at 25 degrees C: approximately 12 minutes. (132-132.2 hours after egg laying; 12-12.2 hours after puparium formation).
moving bubble stage
pupal stage P4(ii)
FlyBase_development_CV
FBdv:00005348
Temporal ordering number - 560.
prepupal stage P4(ii)
Bubble is displaced to anterior end of the puparium, and pupa withdraws to the posterior end. Imaginal head sac is everted and the oral armature of the larva is expelled. Duration at 25 degrees C: approximately 12 minutes. (132-132.2 hours after egg laying; 12-12.2 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
moving bubble stage
FlyBase:FBrf0036849
The pupal stage starts once larval/pupal apolysis is complete as indicated by the expulsion of the larval armature. Early in this stage, the legs and wings reach full extension along the abdomen. The stage ends when the pupal cuticle separates from the underlying epidermis (pupal/adult apolysis), and the eye cup becomes yellow at its periphery. Duration at 25 degrees C: approximately 32 hours. (132.2-164.3 hours after egg laying; 12.2-44.3 hours after puparium formation).
phanerocephalic pupa
FlyBase_development_CV
FBdv:00005349
Temporal ordering number - 570. DISAMBIGUATION: In Drosophila lab vernacular, the term 'pupal stage' is often used to refer to the entire period from formation of the puparium to eclosion. However, this does not correspond to the standard usage of 'pupal stage' for Cyclorrhaphous flies (for discussion see: FBrf0087128). Briefly: formation of the puparium (hardening of the larval cuticle) marks the beginning of the pre-pupal stage. The pupal stage begins following pupal/larval apolysis - detachment of the larval epidermis from the puparium. In Drosophila, the outward sign of the completion of apolysis is the eversion of the head and expulsion of the larval mouthparts (FBrf0036849). We use P-stage to refer to the stage from pupariation to eclosion, and restrict pupal stage to its standard usage.
pupal stage
The pupal stage starts once larval/pupal apolysis is complete as indicated by the expulsion of the larval armature. Early in this stage, the legs and wings reach full extension along the abdomen. The stage ends when the pupal cuticle separates from the underlying epidermis (pupal/adult apolysis), and the eye cup becomes yellow at its periphery. Duration at 25 degrees C: approximately 32 hours. (132.2-164.3 hours after egg laying; 12.2-44.3 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
phanerocephalic pupa
FlyBase:FBrf0036849
Pupal stage P5 starts when the legs and wings reach full extension along the abdomen and ends as the Malpighian tubules become prominent and green. Duration at 25 degrees C: approximately 6 hours, 30 minutes. (132.2-138.7 hours after egg laying; 12.2-18.7 hours after puparium formation).
FlyBase_development_CV
FBdv:00005350
Temporal ordering number - 580.
pupal stage P5
Pupal stage P5 starts when the legs and wings reach full extension along the abdomen and ends as the Malpighian tubules become prominent and green. Duration at 25 degrees C: approximately 6 hours, 30 minutes. (132.2-138.7 hours after egg laying; 12.2-18.7 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
Legs and wings reach full extension along abdomen. Enlarged initial segments of anterior pair Malpighian tubules move from thorax into abdomen. Translucent patch that lacks adhering fat body cells becomes discernible in the middle of the eye region. Pair of white Malpighian tubules becomes visible dorsally in the abdomen. Duration at 25 degrees C: approximately 66 minutes. (132.2-133.3 hours after egg laying; 12.2-13.3 hours after puparium formation).
Malpighian tubules migrating
FlyBase_development_CV
FBdv:00005351
Temporal ordering number - 590.
pupal stage P5(i)
Legs and wings reach full extension along abdomen. Enlarged initial segments of anterior pair Malpighian tubules move from thorax into abdomen. Translucent patch that lacks adhering fat body cells becomes discernible in the middle of the eye region. Pair of white Malpighian tubules becomes visible dorsally in the abdomen. Duration at 25 degrees C: approximately 66 minutes. (132.2-133.3 hours after egg laying; 12.2-13.3 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
Malpighian tubules migrating
FlyBase:FBrf0036849
Malpighian tubules become prominent and green. Duration at 25 degrees C: approximately 5 hours, 25 minutes. (133.3-138.7 hours after egg laying; 13.3-18.7 hours after puparium formation).
white Malpighian tubules stage
FlyBase_development_CV
FBdv:00005352
Temporal ordering number - 600.
pupal stage P5(ii)
Malpighian tubules become prominent and green. Duration at 25 degrees C: approximately 5 hours, 25 minutes. (133.3-138.7 hours after egg laying; 13.3-18.7 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
white Malpighian tubules stage
FlyBase:FBrf0036849
Dark green 'yellow body' appears between the anterior ends of the two Malpighian tubule segments, mid-dorsally at the anterior of the abdomen. Duration at 25 degrees C: approximately 13 hours, 45 minutes. (138.7-152.4 hours after egg laying; 18.7-32.4 hours after puparium formation).
green Malpighian tubules stage
FlyBase_development_CV
FBdv:00005353
Temporal ordering number - 610.
pupal stage P6
Dark green 'yellow body' appears between the anterior ends of the two Malpighian tubule segments, mid-dorsally at the anterior of the abdomen. Duration at 25 degrees C: approximately 13 hours, 45 minutes. (138.7-152.4 hours after egg laying; 18.7-32.4 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
green Malpighian tubules stage
FlyBase:FBrf0036849
The 'yellow body' moves back between the Malpighian tubules. The transparent pupal cuticle separates from the underlying epidermis. Eye cup becomes yellow at its perimeter. Duration at 25 degrees C: approximately 12 hours. (152.4-164.3 hours after egg laying; 32.4-44.3 hours after puparium formation).
yellow body stage
FlyBase_development_CV
FBdv:00005354
Temporal ordering number - 620.
pupal stage P7
The 'yellow body' moves back between the Malpighian tubules. The transparent pupal cuticle separates from the underlying epidermis. Eye cup becomes yellow at its perimeter. Duration at 25 degrees C: approximately 12 hours. (152.4-164.3 hours after egg laying; 32.4-44.3 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
yellow body stage
FlyBase:FBrf0036849
Pale yellow pigmentation spreads inwards across the eye. Eye color becomes bright yellow, then changes to amber. Duration at 25 degrees C: approximately 12 hours 20 minutes. (164.3-176.6 hours after egg laying; 44.3-56.6 hours after puparium formation).
pupal stage P8
yellow-eyed stage
FlyBase_development_CV
FBdv:00005355
Temporal ordering number - 630.
pharate adult stage P8
Pale yellow pigmentation spreads inwards across the eye. Eye color becomes bright yellow, then changes to amber. Duration at 25 degrees C: approximately 12 hours 20 minutes. (164.3-176.6 hours after egg laying; 44.3-56.6 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
yellow-eyed stage
FlyBase:FBrf0036849
Eye color darkens to deep amber, then becomes pale pink. Duration at 25 degrees C: approximately 18 hours. (176.6-194.5 hours after egg laying; 56.6-74.5 hours after puparium formation).
amber-eyed stage
pupal stage P9
FlyBase_development_CV
FBdv:00005356
Temporal ordering number - 640.
pharate adult stage P9
Eye color darkens to deep amber, then becomes pale pink. Duration at 25 degrees C: approximately 18 hours. (176.6-194.5 hours after egg laying; 56.6-74.5 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
amber-eyed stage
FlyBase:FBrf0036849
Eyes become bright red. Orbital and ocellar bristles and vibrissae darken. Duration at 25 degrees C: approximately 6 minutes. (194.5-194.6 hours after egg laying; 74.5-74.6 hours after puparium formation).
pupal stage P10
red-eye bald stage
FlyBase_development_CV
FBdv:00005357
Temporal ordering number - 650.
pharate adult stage P10
Eyes become bright red. Orbital and ocellar bristles and vibrissae darken. Duration at 25 degrees C: approximately 6 minutes. (194.5-194.6 hours after egg laying; 74.5-74.6 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
red-eye bald stage
FlyBase:FBrf0036849
Thoracic bristles become visible, and the tips of the wings turn grey. Duration at 25 degrees C: approximately 2 hours. (194.6-196.6 hours after egg laying; 74.6-76.6 hours after puparium formation).
pupal stage P11
FlyBase_development_CV
FBdv:00005358
Temporal ordering number - 660.
pharate adult stage P11
Thoracic bristles become visible, and the tips of the wings turn grey. Duration at 25 degrees C: approximately 2 hours. (194.6-196.6 hours after egg laying; 74.6-76.6 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
Dorsal thoracic microchaetes and macrochaetes become visible. Duration at 25 degrees C: approximately 80 minutes (194.6-195.5 hours after egg laying; 74.6-75.9 hours after puparium formation).
head bristles stage
pupal stage P11(i)
FlyBase_development_CV
FBdv:00005359
Temporal ordering number - 670.
pharate adult stage P11(i)
Dorsal thoracic microchaetes and macrochaetes become visible. Duration at 25 degrees C: approximately 80 minutes (194.6-195.5 hours after egg laying; 74.6-75.9 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
head bristles stage
FlyBase:FBrf0036849
Tips of folded wings become grey. Duration at 25 degrees C: approximately 45 minutes (195.5-196.6 hours after egg laying; 75.9-76.6 hours after puparium formation).
pupal stage P11(ii)
thoracic bristles stage
FlyBase_development_CV
FBdv:00005360
Temporal ordering number - 680.
pharate adult stage P11(ii)
Tips of folded wings become grey. Duration at 25 degrees C: approximately 45 minutes (195.5-196.6 hours after egg laying; 75.9-76.6 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
thoracic bristles stage
FlyBase:FBrf0036849
Pharate adult stage P12 begins as the abdominal tergite bristles become visible, and ends as the wings darken to black. Duration at 25 degrees C: approximately 2 hours. (196.6-198.6 hours after egg laying; 76.6-78.6 hours after puparium formation).
pupal stage P12
FlyBase_development_CV
FBdv:00005361
Temporal ordering number - 690.
pharate adult stage P12
Pharate adult stage P12 begins as the abdominal tergite bristles become visible, and ends as the wings darken to black. Duration at 25 degrees C: approximately 2 hours. (196.6-198.6 hours after egg laying; 76.6-78.6 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
Bristles of the abdominal tergites become visible, and the wings become grey. Duration at 25 degrees C: approximately 55 minutes. (196.6-197.5 hours after egg laying; 76.6-77.5 hours after puparium formation).
pupal stage P12(i)
wing tips grey stage
FlyBase_development_CV
FBdv:00005362
Temporal ordering number - 700.
pharate adult stage P12(i)
Bristles of the abdominal tergites become visible, and the wings become grey. Duration at 25 degrees C: approximately 55 minutes. (196.6-197.5 hours after egg laying; 76.6-77.5 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
wing tips grey stage
FlyBase:FBrf0036849
Sex combs darken in males. Wings darken to black. Duration at 25 degrees C: approximately 65 minutes. (197.5-198.6 hours after egg laying; 77.5-78.6 hours after puparium formation).
pupal stage P12(ii)
wings grey stage
FlyBase_development_CV
FBdv:00005363
Temporal ordering number - 710.
pharate adult stage P12(ii)
Sex combs darken in males. Wings darken to black. Duration at 25 degrees C: approximately 65 minutes. (197.5-198.6 hours after egg laying; 77.5-78.6 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
wings grey stage
FlyBase:FBrf0036849
Tarsal bristles darken and claws become black. Duration at 25 degrees C: approximately 3 hours, 20 minutes. (198.6-201.9 hours after egg laying; 78.6-81.9 hours after puparium formation).
pupal stage P13
wings black stage
FlyBase_development_CV
FBdv:00005364
Temporal ordering number - 720.
pharate adult stage P13
Tarsal bristles darken and claws become black. Duration at 25 degrees C: approximately 3 hours, 20 minutes. (198.6-201.9 hours after egg laying; 78.6-81.9 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
wings black stage
FlyBase:FBrf0036849
The meconium appears dorsally at the posterior tip of the abdomen. Duration at 25 degrees C: approximately 9 hours, 30 minutes (201.9-211.5 hours after egg laying; 81.9-91.5 hours after puparium formation).
mature bristles stage
pupal stage P14
FlyBase_development_CV
FBdv:00005365
Temporal ordering number - 730.
pharate adult stage P14
The meconium appears dorsally at the posterior tip of the abdomen. Duration at 25 degrees C: approximately 9 hours, 30 minutes (201.9-211.5 hours after egg laying; 81.9-91.5 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
mature bristles stage
FlyBase:FBrf0036849
Pharate adult stage P15 begins with the tanning of the tergites and ends with eclosion. Duration at 25 degrees C: approximately 8 hours, 30 minutes. (211.5-220 hours after egg laying; 91.5-100 hours after puparium formation).
pupal stage P15
FlyBase_development_CV
FBdv:00005366
Temporal ordering number - 740.
pharate adult stage P15
Pharate adult stage P15 begins with the tanning of the tergites and ends with eclosion. Duration at 25 degrees C: approximately 8 hours, 30 minutes. (211.5-220 hours after egg laying; 91.5-100 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
Tanning of the tergites obscures the Malpighian tubules and the 'yellow body'. Legs begin to twitch; fly is able to walk if puparium is removed prematurely. Ptilinum expands by hydrostatic pressure, opening the operculum. Duration at 25 degrees C: approximately 8 hours, 6 minutes. (211.5-219.6 hours after egg laying; 91.5-99.6 hours after puparium formation).
meconium stage
pupal stage P15(i)
FlyBase_development_CV
FBdv:00005367
Temporal ordering number - 750.
pharate adult stage P15(i)
Tanning of the tergites obscures the Malpighian tubules and the 'yellow body'. Legs begin to twitch; fly is able to walk if puparium is removed prematurely. Ptilinum expands by hydrostatic pressure, opening the operculum. Duration at 25 degrees C: approximately 8 hours, 6 minutes. (211.5-219.6 hours after egg laying; 91.5-99.6 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
meconium stage
FlyBase:FBrf0036849
Stage which starts when the operculum opens and ends when eclosion is completed. Duration at 25 degrees C: approximately 24 minutes. (219.6-220 hours after egg laying; 99.6-100 hours after puparium formation).
eclosion stage
pupal stage P15(ii)
FlyBase_development_CV
FBdv:00005368
Temporal ordering number - 760.
pharate adult stage P15(ii)
Stage which starts when the operculum opens and ends when eclosion is completed. Duration at 25 degrees C: approximately 24 minutes. (219.6-220 hours after egg laying; 99.6-100 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
eclosion stage
FlyBase:FBrf0036849
The stage of the Drosophila life-cycle from eclosion to death.
FlyBase_development_CV
FBdv:00005369
Temporal ordering number - 770.
adult stage
The stage of the Drosophila life-cycle from eclosion to death.
FBC:DOS
Newly eclosed adult stage. Animal free of pupal case. Runs rapidly to find site for wing expansion. Wings are folded back and black against a very pale abdomen.
FBdv:00005373
FlyBase_development_CV
adult stage I
FBdv:00005370
Temporal ordering number - 785. The time at which eclosed flies settle down for wing expansion can vary greatly. If they fail to find a suitable site then expansion can be delayed by several hours.
adult stage A1
Newly eclosed adult stage. Animal free of pupal case. Runs rapidly to find site for wing expansion. Wings are folded back and black against a very pale abdomen.
FlyBase:FBrf0049147
Stage, shortly after eclosion, during which the wings expand. During wing expansion, the abdomen pulsates and the hind legs stroke the wings vigorously for several minutes at a time. The stage ends when the wings are folded down over the abdomen, which has become broader and shorter, and the wing cuticle has lost its folds. The stage lasts around 15 minutes at 25'C.
FBdv:00005374
FlyBase_development_CV
adult stage II
FBdv:00005371
Temporal ordering number - 790.
adult stage A2
Stage, shortly after eclosion, during which the wings expand. During wing expansion, the abdomen pulsates and the hind legs stroke the wings vigorously for several minutes at a time. The stage ends when the wings are folded down over the abdomen, which has become broader and shorter, and the wing cuticle has lost its folds. The stage lasts around 15 minutes at 25'C.
FlyBase:FBrf0049147
true
true
true
FlyBase_development_CV
FBdv:00005412
This should be considered as a type of cell rather than as a stage. Please use FBbt:00005412.
gamete
true
The developing adult after pupal-adult apolysis, i.e.- from stage P8 (when yellow eye color first becomes visible through the pupal case), to eclosion. Duration at 25 degrees C: approximately 55.7 hours (164.3-220 hours after egg laying; 44.3-100 hours after puparium formation).
FlyBase_development_CV
FBdv:00006011
Temporal ordering number - 625.
pharate adult stage
The developing adult after pupal-adult apolysis, i.e.- from stage P8 (when yellow eye color first becomes visible through the pupal case), to eclosion. Duration at 25 degrees C: approximately 55.7 hours (164.3-220 hours after egg laying; 44.3-100 hours after puparium formation).
FlyBase:FBrf0036849
FlyBase:FBrf0048355
FlyBase:FBrf0049147
Adult stage immediately after wing expansion, during which tanning of the cuticle is completed. This stage lasts approximately 45 minutes at 25'C.
FBdv:00005375
FlyBase_development_CV
adult stage III
FBdv:00006012
Temporal ordering number - 800.
adult stage A3
Adult stage immediately after wing expansion, during which tanning of the cuticle is completed. This stage lasts approximately 45 minutes at 25'C.
FlyBase:FBrf0049147
david
2008-06-05T04:51:08Z
GO:0007283
FlyBase_development_CV
FBdv:00007000
Temporal ordering number - 20000.
spermatogenesis
The stage of the Drosophila life-cycle from the formation of the puparium (beginning of the prepupal stage) to eclosion.
david
2008-06-05T04:51:40Z
metamorphosis
FlyBase_development_CV
pupal stage
FBdv:00007001
Temporal ordering number - 490. DISAMBIGUATION: In Drosophila lab vernacular, the term 'pupal stage' is often used to refer to the entire period from formation of the puparium to eclosion. However, this does not correspond to the standard usage of 'pupal stage' for cyclorrhaphous flies (for discussion see: FBrf0087128). Briefly: formation of the puparium (hardening of the larval cuticle) marks the beginning of the pre-pupal stage. The pupal stage begins following pupal/larval apolysis - detachment of the larval epidermis from the puparium. In Drosophila, the outward sign of the completion of apolysis is the eversion of the head an expulsion of the larval mouthparts (FBrf0036849). We use P-stage to refer to the stage from pupariation to eclosion, and restrict pupal stage to its standard usage.
P-stage
The stage of the Drosophila life-cycle from the formation of the puparium (beginning of the prepupal stage) to eclosion.
FBC:DOS
Oogenesis stage that begins when nurse cell dumping begins and development of the wax layer begins and ends when the dorsal appendages begin to form.
FlyBase_development_CV
FBdv:00007002
Temporal ordering number - 10140.
oogenesis stage S11a
Oogenesis stage that begins when nurse cell dumping begins and development of the wax layer begins and ends when the dorsal appendages begin to form.
FlyBase:FBrf0043885
Oogenesis stage that begins when endochorion begins to form at the anterior pole, a process which includes the beginning of formation of the dorsal appendages. During this stage, the follicle cells secrete membranous vesicles that form irregular extracellular plaques. This stage ends when dying nurse cells form an anterior cap to the oocyte.
FlyBase_development_CV
FBdv:00007003
Temporal ordering number - 10150.
oogenesis stage S11b
Oogenesis stage that begins when endochorion begins to form at the anterior pole, a process which includes the beginning of formation of the dorsal appendages. During this stage, the follicle cells secrete membranous vesicles that form irregular extracellular plaques. This stage ends when dying nurse cells form an anterior cap to the oocyte.
FlyBase:FBrf0043885
Stage which begins when wandering third instar larva stops crawling. The larva everts its anterior spiracles during this stage.
FlyBase_development_CV
FBdv:00007004
Temporal ordering number - 470.
third instar larval stage L1
Stage which begins when wandering third instar larva stops crawling. The larva everts its anterior spiracles during this stage.
FlyBase:FBrf0036849
The anterior spiracles are fully everted, with 7-9 finger-like projections. The body shortens, withdrawing three apparent abdominal segments and the larva sticks to its substrate.
spiracles everted larva
FlyBase_development_CV
white prepupa
FBdv:00007005
Temporal ordering number - 480.
third instar larval stage L2
The anterior spiracles are fully everted, with 7-9 finger-like projections. The body shortens, withdrawing three apparent abdominal segments and the larva sticks to its substrate.
FlyBase:FBrf0036849
spiracles everted larva
FlyBase:FBrf0036849
white prepupa
FlyBase:FBrf0036849
Oogenesis stage during which the number of nurse cell nuclei at the anterior of the oocyte reduce from 4 to zero. The oocyte chromosomes reach full metaphase I during this stage, at which point meiosis is arrested (until fertilization).
david
2008-11-13T06:27:57Z
FlyBase_development_CV
FBdv:00007006
Temporal ordering number - 10250.
oogenesis stage S13E
Oogenesis stage during which the number of nurse cell nuclei at the anterior of the oocyte reduce from 4 to zero. The oocyte chromosomes reach full metaphase I during this stage, at which point meiosis is arrested (until fertilization).
FlyBase:FBrf0029744
Third instar larva from the beginning of wandering to the beginning of puparium formation.
david
2008-12-11T01:19:53Z
FlyBase_development_CV
FBdv:00007007
Temporal ordering number - 450.
late third instar larval stage
Third instar larva from the beginning of wandering to the beginning of puparium formation.
FBC:DOS
FlyBase_development_CV
FBdv:00007008
occurrent
true
djs93
2009-10-01T05:56:42Z
GO:0032502
FlyBase_development_CV
FBdv:00007009
developmental process
true
A cycle of nuclear division during the embryogenesis of Drosophila melanogaster. The first 13 cycles are synchronous throughout the embryo and occur their timing relative to other developmental processes is invariant. Later nuclear division cycles are asynchronous across the embryo although may be more locally synchronized.
djs93
2009-10-01T05:57:41Z
FlyBase_development_CV
FBdv:00007011
embryonic cycle
A cycle of nuclear division during the embryogenesis of Drosophila melanogaster. The first 13 cycles are synchronous throughout the embryo and occur their timing relative to other developmental processes is invariant. Later nuclear division cycles are asynchronous across the embryo although may be more locally synchronized.
FlyBase:FBrf0049535
FlyBase:FBrf0089570
A temporal subdivision of a Drosophila life, delimited by major transitions in the circumstances of the organism, such as: fertilization; hatching; pupal ecdysis; eclosion.
djs93
2009-10-01T05:59:22Z
life cycle stage
FlyBase_development_CV
FBdv:00007012
life stage
A temporal subdivision of a Drosophila life, delimited by major transitions in the circumstances of the organism, such as: fertilization; hatching; pupal ecdysis; eclosion.
FBC:DOS
Temporal subdivision of life based on time elapsed since some key developmental transition, such as fertilization, hatching or eclosion.
djs93
2010-09-29T12:25:36Z
FlyBase_development_CV
FBdv:00007013
age
Temporal subdivision of life based on time elapsed since some key developmental transition, such as fertilization, hatching or eclosion.
FBC:DOS
Temporal subdivision of adulthood in days post-eclosion.
djs93
2010-09-29T12:28:05Z
FlyBase_development_CV
FBdv:00007014
adult age in days
Temporal subdivision of adulthood in days post-eclosion.
FBC:DOS
The first two hours of embryonic stage 17 at 25'C. (Approximately 16-18 hours at 25'C after egg laying).
djs93
2011-04-26T11:57:15Z
FlyBase_development_CV
FBdv:00007015
Temporal ordering number - 391. Should not be used to stage embryos whose development is at temperatures other than 25'C.
embryonic stage 17(i)
The first two hours of embryonic stage 17 at 25'C. (Approximately 16-18 hours at 25'C after egg laying).
FBC:DOS
Hours 2-4 of embryonic stage 17 at 25'C. (Approximately 18-20 hours at 25'C after egg laying).
djs93
2011-04-26T12:00:15Z
FlyBase_development_CV
FBdv:00007016
Temporal ordering number - 392. Should not be used to stage embryos whose development is at temperatures other than 25'C.
embryonic stage 17(ii)
Hours 2-4 of embryonic stage 17 at 25'C. (Approximately 18-20 hours at 25'C after egg laying).
FBC:DOS
Hours 4-6 of embryonic stage 17 at 25'C. (Approximately 20-22 hours at 25'C after egg laying).
djs93
2011-04-26T12:01:18Z
FlyBase_development_CV
FBdv:00007017
Temporal ordering number - 393. Should not be used to stage embryos whose development is at temperatures other than 25'C.
embryonic stage 17(iii)
Hours 4-6 of embryonic stage 17 at 25'C. (Approximately 20-22 hours at 25'C after egg laying).
FBC:DOS
Hours 6-8 (the last two hours) of embryonic stage 17 at 25'C. (Approximately 22-24 hours at 25'C after egg laying).
djs93
2011-04-26T12:03:14Z
FlyBase_development_CV
FBdv:00007018
Temporal ordering number - 394. Should not be used to stage embryos whose development is at temperatures other than 25'C.
embryonic stage 17(iv)
Hours 6-8 (the last two hours) of embryonic stage 17 at 25'C. (Approximately 22-24 hours at 25'C after egg laying).
FBC:DOS
The substage of the wandering third instar larval stage, prior to the beginning of clearance of the gut.
FlyBase_development_CV
FBdv:00007019
Temporal ordering number - 462. This is commonly assayed by adding 0.5% bromophenol blue to the food and looking for wandering third instar larvae with the same color guts (dark blue) as feeding larvae (Andres and Thummel, 1994). Larvae at this stage are in chromosomal puff stage 1 (Andres and Thummel, 1994).
third instar - uncleared gut stage
The substage of the wandering third instar larval stage, prior to the beginning of clearance of the gut.
FlyBase:FBrf0076598
The substage of the wandering third instar larval stage when the larva has partially cleared its gut contents.
FlyBase_development_CV
FBdv:00007020
Temporal ordering number - 465. This is commonly assayed by adding 0.5% bromophenol blue to the food and looking for wandering third instar larvae with lighter colored guts (light blue) than feeding larvae (Andres and Thummel, 1994). Larvae at this stage are mainly in chromosomal puff stages 2-7 (Andres and Thummel, 1994).
third instar - partially cleared gut stage
The substage of the wandering third instar larval stage when the larva has partially cleared its gut contents.
FlyBase:FBrf0076598
The substage of the wandering third instar larval stage when the larva has cleared its gut contents.
FlyBase_development_CV
FBdv:00007021
Temporal ordering number - 467. This is commonly assayed by adding 0.5% bromophenol blue to the food and looking for wandering third instar larvae with guts lacking any blue stain (Andres and Thummel, 1994). Larvae at this stage are mainly in chromosomal puff stages 7-9 and pupate within 1-6 hours (Andres and Thummel, 1994.
third instar - cleared gut stage
The substage of the wandering third instar larval stage when the larva has cleared its gut contents.
FlyBase:FBrf0076598
The interphase (GO:0051325) of an embryonic cycle.
FlyBase_development_CV
FBdv:00007022
embryonic cycle interphase
The interphase (GO:0051325) of an embryonic cycle.
FBC:DOS
The M-phase (GO:0000279) of an embryonic cycle.
FlyBase_development_CV
FBdv:00007023
embryonic cycle M-phase
The M-phase (GO:0000279) of an embryonic cycle.
FBC:DOS
GO:0008150
FlyBase_development_CV
FBdv:00007024
biological process
The developmental stage that lasts from eclosion of the adult from the pupal case until tanning is complete (the end of adult stage A3).
djs93
2013-01-08T20:06:59Z
FlyBase_development_CV
FBdv:00007025
Temporal ordering number - 782.
immature adult stage
The developmental stage that lasts from eclosion of the adult from the pupal case until tanning is complete (the end of adult stage A3).
FBC:DOS
Life stage from the end of adult stage A3, when tanning is complete, to death.
djs93
2013-01-10T13:03:54Z
FlyBase_development_CV
FBdv:00007026
mature adult stage
Life stage from the end of adult stage A3, when tanning is complete, to death.
FBC:DOS
The day of eclosion.
FlyBase_development_CV
FBdv:00007075
Temporal ordering number - 780.
day 0 of adulthood
The day of eclosion.
FBC:DOS
1st day after eclosion.
FlyBase_development_CV
FBdv:00007076
Temporal ordering number - 810.
day 1 of adulthood
1st day after eclosion.
FBC:DOS
2nd day after eclosion.
FlyBase_development_CV
FBdv:00007077
Temporal ordering number - 820.
day 2 of adulthood
2nd day after eclosion.
FBC:DOS
3rd day after eclosion.
FlyBase_development_CV
FBdv:00007078
Temporal ordering number - 830.
day 3 of adulthood
3rd day after eclosion.
FBC:DOS
4th day after eclosion.
FlyBase_development_CV
FBdv:00007079
Temporal ordering number - 840.
day 4 of adulthood
4th day after eclosion.
FBC:DOS
5th day after eclosion.
FlyBase_development_CV
FBdv:00007080
Temporal ordering number - 850.
day 5 of adulthood
5th day after eclosion.
FBC:DOS
6th day after eclosion.
FlyBase_development_CV
FBdv:00007081
Temporal ordering number - 860.
day 6 of adulthood
6th day after eclosion.
FBC:DOS
7th day after eclosion.
FlyBase_development_CV
FBdv:00007082
Temporal ordering number - 870.
day 7 of adulthood
7th day after eclosion.
FBC:DOS
8th day after eclosion.
FlyBase_development_CV
FBdv:00007083
Temporal ordering number - 880.
day 8 of adulthood
8th day after eclosion.
FBC:DOS
9th day after eclosion.
FlyBase_development_CV
FBdv:00007084
Temporal ordering number - 890.
day 9 of adulthood
9th day after eclosion.
FBC:DOS
10th day after eclosion.
FlyBase_development_CV
FBdv:00007085
Temporal ordering number - 900.
day 10 of adulthood
10th day after eclosion.
FBC:DOS
11th day after eclosion.
FlyBase_development_CV
FBdv:00007086
Temporal ordering number - 910.
day 11 of adulthood
11th day after eclosion.
FBC:DOS
12th day after eclosion.
FlyBase_development_CV
FBdv:00007087
Temporal ordering number - 920.
day 12 of adulthood
12th day after eclosion.
FBC:DOS
13th day after eclosion.
FlyBase_development_CV
FBdv:00007088
Temporal ordering number - 930.
day 13 of adulthood
13th day after eclosion.
FBC:DOS
14th day after eclosion.
FlyBase_development_CV
FBdv:00007089
Temporal ordering number - 940.
day 14 of adulthood
14th day after eclosion.
FBC:DOS
15th day after eclosion.
FlyBase_development_CV
FBdv:00007090
Temporal ordering number - 950.
day 15 of adulthood
15th day after eclosion.
FBC:DOS
16th day after eclosion.
FlyBase_development_CV
FBdv:00007091
Temporal ordering number - 960.
day 16 of adulthood
16th day after eclosion.
FBC:DOS
17th day after eclosion.
FlyBase_development_CV
FBdv:00007092
Temporal ordering number - 970.
day 17 of adulthood
17th day after eclosion.
FBC:DOS
18th day after eclosion.
FlyBase_development_CV
FBdv:00007093
Temporal ordering number - 980.
day 18 of adulthood
18th day after eclosion.
FBC:DOS
19th day after eclosion.
FlyBase_development_CV
FBdv:00007094
Temporal ordering number - 990.
day 19 of adulthood
19th day after eclosion.
FBC:DOS
20th day after eclosion.
FlyBase_development_CV
FBdv:00007095
Temporal ordering number - 1000.
day 20 of adulthood
20th day after eclosion.
FBC:DOS
21st day after eclosion.
FlyBase_development_CV
FBdv:00007096
Temporal ordering number - 1010.
day 21 of adulthood
21st day after eclosion.
FBC:DOS
22nd day after eclosion.
FlyBase_development_CV
FBdv:00007097
Temporal ordering number - 1020.
day 22 of adulthood
22nd day after eclosion.
FBC:DOS
23rd day after eclosion.
FlyBase_development_CV
FBdv:00007098
Temporal ordering number - 1030.
day 23 of adulthood
23rd day after eclosion.
FBC:DOS
24th day after eclosion.
FlyBase_development_CV
FBdv:00007099
Temporal ordering number - 1040.
day 24 of adulthood
24th day after eclosion.
FBC:DOS
25th day after eclosion.
FlyBase_development_CV
FBdv:00007100
Temporal ordering number - 1050.
day 25 of adulthood
25th day after eclosion.
FBC:DOS
26th day after eclosion.
FlyBase_development_CV
FBdv:00007101
Temporal ordering number - 1060.
day 26 of adulthood
26th day after eclosion.
FBC:DOS
27th day after eclosion.
FlyBase_development_CV
FBdv:00007102
Temporal ordering number - 1070.
day 27 of adulthood
27th day after eclosion.
FBC:DOS
28th day after eclosion.
FlyBase_development_CV
FBdv:00007103
Temporal ordering number - 1080.
day 28 of adulthood
28th day after eclosion.
FBC:DOS
29th day after eclosion.
FlyBase_development_CV
FBdv:00007104
Temporal ordering number - 1090.
day 29 of adulthood
29th day after eclosion.
FBC:DOS
30th day after eclosion.
FlyBase_development_CV
FBdv:00007105
Temporal ordering number - 1100.
day 30 of adulthood
30th day after eclosion.
FBC:DOS
31st day after eclosion.
FlyBase_development_CV
FBdv:00007106
Temporal ordering number - 1110.
day 31 of adulthood
31st day after eclosion.
FBC:DOS
32nd day after eclosion.
FlyBase_development_CV
FBdv:00007107
Temporal ordering number - 1120.
day 32 of adulthood
32nd day after eclosion.
FBC:DOS
33rd day after eclosion.
FlyBase_development_CV
FBdv:00007108
Temporal ordering number - 1130.
day 33 of adulthood
33rd day after eclosion.
FBC:DOS
34th day after eclosion.
FlyBase_development_CV
FBdv:00007109
Temporal ordering number - 1140.
day 34 of adulthood
34th day after eclosion.
FBC:DOS
35th day after eclosion.
FlyBase_development_CV
FBdv:00007110
Temporal ordering number - 1150.
day 35 of adulthood
35th day after eclosion.
FBC:DOS
36th day after eclosion.
FlyBase_development_CV
FBdv:00007111
Temporal ordering number - 1160.
day 36 of adulthood
36th day after eclosion.
FBC:DOS
37th day after eclosion.
FlyBase_development_CV
FBdv:00007112
Temporal ordering number - 1170.
day 37 of adulthood
37th day after eclosion.
FBC:DOS
38th day after eclosion.
FlyBase_development_CV
FBdv:00007113
Temporal ordering number - 1180.
day 38 of adulthood
38th day after eclosion.
FBC:DOS
39th day after eclosion.
FlyBase_development_CV
FBdv:00007114
Temporal ordering number - 1190.
day 39 of adulthood
39th day after eclosion.
FBC:DOS
40th day after eclosion.
FlyBase_development_CV
FBdv:00007115
Temporal ordering number - 1200.
day 40 of adulthood
40th day after eclosion.
FBC:DOS
41st day after eclosion.
FlyBase_development_CV
FBdv:00007116
Temporal ordering number - 1210.
day 41 of adulthood
41st day after eclosion.
FBC:DOS
42nd day after eclosion.
FlyBase_development_CV
FBdv:00007117
Temporal ordering number - 1220.
day 42 of adulthood
42nd day after eclosion.
FBC:DOS
43rd day after eclosion.
FlyBase_development_CV
FBdv:00007118
Temporal ordering number - 1230.
day 43 of adulthood
43rd day after eclosion.
FBC:DOS
44th day after eclosion.
FlyBase_development_CV
FBdv:00007119
Temporal ordering number - 1240.
day 44 of adulthood
44th day after eclosion.
FBC:DOS
45th day after eclosion.
FlyBase_development_CV
FBdv:00007120
Temporal ordering number - 1250.
day 45 of adulthood
45th day after eclosion.
FBC:DOS
46th day after eclosion.
FlyBase_development_CV
FBdv:00007121
Temporal ordering number - 1260.
day 46 of adulthood
46th day after eclosion.
FBC:DOS
47th day after eclosion.
FlyBase_development_CV
FBdv:00007122
Temporal ordering number - 1270.
day 47 of adulthood
47th day after eclosion.
FBC:DOS
48th day after eclosion.
FlyBase_development_CV
FBdv:00007123
Temporal ordering number - 1280.
day 48 of adulthood
48th day after eclosion.
FBC:DOS
49th day after eclosion.
FlyBase_development_CV
FBdv:00007124
Temporal ordering number - 1290.
day 49 of adulthood
49th day after eclosion.
FBC:DOS
50th day after eclosion.
FlyBase_development_CV
FBdv:00007125
Temporal ordering number - 1300.
day 50 of adulthood
50th day after eclosion.
FBC:DOS
51st day after eclosion.
FlyBase_development_CV
FBdv:00007126
Temporal ordering number - 1310.
day 51 of adulthood
51st day after eclosion.
FBC:DOS
52nd day after eclosion.
FlyBase_development_CV
FBdv:00007127
Temporal ordering number - 1320.
day 52 of adulthood
52nd day after eclosion.
FBC:DOS
53rd day after eclosion.
FlyBase_development_CV
FBdv:00007128
Temporal ordering number - 1330.
day 53 of adulthood
53rd day after eclosion.
FBC:DOS
54th day after eclosion.
FlyBase_development_CV
FBdv:00007129
Temporal ordering number - 1340.
day 54 of adulthood
54th day after eclosion.
FBC:DOS
55th day after eclosion.
FlyBase_development_CV
FBdv:00007130
Temporal ordering number - 1350.
day 55 of adulthood
55th day after eclosion.
FBC:DOS
56th day after eclosion.
FlyBase_development_CV
FBdv:00007131
Temporal ordering number - 1360.
day 56 of adulthood
56th day after eclosion.
FBC:DOS
57th day after eclosion.
FlyBase_development_CV
FBdv:00007132
Temporal ordering number - 1370.
day 57 of adulthood
57th day after eclosion.
FBC:DOS
58th day after eclosion.
FlyBase_development_CV
FBdv:00007133
Temporal ordering number - 1380.
day 58 of adulthood
58th day after eclosion.
FBC:DOS
59th day after eclosion.
FlyBase_development_CV
FBdv:00007134
Temporal ordering number - 1390.
day 59 of adulthood
59th day after eclosion.
FBC:DOS
60th day after eclosion.
FlyBase_development_CV
FBdv:00007135
Temporal ordering number - 1400.
day 60 of adulthood
60th day after eclosion.
FBC:DOS
A collective term for stages 9 and 10.
FlyBase_development_CV
FBdv:00014201
Temporal ordering number - 270.
early extended germ band stage
A collective term for stages 9 and 10.
FBC:DOS
true
A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle.
M phase of mitotic cell cycle
M-phase of mitotic cell cycle
biological_process
GO:0000087
Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
mitotic M phase
A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle.
GOC:mtg_cell_cycle
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
GO:0007067
MIPS_funcat:10.03.01
MIPS_funcat:10.03.01.01
Wikipedia:Mitosis
biological_process
mitosis
GO:0000278
mitotic cell cycle
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
GOC:mah
ISBN:0815316194
Reactome:69278
A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase.
Wikipedia:M_phase
M-phase
biological_process
GO:0000279
Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
M phase
A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase.
GOC:mtg_cell_cycle
The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
MIPS_funcat:10.03.04
MIPS_funcat:10.03.04.07
biological_process
karyokinesis
GO:0000280
nuclear division
The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
GOC:mah
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
molecular process
GO:0005554
molecular function
molecular_function
GO:0003674
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
molecular_function
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
GOC:pdt
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Wikipedia:Enzyme
enzyme activity
molecular_function
GO:0003824
catalytic activity
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GOC:vw
ISBN:0198506732
enzyme activity
GOC:dph
GOC:tb
true
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
receptor binding
Wikipedia:Ligand_(biochemistry)
receptor ligand
molecular_function
receptor-associated protein activity
GO:0005102
Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'.
signaling receptor binding
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
GOC:bf
GOC:ceb
ISBN:0198506732
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
Wikipedia:Binding_(molecular)
ligand
molecular_function
GO:0005488
Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
binding
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
GOC:ceb
GOC:mah
ISBN:0198506732
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
GO:0001948
GO:0045308
MIPS_funcat:16.01
MIPS_funcat:18.01.07
Reactome:R-HSA-170835
Reactome:R-HSA-170846
protein amino acid binding
glycoprotein binding
molecular_function
GO:0005515
protein binding
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
GOC:go_curators
Reactome:R-HSA-170835
An anchoring protein, ZFYVE9 (SARA), recruits SMAD2/3
Reactome:R-HSA-170846
TGFBR2 recruits TGFBR1
The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).
phosphorus metabolism
biological_process
GO:0006793
phosphorus metabolic process
The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).
GOC:ai
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
MIPS_funcat:01.04
phosphate metabolism
biological_process
phosphate metabolic process
GO:0006796
phosphate-containing compound metabolic process
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
GOC:ai
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
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
MIPS_funcat:10
MIPS_funcat:10.03
Wikipedia:Cell_cycle
cell-division cycle
biological_process
GO:0007049
cell cycle
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
GOC:go_curators
GOC:mtg_cell_cycle
Any process that modulates the frequency, rate or extent of mitosis.
regulation of mitosis
biological_process
GO:0007088
regulation of mitotic nuclear division
Any process that modulates the frequency, rate or extent of mitosis.
GOC:go_curators
Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
Wikipedia:Cell_signaling
biological_process
GO:0007154
cell communication
Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
GOC:mah
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
GO:0023033
MIPS_funcat:30
Wikipedia:Signal_transduction
signaling cascade
signalling cascade
biological_process
signaling pathway
signalling pathway
GO:0007165
Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
signal transduction
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
GOC:go_curators
GOC:mtg_signaling_feb11
signalling pathway
GOC:mah
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
MIPS_funcat:41
biological_process
GO:0007275
Note that this term was 'developmental process'.
multicellular organism development
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
GOC:dph
GOC:ems
GOC:isa_complete
GOC:tb
Any process that modulates the rate or extent of progress through the mitotic cell cycle.
mitotic cell cycle modulation
mitotic cell cycle regulation
modulation of mitotic cell cycle progression
regulation of mitotic cell cycle progression
regulation of progression through mitotic cell cycle
biological_process
mitotic cell cycle regulator
GO:0007346
regulation of mitotic cell cycle
Any process that modulates the rate or extent of progress through the mitotic cell cycle.
GOC:dph
GOC:go_curators
GOC:tb
regulation of progression through mitotic cell cycle
GOC:dph
GOC:tb
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
janelomax
2012-09-19T15:05:24Z
GO:0000004
GO:0007582
GO:0044699
Wikipedia:Biological_process
biological process
physiological process
biological_process
single organism process
single-organism process
GO:0008150
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this.
biological_process
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
GOC:pdt
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
janelomax
2012-10-17T15:46:40Z
GO:0044236
GO:0044710
MIPS_funcat:01
Wikipedia:Metabolism
metabolism
metabolic process resulting in cell growth
metabolism resulting in cell growth
multicellular organism metabolic process
biological_process
single-organism metabolic process
GO:0008152
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
metabolic process
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
GOC:go_curators
ISBN:0198547684
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
GO:0009795
embryogenesis and morphogenesis
Wikipedia:Embryogenesis
embryogenesis
embryonal development
biological_process
GO:0009790
embryo development
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
GOC:go_curators
GOC:isa_complete
GOC:mtg_sensu
Any process that modulates the frequency, rate or extent of replication and segregation of genetic material in the embryo.
embryonic mitotic cell cycle modulation
embryonic mitotic cell cycle regulation
modulation of embryonic mitotic cell cycle progression
regulation of embryonic mitotic cell cycle
regulation of embryonic mitotic cell cycle progression
regulation of progression through embryonic mitotic cell cycle
biological_process
embryonic mitotic cell cycle regulator
GO:0009794
regulation of mitotic cell cycle, embryonic
Any process that modulates the frequency, rate or extent of replication and segregation of genetic material in the embryo.
GOC:dph
GOC:go_curators
GOC:tb
regulation of embryonic mitotic cell cycle
GOC:dph
GOC:tb
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GO:0044252
down regulation of metabolic process
down-regulation of metabolic process
downregulation of metabolic process
negative regulation of metabolism
negative regulation of organismal metabolism
inhibition of metabolic process
inhibition of organismal metabolic process
negative regulation of multicellular organismal metabolic process
biological_process
GO:0009892
negative regulation of metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GO:0044253
positive regulation of metabolism
up regulation of metabolic process
up-regulation of metabolic process
upregulation of metabolic process
activation of metabolic process
positive regulation of multicellular organismal metabolic process
positive regulation of organismal metabolism
stimulation of metabolic process
stimulation of organismal metabolic process
up-regulation of organismal metabolic process
biological_process
GO:0009893
positive regulation of metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GOC:go_curators
Any process that modulates the frequency, rate or extent of signal transduction.
GO:0035466
biological_process
regulation of signaling pathway
regulation of signalling pathway
GO:0009966
regulation of signal transduction
Any process that modulates the frequency, rate or extent of signal transduction.
GOC:sm
regulation of signalling pathway
GOC:mah
Any process that activates or increases the frequency, rate or extent of signal transduction.
GO:0035468
up regulation of signal transduction
up-regulation of signal transduction
upregulation of signal transduction
activation of signal transduction
stimulation of signal transduction
biological_process
positive regulation of signaling pathway
positive regulation of signalling pathway
GO:0009967
positive regulation of signal transduction
Any process that activates or increases the frequency, rate or extent of signal transduction.
GOC:sm
positive regulation of signalling pathway
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
GO:0035467
down regulation of signal transduction
down-regulation of signal transduction
downregulation of signal transduction
inhibition of signal transduction
biological_process
negative regulation of signaling pathway
negative regulation of signalling pathway
GO:0009968
negative regulation of signal transduction
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
GOC:sm
negative regulation of signalling pathway
GOC:mah
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
janelomax
2012-12-11T16:56:55Z
GO:0008151
GO:0044763
GO:0050875
cell physiology
cellular physiological process
cell growth and/or maintenance
biological_process
single-organism cellular process
GO:0009987
cellular process
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:go_curators
GOC:isa_complete
Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
regulation of receptor activity
biological_process
GO:0010469
regulation of signaling receptor activity
Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
GOC:dph
GOC:tb
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
biological_process
GO:0010562
positive regulation of phosphorus metabolic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
GOC:dph
GOC:tb
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
biological_process
GO:0010563
negative regulation of phosphorus metabolic process
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
GOC:dph
GOC:tb
Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
biological_process
GO:0010564
regulation of cell cycle process
Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
GOC:dph
GOC:tb
Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
positive regulation of organelle organisation
biological_process
positive regulation of organelle organization and biogenesis
GO:0010638
positive regulation of organelle organization
Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
GOC:dph
GOC:tb
positive regulation of organelle organisation
GOC:mah
positive regulation of organelle organization and biogenesis
GOC:mah
Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
negative regulation of organelle organisation
biological_process
negative regulation of organelle organization and biogenesis
GO:0010639
negative regulation of organelle organization
Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
GOC:dph
GOC:tb
negative regulation of organelle organisation
GOC:mah
negative regulation of organelle organization and biogenesis
GOC:mah
Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
biological_process
GO:0010646
regulation of cell communication
Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
GOC:dph
GOC:tb
Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
biological_process
GO:0010647
positive regulation of cell communication
Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
GOC:dph
GOC:tb
Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
biological_process
GO:0010648
negative regulation of cell communication
Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
GOC:dph
GOC:tb
Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
tanyaberardini
2009-04-27T09:53:22Z
biological_process
GO:0010948
negative regulation of cell cycle process
Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
GOC:dph
GOC:tb
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
GO:0044235
GO:0071842
MIPS_funcat:42
cell organisation
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
biological_process
cell organization and biogenesis
GO:0016043
cellular component organization
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
GOC:ai
GOC:jl
GOC:mah
cellular component organisation at cellular level
GOC:mah
cellular component organisation in other organism
GOC:mah
cell organization and biogenesis
GOC:mah
true
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Reactome:R-HSA-6788855
Reactome:R-HSA-6788867
phosphokinase activity
molecular_function
GO:0016301
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
kinase activity
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
ISBN:0198506732
Reactome:R-HSA-6788855
FN3KRP phosphorylates PsiAm, RibAm
Reactome:R-HSA-6788867
FN3K phosphorylates ketosamines
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
Wikipedia:Phosphorylation
biological_process
GO:0016310
phosphorylation
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
ISBN:0198506732
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
EC:2
Reactome:R-HSA-1483089
Reactome:R-HSA-1483186
Reactome:R-HSA-5668414
Reactome:R-HSA-6787403
Reactome:R-HSA-8868783
molecular_function
GO:0016740
transferase activity
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
ISBN:0198506732
Reactome:R-HSA-1483089
PE is converted to PS by PTDSS2
Reactome:R-HSA-1483186
PC is converted to PS by PTDSS1
Reactome:R-HSA-5668414
TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK
Reactome:R-HSA-6787403
GTPBP3 and MTO1 transform uridine-34 yielding 5-taurinomethyluridine-34 in tRNA
Reactome:R-HSA-8868783
TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
EC:2.7
molecular_function
GO:0016772
Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
transferase activity, transferring phosphorus-containing groups
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
GOC:jl
ISBN:0198506732
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
regulation of phosphate metabolism
biological_process
GO:0019220
regulation of phosphate metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
GOC:go_curators
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GO:0044246
regulation of metabolism
regulation of multicellular organismal metabolic process
regulation of organismal metabolic process
biological_process
GO:0019222
regulation of metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GOC:go_curators
regulation of organismal metabolic process
GOC:tb
The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.
biological_process
GO:0022402
cell cycle process
The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.
GOC:isa_complete
GOC:mtg_cell_cycle
One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events.
biological_process
GO:0022403
cell cycle phase
One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events.
GOC:mtg_cell_cycle
Any process that modulates the frequency, rate or extent of a signaling process.
2010-02-16T09:30:50Z
biological_process
regulation of signaling process
regulation of signalling process
GO:0023051
regulation of signaling
Any process that modulates the frequency, rate or extent of a signaling process.
GOC:mtg_signal
regulation of signaling process
GOC:bf
regulation of signalling process
GOC:mah
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
janelomax
2010-02-16T09:30:50Z
GO:0023046
GO:0044700
biological signaling
signaling process
signalling
biological_process
signalling process
single organism signaling
GO:0023052
Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
signaling
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
GOC:mtg_signal
GOC:mtg_signaling_feb11
GOC:signaling
signalling process
GOC:mah
Any process that activates, maintains or increases the frequency, rate or extent of a signaling process.
2010-02-16T09:30:50Z
positive regulation of signalling process
biological_process
positive regulation of signaling process
GO:0023056
positive regulation of signaling
Any process that activates, maintains or increases the frequency, rate or extent of a signaling process.
GOC:mtg_signal
positive regulation of signalling process
GOC:mah
positive regulation of signaling process
GOC:bf
Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.
2010-02-16T09:30:50Z
biological_process
negative regulation of signaling process
negative regulation of signalling process
GO:0023057
negative regulation of signaling
Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.
GOC:mtg_signal
negative regulation of signaling process
GOC:bf
negative regulation of signalling process
GOC:mah
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed.
MIPS_funcat:18.02.07
molecular_function
GO:0030545
receptor regulator activity
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed.
GOC:ceb
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased.
receptor activator activity
molecular_function
GO:0030546
signaling receptor activator activity
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased.
GOC:ceb
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
regulation of cellular metabolism
biological_process
GO:0031323
regulation of cellular metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
down regulation of cellular metabolic process
down-regulation of cellular metabolic process
downregulation of cellular metabolic process
negative regulation of cellular metabolism
inhibition of cellular metabolic process
biological_process
GO:0031324
negative regulation of cellular metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
GOC:mah
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
positive regulation of cellular metabolism
up regulation of cellular metabolic process
up-regulation of cellular metabolic process
upregulation of cellular metabolic process
activation of cellular metabolic process
stimulation of cellular metabolic process
biological_process
GO:0031325
positive regulation of cellular metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
down regulation of protein binding
down-regulation of protein binding
downregulation of protein binding
inhibition of protein binding
biological_process
GO:0032091
negative regulation of protein binding
Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
GOC:mah
Any process that activates or increases the frequency, rate or extent of protein binding.
up regulation of protein binding
up-regulation of protein binding
upregulation of protein binding
activation of protein binding
stimulation of protein binding
biological_process
GO:0032092
positive regulation of protein binding
Any process that activates or increases the frequency, rate or extent of protein binding.
GOC:mah
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
janelomax
2012-09-19T16:07:47Z
GO:0044707
GO:0050874
organismal physiological process
biological_process
single-multicellular organism process
GO:0032501
multicellular organismal process
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
GOC:curators
GOC:dph
GOC:isa_complete
GOC:tb
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
janelomax
2012-12-19T12:21:31Z
GO:0044767
development
biological_process
single-organism developmental process
GO:0032502
developmental process
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
GOC:isa_complete
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
regulation of organelle organisation
biological_process
regulation of organelle organization and biogenesis
GO:0033043
regulation of organelle organization
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
GOC:mah
regulation of organelle organisation
GOC:mah
regulation of organelle organization and biogenesis
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
down regulation of kinase activity
down-regulation of kinase activity
downregulation of kinase activity
inhibition of kinase activity
kinase inhibitor
biological_process
GO:0033673
negative regulation of kinase activity
Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GOC:mah
Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
up regulation of kinase activity
up-regulation of kinase activity
upregulation of kinase activity
kinase activator
stimulation of kinase activity
biological_process
GO:0033674
positive regulation of kinase activity
Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GOC:mah
Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
rfoulger
2011-08-01T02:45:27Z
GO:0004872
GO:0019041
receptor activity
receptor activity involved in signal transduction
molecular_function
GO:0038023
signaling receptor activity
Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
GOC:bf
GOC:signaling
receptor activity involved in signal transduction
GOC:bf
Any process that activates or increases the frequency, rate or extent of embryonic development.
up regulation of embryonic development
up-regulation of embryonic development
upregulation of embryonic development
activation of embryonic development
stimulation of embryonic development
biological_process
GO:0040019
positive regulation of embryonic development
Any process that activates or increases the frequency, rate or extent of embryonic development.
GOC:go_curators
Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
biological_process
GO:0042325
regulation of phosphorylation
Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
GOC:jl
Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
down regulation of phosphorylation
down-regulation of phosphorylation
downregulation of phosphorylation
inhibition of phosphorylation
biological_process
GO:0042326
negative regulation of phosphorylation
Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
GOC:jl
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
up regulation of phosphorylation
up-regulation of phosphorylation
upregulation of phosphorylation
activation of phosphorylation
stimulation of phosphorylation
biological_process
GO:0042327
positive regulation of phosphorylation
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
GOC:jl
Any process that activates or increases the activity of an enzyme.
GO:0048554
MIPS_funcat:18.02.01.01
positive regulation of enzyme activity
up regulation of enzyme activity
up-regulation of enzyme activity
upregulation of enzyme activity
activation of enzyme activity
activation of metalloenzyme activity
positive regulation of metalloenzyme activity
stimulation of enzyme activity
stimulation of metalloenzyme activity
up regulation of metalloenzyme activity
up-regulation of metalloenzyme activity
upregulation of metalloenzyme activity
biological_process
GO:0043085
positive regulation of catalytic activity
Any process that activates or increases the activity of an enzyme.
GOC:ebc
GOC:jl
GOC:tb
GOC:vw
positive regulation of enzyme activity
GOC:tb
Any process that stops or reduces the activity of an enzyme.
GO:0048553
down regulation of enzyme activity
down-regulation of enzyme activity
down-regulation of metalloenzyme activity
downregulation of enzyme activity
negative regulation of enzyme activity
down regulation of metalloenzyme activity
downregulation of metalloenzyme activity
inhibition of enzyme activity
inhibition of metalloenzyme activity
negative regulation of metalloenzyme activity
biological_process
GO:0043086
negative regulation of catalytic activity
Any process that stops or reduces the activity of an enzyme.
GOC:ebc
GOC:jl
GOC:tb
GOC:vw
negative regulation of enzyme activity
GOC:tb
Any process that modulates the frequency, rate or extent of protein binding.
biological_process
GO:0043393
regulation of protein binding
Any process that modulates the frequency, rate or extent of protein binding.
GOC:go_curators
Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
biological_process
GO:0043549
regulation of kinase activity
Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GOC:bf
Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
jane
2009-04-21T04:07:27Z
biological_process
GO:0044092
negative regulation of molecular function
Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
GO:jl
Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
jane
2009-04-21T04:11:06Z
biological_process
GO:0044093
positive regulation of molecular function
Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
GO:jl
The chemical reactions and pathways by which individual cells transform chemical substances.
cellular metabolism
biological_process
intermediary metabolism
GO:0044237
cellular metabolic process
The chemical reactions and pathways by which individual cells transform chemical substances.
GOC:go_curators
intermediary metabolism
GOC:mah
A distinct period or stage in a biological process or cycle.
janelomax
2014-07-16T13:12:40Z
biological_process
GO:0044848
Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase.
biological phase
A distinct period or stage in a biological process or cycle.
GOC:jl
The eukaryotic cell cycle in which a cell is duplicated without changing ploidy, occurring in the embryo.
biological_process
GO:0045448
mitotic cell cycle, embryonic
The eukaryotic cell cycle in which a cell is duplicated without changing ploidy, occurring in the embryo.
GOC:go_curators
Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
down regulation of progression through cell cycle
down-regulation of progression through cell cycle
downregulation of progression through cell cycle
negative regulation of cell cycle progression
negative regulation of progression through cell cycle
inhibition of progression through cell cycle
biological_process
GO:0045786
negative regulation of cell cycle
Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
GOC:dph
GOC:go_curators
GOC:tb
Any process that activates or increases the rate or extent of progression through the cell cycle.
positive regulation of cell cycle progression
positive regulation of progression through cell cycle
up regulation of progression through cell cycle
up-regulation of progression through cell cycle
upregulation of progression through cell cycle
activation of progression through cell cycle
stimulation of progression through cell cycle
biological_process
GO:0045787
positive regulation of cell cycle
Any process that activates or increases the rate or extent of progression through the cell cycle.
GOC:go_curators
positive regulation of progression through cell cycle
GOC:dph
GOC:tb
Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother.
down regulation of mitosis
down-regulation of mitosis
downregulation of mitosis
negative regulation of mitosis
inhibition of mitosis
biological_process
GO:0045839
negative regulation of mitotic nuclear division
Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother.
GOC:dph
GOC:go_curators
GOC:tb
Any process that activates or increases the frequency, rate or extent of mitosis.
positive regulation of mitosis
up regulation of mitosis
up-regulation of mitosis
upregulation of mitosis
activation of mitosis
mitogenic activity
stimulation of mitosis
biological_process
GO:0045840
positive regulation of mitotic nuclear division
Any process that activates or increases the frequency, rate or extent of mitosis.
GOC:go_curators
Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle.
down regulation of progression through mitotic cell cycle
down-regulation of progression through mitotic cell cycle
downregulation of progression through mitotic cell cycle
negative regulation of mitotic cell cycle progression
negative regulation of progression through mitotic cell cycle
inhibition of progression through mitotic cell cycle
biological_process
GO:0045930
negative regulation of mitotic cell cycle
Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle.
GOC:dph
GOC:go_curators
GOC:tb
negative regulation of progression through mitotic cell cycle
GOC:dph
GOC:tb
Any process that activates or increases the rate or extent of progression through the mitotic cell cycle.
positive regulation of mitotic cell cycle progression
positive regulation of progression through mitotic cell cycle
up regulation of progression through mitotic cell cycle
up-regulation of progression through mitotic cell cycle
upregulation of progression through mitotic cell cycle
activation of progression through mitotic cell cycle
stimulation of progression through mitotic cell cycle
biological_process
GO:0045931
positive regulation of mitotic cell cycle
Any process that activates or increases the rate or extent of progression through the mitotic cell cycle.
GOC:dph
GOC:go_curators
GOC:tb
positive regulation of progression through mitotic cell cycle
GOC:dph
GOC:tb
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
down regulation of phosphate metabolic process
down-regulation of phosphate metabolic process
downregulation of phosphate metabolic process
negative regulation of phosphate metabolism
inhibition of phosphate metabolic process
biological_process
GO:0045936
negative regulation of phosphate metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
positive regulation of phosphate metabolism
up regulation of phosphate metabolic process
up-regulation of phosphate metabolic process
upregulation of phosphate metabolic process
activation of phosphate metabolic process
stimulation of phosphate metabolic process
biological_process
GO:0045937
positive regulation of phosphate metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
GOC:go_curators
Any process that stops, prevents or reduces the rate or extent of progression through the embryonic mitotic cell cycle.
down regulation of progression through embryonic mitotic cell cycle
down-regulation of progression through embryonic mitotic cell cycle
downregulation of progression through embryonic mitotic cell cycle
negative regulation of embryonic mitotic cell cycle
negative regulation of embryonic mitotic cell cycle progression
negative regulation of progression through embryonic mitotic cell cycle
inhibition of progression through embryonic mitotic cell cycle
biological_process
GO:0045976
negative regulation of mitotic cell cycle, embryonic
Any process that stops, prevents or reduces the rate or extent of progression through the embryonic mitotic cell cycle.
GOC:dph
GOC:go_curators
GOC:tb
negative regulation of embryonic mitotic cell cycle
GOC:dph
GOC:tb
negative regulation of progression through embryonic mitotic cell cycle
GOC:dph
GOC:tb
Any process that activates or increases the frequency, rate or extent of progression through the embryonic mitotic cell cycle.
positive regulation of embryonic mitotic cell cycle
positive regulation of embryonic mitotic cell cycle progression
positive regulation of progression through embryonic mitotic cell cycle
up regulation of mitotic cell cycle, embryonic
up-regulation of mitotic cell cycle, embryonic
upregulation of mitotic cell cycle, embryonic
activation of mitotic cell cycle, embryonic
stimulation of mitotic cell cycle, embryonic
biological_process
GO:0045977
positive regulation of mitotic cell cycle, embryonic
Any process that activates or increases the frequency, rate or extent of progression through the embryonic mitotic cell cycle.
GOC:dph
GOC:go_curators
GOC:tb
positive regulation of embryonic mitotic cell cycle
GOC:dph
GOC:tb
positive regulation of progression through embryonic mitotic cell cycle
GOC:dph
GOC:tb
Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development.
down regulation of embryonic development
down-regulation of embryonic development
downregulation of embryonic development
inhibition of embryonic development
biological_process
GO:0045992
negative regulation of embryonic development
Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development.
GOC:go_curators
Any process that modulates the frequency, rate or extent of embryonic development.
biological_process
GO:0045995
regulation of embryonic development
Any process that modulates the frequency, rate or extent of embryonic development.
GOC:go_curators
The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands).
midori
2010-09-13T04:51:59Z
GO:0071884
receptor agonist activity
signaling molecule
signaling receptor ligand activity
vitamin D receptor activator activity
molecular_function
GO:0048018
Definition discussed in https://github.com/geneontology/go-ontology/issues/14220
receptor ligand activity
The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands).
GOC:kv
GOC:molecular_function_refactoring
GOC:pdt
receptor agonist activity
GOC:molecular_function_refactoring
The creation of two or more organelles by division of one organelle.
biological_process
GO:0048285
organelle fission
The creation of two or more organelles by division of one organelle.
GOC:jid
Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
GO:0043119
positive regulation of physiological process
up regulation of biological process
up-regulation of biological process
upregulation of biological process
activation of biological process
stimulation of biological process
biological_process
GO:0048518
positive regulation of biological process
Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
GOC:jid
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
GO:0043118
down regulation of biological process
down-regulation of biological process
downregulation of biological process
negative regulation of physiological process
inhibition of biological process
biological_process
GO:0048519
negative regulation of biological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
GOC:jid
Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GO:0051242
positive regulation of cellular physiological process
up regulation of cellular process
up-regulation of cellular process
upregulation of cellular process
activation of cellular process
stimulation of cellular process
biological_process
GO:0048522
positive regulation of cellular process
Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:jid
Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GO:0051243
down regulation of cellular process
down-regulation of cellular process
downregulation of cellular process
negative regulation of cellular physiological process
inhibition of cellular process
biological_process
GO:0048523
negative regulation of cellular process
Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:jid
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
biological_process
GO:0048583
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
regulation of response to stimulus
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
GOC:jid
Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
up regulation of response to stimulus
up-regulation of response to stimulus
upregulation of response to stimulus
activation of response to stimulus
stimulation of response to stimulus
biological_process
GO:0048584
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
positive regulation of response to stimulus
Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
GOC:jid
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
down regulation of response to stimulus
down-regulation of response to stimulus
downregulation of response to stimulus
inhibition of response to stimulus
biological_process
GO:0048585
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
negative regulation of response to stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
GOC:jid
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
development of an anatomical structure
biological_process
GO:0048856
anatomical structure development
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
GO_REF:0000021
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
GO:0050791
regulation of physiological process
biological_process
GO:0050789
regulation of biological process
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
GOC:ai
GOC:go_curators
Any process that modulates the activity of an enzyme.
GO:0048552
MIPS_funcat:18.02.01
regulation of enzyme activity
regulation of metalloenzyme activity
biological_process
GO:0050790
regulation of catalytic activity
Any process that modulates the activity of an enzyme.
GOC:ai
GOC:ebc
GOC:vw
Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
biological_process
GO:0050793
regulation of developmental process
Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
GOC:go_curators
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GO:0051244
regulation of cellular physiological process
biological_process
GO:0050794
regulation of cellular process
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are 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
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
GO:0051869
MIPS_funcat:34.11
physiological response to stimulus
biological_process
GO:0050896
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
response to stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
GOC:ai
GOC:bf
Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
down regulation of developmental process
down-regulation of developmental process
downregulation of developmental process
inhibition of developmental process
biological_process
GO:0051093
negative regulation of developmental process
Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
GOC:ai
Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
up regulation of developmental process
up-regulation of developmental process
upregulation of developmental process
activation of developmental process
stimulation of developmental process
biological_process
GO:0051094
positive regulation of developmental process
Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
GOC:ai
Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
biological_process
GO:0051098
regulation of binding
Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
GOC:ai
Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
up regulation of binding
up-regulation of binding
upregulation of binding
activation of binding
stimulation of binding
biological_process
GO:0051099
positive regulation of binding
Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
GOC:ai
Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
down regulation of binding
down-regulation of binding
downregulation of binding
inhibition of binding
biological_process
GO:0051100
negative regulation of binding
Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
GOC:ai
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
regulation of cellular component organisation
biological_process
regulation of cell organisation
regulation of cell organization
regulation of cellular component organization and biogenesis
GO:0051128
regulation of cellular component organization
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
GOC:ai
regulation of cell organisation
GOC:mah
regulation of cell organization
GOC:mah
regulation of cellular component organization and biogenesis
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
down regulation of cell organization
down-regulation of cell organization
downregulation of cell organization
inhibition of cell organization
biological_process
negative regulation of cell organisation
negative regulation of cellular component organization and biogenesis
GO:0051129
negative regulation of cellular component organization
Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
GOC:ai
negative regulation of cell organisation
GOC:mah
negative regulation of cellular component organization and biogenesis
GOC:mah
Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
positive regulation of cell organisation
up regulation of cell organization
up-regulation of cell organization
upregulation of cell organization
activation of cell organization
stimulation of cell organization
biological_process
positive regulation of cellular component organization and biogenesis
GO:0051130
positive regulation of cellular component organization
Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
GOC:ai
positive regulation of cellular component organization and biogenesis
GOC:mah
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
regulation of phosphorus metabolism
biological_process
GO:0051174
regulation of phosphorus metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
GOC:ai
Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.
biological_process
GO:0051239
regulation of multicellular organismal process
Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.
GOC:ai
GOC:dph
GOC:tb
Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
up regulation of multicellular organismal process
up-regulation of multicellular organismal process
upregulation of multicellular organismal process
activation of multicellular organismal process
stimulation of multicellular organismal process
biological_process
GO:0051240
positive regulation of multicellular organismal process
Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
GOC:ai
Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
down regulation of multicellular organismal process
down-regulation of multicellular organismal process
downregulation of multicellular organismal process
inhibition of multicellular organismal process
biological_process
GO:0051241
negative regulation of multicellular organismal process
Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
GOC:ai
The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs.
resting phase
Wikipedia:Interphase
karyostasis
biological_process
GO:0051325
Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
interphase
The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs.
GOC:mtg_cell_cycle
The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs.
interphase of mitotic cell cycle
biological_process
GO:0051329
Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
mitotic interphase
The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs.
GOC:mtg_cell_cycle
Any process that modulates the frequency, rate or extent of transferase activity, the 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.
transferase regulator
biological_process
GO:0051338
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
regulation of transferase activity
Any process that modulates the frequency, rate or extent of transferase activity, the 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.-.-.-
GOC:ai
Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
transferase activator
up regulation of transferase activity
up-regulation of transferase activity
upregulation of transferase activity
activation of transferase activity
stimulation of transferase activity
biological_process
GO:0051347
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
positive regulation of transferase activity
Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
GOC:ai
Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
down regulation of transferase activity
down-regulation of transferase activity
downregulation of transferase activity
transferase inhibitor
inhibition of transferase activity
biological_process
GO:0051348
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
negative regulation of transferase activity
Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
GOC:ai
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
biological_process
GO:0051716
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
cellular response to stimulus
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
GOC:bf
GOC:jl
Any process that modulates the rate or extent of progression through the cell cycle.
GO:0000074
cell cycle modulation
cell cycle regulation
control of cell cycle progression
modulation of cell cycle progression
regulation of cell cycle progression
regulation of progression through cell cycle
biological_process
cell cycle regulator
tumor suppressor
GO:0051726
regulation of cell cycle
Any process that modulates the rate or extent of progression through the cell cycle.
GOC:ai
GOC:dph
GOC:tb
Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
biological_process
GO:0051783
regulation of nuclear division
Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
GOC:ai
Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
down regulation of nuclear division
down-regulation of nuclear division
downregulation of nuclear division
inhibition of nuclear division
biological_process
GO:0051784
negative regulation of nuclear division
Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
GOC:ai
Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
up regulation of nuclear division
up-regulation of nuclear division
upregulation of nuclear division
activation of nuclear division
stimulation of nuclear division
biological_process
GO:0051785
positive regulation of nuclear division
Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
GOC:ai
A compound molecular function in which an effector function is controlled by one or more regulatory components.
molecular_function
GO:0060089
molecular transducer activity
A compound molecular function in which an effector function is controlled by one or more regulatory components.
GOC:dos
GOC:pdt
Any process that modulates a measurable attribute of any biological process, quality or function.
regulation
biological_process
GO:0065007
biological regulation
Any process that modulates a measurable attribute of any biological process, quality or function.
GOC:dph
GOC:isa_complete
GOC:mah
GOC:pr
GOC:vw
Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
regulation of a molecular function
biological_process
GO:0065009
regulation of molecular function
Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
GOC:isa_complete
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
midori
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
Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
tanyaberardini
2009-09-09T11:39:52Z
biological_process
GO:0090068
positive regulation of cell cycle process
Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
GOC:dph
GOC:tb
One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events.
biological_process
GO:0098763
This term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation should be to 'regulation of x/y phase transition' or to a process which occurs during the reported phase (e.g. mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
mitotic cell cycle phase
One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events.
GOC:dos
A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators.
molecular_function
GO:0098772
molecular function regulator
A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators.
GOC:dos
GOC:pt
A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.
pg
2017-03-23T14:44:23Z
biological_process
GO:0140014
mitotic nuclear division
A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.
ISBN:0198547684
Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor.
bf
2012-02-22T11:40:53Z
regulation of receptor ligand
biological_process
GO:1900120
regulation of receptor binding
Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor.
GOC:TermGenie
GOC:signaling
regulation of receptor ligand
GOC:TermGenie
Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.
bf
2012-02-22T11:40:57Z
down regulation of receptor binding
down-regulation of receptor binding
downregulation of receptor binding
inhibition of receptor binding
inhibition of receptor ligand
biological_process
down regulation of receptor-associated protein activity
GO:1900121
negative regulation of receptor binding
Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.
GOC:TermGenie
GOC:signaling
down regulation of receptor binding
GOC:TermGenie
down-regulation of receptor binding
GOC:TermGenie
downregulation of receptor binding
GOC:TermGenie
inhibition of receptor binding
GOC:TermGenie
inhibition of receptor ligand
GOC:TermGenie
down regulation of receptor-associated protein activity
GOC:TermGenie
Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
bf
2012-02-22T11:41:00Z
up regulation of receptor binding
upregulation of receptor binding
activation of receptor binding
biological_process
GO:1900122
positive regulation of receptor binding
Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
GOC:TermGenie
GOC:signaling
up regulation of receptor binding
GOC:TermGenie
upregulation of receptor binding
GOC:TermGenie
activation of receptor binding
GOC:TermGenie
A process that is part of the mitotic cell cycle.
jl
2014-05-22T14:22:34Z
biological_process
GO:1903047
mitotic cell cycle process
A process that is part of the mitotic cell cycle.
GOC:TermGenie
GOC:mtg_cell_cycle
GO_REF:0000060
Any process that modulates the frequency, rate or extent of multicellular organismal development.
tanyaberardini
2010-08-05T11:25:59Z
biological_process
GO:2000026
regulation of multicellular organismal development
Any process that modulates the frequency, rate or extent of multicellular organismal development.
GOC:obol
Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity.
rfoulger
2010-12-02T09:28:47Z
negative regulation of receptor activity
biological_process
GO:2000272
negative regulation of signaling receptor activity
Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity.
GOC:obol
Any process that activates or increases the frequency, rate or extent of signaling receptor activity.
rfoulger
2010-12-02T09:28:50Z
biological_process
GO:2000273
positive regulation of signaling receptor activity
Any process that activates or increases the frequency, rate or extent of signaling receptor activity.
GOC:obol
Any entity that is ordered in discrete units along a linear axis.
Chris Mungall
sequentially ordered entity
Any individual unit of a collection of like units arranged in a linear order
Chris Mungall
An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair.
sequence atomic unit
ready for release
pending final vetting
requires discussion
## Elucidation
This is used when the statement/axiom is assumed to hold true 'eternally'
## How to interpret (informal)
First the "atemporal" FOL is derived from the OWL using the standard
interpretation. This axiom is temporalized by embedding the axiom
within a for-all-times quantified sentence. The t argument is added to
all instantiation predicates and predicates that use this relation.
## Example
Class: nucleus
SubClassOf: part_of some cell
forall t :
forall n :
instance_of(n,Nucleus,t)
implies
exists c :
instance_of(c,Cell,t)
part_of(n,c,t)
## Notes
This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
true
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
infer input from direct reg
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
enabling an MF enables its parts
true
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
involved in BP
This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps"
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).