http://dx.doi.org/10.1186/2041-1480-4-30
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 for the description of Drosophila melanogaster phenotypes.
Drosophila Phenotype Ontology (DPO)
https://creativecommons.org/licenses/by/3.0/
02:09:2021 11:58
FlyBase miscellaneous CV
2021-09-02
definition
definition
textual definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
has ontology root term
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
Person:Alan Ruttenberg
Add as annotation triples in the granting ontology
term replaced by
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
camcur
BrainName official abbreviation
BRAND NAME
EmbDevSlim
FORMULA
FlyTed temp subset for edit tracking purposes
Testis slim
INN
IUPAC NAME
InChI
InChIKey
terms for rd test ontology
SMILES
Abnormal/normal slim
Absent/present slim
Attribute slim
camcur
cell_quality
cur
warning of impending obsoletion
do not annotate
fbcvsubset_mgiribbons
larval olfactory system
lethal phase terms
Relational slim: types of quality that require an additional entity in order to exist
Systematic synonym
Value slim
http://purl.org/dc/elements/1.1/description
uberon
dc-description
true
dc-description
description
http://purl.org/dc/elements/1.1/title
uberon
dc-title
true
dc-title
title
http://purl.org/dc/terms/license
uberon
dcterms-license
true
dcterms-license
license
subset_property
synonym_type_property
consider
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
label
label
is part of
is part of
my brain is part of my body (continuant parthood, two material entities)
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)
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)
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.
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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
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'.
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
part_of
BFO:0000050
OBO_REL:part_of
part_of
external
protein
quality
relationship
uberon
part_of
part_of
part of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
has part
my body has part my brain (continuant parthood, two material entities)
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)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
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.
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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
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'.
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
has_part
BFO:0000051
OBO_REL:has_part
chebi_ontology
external
protein
quality
relationship
uberon
has_part
false
has_part
We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'.
has part
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
djs93
2009-10-09T10:00:53Z
BFO:0000062
OBO_REL:preceded_by
is preceded by
takes place after
uberon
preceded_by
preceded_by
preceded by
is preceded by
SIO:000249
takes place after
Allen:precedes
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
BFO:0000063
uberon
precedes
precedes
precedes
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
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
BFO:0000067
uberon
contains_process
contains_process
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
has_age
FBdv:00018001
relationship
substage_of
substage_of
Creating this relation as a temporary fix, pending adding the axiom occurrent_part_of subproperty of happens_during to RO.
substage_of
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
RO:0000052
fly_anatomy.ontology
characteristic_of
characteristic_of
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
RO:0000053
fly_anatomy.ontology
uberon
bearer_of
has_characteristic
bearer_of
has_characteristic
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
RO:0000056
protein
uberon
participates_in
false
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
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
RO:0000086
protein
uberon
has_quality
false
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
RO:0000087
chebi_ontology
has_role
false
false
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
disposition of
RO:0002002
uberon
has_boundary
has_boundary
has boundary
A part of relation that applies only between occurents.
RO:0002012
FlyBase_development_CV
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
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
<=
Primitive instance level timing relation between events
before or simultaneous with
Relation between occurrents, shares start and end boundaries.
RO:0002082
coincides_with
is_equal_to
uberon
simultaneous_with
simultaneous_with
simultaneous with
Relation between occurrents, shares start and end boundaries.
Allen:is_equal_to
https://orcid.org/0000-0002-6601-2165
David Osumi-Sutherland
t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
before
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
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
David Osumi-Sutherland
starts_at_end_of
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
RO:0002087
directly preceded by
is directly preceded by
is immediately preceded by
starts_at_end_of
FlyBase_development_CV
uberon
immediately_preceded_by
immediately_preceded_by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
SIO:000251
is immediately preceded by
SIO:000251
David Osumi-Sutherland
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
immediately_precedes
immediately_precedes
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
David Osumi-Sutherland
io
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
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
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
x overlaps y if and only if there exists some z such that x has part z and z part of y
BFO_0000051 some (BFO_0000050 some ?Y)
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO:0002131
fly_anatomy.ontology
uberon
overlaps
overlaps
overlaps
true
lactation SubClassOf 'only in taxon' some 'Mammalia'
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.
'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
Chris Mungall
RO:0002160
never_outside_taxon
specific_to
specific_to_taxon
protein
uberon
only_in_taxon
false
only_in_taxon
Down-propagates. The original name for this in the paper is 'specific_to'. Applicable to genes because some genes are lost in sub-species (strains) of a species.
only in taxon
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Chris Mungall
Jennifer Deegan
RO:0002162
uberon
in_taxon
in_taxon
Connects a biological entity to its taxon of origin.
in taxon
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO:0002180
protein
uberon
has_component
false
has_component
For use in recording has_part with a cardinality constraint.
Use: http://purl.obolibrary.org/obo/BFO_0000073 'has cardinal part' ?
has component
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
Terry Meehan
RO:0002202
fly_anatomy.ontology
uberon
develops_from
develops_from
This is the transitive form of the develops from relation
develops from
inverse of develops from
Chris Mungall
David Osumi-Sutherland
Terry Meehan
RO:0002203
fly_anatomy.ontology
uberon
develops_into
develops_into
develops into
process(P1) regulates process(P2) iff:Â 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
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
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
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
Chris Mungall
has function realized in
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
RO_0000053 some (RO_0000054 only ?Y)
RO:0002215
fly_anatomy.ontology
protein
uberon
capable_of
false
capable_of
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
Chris Mungall
has function in
RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
RO:0002216
fly_anatomy.ontology
uberon
capable_of_part_of
capable_of_part_of
capable of part of
true
Chris Mungall
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
inverse of starts with
RO:0002223
uberon
starts
starts
starts
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
RO:0002224
uberon
starts_with
starts_with
starts with
inverse of ends with
RO:0002229
finishes
uberon
ends
ends
ends
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
RO:0002230
uberon
ends_with
ends_with
ends with
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
has start location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
has end location
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
Chris Mungall
consumes
has input
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
Chris Mungall
RO:0002254
uberon
has_developmental_contribution_from
has_developmental_contribution_from
has developmental contribution from
inverse of has developmental contribution from
Chris Mungall
RO:0002255
uberon
developmentally_contributes_to
developmentally_contributes_to
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
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
Because part_of is transitive, inheres in is a sub-relation of inheres in part of
Chris Mungall
inheres in part of
characteristic of part of
true
A relationship that holds via some environmental process
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
evolutionarily related to
A mereological relationship or a topological relationship
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
a particular instances of akt-2 enables some instance of protein kinase activity
Chris Mungall
catalyzes
executes
has
is catalyzing
is executing
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
RO:0002328
uberon
functionally_related_to
functionally_related_to
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
Chris Mungall
false
RO:0002329
uberon
part_of_structure_that_is_capable_of
part_of_structure_that_is_capable_of
part of structure that is capable of
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
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
is member of
member part of
SIO
RO:0002350
uberon
member_of
member_of
member of
has member is a mereological relation between a collection and an item.
SIO
RO:0002351
uberon
has_member
has_member
has member
inverse of has input
Chris Mungall
RO:0002352
uberon
input_of
input_of
input of
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
Chris Mungall
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
Chris Mungall
RO:0002385
uberon
has_potential_to_developmentally_contribute_to
has_potential_to_developmentally_contribute_to
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
RO:0002387
uberon
has_potential_to_develop_into
has_potential_to_develop_into
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
Chris Mungall
has potential to directly develop into
inverse of upstream of
Chris Mungall
causally downstream of
Chris Mungall
immediately causally downstream of
This relation groups causal relations between material entities and causal relations between processes
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
Chris Mungall
immediately causally upstream of
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
affects
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
Chris Mungall
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
Chris Mungall
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
Chris Mungall
involved in negative regulation of
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
Chris Mungall
involved in or reguates
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
Chris Mungall
executes activity in
enables activity in
is active in
true
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
GOC:cjm
GOC:dos
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Chris Mungall
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/MI_0914
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
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
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
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
RO:0002488
begins_to_exist_during
uberon
RO:0002488
existence_starts_during
existence_starts_during
existence starts during
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
Relation between continuant and occurrent, such that c comes into existence at the start of p.
RO:0002489
uberon
existence_starts_with
existence_starts_with
existence starts with
Relation between continuant and occurrent, such that c comes into existence at the start of p.
RO:0002491
uberon
existence_starts_and_ends_during
existence_starts_and_ends_during
existence starts and ends during
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
RO:0002492
ceases_to_exist_during
uberon
RO:0002492
existence_ends_during
existence_ends_during
existence ends during
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
RO:0002493
uberon
existence_ends_with
existence_ends_with
existence ends with
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
RO:0002494
transforms from
uberon
transformation_of
transformation_of
transformation of
transforms from
SIO:000657
RO:0002495
direct_transformation_of
immediately transforms from
uberon
immediate_transformation_of
immediate_transformation_of
immediate transformation of
direct_transformation_of
immediately transforms from
SIO:000658
RO:0002496
uberon
existence_starts_during_or_after
existence_starts_during_or_after
existence starts during or after
RO:0002497
uberon
existence_ends_during_or_before
existence_ends_during_or_before
existence ends during or before
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
Chris Mungall
depends on
q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
Chris Mungall
towards
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between entities
Chris Mungall
causally influenced by (entity-centric)
causally influenced by
Chris Mungall
interaction relation helper property
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
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
A relation that holds between an attribute or a qualifier and another attribute.
Chris Mungall
This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
has modifier
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Chris Mungall
directly regulates (processual)
directly regulates
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
Chris Mungall
has part structure that is capable of
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
capable of positively regulating
Inverse of 'causal agent in process'
process has causal agent
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
directly positively regulates (process to process)
directly positively regulates
Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
directly negatively regulates (process to process)
directly negatively regulates
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
cjm
2018-01-25T23:20:13Z
enables subfunction
cjm
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
cjm
2018-01-26T23:49:51Z
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
cjm
2018-01-26T23:53:14Z
acts upstream of, positive effect
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
cjm
2018-01-26T23:53:22Z
acts upstream of, negative effect
cjm
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
cjm
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
Vasundra Touré
regulates activity of
has_role
has role
by_means
in_response_to
quality
correlates_with
correlates_with
q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
decreased_in_magnitude_relative_to
This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
decreased_in_magnitude_relative_to
q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
PATOC:CJM
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
different_in_magnitude_relative_to
different_in_magnitude_relative_to
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
PATOC:CJM
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
increased_in_magnitude_relative_to
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
increased_in_magnitude_relative_to
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
PATOC:CJM
q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
quality
reciprocal_of
There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.
reciprocal_of
q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
PATOC:CJM
0
100
Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
dos
2018-05-22T16:43:28Z
This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses.
has increased age-specific mortality rate
Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
PMID:24138933
Wikipedia:Infant_mortality
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
occurrent
Occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
per discussion with Barry Smith
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
process
Process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
disposition
Disposition
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
realizable
RealizableEntity
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
quality
Quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
bfo
BFO:0000019
quality
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
sdc
SpecificallyDependentContinuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
per discussion with Barry Smith
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
role
Role
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
object-aggregate
ObjectAggregate
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
bfo
BFO:0000030
object
gdc
GenericallyDependentContinuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
function
Function
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
material
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
bfo
BFO:0000040
material entity
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
immaterial
ImmaterialEntity
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
CARO:0000000
Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.
anatomical entity
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
CAROC:Brownsville2014
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
CARO:0000003
Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development.
connected anatomical structure
Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle.
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome.
portion of organism substance
CARO:0000004
Note - CARO explicitly declares organisms substances to be part of (some) organism.
organism substance
An anatomical entity that has mass.
CARO:0000006
material anatomical entity
Anatomical entity that has no mass.
CARO:0000007
immaterial anatomical entity
Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell.
multicellular organism
Melissa Haendel
9/18/11
CARO:0000012
MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history.
MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history.
MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities.
MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities.
multicellular organism
An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CL:0000000
GO:0005623
CARO:0000013
deprecate and replace with CL or GO term?
cell
Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher.
cell component
CARO:0000014
This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class.
cell part
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism.
CARO:0000032
organism subdivision
0
0
An anatomical structure that has no cells or cell parts as a part.
CARO:0000040
Example. Insect cuticle, eggshell, hair.
acellular anatomical structure
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
CARO:0000042
MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids?
extraembryonic structure
2
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
multi-cell-component structure
CARO:0001000
Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain.
multi-cell-part structure
Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells.
mah
10.7.2011
gross anatomical part
Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
Melissa Haendel
organism or virus
Melissa Haendel
9/18/11
organism or virus or viroid
An anatomical structure that has more than one cell as a part.
djs93
Sun Feb 27 10:53:00 GMT 2011
CARO:0010000
multicellular anatomical structure
There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS
An individual member of a clade of cellular organisms.
mah
organism
mah
7.16.2011
CARO:0010004
A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms.
A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms.
cellular organism
2
Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.
CARO:0000054
disconnected anatomical group
An anatomical structure consisting of one or more cells.
2018-09-28T14:20:19Z
cellular anatomical structure
dos
With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell
Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them.
Important for alignment with Darwin Core class "Organism".
biological entity
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
chemical entity
chebi_ontology
CHEBI:24431
chemical entity
chemical entity
UniProt
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CALOHA:TS-2035
FMA:68646
GO:0005623
KUPO:0000002
VHOG:0001533
WBbt:0004017
XAO:0003012
cell
CL:0000000
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
cell
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CARO:mah
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).
native cell
A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models.
2017-01-30T18:53:32Z
https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913
cell
https://github.com/obophenotype/cell-ontology/issues/448
abnormal cell
A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models.
GOC:add
GOC:cg
GOC:wdd
An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism.
2017-01-30T19:16:26Z
https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12922
cell
tumor cell
tumour cell
https://github.com/obophenotype/cell-ontology/issues/448
neoplastic cell
An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism.
GOC:add
GOC:cg
GOC:wdd
A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell.
tmeehan
2009-12-23T10:53:24Z
cell
increased nucleus size
A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell.
GOC:tfm
fly_anatomy.ontology
FBbt:00000000
germ layer derivative
An individual member of the species Drosophila melanogaster.
CARO:0000012
NCBITaxon:7227
fly_anatomy.ontology
Drosophila
whole organism
FBbt:00000001
organism
An individual member of the species Drosophila melanogaster.
FBC:DOS
The three main divisions of the whole organism formed from groups of segments.
fly_anatomy.ontology
FBbt:00000002
tagma
The three main divisions of the whole organism formed from groups of segments.
FBC:GG
One of the repeated divisions of the whole organism.
fly_anatomy.ontology
FBbt:00000003
segment
One of the repeated divisions of the whole organism.
FBC:GG
fly_anatomy.ontology
FBbt:00000004
head
Any segment (FBbt:00000003) that is part of some head (FBbt:00000004).
fly_anatomy.ontology
FBbt:00000006
head segment
Any segment (FBbt:00000003) that is part of some head (FBbt:00000004).
FlyBase:FBrf0075072
A segment that is anterior to the gnathal segments.
pregnathal segment
preoral segment
fly_anatomy.ontology
cephalic segment
procephalon
FBbt:00000007
procephalic segment
A segment that is anterior to the gnathal segments.
FBC:GG
Segment anterior to the intercalary segment. In the adult it bears the antennae.
fly_anatomy.ontology
FBbt:00000009
antennal segment
Segment anterior to the intercalary segment. In the adult it bears the antennae.
FBC:DOS
.
fly_anatomy.ontology
FBbt:00000052
embryo
.
FlyBase:FBrf0039741
FlyBase:FBrf0041814
A collective term for stages 1-4.
fly_anatomy.ontology
FBbt:00000054
DEPRECATION WARNING.
cleavage stage embryo
A collective term for stages 1-4.
FBC:DOS
Primordium that is a primary subdivision of the embryo into regions based on tissue and cell-type fate and specification. Germ layers first become morphologically distinct during gastrulation. As a result of gastrulation, the endoderm becomes the inner-most layer, the mesoderm becomes the middle layer and the ectoderm becomes the outer layer.
fly_anatomy.ontology
FBbt:00000110
germ layer
Primordium that is a primary subdivision of the embryo into regions based on tissue and cell-type fate and specification. Germ layers first become morphologically distinct during gastrulation. As a result of gastrulation, the endoderm becomes the inner-most layer, the mesoderm becomes the middle layer and the ectoderm becomes the outer layer.
FBC:DOS
The outermost germ layer of the embryo.
fly_anatomy.ontology
FBbt:00000111
ectoderm
The outermost germ layer of the embryo.
FBC:GG
The region of the ectoderm anterior to the cephalic furrow.
fly_anatomy.ontology
FBbt:00000119
anterior ectoderm
The region of the ectoderm anterior to the cephalic furrow.
FBC:DOS
Any tagma (FBbt:00000002) that is part of some embryo (FBbt:00000052).
fly_anatomy.ontology
FBbt:00000137
embryonic tagma
Any tagma (FBbt:00000002) that is part of some embryo (FBbt:00000052).
FBC:Autogenerated
Any segment (FBbt:00000003) that is part of some embryo (FBbt:00000052).
fly_anatomy.ontology
FBbt:00000154
embryonic segment
Any segment (FBbt:00000003) that is part of some embryo (FBbt:00000052).
FBC:Autogenerated
Any head (FBbt:00000004) that is part of some embryo (FBbt:00000052).
fly_anatomy.ontology
FBbt:00000155
embryonic head
Any head (FBbt:00000004) that is part of some embryo (FBbt:00000052).
FBC:Autogenerated
Any segment (FBbt:00000003) that is part of some embryonic head (FBbt:00000155).
fly_anatomy.ontology
FBbt:00000157
embryonic head segment
Any segment (FBbt:00000003) that is part of some embryonic head (FBbt:00000155).
FlyBase:FBrf0075072
Any procephalic segment (FBbt:00000007) that is part of some embryonic head (FBbt:00000155).
fly_anatomy.ontology
FBbt:00000158
embryonic procephalic segment
Any procephalic segment (FBbt:00000007) that is part of some embryonic head (FBbt:00000155).
FBC:Autogenerated
Any antennal segment (FBbt:00000009) that is part of some embryonic head (FBbt:00000155).
fly_anatomy.ontology
FBbt:00000160
embryonic antennal segment
Any antennal segment (FBbt:00000009) that is part of some embryonic head (FBbt:00000155).
FBC:Autogenerated
Region that gives rise to the neuroblasts of the central nervous system (Bossing et al., 1996). An anterior region (procephalic neurogenic region) gives rise to the brain and a posterior, ventral region (ventral neuroectoderm) gives rise to the ventral nerve cord and gnathal ganglia (Bossing et al., 1996).
fly_anatomy.ontology
FBbt:00001057
neurogenic region
Region that gives rise to the neuroblasts of the central nervous system (Bossing et al., 1996). An anterior region (procephalic neurogenic region) gives rise to the brain and a posterior, ventral region (ventral neuroectoderm) gives rise to the ventral nerve cord and gnathal ganglia (Bossing et al., 1996).
FlyBase:FBrf0089570
FlyBase:FBrf0090460
FlyBase:FBrf0098344
Primordium of the early extended germ band embryo that will give rise to the larval Bolwig organ, larval optic anlage and adult eye. It is a dorsoposterior strip of the embryonic procephalon that invaginates at stages 12-13. It can be subdivided into 4 different regions. The most anterior gives rise to the embryonic primordium of adult eye. Posterior to it, the anterior lip develops into the embryonic inner optic lobe primordium, that will give rise to the larval inner optic anlage. Posteriorly, the posterior lip develops into the embryonic outer optic lobe primordium, that will give rise to the larval outer optic anlage. The most posterior region will develop into the Bolwig organ primordium.
optic lobe placode
optic lobe primordium
fly_anatomy.ontology
P2 VisSys
FBbt:00001059
visual primordium
Primordium of the early extended germ band embryo that will give rise to the larval Bolwig organ, larval optic anlage and adult eye. It is a dorsoposterior strip of the embryonic procephalon that invaginates at stages 12-13. It can be subdivided into 4 different regions. The most anterior gives rise to the embryonic primordium of adult eye. Posterior to it, the anterior lip develops into the embryonic inner optic lobe primordium, that will give rise to the larval inner optic anlage. Posteriorly, the posterior lip develops into the embryonic outer optic lobe primordium, that will give rise to the larval outer optic anlage. The most posterior region will develop into the Bolwig organ primordium.
FlyBase:FBrf0089570
FlyBase:FBrf0151275
optic lobe placode
FlyBase:FBrf0151275
P2 VisSys
FBC:DOS
The ventrally/medially located ectodermal region of the trunk from which neuroblasts delaminate to form the ventral nerve cord and gnathal ganglia. This region becomes distinct during stage 8 when its cells become enlarged compared to those in the adjacent dorsal ectoderm.
FBbt:00000113
P2 VenEc
VenEc
vNR
ventral neurogenic region
fly_anatomy.ontology
neurectoderm
neuroectoderm
FBbt:00001061
ventral neurectoderm
The ventrally/medially located ectodermal region of the trunk from which neuroblasts delaminate to form the ventral nerve cord and gnathal ganglia. This region becomes distinct during stage 8 when its cells become enlarged compared to those in the adjacent dorsal ectoderm.
FlyBase:FBrf0076117
FlyBase:FBrf0089570
vNR
FlyBase:FBrf0090460
ventral neurogenic region
FlyBase:FBrf0090460
An equivalence group of the neurectoderm where all cells can, although only one will, become a neural progenitor cell.
fly_anatomy.ontology
FBbt:00001135
proneural cluster
An equivalence group of the neurectoderm where all cells can, although only one will, become a neural progenitor cell.
FlyBase:FBrf0074477
FlyBase:FBrf0089570
fly_anatomy.ontology
SOP
sensillum precursor
sensory organ mother cell
sensory organ precursor cell
FBbt:00001137
sensory mother cell
Embryonic structure that will develop into a larval imaginal tissue, which will later form an adult structure (Cohen, 1993).
embryonic imaginal precursor
fly_anatomy.ontology
FBbt:00001648
embryonic imaginal tissue
Embryonic structure that will develop into a larval imaginal tissue, which will later form an adult structure (Cohen, 1993).
FlyBase:FBrf0064789
Population of contiguous, morphologically distinct cells of the embryo that will proliferate to form an imaginal disc in the larva. During early embryogenesis the precursor is part of the epithelial sheet before segregating from the epithelial sheet by late embryogenesis (Cohen, 1993).
fly_anatomy.ontology
imaginal disc specific anlage
FBbt:00001649
imaginal disc primordium
Population of contiguous, morphologically distinct cells of the embryo that will proliferate to form an imaginal disc in the larva. During early embryogenesis the precursor is part of the epithelial sheet before segregating from the epithelial sheet by late embryogenesis (Cohen, 1993).
FBC:SPR
FlyBase:FBrf0064789
Primordium from which the eye-antennal disc develops.
fly_anatomy.ontology
eye-antennal disc specific anlage
FBbt:00001652
eye-antennal disc primordium
Primordium from which the eye-antennal disc develops.
FBC:SPR
fly_anatomy.ontology
FBbt:00001727
larva
Any tagma (FBbt:00000002) that is part of some larva (FBbt:00001727).
fly_anatomy.ontology
FBbt:00001728
larval tagma
Any tagma (FBbt:00000002) that is part of some larva (FBbt:00001727).
FBC:Autogenerated
Any segment (FBbt:00000003) that is part of some larva (FBbt:00001727).
fly_anatomy.ontology
FBbt:00001729
larval segment
Any segment (FBbt:00000003) that is part of some larva (FBbt:00001727).
FBC:Autogenerated
Any head (FBbt:00000004) that is part of some larva (FBbt:00001727).
fly_anatomy.ontology
FBbt:00001730
larval head
Any head (FBbt:00000004) that is part of some larva (FBbt:00001727).
FBC:Autogenerated
Any segment (FBbt:00000003) that is part of some larval head (FBbt:00001730).
fly_anatomy.ontology
FBbt:00001732
larval head segment
Any segment (FBbt:00000003) that is part of some larval head (FBbt:00001730).
FlyBase:FBrf0075072
Any procephalic segment (FBbt:00000007) that is part of some larval head (FBbt:00001730).
fly_anatomy.ontology
FBbt:00001733
larval procephalic segment
Any procephalic segment (FBbt:00000007) that is part of some larval head (FBbt:00001730).
FBC:Autogenerated
Any antennal segment (FBbt:00000009) that is part of some larval head (FBbt:00001730).
fly_anatomy.ontology
FBbt:00001735
larval antennal segment
Any antennal segment (FBbt:00000009) that is part of some larval head (FBbt:00001730).
FBC:Autogenerated
Imaginal tissue that is found in the larva and will develop into an adult structure during metamorphosis.
embryonic/larval imaginal precursor
larval imaginal precursor
fly_anatomy.ontology
FBbt:00001760
larval imaginal tissue
Imaginal tissue that is found in the larva and will develop into an adult structure during metamorphosis.
FlyBase:FBrf0064789
A sac shaped epithelial structure in the larva that gives rise to part of the adult integumentary system. One side of the sac consists of peripodial epithelium, the other of columnar epithelium. A single anterior-posterior compartment boundary bisects both peripodial membrane and columnar epithelium. Cells do not cross this boundary during growth and development of the disc.
fly_anatomy.ontology
imaginal disk
FBbt:00001761
imaginal disc
A sac shaped epithelial structure in the larva that gives rise to part of the adult integumentary system. One side of the sac consists of peripodial epithelium, the other of columnar epithelium. A single anterior-posterior compartment boundary bisects both peripodial membrane and columnar epithelium. Cells do not cross this boundary during growth and development of the disc.
FBC:GG
Imaginal disc that, in the adults, gives rise to the eye, antenna, head capsule (including all bristles and external membranes) and the maxillary palps (Cohen, 1993).
fly_anatomy.ontology
FBbt:00001766
Figure 12 from Cohen (1993, Bate, Martinez Arias, 1993: 747--841) provides a fate map of the eye-antennal disc.
eye-antennal disc
Imaginal disc that, in the adults, gives rise to the eye, antenna, head capsule (including all bristles and external membranes) and the maxillary palps (Cohen, 1993).
FlyBase:FBrf0064789
Anterior, bulbous portion of the eye-antennal disc that gives rise to the eye as well as contributing to the head capsule (Cohen, 1993).
fly_anatomy.ontology
FBbt:00001768
Figure 12 from Cohen (1993, Bate, Martinez Arias, 1993: 747--841) provides a fate map of the eye-antennal disc.
eye disc
Anterior, bulbous portion of the eye-antennal disc that gives rise to the eye as well as contributing to the head capsule (Cohen, 1993).
FlyBase:FBrf0064789
Nervous system of the embryo/larva.
FBbt:00005719
VFB:FBbt_00001911
larval nervous system
fly_anatomy.ontology
FBbt:00001911
embryonic/larval nervous system
Nervous system of the embryo/larva.
FlyBase:FBrf0045359
FlyBase:FBrf0075072
FlyBase:FBrf0105282
Any sense organ (FBbt:00005155) that is part of some larva (FBbt:00001727).
VFB:FBbt_00002639
larval sense organ
fly_anatomy.ontology
FBbt:00002639
embryonic/larval sense organ
Any sense organ (FBbt:00005155) that is part of some larva (FBbt:00001727).
FBC:Autogenerated
Any sense organ (FBbt:00005155) that is part of some larval antennal segment (FBbt:00001735).
VFB:FBbt_00002654
larval antennal segment sensillum
fly_anatomy.ontology
FBbt:00002654
embryonic/larval antennal segment sensillum
Any sense organ (FBbt:00005155) that is part of some larval antennal segment (FBbt:00001735).
FBC:Autogenerated
The prepupa is the name given to the organism at the period of the life cycle that 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 is approximately 12 hours. It occurs 120-132.2 hours after egg laying, and is the period of 0-12.2 hours after puparium formation.
fly_anatomy.ontology
PP
FBbt:00002952
prepupa
The prepupa is the name given to the organism at the period of the life cycle that 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 is approximately 12 hours. It occurs 120-132.2 hours after egg laying, and is the period of 0-12.2 hours after puparium formation.
FlyBase:FBrf0036849
FlyBase:FBrf0048355
The pupa is the name given to the organism at the period of the life cycle that begins 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. The duration of this stage is approximately 32 hours at 25 degrees C, and spans from 132.2-164.3 hours after egg laying, or is the period of 12.2-44.3 hours after puparium formation.
fly_anatomy.ontology
P
FBbt:00002953
pupa
The pupa is the name given to the organism at the period of the life cycle that begins 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. The duration of this stage is approximately 32 hours at 25 degrees C, and spans from 132.2-164.3 hours after egg laying, or is the period of 12.2-44.3 hours after puparium formation.
FlyBase:FBrf0036849
FlyBase:FBrf0048355
.
fly_anatomy.ontology
imago
FBbt:00003004
adult
.
FlyBase:FBrf0036849
Any tagma (FBbt:00000002) that is part of some adult (FBbt:00003004).
fly_anatomy.ontology
FBbt:00003005
adult tagma
Any tagma (FBbt:00000002) that is part of some adult (FBbt:00003004).
FBC:Autogenerated
Segment of the adult.
fly_anatomy.ontology
FBbt:00003006
adult segment
Segment of the adult.
FBC:SPR
Head of the adult organism.
fly_anatomy.ontology
FBbt:00003007
adult head
Head of the adult organism.
FBC:SPR
Segment of the adult head.
fly_anatomy.ontology
FBbt:00003009
adult head segment
Segment of the adult head.
FlyBase:FBrf0064788
Any procephalic segment (FBbt:00000007) that is part of some adult head (FBbt:00003007).
fly_anatomy.ontology
FBbt:00003010
adult procephalic segment
Any procephalic segment (FBbt:00000007) that is part of some adult head (FBbt:00003007).
FBC:Autogenerated
Any antennal segment (FBbt:00000009) that is part of some adult head (FBbt:00003007).
FBbt:00004512
adult antennal structure
fly_anatomy.ontology
FBbt:00003012
adult antennal segment
Any antennal segment (FBbt:00000009) that is part of some adult head (FBbt:00003007).
FBC:Autogenerated
Any nervous system (FBbt:00005093) that is part of some adult (FBbt:00003004).
VFB:FBbt_00003559
fly_anatomy.ontology
FBbt:00003559
adult nervous system
Any nervous system (FBbt:00005093) that is part of some adult (FBbt:00003004).
FlyBase:FBrf0002482
FlyBase:FBrf0007196
FlyBase:FBrf0007735
FlyBase:FBrf0034076
Any sense organ (FBbt:00005155) that is part of some adult (FBbt:00003004).
VFB:FBbt_00004113
fly_anatomy.ontology
FBbt:00004113
adult sense organ
Any sense organ (FBbt:00005155) that is part of some adult (FBbt:00003004).
FlyBase:FBrf0007734
FlyBase:FBrf0031004
Any developing material anatomical entity (FBbt:00007006) that is part of some embryo (FBbt:00000052).
fly_anatomy.ontology
FBbt:00004208
developing embryonic structure
Any developing material anatomical entity (FBbt:00007006) that is part of some embryo (FBbt:00000052).
FBC:Autogenerated
A collective term for stages 11 and 12.
fly_anatomy.ontology
FBbt:00004450
late extended germ band embryo
A collective term for stages 11 and 12.
FBC:DOS
A bilaterally paired compound sense organ of the adult head that functions in visual perception.
VFB:FBbt_00004508
fly_anatomy.ontology
compound eye
FBbt:00004508
eye
A bilaterally paired compound sense organ of the adult head that functions in visual perception.
FBC:DOS
A division of the whole organism into specialized systems.
fly_anatomy.ontology
FBbt:00004856
organ system
A division of the whole organism into specialized systems.
FBC:GG
All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems.
VFB:FBbt_00005093
fly_anatomy.ontology
FBbt:00005093
nervous system
All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems.
FlyBase:FBrf0166419
Multicellular anatomical structure with largely bona fide boundary that transduces some sensory stimulus to the nervous system.
VFB:FBbt_00005155
fly_anatomy.ontology
FBbt:00005155
sense organ
Multicellular anatomical structure with largely bona fide boundary that transduces some sensory stimulus to the nervous system.
FBC:DOS
A light sensitive sense organ.
VFB:FBbt_00005162
fly_anatomy.ontology
FBbt:00005162
photoreceptor
A light sensitive sense organ.
FBC:GG
Any somatic cell (FBbt:00100318) that overlaps some sense organ (FBbt:00005155).
fly_anatomy.ontology
SOC
FBbt:00005163
sensory organ cell
Any somatic cell (FBbt:00100318) that overlaps some sense organ (FBbt:00005155).
FBC:Autogenerated
Precursor cell that gives rise to an external sensory organ.
fly_anatomy.ontology
FBbt:00005164
external sensory organ precursor cell
Precursor cell that gives rise to an external sensory organ.
FlyBase:FBrf0111371
Sensory organ that has external structures that detect mechanical or chemical stimuli.
VFB:FBbt_00005168
eo
es
fly_anatomy.ontology
sensillum
FBbt:00005168
external sensory organ
Sensory organ that has external structures that detect mechanical or chemical stimuli.
FlyBase:FBrf0064796
es
FlyBase:FBrf0064796
fly_anatomy.ontology
FBbt:00005290
DEPRECATION WARNING.
pre-blastoderm embryo
Nuclear divisions 1 and 2. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying).
fly_anatomy.ontology
FBbt:00005291
DEPRECATION WARNING.
stage 1 embryo
Nuclear divisions 1 and 2. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying).
FlyBase:FBrf0089570
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).
fly_anatomy.ontology
FBbt:00005293
DEPRECATION WARNING.
stage 2 embryo
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
Nuclear division 9. The cleavage nuclei complete there 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).
fly_anatomy.ontology
FBbt:00005301
DEPRECATION WARNING.
stage 3 embryo
Nuclear division 9. The cleavage nuclei complete there 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
A collective term for stages 3-5.
fly_anatomy.ontology
FBbt:00005304
DEPRECATION WARNING.
blastoderm embryo
A collective term for stages 3-5.
FBC:DOS
A blastoderm embryo prior to cellularization (corresponds to embryonic stages 3 and 4).
fly_anatomy.ontology
FBbt:00005305
DEPRECATION WARNING.
syncytial blastoderm embryo
A blastoderm embryo prior to cellularization (corresponds to embryonic stages 3 and 4).
FBC:DOS
FBC:GG
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).
fly_anatomy.ontology
FBbt:00005306
DEPRECATION WARNING.
stage 4 embryo
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
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 C: approximately 40 minutes (130-170 minutes after egg laying).
fly_anatomy.ontology
cellular blastoderm embryo
FBbt:00005311
DEPRECATION WARNING.
stage 5 embryo
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 C: approximately 40 minutes (130-170 minutes after egg laying).
FBC:DOS
FBC:MA
FlyBase:FBrf0089570
A collective term for stages 6-8, during which complex morphogenetic movements result in the formation of the three germ layers; ectoderm, mesoderm and endoderm.
fly_anatomy.ontology
FBbt:00005317
DEPRECATION WARNING.
gastrula embryo
A collective term for stages 6-8, during which complex morphogenetic movements result in the formation of the three germ layers; ectoderm, mesoderm and endoderm.
FBC:DOS
FBC:GG
A collective term for stages 9-12.
fly_anatomy.ontology
FBbt:00005321
DEPRECATION WARNING.
extended germ band embryo
A collective term for stages 9-12.
FBC:DOS
A collective term for stages 13-15.
fly_anatomy.ontology
contracted germ band embryo
head involution embryo
FBbt:00005331
DEPRECATION WARNING.
dorsal closure embryo
A collective term for stages 13-15.
FBC:DOS
A collective term for stages 16 and 17.
fly_anatomy.ontology
FBbt:00005333
DEPRECATION WARNING.
late embryo
A collective term for stages 16 and 17.
FBC:DOS
Domain that does not yet coincide 1:1 with a later organ. Anlagen in statu nascendi are typically defined for the early blastoderm by the expression domains of genes which, in the late blastoderm or later, are expressed in specific anlagen, but initially come on in larger domains.
fly_anatomy.ontology
A0
FBbt:00005413
anlage in statu nascendi
Domain that does not yet coincide 1:1 with a later organ. Anlagen in statu nascendi are typically defined for the early blastoderm by the expression domains of genes which, in the late blastoderm or later, are expressed in specific anlagen, but initially come on in larger domains.
FlyBase:FBrf0155831
FlyBase:FBrf0178740
Anlage in statu nascendi of the visual system in a stage 5 embryo that will give rise to the visual system anlage.
Asn VisSys
fly_anatomy.ontology
A0Vis
FBbt:00005425
visual anlage in statu nascendi
Anlage in statu nascendi of the visual system in a stage 5 embryo that will give rise to the visual system anlage.
FBC:VH
Asn VisSys
FBC:DOS
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
fly_anatomy.ontology
FBbt:00005426
anlage
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
FlyBase:FBrf0089570
FlyBase:FBrf0178740
fly_anatomy.ontology
FBbt:00005427
ectoderm anlage
Anlage of the visual system in the gastrula embryo that will give rise to the visual primordium.
A VisSys
fly_anatomy.ontology
AVis
FBbt:00005434
visual anlage
Anlage of the visual system in the gastrula embryo that will give rise to the visual primordium.
FBC:VH
A VisSys
FBC:DOS
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue.
fly_anatomy.ontology
P
placode
FBbt:00005495
primordium
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue.
FBC:DOS
FlyBase:FBrf0089570
FlyBase:FBrf0178740
Early primordium of the late extended germ band and dorsal closure embryo that will give rise to the adult eye. It develops from the visual primordium.
adult eye primordium early
fly_anatomy.ontology
FBbt:00005515
early embryonic primordium of adult eye
Early primordium of the late extended germ band and dorsal closure embryo that will give rise to the adult eye. It develops from the visual primordium.
FBC:DOS
FBC:VH
FlyBase:FBrf0089570
FlyBase:FBrf0151275
fly_anatomy.ontology
P2 iVenEp
venEpiP2
FBbt:00005533
ventral epidermis primordium
P2 iVenEp
FBC:DOS
.
fly_anatomy.ontology
P2 VenEc
venEc
FBbt:00005558
ventral ectoderm
.
FlyBase:FBrf0089570
P2 VenEc
FBC:DOS
Any sense organ (FBbt:00005155) that is part of some antennal segment (FBbt:00000009).
FBbt:00004171
VFB:FBbt_00005806
antennal sensillum
fly_anatomy.ontology
FBbt:00005806
antennal sense organ
Any sense organ (FBbt:00005155) that is part of some antennal segment (FBbt:00000009).
FBC:Autogenerated
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.
fly_anatomy.ontology
FBbt:00006011
pharate adult
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.
FlyBase:FBrf0049147
Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.
CARO:0000003
fly_anatomy.ontology
FBbt:00007001
anatomical structure
Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.
CARO:MAH
FBC:DOS
Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CARO:0000013
CL:0000000
fly_anatomy.ontology
FBbt:00007002
cell
Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CARO:MAH
Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships.
CARO:0000043
fly_anatomy.ontology
FBbt:00007003
portion of tissue
Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships.
CARO:MAH
Portion of tissue, that consists of one or more layers of cells with distinct apical-basal polarity, connected to each other by cell junctions.
CARO:0000066
fly_anatomy.ontology
FBbt:00007005
epithelium
Portion of tissue, that consists of one or more layers of cells with distinct apical-basal polarity, connected to each other by cell junctions.
CARO:MAH
fly_anatomy.ontology
FBbt:00007006
developing material anatomical entity
fly_anatomy.ontology
FBbt:00007008
somatic precursor cell
Anatomical structure that is a primary subdivision of whole organism. The mereological sum of these is the whole organism.
CARO:0000032
fly_anatomy.ontology
FBbt:00007009
organism subdivision
Anatomical structure that is a primary subdivision of whole organism. The mereological sum of these is the whole organism.
CARO:MAH
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which, through specific morphogenetic processes, forms a single distinct structural unit demarcated by bona fide boundaries from other distinct structural units of different types.
CARO:0000055
fly_anatomy.ontology
FBbt:00007010
multi-tissue structure
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which, through specific morphogenetic processes, forms a single distinct structural unit demarcated by bona fide boundaries from other distinct structural units of different types.
CARO:MAH
CARO:0000006
fly_anatomy.ontology
FBbt:00007016
material anatomical entity
The region of the ectoderm posterior to the cephalic furrow.
fly_anatomy.ontology
FBbt:00007045
trunk ectoderm
The region of the ectoderm posterior to the cephalic furrow.
FBC:DOS
An anatomical structure consisting of multiple cell cluster organs and which does not contain portions of tissue.
david
2008-10-21T12:20:23Z
fly_anatomy.ontology
FBbt:00007230
compound cell cluster organ
An anatomical structure consisting of multiple cell cluster organs and which does not contain portions of tissue.
FBC:DOS
Any compound cell cluster organ (FBbt:00007230) that capable of some detection of stimulus involved in sensory perception (GO:0050906).
david
2008-10-21T02:09:38Z
FBbt:00002653
VFB:FBbt_00007234
compound sensillum
fly_anatomy.ontology
FBbt:00007234
compound sense organ
Any compound cell cluster organ (FBbt:00007230) that capable of some detection of stimulus involved in sensory perception (GO:0050906).
FBC:Autogenerated
Compound sense organ that is located within the epidermis.
david
2008-10-21T02:23:08Z
VFB:FBbt_00007235
fly_anatomy.ontology
FBbt:00007235
external compound sense organ
Compound sense organ that is located within the epidermis.
FlyBase:FBrf0089570
Material anatomical entity generated by coordinated expression of the organism's own genome and whose component parts are not all connected to each other.
david
2008-11-04T03:09:28Z
fly_anatomy.ontology
FBbt:00007276
anatomical group
Material anatomical entity generated by coordinated expression of the organism's own genome and whose component parts are not all connected to each other.
FBC:DOS
An anatomical group whose component structures share a common function.
david
2008-11-04T03:18:01Z
fly_anatomy.ontology
FBbt:00007278
non-connected functional system
An anatomical group whose component structures share a common function.
FBC:DOS
Any sense organ (FBbt:00005155) that is part of some larval head (FBbt:00001730).
david
2008-11-05T10:34:14Z
VFB:FBbt_00007280
larval head sense organ
fly_anatomy.ontology
FBbt:00007280
embryonic/larval head sense organ
Any sense organ (FBbt:00005155) that is part of some larval head (FBbt:00001730).
FBC:Autogenerated
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of sound.
fly_anatomy.ontology
FBbt:00007685
auditory system
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of sound.
FBC:DOS
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of mechanical stimuli.
fly_anatomy.ontology
FBbt:00007687
mechanosensory system
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of mechanical stimuli.
FBC:DOS
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of smell.
fly_anatomy.ontology
FBbt:00007688
olfactory system
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of smell.
FBC:DOS
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of chemical stimuli.
fly_anatomy.ontology
FBbt:00007689
chemosensory system
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of chemical stimuli.
FBC:DOS
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of taste.
fly_anatomy.ontology
FBbt:00007690
gustatory system
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of taste.
FBC:DOS
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception.
fly_anatomy.ontology
FBbt:00007692
Note - the relationship of this class to the nervous system is overlap. This allows for sense organ components that function in the transduction of sensory signals but that are not considered to be part of the nervous system to be part of sensory systems.
sensory system
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception.
FBC:DOS
A collective term for stages 9 and 10.
fly_anatomy.ontology
FBbt:00014201
early extended germ band embryo
A collective term for stages 9 and 10.
FBC:DOS
Any germ layer derivative (FBbt:00000000) that develops from some ectoderm (FBbt:00000111).
FBbt:00005253
fly_anatomy.ontology
FBbt:00025990
ectodermal derivative
Any germ layer derivative (FBbt:00000000) that develops from some ectoderm (FBbt:00000111).
FBC:DOS
.
fly_anatomy.ontology
FBbt:00025991
anterior ectoderm derivative
.
FBC:DOS
.
fly_anatomy.ontology
FBbt:00025993
ventral ectoderm derivative
.
FBC:DOS
Any group of similar imaginal cells, such as an imaginal disc, imaginal ring or imaginal island, or a precursor tissue that forms one of them. These tissues develop separately from other embryonic and larval tissues and they generate adult structures during metamorphosis.
http://orcid.org/0000-0002-1373-1705
2018-08-15T09:31:08Z
imaginal structure
fly_anatomy.ontology
FBbt:00047552
imaginal tissue
Any group of similar imaginal cells, such as an imaginal disc, imaginal ring or imaginal island, or a precursor tissue that forms one of them. These tissues develop separately from other embryonic and larval tissues and they generate adult structures during metamorphosis.
FlyBase:FBrf0064789
imaginal structure
FlyBase:FBrf0053815
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of light.
http://orcid.org/0000-0002-1373-1705
2018-09-18T13:08:28Z
fly_anatomy.ontology
FBbt:00047735
visual system
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of light.
FBC:CP
david
2008-06-30T04:15:23Z
fly_anatomy.ontology
FBbt:00057001
anterior-posterior subdivision of organism
Anatomical structure that has multiple cells as parts.
djs93
2010-11-02T02:25:04Z
fly_anatomy.ontology
FBbt:00100313
multicellular structure
Anatomical structure that has multiple cells as parts.
FBC:DOS
djs93
2010-11-04T08:35:02Z
fly_anatomy.ontology
FBbt:00100318
somatic cell
Primordium of the late embryo that develops from the early primordium, and will give rise to the adult eye.
adult eye primordium late
fly_anatomy.ontology
FBbt:00105515
late embryonic primordium of adult eye
Primordium of the late embryo that develops from the early primordium, and will give rise to the adult eye.
FBC:DOS
FBC:VH
FlyBase:FBrf0089570
FlyBase:FBrf0151275
Nervous system of the pupa.
mmc46
2013-01-04T10:01:28Z
VFB:FBbt_00110192
fly_anatomy.ontology
FBbt:00110192
pupal nervous system
Nervous system of the pupa.
FBC:MMC
fly_anatomy.ontology
FBbt:01000119
anterior ectoderm anlage
Anatomical entity which is part_of Drosophila melanogaster.
FBbt_root:00000000
fly_anatomy.ontology
Drosophila
FBbt:10000000
anatomical entity
Anatomical entity which is part_of Drosophila melanogaster.
CARO:MAH
Primordium of the embryo that will give rise to the adult eye. It corresponds to the most anterior region that develops from the visual primordium.
P1 Eye
adult eye primordium
fly_anatomy.ontology
FBbt:10005249
embryonic primordium of adult eye
Primordium of the embryo that will give rise to the adult eye. It corresponds to the most anterior region that develops from the visual primordium.
FlyBase:FBrf0089570
FlyBase:FBrf0151275
P1 Eye
FBC:DOS
Phenotype that is any abnormality in thermotaxis (GO:0043052). 'thermotaxis' is defined as: 'The directed movement of a motile cell or organism in response to a temperature gradient. Movement may be towards either a higher or lower temperature.'
thermotaxis behavior defective
thermotaxis behaviour defective
thermotaxis defective
phenotypic_class
FBcv:0000002
abnormal thermotaxis
Phenotype that is any abnormality in thermotaxis (GO:0043052). 'thermotaxis' is defined as: 'The directed movement of a motile cell or organism in response to a temperature gradient. Movement may be towards either a higher or lower temperature.'
FBC:DOS
GOC:cab1
WB_REF:cgc467
A phenotype that is a reduction in the ability of males to produce fertilized eggs as a result of mating, but only to > 50% of wild-type.
phenotypic_class
FBcv:0000006
male semi-fertile
A phenotype that is a reduction in the ability of males to produce fertilized eggs as a result of mating, but only to > 50% of wild-type.
FBC:AO
FBC:CP
FBC:DOS
A phenotype that is a reduction in the ability of females to produce fertilized eggs as a result of mating, but only to > 50% of wild-type.
phenotypic_class
FBcv:0000007
female semi-fertile
A phenotype that is a reduction in the ability of females to produce fertilized eggs as a result of mating, but only to > 50% of wild-type.
FBC:AO
FBC:CP
FBC:DOS
Genotype g1 is a modifier of variegation if, and only if, some genotype g2 has a variegated phenotype and the degree of variegation caused by g1g2 is significantly different from that caused by g2 alone.
phenotypic_class
variegation
FBcv:0000008
modifier of variegation
Genotype g1 is a modifier of variegation if, and only if, some genotype g2 has a variegated phenotype and the degree of variegation caused by g1g2 is significantly different from that caused by g2 alone.
FBC:DOS
variegation
FBC:DOS
Phenotype that is the partial or full transformation of one or more segments (FBbt:00000003) or segmental appendages from one identity to another. For example, in antennapedia an antenna is partially or fully transformed into a leg.
phenotypic_class
FBcv:0000316
homeotic
Phenotype that is the partial or full transformation of one or more segments (FBbt:00000003) or segmental appendages from one identity to another. For example, in antennapedia an antenna is partially or fully transformed into a leg.
FBC:DOS
Phenotype that is any abnormality in dorsal/ventral axis specification (GO:0009950). 'dorsal/ventral axis specification' is defined as: 'The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.'
dorsal/ventral axis specification defective
phenotypic_class
dorsal-ventral polarity
FBcv:0000324
abnormal dorsal/ventral axis specification
Phenotype that is any abnormality in dorsal/ventral axis specification (GO:0009950). 'dorsal/ventral axis specification' is defined as: 'The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.'
FBC:DOS
GOC:dph
GOC:go_curators
GOC:tb
dorsal-ventral polarity
FBC:DOS
A phenotype that is an expansion of the developing embryonic nervous system at the expense of developing ventral epidermis.
djs93
2011-09-13T02:42:10Z
phenotypic_class
FBcv:0000325
Typically this is caused by and expansion of the population of neuroblasts at the expense of prospective epidermis, both of which originate in the ventral ectoderm.
neurogenic phenotype
A phenotype that is an expansion of the developing embryonic nervous system at the expense of developing ventral epidermis.
FlyBase:FBrf0040185
phenotypic_class
FBcv:0000347
phenotypic class
The canonical phenotype of a wild-type Drosophilid.
phenotypic_class
FBcv:0000348
wild-type
The canonical phenotype of a wild-type Drosophilid.
FBC:DOS
A phenotype that is survival to mature adulthood, where mature is defined as after adult stage A3 (FBdv:00006012).
phenotypic_class
FBcv:0000349
Note, this term should not be used with the qualifier 'partially'. Use semi-viable or semi-lethal instead.
viable
A phenotype that is survival to mature adulthood, where mature is defined as after adult stage A3 (FBdv:00006012).
FBC:DOS
5
50
5
50
A phenotype of a population that is the death of some significant proportion of animals in that population, but less that half, prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012).
semi-viable
phenotypic_class
FBcv:0000350
partially lethal - majority live
A phenotype of a population that is the death of some significant proportion of animals in that population, but less that half, prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012).
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population at some stage or stages prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012).
phenotypic_class
FBcv:0000351
Note on usage: lethal is appropriate in cases where escaper adults are very rare. The lethal phase prior to becoming a mature adult may be further specified using children terms which specify stage.
lethal
A phenotype of a population that is the death of all animals in that population at some stage or stages prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012).
FBC:DOS
FBC:KM
50
98
50
98
A phenotype of a population that is the death of a majority of animals in that population prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012).
semi-lethal
phenotypic_class
FBcv:0000352
Stages during which there is significant death prior to mature adulthood can be indicated using one or more stage qualifiers.
partially lethal - majority die
A phenotype of a population that is the death of a majority of animals in that population prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012).
FBC:DOS
FBC:KM
FBC:NB
A phenotype that is a failure of mutant cells to survive.
phenotypic_class
FBcv:0000353
Typically, this phenotype is assayed in clones of cells.
cell lethal
A phenotype that is a failure of mutant cells to survive.
FBC:DOS
A post-embryonic, macroscopic, anatomical phenotype.
phenotypic_class
FBcv:0000354
visible
A post-embryonic, macroscopic, anatomical phenotype.
FBC:DOS
Phenotype that is any abnormality in eye color compared to wild-type.
eye color defective
eye colour defective
phenotypic_class
FBcv:0000355
abnormal eye color
Phenotype that is any abnormality in eye color compared to wild-type.
FBC:DOS
A phenotype that is any abnormality in body color compared to wild-type.
body color defective
body colour defective
phenotypic_class
FBcv:0000356
abnormal body color
A phenotype that is any abnormality in body color compared to wild-type.
FBC:DOS
A phenotype that is any abnormality in the size of the whole body or some body part compared to wild-type.
size defective
phenotypic_class
FBcv:0000357
abnormal size
A phenotype that is any abnormality in the size of the whole body or some body part compared to wild-type.
FBC:DOS
Phenotype that is a decrease in body size compared to identically raised wild-type controls.
small body
phenotypic_class
FBcv:0000358
decreased body size
Phenotype that is a decrease in body size compared to identically raised wild-type controls.
FBC:DOS
Phenotype that is a decrease in the number of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. This phenotype is not necessarily accompanied by decreased growth - there may be fewer cells in an otherwise normal volume of tissue.
reduced cell number
phenotypic_class
FBcv:0000359
decreased cell number
Phenotype that is a decrease in the number of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. This phenotype is not necessarily accompanied by decreased growth - there may be fewer cells in an otherwise normal volume of tissue.
FBC:DOS
Phenotype that is a decrease in the size of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. This phenotype is not necessarily accompanied by decreased growth of a tissue - there may be more cells in an otherwise normal volume of tissue.
reduced cell size
phenotypic_class
FBcv:0000360
Note that defects in cell size are not necessarily the result of defects in cell growth. A change in the rate of cell division in the absence of any change in cell growth rate can result in smaller or larger cells.
decreased cell size
Phenotype that is a decrease in the size of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. This phenotype is not necessarily accompanied by decreased growth of a tissue - there may be more cells in an otherwise normal volume of tissue.
FBC:DOS
Phenotype that is an increase in body size compared to identically raised wild-type controls.
large body
phenotypic_class
FBcv:0000361
increased body size
Phenotype that is an increase in body size compared to identically raised wild-type controls.
FBC:DOS
Phenotype that is an increase in the number of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type.
phenotypic_class
FBcv:0000362
This phenotype is not necessarily accompanied by overgrowth of a tissue - there may be more cells in an otherwise normal volume of tissue. It is not necessarily due to an increase in cell growth -it may be the result of an increase in the division rate at normal growth rates. It may not even be due to an increase in the cell division rate - a reduced rate of cell death while the division rate is normal could also achieve it.
increased cell number
Phenotype that is an increase in the number of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type.
FBC:DOS
Phenotype that is an increase in the size of cells compared to wild-type.
phenotypic_class
FBcv:0000363
May be due to an increase in the cell growth rate or to a reduced rate of cell division along with a normal rate of cell growth.
increased cell size
Phenotype that is an increase in the size of cells compared to wild-type.
FBC:DOS
A phenotype that is the inability to produce fertilized eggs as a result of mating.
phenotypic_class
FBcv:0000364
The cause of sterility may be physical or behavioral. Note, this term should not be used with the qualifier 'partially'. Use semi-sterile or semi-fertile instead.
sterile
A phenotype that is the inability to produce fertilized eggs as a result of mating.
FBC:AO
FBC:CP
FBC:DOS
A phenotype that is a reduction in the ability to produce fertilized eggs as a result of mating to below 50% of wild-type.
phenotypic_class
FBcv:0000365
semi-sterile
A phenotype that is a reduction in the ability to produce fertilized eggs as a result of mating to below 50% of wild-type.
FBC:AO
FBC:CP
FBC:DOS
A phenotype that is the inability of females to produce fertilized eggs as a result of mating.
phenotypic_class
FBcv:0000366
The cause of sterility may be physical or behavioral. Note: this term should not be used with the qualifier 'partially' - use semi-sterile or semi-fertile instead.
female sterile
A phenotype that is the inability of females to produce fertilized eggs as a result of mating.
FBC:AO
FBC:CP
FBC:DOS
A phenotype that is a reduction in the ability of females to produce fertilized eggs as a result of mating to below 50% of wild-type.
phenotypic_class
FBcv:0000367
female semi-sterile
A phenotype that is a reduction in the ability of females to produce fertilized eggs as a result of mating to below 50% of wild-type.
FBC:AO
FBC:CP
FBC:DOS
A phenotype of female sterility due to defects in the female germline.
female sterile germ-line-dependent
phenotypic_class
FBcv:0000368
female sterile germline-dependent
A phenotype of female sterility due to defects in the female germline.
FBC:DOS
A phenotype of female sterility due to defects in somatic cells of the ovary (FBbt:00006030), or of the products of these cells (such as eggshell).
phenotypic_class
FBcv:0000369
female sterile soma-dependent
A phenotype of female sterility due to defects in somatic cells of the ovary (FBbt:00006030), or of the products of these cells (such as eggshell).
FBC:DOS
A phenotype that is the inability of males to produce fertilized eggs as a result of mating.
phenotypic_class
FBcv:0000370
The cause of sterility may be physical or behavioral. Note - this term should not be used with the qualifier 'partially' - use semi-sterile or semi-fertile instead.
male sterile
A phenotype that is the inability of males to produce fertilized eggs as a result of mating.
FBC:AO
FBC:CP
FBC:DOS
A phenotype that is a reduction in the ability of males to produce fertilized eggs as a result of mating to below 50% of wild-type.
phenotypic_class
FBcv:0000371
male semi-sterile
A phenotype that is a reduction in the ability of males to produce fertilized eggs as a result of mating to below 50% of wild-type.
FBC:AO
FBC:CP
FBC:DOS
A phenotype of male sterility due to defects in the male germline.
male sterile germ-line-dependent
phenotypic_class
FBcv:0000372
male sterile germline-dependent
A phenotype of male sterility due to defects in the male germline.
FBC:DOS
A phenotype of male sterility due to defects in somatic cells of the testis (FBbt:00006031) or of the products of these cells.
phenotypic_class
FBcv:0000373
male sterile soma-dependent
A phenotype of male sterility due to defects in somatic cells of the testis (FBbt:00006031) or of the products of these cells.
FBC:DOS
A phenotype that is the ability to produce fertilized eggs as a result of mating.
phenotypic_class
FBcv:0000374
Note, this term should not be used with the qualifier 'partially'. Use semi-sterile or semi-fertile instead.
fertile
A phenotype that is the ability to produce fertilized eggs as a result of mating.
FBC:AO
FBC:CP
FBC:DOS
A phenotype that is a reduction in the ability to produce fertilized eggs as a result of mating, but only to > 50% of wild-type.
phenotypic_class
FBcv:0000375
semi-fertile
A phenotype that is a reduction in the ability to produce fertilized eggs as a result of mating, but only to > 50% of wild-type.
FBC:AO
FBC:CP
FBC:DOS
A phenotype that is the ability of males to produce fertilized eggs as a result of mating.
phenotypic_class
FBcv:0000376
Note - this term should not be used with the qualifier 'partially' - use male semi-sterile or male semi-fertile instead.
male fertile
A phenotype that is the ability of males to produce fertilized eggs as a result of mating.
FBC:AO
FBC:CP
FBC:DOS
A phenotype that is the ability of females to produce fertilized eggs as a result of mating.
phenotypic_class
FBcv:0000377
Note - this term should not be used with the qualifier 'partially' - use female semi-sterile or female semi-fertile instead.
female fertile
A phenotype that is the ability of females to produce fertilized eggs as a result of mating.
FBC:AO
FBC:CP
FBC:DOS
A phenotype in which all offspring are sterile. Typically, this is due to maternal effect sterility resulting from defects in pole cell development.
phenotypic_class
FBcv:0000378
grandchildless
A phenotype in which all offspring are sterile. Typically, this is due to maternal effect sterility resulting from defects in pole cell development.
ISBN:978-0-87969-321-3
Genotype g1 is an enhancer of variegation if, and only if, some genotype g2 has a variegated phenotype and the degree of variegation caused by g1g2 is greater than that caused by g2 alone.
phenotypic_class
FBcv:0000379
Typically, g2 is a chromosomal aberration or an insertion.
enhancer of variegation
Genotype g1 is an enhancer of variegation if, and only if, some genotype g2 has a variegated phenotype and the degree of variegation caused by g1g2 is greater than that caused by g2 alone.
FBC:DOS
Genotype g1 is a non-enhancer of variegation of the phenotype due to genotype g2 if, and only if, g2 has a variegated phenotype and the degree of variegation caused by g1g2 is not greater than that caused by g2 alone.
phenotypic_class
FBcv:0000380
non-enhancer of variegation
Genotype g1 is a non-enhancer of variegation of the phenotype due to genotype g2 if, and only if, g2 has a variegated phenotype and the degree of variegation caused by g1g2 is not greater than that caused by g2 alone.
FBC:DOS
Genotype g1 is a suppressor of variegation if, and only if, some genotype g2 has a variegated phenotype and the degree of variegation caused by g1g2 is less than that caused by to g2 alone.
phenotypic_class
FBcv:0000381
Typically, g2 is a chromosomal aberration or an insertion.
suppressor of variegation
Genotype g1 is a suppressor of variegation if, and only if, some genotype g2 has a variegated phenotype and the degree of variegation caused by g1g2 is less than that caused by to g2 alone.
FBC:DOS
Genotype g1 is a non-suppressor of variegation of the phenotype due to genotype g2 if, and only if, g2 has a variegated phenotype and the degree of variegation caused by g1g2 is not less than that caused by g2 alone.
phenotypic_class
FBcv:0000382
non-suppressor of variegation
Genotype g1 is a non-suppressor of variegation of the phenotype due to genotype g2 if, and only if, g2 has a variegated phenotype and the degree of variegation caused by g1g2 is not less than that caused by g2 alone.
FBC:DOS
A phenotype that is the inability to synthesize some organic compound that can be synthesized by wild-type animals, and that is required for normal growth and/or development.
phenotypic_class
FBcv:0000383
auxotroph
A phenotype that is the inability to synthesize some organic compound that can be synthesized by wild-type animals, and that is required for normal growth and/or development.
http://en.wikipedia.org/wiki/Auxotrophic
Phenotype that is any abnormality in aging (GO:0007568). 'aging' is defined as: 'A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).'
aging defective
phenotypic_class
FBcv:0000384
abnormal aging
Phenotype that is any abnormality in aging (GO:0007568). 'aging' is defined as: 'A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).'
GOC:PO_curators
5
5
Phenotype that is a shorter adult life-span than wild-type.
increased adult mortality
phenotypic_class
FBcv:0000385
short lived
Phenotype that is a shorter adult life-span than wild-type.
FBC:DOS
Phenotype that is a longer adult life-span than wild-type.
phenotypic_class
FBcv:0000386
long lived
Phenotype that is a longer adult life-span than wild-type.
FBC:DOS
Phenotype that is any abnormality in behavior (GO:0007610). 'behavior' is defined as: 'The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.'
behavior defective
behaviour defective
behavioural
phenotypic_class
behavioral
FBcv:0000387
abnormal behavior
Phenotype that is any abnormality in behavior (GO:0007610). 'behavior' is defined as: 'The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.'
GOC:ems
GOC:jl
ISBN:0395448956
PMID:20160973
Phenotype that is a change in the strong tendency, seen in wild-type Drosophila melanogaster, to climb - a behavior otherwise known as negative gravitaxis (GO:0048060 ; movement away from the source of gravity).
gravitaxis defective
phenotypic_class
geotaxis behaviour defective
gravitaxis behavior defective
FBcv:0000388
Note, this term should not be used when flies have climbing defects purely as a consequence of locomotion defects, use 'locomotor behavior defective' instead.
abnormal gravitaxis
Phenotype that is a change in the strong tendency, seen in wild-type Drosophila melanogaster, to climb - a behavior otherwise known as negative gravitaxis (GO:0048060 ; movement away from the source of gravity).
FBC:DOS
Phenotype that is a disposition to paralysis under conditions that do not cause paralysis in a wild-type animal. Paralysis is defined as an inability to exhibit `multicellular organismal movement` (GO:0050879)
phenotypic_class
FBcv:0000389
paralytic
Phenotype that is a disposition to paralysis under conditions that do not cause paralysis in a wild-type animal. Paralysis is defined as an inability to exhibit `multicellular organismal movement` (GO:0050879)
FBC:DOS
A phenotype consisting of decreased frequency of `multicellular organismal movement` (GO:0050879) compared to wild-type.
phenotypic_class
FBcv:0000390
hypoactive
A phenotype consisting of decreased frequency of `multicellular organismal movement` (GO:0050879) compared to wild-type.
FBC:DOS
A phenotype exhibited following mechanical shock and consisting of a brief period of intense, uncoordinated motor activity (legs and wings flailing, abdomen coiling) followed by a prolonged period of paralysis.
phenotypic_class
easily shocked
FBcv:0000391
bang sensitive
A phenotype exhibited following mechanical shock and consisting of a brief period of intense, uncoordinated motor activity (legs and wings flailing, abdomen coiling) followed by a prolonged period of paralysis.
FlyBase:FBrf0022877
easily shocked
FlyBase:FBrf0022877
A phenotype consisting of increased frequency of `multicellular organismal movement` (GO:0050879) compared to wild-type.
phenotypic_class
FBcv:0000392
hyperactive
A phenotype consisting of increased frequency of `multicellular organismal movement` (GO:0050879) compared to wild-type.
FBC:DOS
Phenotype that is any abnormality in response to pain (GO:0048265). 'response to pain' is defined as: '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 pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.'
pain response defective
phenotypic_class
FBcv:0000393
abnormal pain response
Phenotype that is any abnormality in response to pain (GO:0048265). 'response to pain' is defined as: '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 pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.'
FBC:DOS
GOC:jid
PMID:10203867
PMID:12723742
PMID:12843304
Wikipedia:Pain
Phenotype that is any abnormality in circadian rhythm (GO:0007623). 'circadian rhythm' is defined as: 'Any biological process in an organism that recurs with a regularity of approximately 24 hours.'
circadian rhythm defective
phenotypic_class
FBcv:0000394
abnormal circadian rhythm
Phenotype that is any abnormality in circadian rhythm (GO:0007623). 'circadian rhythm' is defined as: 'Any biological process in an organism that recurs with a regularity of approximately 24 hours.'
FBC:DOS
GOC:bf
GOC:go_curators
Phenotype that is any abnormality in locomotor rhythm (GO:0045475). 'locomotor rhythm' is defined as: 'The rhythm of the locomotor activity of an organism during its 24 hour activity cycle.'
locomotor rhythm defective
phenotypic_class
FBcv:0000395
abnormal locomotor rhythm
Phenotype that is any abnormality in locomotor rhythm (GO:0045475). 'locomotor rhythm' is defined as: 'The rhythm of the locomotor activity of an organism during its 24 hour activity cycle.'
FBC:DOS
GOC:go_curators
Phenotype that is any abnormality in eclosion rhythm (GO:0008062). 'eclosion rhythm' is defined as: 'The timing of the emergence of the adult fly from its pupal case, which usually occurs at dawn.'
eclosion rhythm defective
phenotypic_class
FBcv:0000396
abnormal eclosion rhythm
Phenotype that is any abnormality in eclosion rhythm (GO:0008062). 'eclosion rhythm' is defined as: 'The timing of the emergence of the adult fly from its pupal case, which usually occurs at dawn.'
FBC:DOS
PMID:11715043
Phenotype that is any abnormality in learning (GO:0007612). 'learning' is defined as: 'Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.'
learning defective
phenotypic_class
FBcv:0000397
abnormal learning
Phenotype that is any abnormality in learning (GO:0007612). 'learning' is defined as: 'Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.'
FBC:DOS
ISBN:0582227089
ISBN:0721662544
Phenotype that is any abnormality in memory (GO:0007613). 'memory' is defined as: 'The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).'
memory defective
phenotypic_class
FBcv:0000398
abnormal memory
Phenotype that is any abnormality in memory (GO:0007613). 'memory' is defined as: 'The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).'
FBC:DOS
GOC:curators
ISBN:0582227089
Phenotype that is any abnormality in courtship behavior (GO:0007619). 'courtship behavior' is defined as: 'The behavior of an organism for the purpose of attracting sexual partners.'
courtship behavior defective
phenotypic_class
FBcv:0000399
abnormal courtship behavior
Phenotype that is any abnormality in courtship behavior (GO:0007619). 'courtship behavior' is defined as: 'The behavior of an organism for the purpose of attracting sexual partners.'
FBC:DOS
GOC:ai
GOC:dph
Phenotype that is any abnormality in mating (GO:0007618). 'mating' is defined as: 'The pairwise union of individuals for the purpose of sexual reproduction, ultimately resulting in the formation of zygotes.'
mating defective
phenotypic_class
FBcv:0000400
abnormal mating
Phenotype that is any abnormality in mating (GO:0007618). 'mating' is defined as: 'The pairwise union of individuals for the purpose of sexual reproduction, ultimately resulting in the formation of zygotes.'
FBC:DOS
GOC:jl
ISBN:0387520546
Phenotype that is any abnormality in circadian mating behavior (GO:0035648). 'circadian mating behavior' is defined as: 'The fluctuation in mating behavior that occurs over an approximately 24 hour cycle.'
mating rhythm defective
phenotypic_class
FBcv:0000401
abnormal mating rhythm
Phenotype that is any abnormality in circadian mating behavior (GO:0035648). 'circadian mating behavior' is defined as: 'The fluctuation in mating behavior that occurs over an approximately 24 hour cycle.'
FBC:DOS
GOC:bf
GOC:dos
PMID:11470898
PMID:17276917
Phenotype that is any abnormality in male courtship behavior, veined wing generated song production (GO:0045433). This is defined as 'The process during wing vibration where the male insect produces a species-specific acoustic signal called a love song.'
singing defective
song defective
song production defective
phenotypic_class
FBcv:0000402
abnormal song
Phenotype that is any abnormality in male courtship behavior, veined wing generated song production (GO:0045433). This is defined as 'The process during wing vibration where the male insect produces a species-specific acoustic signal called a love song.'
FBC:DOS
GOC:mtg_sensu
PMID:11092827
singing defective
FBC:SM
song production defective
FBC:SM
Phenotype that is any abnormality in chemosensory behavior (GO:0007635). 'chemosensory behavior' is defined as: 'Behavior that is dependent upon the sensation of chemicals.'.'
chemosensitive behavior defective
chemosensitive behaviour defective
phenotypic_class
FBcv:0000403
abnormal chemosensitive behavior
Phenotype that is any abnormality in chemosensory behavior (GO:0007635). 'chemosensory behavior' is defined as: 'Behavior that is dependent upon the sensation of chemicals.'.'
FBC:DOS
GOC:go_curators
Phenotype that is any abnormality in sensory perception of smell (GO:0007608). 'sensory perception of smell' is defined as: 'The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process.'
olfaction defective
smell perception defective
phenotypic_class
FBcv:0000404
abnormal smell perception
Phenotype that is any abnormality in sensory perception of smell (GO:0007608). 'sensory perception of smell' is defined as: 'The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process.'
FBC:DOS
GOC:ai
Phenotype that is any abnormality in sensory perception of taste (GO:0050909). 'sensory perception of taste' is defined as: 'The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process.'
gustation defective
taste defective
taste perception defective
phenotypic_class
FBcv:0000405
abnormal taste perception
Phenotype that is any abnormality in sensory perception of taste (GO:0050909). 'sensory perception of taste' is defined as: 'The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process.'
FBC:DOS
GOC:ai
Phenotype that is any abnormality in or absense of proboscis extension reflex in response to a sugar stimulus via taste sensilla on the tarsus.
tarsal response defective
phenotypic_class
FBcv:0000406
abnormal tarsal response
Phenotype that is any abnormality in or absense of proboscis extension reflex in response to a sugar stimulus via taste sensilla on the tarsus.
FBC:DOS
Phenotype that is any abnormality in sensory perception of sound (GO:0007605). 'sensory perception of sound' is defined as: 'The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.'
auditory perception defective
phenotypic_class
auditory system defective
FBcv:0000407
abnormal auditory perception
Phenotype that is any abnormality in sensory perception of sound (GO:0007605). 'sensory perception of sound' is defined as: 'The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.'
FBC:DOS
GOC:ai
Phenotype that is any abnormality in response to stress (GO:0006950). 'response to stress' is defined as: 'Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).'
stress response defective
environmental stress response defective
phenotypic_class
FBcv:0000408
abnormal stress response
Phenotype that is any abnormality in response to stress (GO:0006950). 'response to stress' is defined as: 'Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).'
FBC:DOS
GOC:mah
Phenotype that is any abnormality in response to osmotic stress (GO:0006970). 'response to osmotic stress' is defined as: 'Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.'
osmotic stress response defective
phenotypic_class
FBcv:0000409
abnormal osmotic stress response
Phenotype that is any abnormality in response to osmotic stress (GO:0006970). 'response to osmotic stress' is defined as: 'Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.'
FBC:DOS
GOC:jl
Phenotype that is any abnormality in response to heat (GO:0009408). 'response to heat' is defined as: '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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.'
heat stress response defective
phenotypic_class
FBcv:0000410
abnormal heat stress response
Phenotype that is any abnormality in response to heat (GO:0009408). 'response to heat' is defined as: '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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.'
FBC:DOS
GOC:lr
Phenotype that is any abnormality in visual behavior (GO:0007632). 'visual behavior' is defined as: 'The behavior of an organism in response to a visual stimulus.'
visual behavior defective
visual behaviour defective
phenotypic_class
FBcv:0000411
abnormal visual behavior
Phenotype that is any abnormality in visual behavior (GO:0007632). 'visual behavior' is defined as: 'The behavior of an organism in response to a visual stimulus.'
FBC:DOS
GOC:jid
GOC:pr
Phenotype that is any abnormality in optomotor response: a motor response during flight or walking that serves to stabilize both image formation on the retina and locomotor course.
optomotor behaviour defective
optomotor response defective
phenotypic_class
FBcv:0000412
abnormal optomotor response
Phenotype that is any abnormality in optomotor response: a motor response during flight or walking that serves to stabilize both image formation on the retina and locomotor course.
FBC:DOS
Phenotype that is any abnormality in phototaxis (GO:0042331). 'phototaxis' is defined as: 'The directed movement of a motile cell or organism in response to light.'
phototaxis defective
phenotypic_class
phototaxis behaviour defective
FBcv:0000413
abnormal phototaxis
Phenotype that is any abnormality in phototaxis (GO:0042331). 'phototaxis' is defined as: 'The directed movement of a motile cell or organism in response to light.'
FBC:DOS
GOC:jl
ISBN:0192800981
Phenotype that is any abnormality in locomotory behavior (GO:0007626). 'locomotory behavior' is defined as: 'The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.'
locomotor behavior defective
locomotor behaviour defective
phenotypic_class
FBcv:0000414
abnormal locomotor behavior
Phenotype that is any abnormality in locomotory behavior (GO:0007626). 'locomotory behavior' is defined as: 'The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.'
FBC:DOS
GOC:dph
Phenotype that is a reduced ability to jump or a reduced jump response. This may be due to neurological or muscular defects.
jumping defective
phenotypic_class
FBcv:0000415
abnormal jumping
Phenotype that is a reduced ability to jump or a reduced jump response. This may be due to neurological or muscular defects.
FBC:DOS
Phenotype that is abnormal co-ordination of motor activity.
phenotypic_class
FBcv:0000416
uncoordinated
Phenotype that is abnormal co-ordination of motor activity.
FBC:CP
FBC:DOS
Phenotype that is any abnormality in flight (GO:0060361). 'flight' is defined as: 'Self-propelled movement of an organism from one location to another through the air, usually by means of active wing movement.'
flight defective
flight behaviour defective
phenotypic_class
FBcv:0000417
This term is agnostic as to the causes of defects in flight. An animal's flight may be defective for mechanical, behavioral or sensory reasons.
abnormal flight
Phenotype that is any abnormality in flight (GO:0060361). 'flight' is defined as: 'Self-propelled movement of an organism from one location to another through the air, usually by means of active wing movement.'
FBC:DOS
GOC:dph
Phenotype that is the absence of flight (GO:0060361). 'flight' is defined as: 'Self-propelled movement of an organism from one location to another through the air, usually by means of active wing movement.'
phenotypic_class
FBcv:0000418
This term is agnostic as to the causes of flightlessness. An animal may be flightless for mechanical or behavioral reasons.
flightless
Phenotype that is the absence of flight (GO:0060361). 'flight' is defined as: 'Self-propelled movement of an organism from one location to another through the air, usually by means of active wing movement.'
FBC:DOS
GOC:dph
Phenotype that is any abnormality in feeding behavior (GO:0007631). 'feeding behavior' is defined as: 'Behavior associated with the intake of food.'
feeding behavior defective
feeding behaviour defective
phenotypic_class
FBcv:0000419
abnormal feeding behavior
Phenotype that is any abnormality in feeding behavior (GO:0007631). 'feeding behavior' is defined as: 'Behavior associated with the intake of food.'
FBC:DOS
GOC:mah
Phenotype that is any abnormality in grooming behavior (GO:0007625). 'grooming behavior' is defined as: 'The specific behavior of an organism relating to grooming, cleaning and brushing to remove dirt and parasites.'
grooming behavior defective
grooming behaviour defective
phenotypic_class
FBcv:0000420
abnormal grooming behavior
Phenotype that is any abnormality in grooming behavior (GO:0007625). 'grooming behavior' is defined as: 'The specific behavior of an organism relating to grooming, cleaning and brushing to remove dirt and parasites.'
FBC:DOS
GOC:jl
GOC:pr
Phenotype that is any abnormality in or loss of a stereotypical behavioral response to touch.
touch response defective
touch sensitivity defective
phenotypic_class
FBcv:0000421
This phenotype is commonly assayed by scoring larval avoidance responses following stroking of the thoracic segments (see Kernan et al., 1994). On its own, this is not sufficient evidence for an abnormality in sensory perception of touch, as motor defects can also cause this phenotype.
abnormal touch response
Phenotype that is any abnormality in or loss of a stereotypical behavioral response to touch.
FlyBase:FBrf0073546
Phenotype that is any abnormality in entrainment of circadian clock by photoperiod (GO:0043153), which is defined as: 'The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night).'
phenotypic_class
FBcv:0000422
photoperiod response variant
Phenotype that is any abnormality in entrainment of circadian clock by photoperiod (GO:0043153), which is defined as: 'The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night).'
FBC:DOS
GOC:jl
Phenotype that is any abnormality in DNA repair (GO:0006281). 'DNA repair' is defined as: 'The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.'
DNA repair defective
phenotypic_class
FBcv:0000423
abnormal DNA repair
Phenotype that is any abnormality in DNA repair (GO:0006281). 'DNA repair' is defined as: 'The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.'
FBC:DOS
PMID:11563486
Phenotype that is a change in the amount of cell death in a whole animal or in some specific organ tissue or clone of cells compared to wild-type. This may be due to effects on the regulation of cell death (GO:0010941) or in cell death (GO:0008219) pathways themselves.
cell death defective
apoptosis defective
pcd defective
programmed cell death defective
phenotypic_class
FBcv:0000424
abnormal cell death
Phenotype that is a change in the amount of cell death in a whole animal or in some specific organ tissue or clone of cells compared to wild-type. This may be due to effects on the regulation of cell death (GO:0010941) or in cell death (GO:0008219) pathways themselves.
FBC:DOS
Phenotype that is an increase in the amount of cell death in a whole animal or in some specific organ tissue or clone of cells compared to wild-type.
pcd increase
programmed cell death increase
phenotypic_class
FBcv:0000425
increased cell death
Phenotype that is an increase in the amount of cell death in a whole animal or in some specific organ tissue or clone of cells compared to wild-type.
FBC:DOS
Phenotype that is a decrease in the amount of cell death in a whole animal or in some specific organ tissue or clone of cells compared to wild-type.
pcd decrease
programmed cell death decrease
phenotypic_class
FBcv:0000426
decreased cell death
Phenotype that is a decrease in the amount of cell death in a whole animal or in some specific organ tissue or clone of cells compared to wild-type.
FBC:DOS
Phenotype that is any abnormality in cell growth (GO:0016049). 'cell growth' is defined as: 'The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.'
cell growth defective
phenotypic_class
FBcv:0000427
Note that defects in cell size are not necessarily the result of defects in cell growth. A change in the rate of cell division in the absence of any change in cell growth rate can result in smaller or larger cells.
abnormal cell growth
Phenotype that is any abnormality in cell growth (GO:0016049). 'cell growth' is defined as: 'The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.'
FBC:DOS
GOC:ai
Phenotype that is any abnormality in the size of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type.
cell size defective
phenotypic_class
FBcv:0000428
abnormal cell size
Phenotype that is any abnormality in the size of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type.
FBC:DOS
Phenotype that is any abnormality in the shape (PATO:0000052) of some cell compared to wild-type.
cell shape defective
phenotypic_class
FBcv:0000429
abnormal cell shape
Phenotype that is any abnormality in the shape (PATO:0000052) of some cell compared to wild-type.
FBC:DOS
Phenotype that is any abnormality in the asymmetric distribution of components within a cell. For example an epithelial cell is 'cell polarity defective' if it lacks the normal asymmetric distribution of proteins or cell components such as junctions or villi along its apical-basal axis.
cell polarity defective
phenotypic_class
abnormal cell polarity
Phenotype that is any abnormality in the asymmetric distribution of components within a cell. For example an epithelial cell is 'cell polarity defective' if it lacks the normal asymmetric distribution of proteins or cell components such as junctions or villi along its apical-basal axis.
FBC:DOS
Phenotype that is any abnormality in meiotic cell cycle (GO:0051321). 'meiotic cell cycle' is defined as: 'Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.'
meiotic cell cycle defective
phenotypic_class
meiotic
FBcv:0000431
abnormal meiotic cell cycle
Phenotype that is any abnormality in meiotic cell cycle (GO:0051321). 'meiotic cell cycle' is defined as: 'Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.'
FBC:DOS
GOC:ai
Phenotype that is any abnormality in mitotic cell cycle (GO:0000278). 'mitotic cell cycle' is defined as: '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.'
mitotic cell cycle defective
phenotypic_class
mitotic
FBcv:0000432
abnormal mitotic cell cycle
Phenotype that is any abnormality in mitotic cell cycle (GO:0000278). 'mitotic cell cycle' is defined as: '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.'
FBC:DOS
GOC:mah
ISBN:0815316194
Reactome:69278
Phenotype that is any abnormality in cytokinesis (GO:0000910). 'cytokinesis' is defined as: 'The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.'
cytokinesis defective
phenotypic_class
FBcv:0000433
abnormal cytokinesis
Phenotype that is any abnormality in cytokinesis (GO:0000910). 'cytokinesis' is defined as: 'The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.'
FBC:DOS
GOC:mtg_cell_cycle
Phenotype that is any abnormality in the electrophysiological properties of some class of neurons, muscles or other anatomical structure of the nervous system. Examples of these phenotypes at the neuron class level include defects in spontaneous or evoked excitatory junction potential. Examples at a more gross anatomical level include abnormal retinal electrophysiology (e.g.- measured by an electroretinogram).
neurophysiology defective
phenotypic_class
FBcv:0000434
abnormal neurophysiology
Phenotype that is any abnormality in the electrophysiological properties of some class of neurons, muscles or other anatomical structure of the nervous system. Examples of these phenotypes at the neuron class level include defects in spontaneous or evoked excitatory junction potential. Examples at a more gross anatomical level include abnormal retinal electrophysiology (e.g.- measured by an electroretinogram).
FBC:DOS
Phenotype that is any abnormality in the anatomy of the nervous system (FBbt:00005093). 'nervous system' is defined as: 'All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems.'
neuroanatomy defective
phenotypic_class
FBcv:0000435
abnormal neuroanatomy
Phenotype that is any abnormality in the anatomy of the nervous system (FBbt:00005093). 'nervous system' is defined as: 'All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems.'
FBC:DOS
FlyBase:FBrf0166419
Phenotype that is any abnormality in sex determination (GO:0007530). 'sex determination' is defined as: 'Any process that establishes and transmits the specification of sexual status of an individual organism.'
sex-determination defective
phenotypic_class
FBcv:0000436
abnormal sex-determination
Phenotype that is any abnormality in sex determination (GO:0007530). 'sex determination' is defined as: 'Any process that establishes and transmits the specification of sexual status of an individual organism.'
FBC:DOS
ISBN:0198506732
FBcv:0000436
phenotypic_class
FBcv:0000437
This term was obsoleted because it was felt that the evidence provided in papers is not enough to annotate with this term. mc161014
dosage compensation defective
true
Phenotype that is a difference in electrophoretic migration of a gene product compared to wild-type.
phenotypic_class
FBcv:0000438
electrophoretic variant
Phenotype that is a difference in electrophoretic migration of a gene product compared to wild-type.
FBC:DOS
Phenotype that is a decreased sensitivity (compared to wild-type) to the toxic effects of some specified chemical. The phrase 'toxic effects' here refers to reversible effects such as inebriation and sedation as well as sustained damage, developmental defects and death.
phenotypic_class
FBcv:0000439
chemical resistant
Phenotype that is a decreased sensitivity (compared to wild-type) to the toxic effects of some specified chemical. The phrase 'toxic effects' here refers to reversible effects such as inebriation and sedation as well as sustained damage, developmental defects and death.
FBC:DOS
Phenotype that is an increased sensitivity (compared to wild-type) to the toxic effects of some specified chemical. The phrase 'toxic effects' here refers to reversible effects such as inebriation and sedation as well as sustained damage, developmental defects and death.
phenotypic_class
FBcv:0000440
chemical sensitive
Phenotype that is an increased sensitivity (compared to wild-type) to the toxic effects of some specified chemical. The phrase 'toxic effects' here refers to reversible effects such as inebriation and sedation as well as sustained damage, developmental defects and death.
FBC:DOS
Phenotype that is a decreased tendency for radiation exposure to cause toxic effects.
phenotypic_class
FBcv:0000441
radiation resistant
Phenotype that is a decreased tendency for radiation exposure to cause toxic effects.
FBC:DOS
Phenotype that is an increased tendency for radiation exposure to cause toxic effects.
phenotypic_class
FBcv:0000442
radiation sensitive
Phenotype that is an increased tendency for radiation exposure to cause toxic effects.
FBC:DOS
Dominant phenotype consisting of short slender bristles and delayed development. Homozygotes are cell lethal.
phenotypic_class
FBcv:0000443
The phenotype may be a general result of mutations in essential components of the protein synthesis pathway, as a number of Minutes encode ribosomal proteins. In an animal that is heterozygous for a Minute mutation, cells with two wild-type alleles of the affected gene have a growth advantage. Many developmental studies take advantage of this fact to give somatic clones a growth advantage. The term 'Minute' should not be used to annotate the resulting phenotypes.
Minute
Dominant phenotype consisting of short slender bristles and delayed development. Homozygotes are cell lethal.
FlyBase:FBrf0066905
Phenotype that is an increase in size of a tissue or organ due to increased numbers of cells, where the affected tissue or organ maintains its normal form.
hyperplastic
phenotypic_class
FBcv:0000444
hyperplasia
Phenotype that is an increase in size of a tissue or organ due to increased numbers of cells, where the affected tissue or organ maintains its normal form.
ISBN:9780198506737
Phenotype that is characterized by the formation of abnormal masses of tissue (tumors) as the result of neoplasia.
FBcv:0000723
phenotypic_class
FBcv:0000445
Obsoleted as this is the same phenotype as neoplasia.
tumorigenic
true
Phenotype that is characterized by the formation of abnormal masses of tissue (tumors) as the result of neoplasia.
FBC:DOS
Phenotype characterized by the formation of lumps of melanotic tissue inside the body in the absence of foreign bodies.
melanotic 'tumor'
phenotypic_class
FBcv:0000446
Melanotic capsules are formed around foreign bodies in wild-type animals as part of the immune response, for example as a protection against parasitoid wasps. Some, but not all melanotic mass phenotypes involve ectopic activation of this immune response. While melanotic masses are commonly referred to as melanotic tumors in the historical literature, this is a misnomer as they are rarely neoplastic.
melanotic mass phenotype
Phenotype characterized by the formation of lumps of melanotic tissue inside the body in the absence of foreign bodies.
FlyBase:FBrf0094387
FlyBase:FBrf0194475
Phenotype characterized by closely associated necrosis and melanization.
phenotypic_class
FBcv:0000447
melanotic necrosis
Phenotype characterized by closely associated necrosis and melanization.
FlyBase:FBrf0155704
Phenotype that is any abnormality in immune response (GO:0006955). 'immune response' is defined as: 'Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.'
immune response defective
phenotypic_class
FBcv:0000448
abnormal immune response
Phenotype that is any abnormality in immune response (GO:0006955). 'immune response' is defined as: 'Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.'
FBC:DOS
GOC:add
GO_REF:0000022
Phenotype that is any abnormality in establishment of planar polarity (GO:0001736). 'establishment of planar polarity' is defined as: 'Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates.'
tissue polarity defective
planar polarity defective
phenotypic_class
FBcv:0000449
For apical-basal polarity phenotypes of epithelia, the appropriate term is 'cell polarity defective'.
abnormal planar polarity
Phenotype that is any abnormality in establishment of planar polarity (GO:0001736). 'establishment of planar polarity' is defined as: 'Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates.'
GOC:dph
Phenotype that is a change in the rate of some developmental process (GO:0032502) taking place prior to mature adulthood (defined as adult stage A3), compared to wild-type. Note, developmental processes include stages in development of the whole animal (e.g.- larval development) as well as specific sub-processes, such as dorsal closure.
developmental rate defective
phenotypic_class
FBcv:0000450
A more complete formalization would require a clause specifying stage. It might be possible to do this in OWL using the same system as we are using for lethal phase.
abnormal developmental rate
Phenotype that is a change in the rate of some developmental process (GO:0032502) taking place prior to mature adulthood (defined as adult stage A3), compared to wild-type. Note, developmental processes include stages in development of the whole animal (e.g.- larval development) as well as specific sub-processes, such as dorsal closure.
FBC:DOS
Phenotype that is any abnormality in wound healing (GO:0042060). 'wound healing' is defined as: 'The series of events that restore integrity to a damaged tissue, following an injury.'
wound healing defective
phenotypic_class
FBcv:0000451
abnormal wound healing
Phenotype that is any abnormality in wound healing (GO:0042060). 'wound healing' is defined as: 'The series of events that restore integrity to a damaged tissue, following an injury.'
GOC:bf
PMID:15269788
Phenotype that is an abnormality in body size compared to wild-type animals raised under the same conditions as the animals exhibiting the phenotype.
body size defective
phenotypic_class
FBcv:0000665
abnormal body size
Phenotype that is an abnormality in body size compared to wild-type animals raised under the same conditions as the animals exhibiting the phenotype.
FBC:DOS
Phenotype that is any abnormality in cell adhesion (GO:0007155). 'cell adhesion' is defined as: 'The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.'
cell adhesion defective
phenotypic_class
FBcv:0000668
abnormal cell adhesion
Phenotype that is any abnormality in cell adhesion (GO:0007155). 'cell adhesion' is defined as: 'The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.'
FBC:DOS
GOC:hb
GOC:pf
Phenotype that is any abnormality in hatching behavior (GO:0035187). 'hatching behavior' is defined as: 'The specific behavior of an organism during the emergence from an egg shell. In Drosophila for example, the larva swings its head reiteratively through a semicircular arc, using its mouth hooks to tear apart the chorion in front of it and thus free itself from within the egg shell.'
hatching behavior defective
hatching behaviour defective
phenotypic_class
FBcv:0000669
abnormal hatching behavior
Phenotype that is any abnormality in hatching behavior (GO:0035187). 'hatching behavior' is defined as: 'The specific behavior of an organism during the emergence from an egg shell. In Drosophila for example, the larva swings its head reiteratively through a semicircular arc, using its mouth hooks to tear apart the chorion in front of it and thus free itself from within the egg shell.'
FBC:DOS
GOC:pr
PMID:10436051
Phenotype that is any abnormality in eclosion (GO:0007562). 'eclosion' is defined as: 'The emergence of an adult insect from a pupa case.'
eclosion defective
phenotypic_class
FBcv:0000670
abnormal eclosion
Phenotype that is any abnormality in eclosion (GO:0007562). 'eclosion' is defined as: 'The emergence of an adult insect from a pupa case.'
FBC:DOS
GOC:dgh
GOC:dos
GOC:mah
ISBN:0198600461
Phenotype that is any abnormality in cell cycle (GO:0007049). 'cell cycle' is defined as: '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.'
cell cycle defective
phenotypic_class
FBcv:0000671
abnormal cell cycle
Phenotype that is any abnormality in cell cycle (GO:0007049). 'cell cycle' is defined as: '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.'
FBC:DOS
GOC:go_curators
GOC:mtg_cell_cycle
Phenotype that is any abnormality in endomitotic cell cycle (GO:0007113). 'endomitotic cell cycle' is defined as: 'A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell.'
endocycle defective
endomitotic cell cycle defective
phenotypic_class
FBcv:0000672
abnormal endomitotic cell cycle
Phenotype that is any abnormality in endomitotic cell cycle (GO:0007113). 'endomitotic cell cycle' is defined as: 'A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell.'
FBC:DOS
GOC:curators
GOC:dos
GOC:expert_vm
Phenotype that is any abnormality in circadian behavior (GO:0048512). 'circadian behavior' is defined as: 'The specific behavior of an organism that recurs with a regularity of approximately 24 hours.'
djs93
2009-11-30T11:06:35Z
circadian behavior defective
phenotypic_class
FBcv:0000679
abnormal circadian behavior
Phenotype that is any abnormality in circadian behavior (GO:0048512). 'circadian behavior' is defined as: 'The specific behavior of an organism that recurs with a regularity of approximately 24 hours.'
FBC:DOS
GOC:bf
GOC:go_curators
GOC:pr
Phenotype that is any abnormality in proboscis extension reflex (GO:0007637). 'proboscis extension reflex' is defined as: 'The extension, through direct muscle actions, of the proboscis (the trunk-like extension of the mouthparts on the adult external head) in response to a nutritional stimulus.'
proboscis extension reflex defective
phenotypic_class
FBcv:0000680
abnormal proboscis extension reflex
Phenotype that is any abnormality in proboscis extension reflex (GO:0007637). 'proboscis extension reflex' is defined as: 'The extension, through direct muscle actions, of the proboscis (the trunk-like extension of the mouthparts on the adult external head) in response to a nutritional stimulus.'
FB:FBrf0044924
FBC:DOS
GOC:jid
Phenotype that is any abnormality in sensory perception (GO:0007600). 'sensory perception' is defined as: 'The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.'
djs93
2010-02-23T12:28:26Z
sensory perception defective
phenotypic_class
FBcv:0000681
abnormal sensory perception
Phenotype that is any abnormality in sensory perception (GO:0007600). 'sensory perception' is defined as: 'The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.'
FBC:DOS
GOC:ai
GOC:dph
Phenotype that is any abnormality in sensory perception of touch (GO:0050975). 'sensory perception of touch' is defined as: 'The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach).'
touch perception defective
phenotypic_class
FBcv:0000682
abnormal touch perception
Phenotype that is any abnormality in sensory perception of touch (GO:0050975). 'sensory perception of touch' is defined as: 'The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach).'
FBC:DOS
GOC:ai
Phenotype that is any abnormality in response to temperature stimulus (GO:0009266). 'response to temperature stimulus' is defined as: '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 temperature stimulus.'
djs93
2010-02-23T12:51:02Z
temperature response defective
phenotypic_class
FBcv:0000683
abnormal temperature response
Phenotype that is any abnormality in response to temperature stimulus (GO:0009266). 'response to temperature stimulus' is defined as: '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 temperature stimulus.'
FBC:DOS
GOC:hb
Phenotype that is any abnormality in response to cold (GO:0009409). 'response to cold' is defined as: '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 cold stimulus, a temperature stimulus below the optimal temperature for that organism.'
djs93
2010-02-23T02:11:27Z
cold stress response defective
phenotypic_class
FBcv:0000684
abnormal cold stress response
Phenotype that is any abnormality in response to cold (GO:0009409). 'response to cold' is defined as: '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 cold stimulus, a temperature stimulus below the optimal temperature for that organism.'
FBC:DOS
GOC:lr
Phenotype that is any abnormality in axis specification (GO:0009798). 'axis specification' is defined as: 'The establishment, maintenance and elaboration of a pattern along a line or around a point.'
axis specification defective
phenotypic_class
FBcv:0000686
This phenotypic class does not encompass planar polarity.
abnormal axis specification
Phenotype that is any abnormality in axis specification (GO:0009798). 'axis specification' is defined as: 'The establishment, maintenance and elaboration of a pattern along a line or around a point.'
FBC:DOS
GOC:dph
GOC:go_curators
GOC:isa_complete
A phenotype that is a disruption in the wild-type pattern of segments or parasegments of the embryo or larva.
phenotypic_class
FBcv:0000698
Commonly assayed on the basis of phenotypic effects on segmentally repeated cuticular patterns.
embryonic/larval segmentation phenotype
A phenotype that is a disruption in the wild-type pattern of segments or parasegments of the embryo or larva.
FlyBase:FBrf0035438
Embryonic/larval segmentation phenotype that is the complete or partial loss of alternate segments or parasegments.
phenotypic_class
FBcv:0000699
Commonly assayed on the basis of phenotypic effects on segmentally repeated cuticular patterns.
pair rule phenotype
Embryonic/larval segmentation phenotype that is the complete or partial loss of alternate segments or parasegments.
FlyBase:FBrf0035438
Embryonic/larval segmentation phenotype that is the complete or partial loss of even segments.
phenotypic_class
FBcv:0000700
Commonly assayed on the basis of phenotypic effects on segmentally repeated cuticular patterns.
even pair-rule phenotype
Embryonic/larval segmentation phenotype that is the complete or partial loss of even segments.
FlyBase:FBrf0035438
Embryonic/larval segmentation phenotype that is the complete or partial loss of odd segments.
phenotypic_class
FBcv:0000701
Commonly assayed on the basis of phenotypic effects on segmentally repeated cuticular patterns.
odd pair-rule phenotype
Embryonic/larval segmentation phenotype that is the complete or partial loss of odd segments.
FlyBase:FBrf0035438
Embryonic/larval segmentation phenotype in which some fraction of each segment (along the anterior-posterior axis) is deleted and replaced by a mirror image duplication of the remaining part of the segment.
phenotypic_class
FBcv:0000702
Commonly assayed on the basis of phenotypic effects on segmentally repeated cuticular patterns.
segment polarity phenotype
Embryonic/larval segmentation phenotype in which some fraction of each segment (along the anterior-posterior axis) is deleted and replaced by a mirror image duplication of the remaining part of the segment.
FlyBase:FBrf0035438
Embryonic/larval segmentation phenotype that is the complete loss of a contiguous stretch of 2 or more segments.
phenotypic_class
FBcv:0000703
Commonly assayed on the basis of phenotypic effects on segmentally repeated cuticular patterns.
gap phenotype
Embryonic/larval segmentation phenotype that is the complete loss of a contiguous stretch of 2 or more segments.
FlyBase:FBrf0035438
Phenotype that is any abnormality in sleep (GO:0030431). 'sleep' is defined as: 'Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain.'
djs93
2010-09-20T12:06:13Z
sleep defective
phenotypic_class
FBcv:0000705
abnormal sleep
Phenotype that is any abnormality in sleep (GO:0030431). 'sleep' is defined as: 'Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain.'
FBC:DOS
ISBN:0192800981
Phenotype that is any abnormality in entry into diapause (GO:0055115). 'entry into diapause' is defined as: 'The dormancy process that results in entry into diapause. Diapause is a neurohormonally mediated, dynamic state of low metabolic activity. Associated characteristics of this form of dormancy include reduced morphogenesis, increased resistance to environmental extremes, and altered or reduced behavioral activity. Full expression develops in a species-specific manner, usually in response to a number of environmental stimuli that precede unfavorable conditions. Once diapause has begun, metabolic activity is suppressed even if conditions favorable for development prevail. Once initiated, only certain stimuli are capable of releasing the organism from this state, and this characteristic is essential in distinguishing diapause from hibernation.'
djs93
2010-09-20T12:06:28Z
diapause defective
phenotypic_class
FBcv:0000706
abnormal diapause
Phenotype that is any abnormality in entry into diapause (GO:0055115). 'entry into diapause' is defined as: 'The dormancy process that results in entry into diapause. Diapause is a neurohormonally mediated, dynamic state of low metabolic activity. Associated characteristics of this form of dormancy include reduced morphogenesis, increased resistance to environmental extremes, and altered or reduced behavioral activity. Full expression develops in a species-specific manner, usually in response to a number of environmental stimuli that precede unfavorable conditions. Once diapause has begun, metabolic activity is suppressed even if conditions favorable for development prevail. Once initiated, only certain stimuli are capable of releasing the organism from this state, and this characteristic is essential in distinguishing diapause from hibernation.'
FBC:DOS
GOC:ds
GOC:jid
GOC:mah
Phenotype that is any abnormality in entry into reproductive diapause (GO:0055116). 'entry into reproductive diapause' is defined as: 'The dormancy process that results in entry into reproductive diapause. Reproductive diapause is a form of diapause where the organism itself will remain fully active, including feeding and other routine activities, but the reproductive organs experience a tissue-specific reduction in metabolism, with characteristic triggering and releasing stimuli.'
djs93
2010-09-20T12:21:29Z
reproductive diapause defective
phenotypic_class
FBcv:0000707
abnormal reproductive diapause
Phenotype that is any abnormality in entry into reproductive diapause (GO:0055116). 'entry into reproductive diapause' is defined as: 'The dormancy process that results in entry into reproductive diapause. Reproductive diapause is a form of diapause where the organism itself will remain fully active, including feeding and other routine activities, but the reproductive organs experience a tissue-specific reduction in metabolism, with characteristic triggering and releasing stimuli.'
FBC:DOS
GOC:ds
GOC:jid
GOC:mah
Phenotype that is any abnormality in response to starvation (GO:0042594). 'response to starvation' is defined as: '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 starvation stimulus, deprivation of nourishment.'
starvation stress response defective
phenotypic_class
FBcv:0000708
abnormal starvation stress response
Phenotype that is any abnormality in response to starvation (GO:0042594). 'response to starvation' is defined as: '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 starvation stimulus, deprivation of nourishment.'
FBC:DOS
GOC:go_curators
Phenotype that is an increase or decrease in the number of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. This phenotype is not necessarily accompanied by defects in cell growth - there may be a greater or lesser number of cells in an otherwise normal volume of tissue.
cell number defective
phenotypic_class
FBcv:0000709
abnormal cell number
Phenotype that is an increase or decrease in the number of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. This phenotype is not necessarily accompanied by defects in cell growth - there may be a greater or lesser number of cells in an otherwise normal volume of tissue.
FBC:DOS
Phenotype that is a inability to jump. This may be due to neurological or muscular defects.
djs93
2011-03-10T04:57:06Z
phenotypic_class
FBcv:0000713
jumpless
Phenotype that is a inability to jump. This may be due to neurological or muscular defects.
FBC:DOS
Phenotype that is any abnormality in cell migration (GO:0016477). 'cell migration' is defined as: 'The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.'
cell migration defective
phenotypic_class
FBcv:0000716
abnormal cell migration
Phenotype that is any abnormality in cell migration (GO:0016477). 'cell migration' is defined as: 'The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.'
FBC:DOS
GOC:cjm
GOC:dph
GOC:ems
GOC:pf
Wikipedia:Cell_migration
Phenotype that is an increase in the rate of cell growth (GO:0016049) in a whole animal or in some specific organ tissue or clone of cells compared to wild-type.
phenotypic_class
FBcv:0000717
increased cell growth
Phenotype that is an increase in the rate of cell growth (GO:0016049) in a whole animal or in some specific organ tissue or clone of cells compared to wild-type.
FBC:DOS
Phenotype that is an decrease in the rate of cell growth (GO:0016049) in a whole animal or in some specific organ tissue or clone of cells compared to wild-type.
phenotypic_class
FBcv:0000718
decreased cell growth
Phenotype that is an decrease in the rate of cell growth (GO:0016049) in a whole animal or in some specific organ tissue or clone of cells compared to wild-type.
FBC:DOS
Phenotype that is a decrease in size of an initially normally sized organ or tissue due to wasting away of cells.
djs93
2011-03-10T05:59:04Z
phenotypic_class
FBcv:0000719
atrophy
Phenotype that is a decrease in size of an initially normally sized organ or tissue due to wasting away of cells.
FBC:DOS
Phenotype that is any abnormality or in or absence of a jump response (GO:0007630). The jump response in Drosophila is a reflex escape response that can be triggered by a number of signals including odor and light. Standard assays are commonly used to test odor and light induced jump response.
djs93
2011-03-11T08:03:28Z
jump response defective
phenotypic_class
FBcv:0000720
abnormal jump response
Phenotype that is any abnormality or in or absence of a jump response (GO:0007630). The jump response in Drosophila is a reflex escape response that can be triggered by a number of signals including odor and light. Standard assays are commonly used to test odor and light induced jump response.
FlyBase:FBrf0187887
FlyBase:FBrf0191819
Phenotype that is any abnormality in mating behavior (GO:0007617). 'mating behavior' is defined as: 'The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes.'
mating behavior defective
phenotypic_class
FBcv:0000721
abnormal mating behavior
Phenotype that is any abnormality in mating behavior (GO:0007617). 'mating behavior' is defined as: 'The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes.'
FBC:DOS
GOC:ai
GOC:dph
Phenotype that consists of abnormal growth of a tissue or organ due to increased numbers of cells, but in which the affected tissue or organ does not maintain its normal form.
neoplasm
neoplastic
tumorigenesis
tumorigenic
phenotypic_class
FBcv:0000723
neoplasia
Phenotype that consists of abnormal growth of a tissue or organ due to increased numbers of cells, but in which the affected tissue or organ does not maintain its normal form.
FBC:DOS
Phenotype that is a reduction in size of an organ or tissue compared to wild-type due to reduced numbers of cells being produced during its development or growth.
phenotypic_class
FBcv:0000724
This term should not be used where an organ or tissue is reduced in size due to the wasting away of existing cells.
hypoplasia
Phenotype that is a reduction in size of an organ or tissue compared to wild-type due to reduced numbers of cells being produced during its development or growth.
FBC:DOS
Phenotype that is any abnormality in response to oxidative stress (GO:0006979). 'response to oxidative stress' is defined as: '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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.'
oxidative stress response defective
phenotypic_class
FBcv:0000725
abnormal oxidative stress response
Phenotype that is any abnormality in response to oxidative stress (GO:0006979). 'response to oxidative stress' is defined as: '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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.'
FBC:DOS
GOC:jl
PMID:12115731
Embryonic/larval segmentation phenotype that is the complete or partial loss of terminal regions of the embryo/larva: the acron, telson and immediately adjacent segments.
djs93
2011-09-13T02:31:53Z
phenotypic_class
FBcv:0000734
terminal phenotype
Embryonic/larval segmentation phenotype that is the complete or partial loss of terminal regions of the embryo/larva: the acron, telson and immediately adjacent segments.
FBC:DOS
A phenotype in which the aging process (GO:0007568) is slower than in wild-type.
phenotypic_class
FBcv:0000791
delayed aging
A phenotype in which the aging process (GO:0007568) is slower than in wild-type.
FBC:DOC
A phenotype in which the aging process (GO:0007568) is accelerated compared to wild-type.
phenotypic_class
FBcv:0000792
premature aging
A phenotype in which the aging process (GO:0007568) is accelerated compared to wild-type.
FBC:DOC
Phenotype that is a defect in endocytosis (GO:0006897). 'endocytosis' is defined as: 'A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.'
abnormal endocytosis
phenotypic_class
FBcv:0001324
Obsoleted as this is phenotype is too molecular to be captured by FlyBase phenotype curation and will be captured by GO curation [FBC:CP].
endocytosis defective
true
Phenotype that is a defect in endocytosis (GO:0006897). 'endocytosis' is defined as: 'A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.'
FBC:DOS
Phenotype that is a defect in exocytosis (GO:0006887). 'exocytosis' is defined as: 'A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.'
abnormal exocytosis
phenotypic_class
FBcv:0001325
Obsoleted as this is phenotype is too molecular to be captured by FlyBase phenotype curation and will be captured by GO curation [FBC:CP].
exocytosis defective
true
Any abnormality in or loss of some anatomical structure or biological process compared to wild-type.
phenotypic class
phenotypic_class
FBcv:0001347
The subclasses of this term classify Drosophila phenotypes into different common categories. They have been chosen by FlyBase to reflect phenotype terms most often reported by Drosophila researchers in the published literature.
phenotype
Any abnormality in or loss of some anatomical structure or biological process compared to wild-type.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population at some stage or stages prior to eclosion from the pupal case (the end of the P-stage).
pupal lethal
lethal - all die before end of pharate adult stage
phenotypic_class
As the P-Stage and the 'pharate adult stage' have the same end, there is no need for a separate term for 'lethal - all die before end of pharate adult stage.
lethal - all die before end of P-stage
A phenotype of a population that is the death of all animals in that population at some stage or stages prior to eclosion from the pupal case (the end of the P-stage).
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population at some stage or stages before the end of the first instar larval stage.
phenotypic_class
lethal - all die before end of first instar larval stage
A phenotype of a population that is the death of all animals in that population at some stage or stages before the end of the first instar larval stage.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population at some stage or stages before the end of the larval stage.
larval lethal
lethal - all die before end of third instar larval stage
phenotypic_class
As the larval stage and third instar larval stage have the same end, there is no need for a separate term for 'lethal - all die before end of third instar larval stage'.
lethal - all die before end of larval stage
A phenotype of a population that is the death of all animals in that population at some stage or stages before the end of the larval stage.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population at some stage or stages before the end of the second instar larval stage.
phenotypic_class
lethal - all die before end of second instar larval stage
A phenotype of a population that is the death of all animals in that population at some stage or stages before the end of the second instar larval stage.
FBC:DOS
5
5
A phenotype that is an increase in the rate of death in a population at any stage of life (during development or adulthood), over the rate seen in a wild type control population.
phenotypic_class
increased mortality
A phenotype that is an increase in the rate of death in a population at any stage of life (during development or adulthood), over the rate seen in a wild type control population.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population during the P-stage.
pupal lethal
phenotypic_class
lethal - all die during P-stage
A phenotype of a population that is the death of all animals in that population during the P-stage.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population during the first instar larval stage.
phenotypic_class
lethal - all die during first instar larval stage
A phenotype of a population that is the death of all animals in that population during the first instar larval stage.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population during the larval stage.
larval lethal
phenotypic_class
lethal - all die during larval stage
A phenotype of a population that is the death of all animals in that population during the larval stage.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population during the second instar larval stage.
phenotypic_class
lethal - all die during second instar larval stage
A phenotype of a population that is the death of all animals in that population during the second instar larval stage.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population during the third instar larval stage.
phenotypic_class
lethal - all die during third instar larval stage
A phenotype of a population that is the death of all animals in that population during the third instar larval stage.
FBC:DOS
50
50
A phenotype of a population that is the death of the majority of animals in that population during the P-stage.
phenotypic_class
majority die during P-stage
A phenotype of a population that is the death of the majority of animals in that population during the P-stage.
FBC:DOS
50
50
A phenotype of a population that is the death of the majority of animals in that population during the first instar larval stage.
phenotypic_class
majority die during first instar larval stage
A phenotype of a population that is the death of the majority of animals in that population during the first instar larval stage.
FBC:DOS
50
50
A phenotype of a population that is the death of the majority of animals in that population during the larval stage.
phenotypic_class
majority die during larval stage
A phenotype of a population that is the death of the majority of animals in that population during the larval stage.
FBC:DOS
50
50
A phenotype of a population that is the death of the majority of animals in that population during the second instar larval stage.
phenotypic_class
majority die during second instar larval stage
A phenotype of a population that is the death of the majority of animals in that population during the second instar larval stage.
FBC:DOS
50
50
A phenotype of a population that is the death of the majority of animals in that population during the third instar larval stage.
phenotypic_class
majority die during third instar larval stage
A phenotype of a population that is the death of the majority of animals in that population during the third instar larval stage.
FBC:DOS
5
98
5
98
A phenotype of a population that is the death of some significant proportion of animals in that population prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012).
phenotypic_class
partially lethal
A phenotype of a population that is the death of some significant proportion of animals in that population prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012).
FBC:DOS
FBC:KM
5
5
A phenotype of a population that is the death of a significant proportion of animals in that population prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012).
phenotypic_class
increased mortality during development
A phenotype of a population that is the death of a significant proportion of animals in that population prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012).
FBC:DOS
5
5
A phenotype of a population that is the death of a significant proportion of animals in that population during the P-stage.
phenotypic_class
some die during P-stage
A phenotype of a population that is the death of a significant proportion of animals in that population during the P-stage.
FBC:DOS
5
5
A phenotype of a population that is the death of a significant proportion of animals in that population during the first instar larval stage.
phenotypic_class
some die during first instar larval stage
A phenotype of a population that is the death of a significant proportion of animals in that population during the first instar larval stage.
FBC:DOS
5
5
A phenotype of a population that is the death of a significant proportion of animals in that population during the second instar larval stage.
phenotypic_class
some die during second instar larval stage
A phenotype of a population that is the death of a significant proportion of animals in that population during the second instar larval stage.
FBC:DOS
5
5
A phenotype of a population that is the death of a significant proportion of animals in that population during the larval stage.
phenotypic_class
some die during larval stage
A phenotype of a population that is the death of a significant proportion of animals in that population during the larval stage.
FBC:DOS
5
5
A phenotype of a population that is the death of a significant proportion of animals in that population during the third instar larval stage.
phenotypic_class
some die during third instar larval stage
A phenotype of a population that is the death of a significant proportion of animals in that population during the third instar larval stage.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population during the pharate adult stage.
phenotypic_class
lethal - all die during pharate adult stage
A phenotype of a population that is the death of all animals in that population during the pharate adult stage.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population at some stage or stages before the end of the prepupal stage.
phenotypic_class
lethal - all die before end of prepupal stage
A phenotype of a population that is the death of all animals in that population at some stage or stages before the end of the prepupal stage.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population at some stage or stages before the end of the pupal stage.
pupal lethal
phenotypic_class
lethal - all die before end of pupal stage
A phenotype of a population that is the death of all animals in that population at some stage or stages before the end of the pupal stage.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population during the pupal stage.
pupal lethal
phenotypic_class
lethal - all die during pupal stage
A phenotype of a population that is the death of all animals in that population during the pupal stage.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population during the prepupal stage.
phenotypic_class
lethal - all die during prepupal stage
A phenotype of a population that is the death of all animals in that population during the prepupal stage.
FBC:DOS
A phenotype of a population that is the death of all animals in that population at some stage or stages before the end of the embryonic stage.
FBcv:0002033
phenotypic_class
Obsoleted due to equivalence with FBcv:0002033 'lethal - all die during embryonic stage'.
lethal - all die before end of embryonic stage
true
A phenotype of a population that is the death of all animals in that population at some stage or stages before the end of the embryonic stage.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population during the embryonic stage.
embryonic lethal
phenotypic_class
lethal - all die during embryonic stage
98
Need to add local reflexivity to part_of for this to work. And really need to be using continuant part of.
A phenotype of a population that is the death of all animals in that population during the embryonic stage.
FBC:DOS
50
50
A phenotype of a population that is the death of the majority of animals in that population during the pupal stage.
phenotypic_class
majority die during pupal stage
A phenotype of a population that is the death of the majority of animals in that population during the pupal stage.
FBC:DOS
50
50
A phenotype of a population that is the death of the majority of animals in that population during the prepupal stage.
phenotypic_class
majority die during prepupal stage
A phenotype of a population that is the death of the majority of animals in that population during the prepupal stage.
FBC:DOS
50
50
A phenotype of a population that is the death of the majority of animals in that population during the pharate adult stage.
phenotypic_class
majority die during pharate adult stage
A phenotype of a population that is the death of the majority of animals in that population during the pharate adult stage.
FBC:DOS
50
50
A phenotype of a population that is the death of the majority of animals in that population during the embryonic stage.
phenotypic_class
This term is agnostic about whether any survive to adulthood.
majority die during embryonic stage
A phenotype of a population that is the death of the majority of animals in that population during the embryonic stage.
FBC:DOS
5
5
A phenotype of a population that is the death of a significant proportion of animals in that population during the pharate adult stage.
phenotypic_class
some die during pharate adult stage
A phenotype of a population that is the death of a significant proportion of animals in that population during the pharate adult stage.
FBC:DOS
5
5
A phenotype of a population that is the death of a significant proportion of animals in that population during the pupal stage.
phenotypic_class
some die during pupal stage
A phenotype of a population that is the death of a significant proportion of animals in that population during the pupal stage.
FBC:DOS
5
5
A phenotype of a population that is the death of a significant proportion of animals in that population during the prepupal stage.
phenotypic_class
some die during prepupal stage
A phenotype of a population that is the death of a significant proportion of animals in that population during the prepupal stage.
FBC:DOS
5
5
A phenotype of a population that is the death of a significant proportion of animals in that population during the embryonic stage.
phenotypic_class
some die during embryonic stage
A phenotype of a population that is the death of a significant proportion of animals in that population during the embryonic stage.
FBC:DOS
98
98
A phenotype of a population that is the death of all animals in that population as immature adults (after eclosion but before the end of adult stage A3 (FBdv:00006012)).
phenotypic_class
lethal - all die during immature adult stage
A phenotype of a population that is the death of all animals in that population as immature adults (after eclosion but before the end of adult stage A3 (FBdv:00006012)).
FBC:DOS
50
50
A phenotype of a population that is the death of the majority of animals in that population as immature adults (after eclosion but before the end of adult stage A3 (FBdv:00006012)).
phenotypic_class
majority die during immature adult stage
A phenotype of a population that is the death of the majority of animals in that population as immature adults (after eclosion but before the end of adult stage A3 (FBdv:00006012)).
FBC:DOS
5
5
A phenotype of a population that is the death of some significant number of animals in that population as immature adults (after eclosion but before the end of adult stage A3 (FBdv:00006012)).
phenotypic_class
some die during immature adult stage
A phenotype of a population that is the death of some significant number of animals in that population as immature adults (after eclosion but before the end of adult stage A3 (FBdv:00006012)).
FBC:DOS
Phenotype that is any abnormality in sensory perception of light stimulus (GO:0050953). 'sensory perception of light stimulus' is defined as: 'The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.'
visual perception defective
phenotypic_class
FBcv:0004000
abnormal visual perception
Phenotype that is any abnormality in sensory perception of light stimulus (GO:0050953). 'sensory perception of light stimulus' is defined as: 'The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.'
FBC:MMC
GOC:ai
Phenotype that is any abnormality in copulation (GO:0007620). 'copulation' is defined as: 'The act of sexual union between male and female, involving the transfer of sperm.'
copulation defective
phenotypic_class
FBcv:0006000
abnormal copulation
Phenotype that is any abnormality in copulation (GO:0007620). 'copulation' is defined as: 'The act of sexual union between male and female, involving the transfer of sperm.'
FBC:TEMJ
ISBN:0721662544
Phenotype that is an increase in the number of gametes produced.
phenotypic_class
FBcv:0006001
increased fecundity
Phenotype that is an increase in the number of gametes produced.
FBC:TEMJ
Phenotype that is a decrease in the number of gametes produced.
phenotypic_class
FBcv:0006002
decreased fecundity
Phenotype that is a decrease in the number of gametes produced.
FBC:TEMJ
population of Drosophila
Phenotype that is any abnormality in oviposition (GO:0007620). 'oviposition' is defined as: 'The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water.'.
oviposition defective
phenotypic_class
FBcv:0006004
This term should only be used to report defects specifically in oviposition, as opposed to an overall loss of fertility. If a difference in "oviposition rate" is measured by authors as a proxy for sterility/fertility, it would be better to use the terms "sterile", "semi-sterile", or "semi-fertile", as appropriate.
abnormal oviposition
Phenotype that is any abnormality in oviposition (GO:0007620). 'oviposition' is defined as: 'The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water.'.
FBC:TEMJ
GOC:ems
A phenotype that is an increased occurrence of cell division (GO:0051301). 'cell division' is defined as 'The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.'.
phenotypic_class
FBcv:0006005
increased occurrence of cell division
A phenotype that is an increased occurrence of cell division (GO:0051301). 'cell division' is defined as 'The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.'.
FBC:TEMJ
GOC:di
GOC:go_curators
GOC:pr
A phenotype that is a decreased occurrence of cell division (GO:0051301). 'cell division' is defined as 'The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.'.
phenotypic_class
FBcv:0006006
decreased occurrence of cell division
A phenotype that is a decreased occurrence of cell division (GO:0051301). 'cell division' is defined as 'The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.'.
FBC:TEMJ
GOC:di
GOC:go_curators
GOC:pr
population of cells
Phenotype that is any abnormality in anesthesia-resistant memory (GO:0007615). 'anesthesia-resistant memory' is defined as: 'The memory process that results in the formation of consolidated memory resistant to disruption of the patterned activity of the brain, without requiring protein synthesis.'
2020-12-15T14:46:41Z
phenotypic_class
FBcv:0007500
abnormal anesthesia-resistant memory
Phenotype that is any abnormality in anesthesia-resistant memory (GO:0007615). 'anesthesia-resistant memory' is defined as: 'The memory process that results in the formation of consolidated memory resistant to disruption of the patterned activity of the brain, without requiring protein synthesis.'
PMID:15143285
PMID:17088531
Phenotype that is any abnormality in short-term memory (GO:0007614). 'short-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation.'
2020-12-15T14:50:19Z
phenotypic_class
FBcv:0007501
abnormal short-term memory
Phenotype that is any abnormality in short-term memory (GO:0007614). 'short-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation.'
ISBN:0582227089
http://hebb.mit.edu/courses/9.03/lecture4.html
Phenotype that is any abnormality in medium-term memory (GO:0072375). 'medium-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information received at a time ago that is intermediate between that of short and long term memory (30min - 7hrs in Drosophila melanogaster).'
2020-12-15T14:51:08Z
phenotypic_class
FBcv:0007502
abnormal medium-term memory
Phenotype that is any abnormality in medium-term memory (GO:0072375). 'medium-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information received at a time ago that is intermediate between that of short and long term memory (30min - 7hrs in Drosophila melanogaster).'
GOC:sart
PMID:14659098
PMID:7923375
Phenotype that is any abnormality in long-term memory (GO:0007616). 'long-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.'
2020-12-15T14:51:45Z
phenotypic_class
FBcv:0007503
abnormal long-term memory
Phenotype that is any abnormality in long-term memory (GO:0007616). 'long-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.'
ISBN:0582227089
http://hebb.mit.edu/courses/9.03/lecture4.html
Phenotype that is any abnormality in body weight compared to identically raised wild-type controls.
2020-12-15T15:47:07Z
phenotypic_class
FBcv:0007504
abnormal body weight
Phenotype that is any abnormality in body weight compared to identically raised wild-type controls.
FBC:CP
Phenotype that is an increase in body weight compared to identically raised wild-type controls.
2020-12-15T15:50:18Z
phenotypic_class
FBcv:0007505
increased body weight
Phenotype that is an increase in body weight compared to identically raised wild-type controls.
FBC:CP
Phenotype that is a decrease in body weight compared to identically raised wild-type controls.
2020-12-15T15:50:44Z
phenotypic_class
FBcv:0007506
decreased body weight
Phenotype that is a decrease in body weight compared to identically raised wild-type controls.
FBC:CP
A phenotype that is an increase in the size of the whole body or some body part compared to wild-type.
2020-12-15T15:52:00Z
phenotypic_class
FBcv:0007507
increased size
A phenotype that is an increase in the size of the whole body or some body part compared to wild-type.
FBC:CP
A phenotype that is a decrease in the size of the whole body or some body part compared to wild-type.
2020-12-15T15:52:59Z
phenotypic_class
FBcv:0007508
decreased size
A phenotype that is a decrease in the size of the whole body or some body part compared to wild-type.
FBC:CP
Phenotype that is an increase in the rate of phototaxis (GO:0042331). 'phototaxis' is defined as: 'The directed movement of a motile cell or organism in response to light.'
2020-12-16T09:10:39Z
phenotypic_class
FBcv:0007509
increased rate of phototaxis
Phenotype that is an increase in the rate of phototaxis (GO:0042331). 'phototaxis' is defined as: 'The directed movement of a motile cell or organism in response to light.'
FBC:CP
GOC:jl
ISBN:0192800981
Phenotype that is a decrease in the rate of phototaxis (GO:0042331). 'phototaxis' is defined as: 'The directed movement of a motile cell or organism in response to light.'
2020-12-16T09:20:20Z
phenotypic_class
FBcv:0007510
decreased rate of phototaxis
Phenotype that is a decrease in the rate of phototaxis (GO:0042331). 'phototaxis' is defined as: 'The directed movement of a motile cell or organism in response to light.'
FBC:CP
GOC:jl
ISBN:0192800981
Phenotype that is an increase in the rate of cell adhesion (GO:0007155). 'cell adhesion' is defined as: 'The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.'
2020-12-16T09:21:22Z
phenotypic_class
FBcv:0007511
increased rate of cell adhesion
Phenotype that is an increase in the rate of cell adhesion (GO:0007155). 'cell adhesion' is defined as: 'The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.'
FBC:CP
GOC:hb
GOC:pf
Phenotype that is a decrease in the rate of cell adhesion (GO:0007155). 'cell adhesion' is defined as: 'The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.'
2020-12-16T09:22:22Z
phenotypic_class
FBcv:0007512
decreased rate of cell adhesion
Phenotype that is a decrease in the rate of cell adhesion (GO:0007155). 'cell adhesion' is defined as: 'The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.'
FBC:CP
GOC:hb
GOC:pf
Phenotype that is an increase in the total amount or frequency of sleep (GO:0030431) over a given time interval, compared to wild-type. 'sleep' is defined as: 'Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain.'
2020-12-16T12:02:45Z
phenotypic_class
FBcv:0007513
increased sleep
Phenotype that is an increase in the total amount or frequency of sleep (GO:0030431) over a given time interval, compared to wild-type. 'sleep' is defined as: 'Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain.'
FBC:CP
ISBN:0192800981
Phenotype that is a decrease in the total amount or frequency of sleep (GO:0030431) over a given time interval, compared to wild-type. 'sleep' is defined as: 'Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain.'
2020-12-16T12:12:40Z
phenotypic_class
FBcv:0007514
decreased sleep
Phenotype that is a decrease in the total amount or frequency of sleep (GO:0030431) over a given time interval, compared to wild-type. 'sleep' is defined as: 'Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain.'
FBC:CP
ISBN:0192800981
Phenotype that is an increase in the total amount or frequency of feeding behavior (GO:0007631) over a given time interval, compared to wild-type. 'feeding behavior' is defined as: 'Behavior associated with the intake of food.'
2020-12-16T12:14:26Z
phenotypic_class
FBcv:0007515
increased feeding behavior
Phenotype that is an increase in the total amount or frequency of feeding behavior (GO:0007631) over a given time interval, compared to wild-type. 'feeding behavior' is defined as: 'Behavior associated with the intake of food.'
FBC:DOS
GOC:mah
Phenotype that is a decrease in the total amount or frequency of feeding behavior (GO:0007631) over a given time interval, compared to wild-type. 'feeding behavior' is defined as: 'Behavior associated with the intake of food.'
2020-12-16T12:16:19Z
phenotypic_class
FBcv:0007516
decreased feeding behavior
Phenotype that is a decrease in the total amount or frequency of feeding behavior (GO:0007631) over a given time interval, compared to wild-type. 'feeding behavior' is defined as: 'Behavior associated with the intake of food.'
FBC:DOS
GOC:mah
Phenotype that is an increase in the efficacy of memory (GO:0007613) relative to controls. 'memory' is defined as: 'The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).'
2021-08-06T11:45:09Z
phenotypic_class
FBcv:0007517
This will usually be measured as an increased magnitude/rate of a behavioral output associated with memory formation.
increased memory
Phenotype that is an increase in the efficacy of memory (GO:0007613) relative to controls. 'memory' is defined as: 'The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).'
FBC:CP
GOC:curators
ISBN:0582227089
Phenotype that is a decrease in the efficacy of memory (GO:0007613) relative to controls. 'memory' is defined as: 'The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).'
2021-08-06T11:55:18Z
phenotypic_class
FBcv:0007518
This will usually be measured as a decreased magnitude/rate of a behavioral output associated with memory formation.
decreased memory
Phenotype that is a decrease in the efficacy of memory (GO:0007613) relative to controls. 'memory' is defined as: 'The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).'
FBC:CP
GOC:curators
ISBN:0582227089
Phenotype that is an increase in the efficacy of short-term memory (GO:0007614) relative to controls. 'short-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation.'
2021-08-06T11:56:41Z
phenotypic_class
FBcv:0007519
This will usually be measured as an increased magnitude/rate of a behavioral output associated with short-term memory formation.
increased short-term memory
Phenotype that is an increase in the efficacy of short-term memory (GO:0007614) relative to controls. 'short-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation.'
FBC:CP
ISBN:0582227089
http://hebb.mit.edu/courses/9.03/lecture4.html
Phenotype that is a decrease in the efficacy of short-term memory (GO:0007614) relative to controls. 'short-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation.'
2021-08-06T11:57:17Z
phenotypic_class
FBcv:0007520
This will usually be measured as a decreased magnitude/rate of a behavioral output associated with short-term memory formation.
decreased short-term memory
Phenotype that is a decrease in the efficacy of short-term memory (GO:0007614) relative to controls. 'short-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation.'
FBC:CP
ISBN:0582227089
http://hebb.mit.edu/courses/9.03/lecture4.html
Phenotype that is an increase in the efficacy of long-term memory (GO:0007616) relative to controls. 'long-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.'
2021-08-06T12:02:59Z
phenotypic_class
FBcv:0007521
This will usually be measured as an increased magnitude/rate of a behavioral output associated with long-term memory formation.
increased long-term memory
Phenotype that is an increase in the efficacy of long-term memory (GO:0007616) relative to controls. 'long-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.'
FBC:CP
ISBN:0582227089
http://hebb.mit.edu/courses/9.03/lecture4.html
Phenotype that is a decrease in the efficacy of long-term memory (GO:0007616) relative to controls. 'long-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.'
2021-08-06T12:04:30Z
phenotypic_class
FBcv:0007522
This will usually be measured as a decreased magnitude/rate of a behavioral output associated with long-term memory formation.
decreased long-term memory
Phenotype that is a decrease in the efficacy of long-term memory (GO:0007616) relative to controls. 'long-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.'
FBC:CP
ISBN:0582227089
http://hebb.mit.edu/courses/9.03/lecture4.html
Phenotype that is an increase in the efficacy of anesthesia-resistant memory (GO:0007615) relative to controls. 'anesthesia-resistant memory' is defined as: 'The memory process that results in the formation of consolidated memory resistant to disruption of the patterned activity of the brain, without requiring protein synthesis.'
2021-08-06T12:08:22Z
phenotypic_class
FBcv:0007523
This will usually be measured as an increased magnitude/rate of a behavioral output associated with anesthesia-resistant memory formation.
increased anesthesia-resistant memory
Phenotype that is an increase in the efficacy of anesthesia-resistant memory (GO:0007615) relative to controls. 'anesthesia-resistant memory' is defined as: 'The memory process that results in the formation of consolidated memory resistant to disruption of the patterned activity of the brain, without requiring protein synthesis.'
FBC:CP
PMID:15143285
PMID:17088531
Phenotype that is a decrease in the efficacy of anesthesia-resistant memory (GO:0007615) relative to controls. 'anesthesia-resistant memory' is defined as: 'The memory process that results in the formation of consolidated memory resistant to disruption of the patterned activity of the brain, without requiring protein synthesis.'
2021-08-06T12:10:03Z
phenotypic_class
FBcv:0007524
This will usually be measured as a decreased magnitude/rate of a behavioral output associated with anesthesia-resistant memory formation.
decreased anesthesia-resistant memory
Phenotype that is a decrease in the efficacy of anesthesia-resistant memory (GO:0007615) relative to controls. 'anesthesia-resistant memory' is defined as: 'The memory process that results in the formation of consolidated memory resistant to disruption of the patterned activity of the brain, without requiring protein synthesis.'
FBC:CP
PMID:15143285
PMID:17088531
Phenotype that is an increase in the efficacy of medium-term memory (GO:0072375) relative to controls. 'medium-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information received at a time ago that is intermediate between that of short and long term memory (30min - 7hrs in Drosophila melanogaster).'
2021-08-06T12:11:31Z
phenotypic_class
FBcv:0007525
This will usually be measured as an increased magnitude/rate of a behavioral output associated with medium-term memory formation.
increased medium-term memory
Phenotype that is an increase in the efficacy of medium-term memory (GO:0072375) relative to controls. 'medium-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information received at a time ago that is intermediate between that of short and long term memory (30min - 7hrs in Drosophila melanogaster).'
FBC:CP
GOC:sart
PMID:14659098
PMID:7923375
Phenotype that is a decrease in the efficacy of medium-term memory (GO:0072375) relative to controls. 'medium-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information received at a time ago that is intermediate between that of short and long term memory (30min - 7hrs in Drosophila melanogaster).'
2021-08-06T12:12:48Z
phenotypic_class
FBcv:0007526
This will usually be measured as a decreased magnitude/rate of a behavioral output associated with medium-term memory formation.
decreased medium-term memory
Phenotype that is a decrease in the efficacy of medium-term memory (GO:0072375) relative to controls. 'medium-term memory' is defined as: 'The memory process that deals with the storage, retrieval and modification of information received at a time ago that is intermediate between that of short and long term memory (30min - 7hrs in Drosophila melanogaster).'
FBC:CP
GOC:sart
PMID:14659098
PMID:7923375
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
Embryonic stages 4 and 5.
blastoderm
FlyBase_development_CV
FBdv:00005304
Temporal ordering number - 160.
blastoderm stage
Embryonic stages 4 and 5.
FBC:DOS
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
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
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
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
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
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).
UBERON:8000000
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).
UBERON:8000001
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).
UBERON:8000002
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
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
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
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
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
djs93
2009-10-01T05:56:42Z
GO:0032502
FlyBase_development_CV
FBdv:00007009
developmental process
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
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
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
The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
GO:0019952
GO:0050876
Wikipedia:Reproduction
reproductive physiological process
biological_process
GO:0000003
reproduction
The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
GOC:go_curators
GOC:isa_complete
GOC:jl
ISBN:0198506732
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
GO:0007067
Wikipedia:Mitosis
biological_process
mitosis
GO:0000278
Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.
mitotic cell cycle
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
GOC:mah
ISBN:0815316194
Reactome:69278
The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
biological_process
karyokinesis
GO:0000280
nuclear division
The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
GOC:mah
The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
GO:0007104
GO:0016288
GO:0033205
Wikipedia:Cytokinesis
cell cycle cytokinesis
cytokinesis involved in cell cycle
biological_process
GO:0000910
Note that this term should not be used for direct annotation. When annotating eukaryotic species, mitotic or meiotic cytokinesis should always be specified for manual annotation and for prokaryotic species use 'FtsZ-dependent cytokinesis ; GO:0043093' or Cdv-dependent cytokinesis ; GO:0061639. Also, note that cytokinesis does not necessarily result in physical separation and detachment of the two daughter cells from each other.
cytokinesis
The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
GOC:mtg_cell_cycle
cytokinesis involved in cell cycle
GOC:dph
GOC:tb
Any process that modulates the frequency, rate, extent or direction of cell growth.
biological_process
GO:0001558
regulation of cell growth
Any process that modulates the frequency, rate, extent or direction of cell growth.
GOC:go_curators
Cell migration that is accomplished by extension and retraction of a pseudopodium.
ameboid cell migration
amoeboid cell migration
amoeboidal cell migration
biological_process
GO:0001667
Note that this term refers to a mode of migration rather than to any particular cell type.
ameboidal-type cell migration
Cell migration that is accomplished by extension and retraction of a pseudopodium.
GOC:dph
formation of primary germ layer
ectoderm formation
endoderm formation
mesoderm formation
Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates.
establishment of planar cell polarity
biological_process
GO:0001736
establishment of planar polarity
Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates.
GOC:dph
The morphogenetic process in which the anatomical structures of a polarized epithelium are generated and organized. A polarized epithelium is an epithelium where the epithelial sheet is oriented with respect to the planar axis.
epithelial polarization
biological_process
GO:0001738
morphogenesis of a polarized epithelium
The morphogenetic process in which the anatomical structures of a polarized epithelium are generated and organized. A polarized epithelium is an epithelium where the epithelial sheet is oriented with respect to the planar axis.
GOC:dph
epithelial polarization
GOC:dph
embryonic epithelial tube formation
neural tube formation
The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
epithelium morphogenesis
biological_process
GO:0002009
morphogenesis of an epithelium
The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
GOC:dph
GOC:jl
GOC:tb
ISBN:0198506732
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
Wikipedia:Immune_system
biological_process
GO:0002376
Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501).
immune system process
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
GOC:add
GO_REF:0000022
Any process that modulates the frequency, rate, or extent of an immune system process.
biological_process
GO:0002682
regulation of immune system process
Any process that modulates the frequency, rate, or extent of an immune system process.
GOC:add
The pattern specification process that results in the subdivision of an axis or axes in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment.
biological_process
pattern formation
GO:0003002
regionalization
The pattern specification process that results in the subdivision of an axis or axes in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment.
GOC:dph
GOC:isa_complete
pattern formation
GOC:dph
A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring.
puberty
biological_process
reproductive developmental process
GO:0003006
developmental process involved in reproduction
A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring.
GOC:dph
GOC:isa_complete
puberty
GOC:dph
reproductive developmental process
GOC:dph
GOC:tb
A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective.
organ system process
biological_process
GO:0003008
system process
A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective.
GOC:mtg_cardio
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
catalytic activity
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
GO:0008372
NIF_Subcellular:sao1337158144
cell or subcellular entity
cellular component
cellular_component
subcellular entity
GO:0005575
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
cellular_component
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
GOC:pdt
NIF_Subcellular:sao1337158144
subcellular entity
NIF_Subcellular:nlx_subcell_100315
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.
https://github.com/geneontology/go-ontology/issues/17776
Wikipedia:Intracellular
internal to cell
intracellular
protoplasm
cellular_component
nucleocytoplasm
protoplast
GO:0005622
intracellular anatomical structure
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.
ISBN:0198506732
nucleocytoplasm
GOC:mah
protoplast
GOC:mah
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
NIF_Subcellular:sao1702920020
Wikipedia:Cell_nucleus
cell nucleus
horsetail nucleus
cellular_component
GO:0005634
nucleus
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
GOC:go_curators
horsetail nucleus
GOC:al
GOC:mah
GOC:vw
PMID:15030757
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
GO:0005636
Wikipedia:Nuclear_envelope
cellular_component
GO:0005635
nuclear envelope
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
ISBN:0198547684
The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
Wikipedia:Cytoplasm
cellular_component
GO:0005737
cytoplasm
The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
ISBN:0198547684
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
Wikipedia:Vacuole
cellular_component
vacuolar carboxypeptidase Y
GO:0005773
vacuole
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
GOC:mtg_sensu
ISBN:0198506732
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0005904
juxtamembrane
NIF_Subcellular:sao1663586795
Wikipedia:Cell_membrane
cell membrane
cellular membrane
cytoplasmic membrane
plasmalemma
bacterial inner membrane
inner endospore membrane
plasma membrane lipid bilayer
cellular_component
GO:0005886
plasma membrane
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
ISBN:0716731363
cellular membrane
NIF_Subcellular:sao6433132645
plasma membrane lipid bilayer
GOC:mah
The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
Wikipedia:Cell_cortex
cellular_component
cell periphery
peripheral cytoplasm
GO:0005938
cell cortex
The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
GOC:mah
ISBN:0815316194
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
GO:0055134
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
biological_process
nucleobase, nucleoside and nucleotide metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
GO:0006139
nucleobase-containing compound metabolic process
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
GOC:ai
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
GOC:dph
GOC:tb
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
GO:0055132
DNA metabolism
cellular DNA metabolism
biological_process
GO:0006259
DNA metabolic process
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
ISBN:0198506732
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
Wikipedia:DNA_repair
biological_process
GO:0006281
DNA repair
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
PMID:11563486
Any process that modulates the frequency, rate or extent of DNA repair.
biological_process
GO:0006282
regulation of DNA repair
Any process that modulates the frequency, rate or extent of DNA repair.
GOC:go_curators
The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
aromatic compound metabolism
aromatic hydrocarbon metabolic process
aromatic hydrocarbon metabolism
biological_process
GO:0006725
cellular aromatic compound metabolic process
The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
GOC:ai
ISBN:0198506732
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
nitrogen compound metabolism
biological_process
GO:0006807
nitrogen compound metabolic process
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
GOC:jl
ISBN:0198506732
The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
cellular component motion
cellular component movement
biological_process
cell movement
GO:0006928
Note that in GO cellular components include whole cells (cell is_a cellular component).
movement of cell or subcellular component
The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
GOC:dgh
GOC:dph
GOC:jl
GOC:mlg
cellular component motion
GOC:dph
GOC:jl
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
biological_process
response to abiotic stress
response to biotic stress
GO:0006950
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
response to stress
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
GOC:mah
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
biological_process
GO:0006955
immune response
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
GOC:add
GO_REF:0000022
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.
osmotic response
osmotic stress response
biological_process
GO:0006970
response to osmotic stress
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.
GOC:jl
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
GO:0034984
response to DNA damage stimulus
DNA damage response
cellular DNA damage response
response to genotoxic stress
biological_process
GO:0006974
cellular response to DNA damage 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 indicating damage to its DNA from environmental insults or errors during metabolism.
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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
biological_process
GO:0006979
response to oxidative stress
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
GOC:jl
PMID:12115731
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.
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
A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell.
Wikipedia:Mitosis#Endomitosis
biological_process
endomitosis
GO:0007113
Note that this term should not be confused with 'abortive mitotic cell cycle ; GO:0033277'. Although abortive mitosis is sometimes called endomitosis, GO:0033277 refers to a process in which a mitotic spindle forms and chromosome separation begins.
endomitotic cell cycle
A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell.
GOC:curators
GOC:dos
GOC:expert_vm
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
dos
2014-04-15T15:59:10Z
GO:0098602
Wikipedia:Cell_adhesion
biological_process
cell adhesion molecule activity
single organism cell adhesion
GO:0007155
cell adhesion
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
GOC:hb
GOC:pf
Coordinated organization of groups of cells in a tissue, such that they all orient to similar coordinates.
biological_process
GO:0007164
establishment of tissue polarity
Coordinated organization of groups of cells in a tissue, such that they all orient to similar coordinates.
GOC:jid
The 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).
https://github.com/geneontology/go-ontology/issues/21234
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
gastrulation
Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.
biological_process
pattern biosynthesis
pattern formation
GO:0007389
pattern specification process
Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.
GOC:go_curators
GOC:isa_complete
ISBN:0521436125
ectoderm development
nervous system development
endoderm development
mesoderm development
Any process that establishes and transmits the specification of sexual status of an individual organism.
Wikipedia:Sex-determination_system
biological_process
GO:0007530
sex determination
Any process that establishes and transmits the specification of sexual status of an individual organism.
ISBN:0198506732
The emergence of an adult insect from a pupa case.
Wikipedia:Pupa#Emergence
biological_process
GO:0007562
eclosion
The emergence of an adult insect from a pupa case.
GOC:dgh
GOC:dos
GOC:mah
ISBN:0198600461
Any process that modulates the frequency, rate or extent of the emergence of an insect from a pupa-case or of a larva from an egg.
biological_process
GO:0007563
regulation of eclosion
Any process that modulates the frequency, rate or extent of the emergence of an insect from a pupa-case or of a larva from an egg.
GOC:go_curators
ISBN:0198600461
A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
GO:0016280
Wikipedia:Aging
ageing
biological_process
GO:0007568
aging
A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
GOC:PO_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 nutrient stimulus.
response to nutrients
nutritional response pathway
biological_process
GO:0007584
response to nutrient
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 nutrient stimulus.
GOC:go_curators
The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
Wikipedia:Perception
biological_process
GO:0007600
sensory perception
The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
GOC:ai
GOC:dph
The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
Wikipedia:Visual_perception
sense of sight
sensory visual perception
vision
biological_process
GO:0007601
visual perception
The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
GOC:ai
The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
Wikipedia:Hearing_(sense)
hearing
perception of sound
biological_process
GO:0007605
sensory perception of sound
The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
GOC:ai
The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
chemosensory perception
biological_process
GO:0007606
sensory perception of chemical stimulus
The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
GOC:ai
The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process.
Wikipedia:Olfaction
olfaction
scent perception
sense of smell
smell perception
biological_process
GO:0007608
sensory perception of smell
The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process.
GOC:ai
The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
jl
2012-09-20T14:06:08Z
GO:0023032
GO:0044708
GO:0044709
Wikipedia:Behavior
behavioral response to stimulus
behaviour
behavioural response to stimulus
biological_process
single-organism behavior
GO:0007610
1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.
2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).
behavior
The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
GOC:ems
GOC:jl
ISBN:0395448956
PMID:20160973
The acquisition and processing of information and/or the storage and retrieval of this information over time.
biological_process
GO:0007611
learning or memory
The acquisition and processing of information and/or the storage and retrieval of this information over time.
GOC:jid
PMID:8938125
Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
Wikipedia:Learning
biological_process
GO:0007612
learning
Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
ISBN:0582227089
ISBN:0721662544
The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
Wikipedia:Memory
biological_process
GO:0007613
memory
The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
GOC:curators
ISBN:0582227089
The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation.
Wikipedia:Short-term_memory
biological_process
GO:0007614
short-term memory
The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation.
ISBN:0582227089
http://hebb.mit.edu/courses/9.03/lecture4.html
The memory process that results in the formation of consolidated memory resistant to disruption of the patterned activity of the brain, without requiring protein synthesis.
biological_process
GO:0007615
anesthesia-resistant memory
The memory process that results in the formation of consolidated memory resistant to disruption of the patterned activity of the brain, without requiring protein synthesis.
PMID:15143285
PMID:17088531
The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.
Wikipedia:Long-term_memory
biological_process
GO:0007616
long-term memory
The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.
ISBN:0582227089
http://hebb.mit.edu/courses/9.03/lecture4.html
The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes.
Wikipedia:Mating_behaviour
mating behaviour
biological_process
GO:0007617
mating behavior
The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes.
GOC:ai
GOC:dph
The pairwise union of individuals for the purpose of sexual reproduction, ultimately resulting in the formation of zygotes.
biological_process
GO:0007618
mating
The pairwise union of individuals for the purpose of sexual reproduction, ultimately resulting in the formation of zygotes.
GOC:jl
ISBN:0387520546
The behavior of an organism for the purpose of attracting sexual partners.
courtship behaviour
biological_process
GO:0007619
courtship behavior
The behavior of an organism for the purpose of attracting sexual partners.
GOC:ai
GOC:dph
The act of sexual union between male and female, involving the transfer of sperm.
biological_process
GO:0007620
copulation
The act of sexual union between male and female, involving the transfer of sperm.
ISBN:0721662544
The specific behavior of an organism that recur with measured regularity.
rhythmic behavioral response to stimulus
rhythmic behaviour
rhythmic behavioural response to stimulus
biological_process
GO:0007622
rhythmic behavior
The specific behavior of an organism that recur with measured regularity.
GOC:jl
GOC:pr
Any biological process in an organism that recurs with a regularity of approximately 24 hours.
GO:0050895
Wikipedia:Circadian_rhythm
circadian process
biological_process
circadian response
response to circadian rhythm
GO:0007623
circadian rhythm
Any biological process in an organism that recurs with a regularity of approximately 24 hours.
GOC:bf
GOC:go_curators
The specific behavior of an organism relating to grooming, cleaning and brushing to remove dirt and parasites.
groom
grooming behaviour
biological_process
GO:0007625
grooming behavior
The specific behavior of an organism relating to grooming, cleaning and brushing to remove dirt and parasites.
GOC:jl
GOC:pr
The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
behavior via locomotion
locomotion in response to stimulus
locomotory behavioral response to stimulus
locomotory behaviour
locomotory behavioural response to stimulus
biological_process
GO:0007626
locomotory behavior
The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
GOC:dph
The sudden, usually upward, movement off the ground or other surface through sudden muscular effort in the legs, following exposure to an external stimulus.
biological_process
GO:0007630
jump response
The sudden, usually upward, movement off the ground or other surface through sudden muscular effort in the legs, following exposure to an external stimulus.
GOC:jid
ISBN:0198606907
Behavior associated with the intake of food.
https://github.com/geneontology/go-ontology/issues/18547
jl
2011-10-27T03:53:33Z
GO:0044366
GO:0044367
GO:0044368
GO:0044369
GO:0044370
GO:0044371
GO:0044372
Wikipedia:List_of_feeding_behaviours
behavioral response to food
behavioural response to food
feeding behaviour
eating
feeding from phloem of other organism
feeding from plant phloem
feeding from tissue of other organism
feeding from vascular tissue of another organism
feeding from xylem of other organism
feeding on blood of other organism
feeding on or from other organism
feeding on plant sap
hematophagy
injection of substance into other organism during feeding on blood of other organism
taking of blood meal
biological_process
GO:0007631
See also the biological process term 'behavior ; GO:0007610'.
feeding behavior
Behavior associated with the intake of food.
GOC:mah
The behavior of an organism in response to a visual stimulus.
behavioral response to visual stimulus
behavioural response to visual stimulus
visual behaviour
biological_process
GO:0007632
visual behavior
The behavior of an organism in response to a visual stimulus.
GOC:jid
GOC:pr
The behavior of an organism pertaining to movement of the eyes and of objects in the visual field, as in nystagmus.
optokinetic behaviour
biological_process
GO:0007634
optokinetic behavior
The behavior of an organism pertaining to movement of the eyes and of objects in the visual field, as in nystagmus.
GOC:jid
GOC:pr
Behavior that is dependent upon the sensation of chemicals.
behavioral response to chemical stimulus
behavioural response to chemical stimulus
chemosensory behaviour
biological_process
GO:0007635
chemosensory behavior
Behavior that is dependent upon the sensation of chemicals.
GOC:go_curators
The extension, through direct muscle actions, of the proboscis (the trunk-like extension of the mouthparts on the adult external head) in response to a nutritional stimulus.
behavioral response to nutritional stimulus, proboscis extension
proboscis extension in response to nutritional stimulus
biological_process
GO:0007637
proboscis extension reflex
The extension, through direct muscle actions, of the proboscis (the trunk-like extension of the mouthparts on the adult external head) in response to a nutritional stimulus.
FB:FBrf0044924
GOC:jid
The behavior of a male, for the purpose of attracting a sexual partner. An example of this process is found in Drosophila melanogaster.
GO:0016542
male courtship behaviour
biological_process
GO:0008049
male courtship behavior
The behavior of a male, for the purpose of attracting a sexual partner. An example of this process is found in Drosophila melanogaster.
GOC:mtg_sensu
GOC:pr
The timing of the emergence of the adult fly from its pupal case, which usually occurs at dawn.
biological_process
GO:0008062
eclosion rhythm
The timing of the emergence of the adult fly from its pupal case, which usually occurs at dawn.
PMID:11715043
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.
biological process
physiological process
jl
2012-09-19T15:05:24Z
GO:0000004
GO:0007582
GO:0044699
Wikipedia:Biological_process
biological process
physiological process
biological_process
single organism process
single-organism process
GO:0008150
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that 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 ND, no data, is used to indicate this.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological_process
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
GOC:pdt
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
jl
2012-10-17T15:46:40Z
GO:0044236
GO:0044710
Wikipedia:Metabolism
metabolism
metabolic process resulting in cell growth
metabolism resulting in cell growth
multicellular organism metabolic process
biological_process
single-organism metabolic process
GO:0008152
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
metabolic process
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
GOC:go_curators
ISBN:0198547684
Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
biological_process
accidental cell death
necrosis
GO:0008219
This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term.
cell death
Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
GOC:mah
GOC:mtg_apoptosis
PMID:25236395
Locomotory behavior in a fully developed and mature organism.
adult locomotory behaviour
biological_process
GO:0008344
See also the biological process term 'locomotory behavior ; GO:0007626'.
adult locomotory behavior
Locomotory behavior in a fully developed and mature organism.
GOC:ai
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 temperature stimulus.
response to thermal stimulus
biological_process
GO:0009266
response to temperature 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 temperature stimulus.
GOC:hb
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
response to electromagnetic radiation stimulus
response to radiation stimulus
biological_process
GO:0009314
Note that 'radiation' refers to electromagnetic radiation of any wavelength.
response to radiation
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
GOC:jl
Wikipedia:Electromagnetic_radiation
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
GO:0006951
response to heat shock
biological_process
GO:0009408
response to heat
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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
GOC:lr
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 cold stimulus, a temperature stimulus below the optimal temperature for that organism.
biological_process
freezing tolerance
GO:0009409
response to cold
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 cold stimulus, a temperature stimulus below the optimal temperature for that organism.
GOC:lr
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
biological_process
GO:0009416
response to light stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
GOC:go_curators
ISBN:0582227089
The directed movement of a motile cell or organism in response to physical parameters involved in energy generation, such as light, oxygen, and oxidizable substrates.
energytaxis
taxis in response to energy source
biological_process
GO:0009453
energy taxis
The directed movement of a motile cell or organism in response to physical parameters involved in energy generation, such as light, oxygen, and oxidizable substrates.
GOC:jl
PMID:11029423
The series of events in which an external stimulus is received by a cell and converted into a molecular signal.
biological_process
perception of external stimulus
GO:0009581
detection of external stimulus
The series of events in which an external stimulus is received by a cell and converted into a molecular signal.
GOC:hb
The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal.
biological_process
perception of abiotic stimulus
GO:0009582
detection of abiotic stimulus
The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal.
GOC:hb
The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal.
detection of light
biological_process
perception of light
GO:0009583
detection of light stimulus
The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal.
GOC:go_curators
The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm.
biological_process
perception of visible light
GO:0009584
detection of visible light
The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm.
GOC:go_curators
ISBN:0198506732
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.
response to environmental stimulus
biological_process
GO:0009605
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
response to external stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.
GOC:hb
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
GO:0002245
physiological response to wounding
biological_process
GO:0009611
response to wounding
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
GOC:go_curators
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus.
https://github.com/geneontology/go-ontology/issues/16572
response to abiotic stress
biological_process
GO:0009628
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
response to abiotic stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus.
GOC:hb
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 gravitational stimulus.
response to gravitational stimulus
biological_process
GO:0009629
response to gravity
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 gravitational stimulus.
GOC:hb
Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detection of, or exposure to, a period of light or dark of a given length, measured relative to a particular duration known as the 'critical day length'. The critical day length varies between species.
Wikipedia:Photoperiodism
response to day length
response to night length
response to photoperiod
biological_process
GO:0009648
photoperiodism
Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detection of, or exposure to, a period of light or dark of a given length, measured relative to a particular duration known as the 'critical day length'. The critical day length varies between species.
GOC:jid
GOC:pj
ISBN:0582015952
ISBN:0697037754
ISBN:0709408862
The synchronization of a circadian rhythm to environmental time cues such as light.
biological_process
regulation of circadian rhythm phase
GO:0009649
entrainment of circadian clock
The synchronization of a circadian rhythm to environmental time cues such as light.
GOC:jid
The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
embryogenesis and morphogenesis
Wikipedia:Morphogenesis
anatomical structure organization
morphogenesis
biological_process
GO:0009653
anatomical structure morphogenesis
The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
GOC:go_curators
ISBN:0521436125
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
GO:0009795
embryogenesis and morphogenesis
Wikipedia:Embryogenesis
embryogenesis
embryonal development
biological_process
GO:0009790
embryo development
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
GOC:go_curators
GOC:isa_complete
GOC:mtg_sensu
post-embryonic development
embryo development ending in birth or egg hatching
The establishment, maintenance and elaboration of a pattern along a line or around a point.
biological_process
axis determination
GO:0009798
axis specification
The establishment, maintenance and elaboration of a pattern along a line or around a point.
GOC:dph
GOC:go_curators
GOC:isa_complete
Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
histogenesis and organogenesis
biological_process
GO:0009887
animal organ morphogenesis
Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
GOC:dgh
GOC:go_curators
ISBN:0471245208
ISBN:0721662544
The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
histogenesis and organogenesis
Wikipedia:Histogenesis
histogenesis
biological_process
GO:0009888
tissue development
The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
ISBN:0471245208
The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
dorsal-ventral axis specification
dorsoventral axis specification
biological_process
dorsal/ventral axis determination
GO:0009950
dorsal/ventral axis specification
The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
GOC:dph
GOC:go_curators
GOC:tb
dorsal-ventral axis specification
GOC:mah
dorsoventral axis specification
GOC:mah
dorsal/ventral axis determination
GOC:dph
The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
dorsal-ventral pattern formation
dorsoventral pattern formation
dorsal/ventral pattern specification
biological_process
GO:0009953
dorsal/ventral pattern formation
The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
GOC:dph
GOC:go_curators
GOC:isa_complete
GOC:tb
dorsal-ventral pattern formation
GOC:mah
dorsoventral pattern formation
GOC:mah
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
jl
2012-12-11T16:56:55Z
GO:0008151
GO:0044763
GO:0050875
cell physiology
cellular physiological process
cell growth and/or maintenance
biological_process
single-organism cellular process
GO:0009987
cellular process
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:go_curators
GOC:isa_complete
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an extracellular stimulus.
biological_process
GO:0009991
response to extracellular stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an extracellular stimulus.
GOC:go_curators
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 modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
biological_process
GO:0010941
regulation of cell death
Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
GOC:dph
GOC:tb
A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
Wikipedia:Endomembrane_system
cellular_component
GO:0012505
endomembrane system
A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
GOC:lh
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
2014-03-06T11:37:54Z
GO:0098589
GO:0098805
Wikipedia:Biological_membrane
membrane region
region of membrane
whole membrane
cellular_component
GO:0016020
membrane
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
GOC:dos
GOC:mah
ISBN:0815316194
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
GO:0044235
GO:0071842
cell organisation
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
biological_process
cell organization and biogenesis
GO:0016043
cellular component organization
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
GOC:ai
GOC:jl
GOC:mah
cellular component organisation at cellular level
GOC:mah
cellular component organisation in other organism
GOC:mah
cell organization and biogenesis
GOC:mah
The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
GO:0048591
cellular growth
growth of cell
biological_process
cell expansion
metabolic process resulting in cell growth
metabolism resulting in cell growth
non-developmental cell growth
non-developmental growth of a unicellular organism
GO:0016049
cell growth
The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
GOC:ai
non-developmental cell growth
GOC:mah
non-developmental growth of a unicellular organism
GOC:mah
true
kinase activity
morphogenesis of embryonic epithelium
The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
Wikipedia:Cell_migration
biological_process
GO:0016477
cell migration
The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
GOC:cjm
GOC:dph
GOC:ems
GOC:pf
Wikipedia:Cell_migration
The process during courtship where the male insect vibrates his wings. An example of this is found in Drosophila melanogaster.
male courtship behaviour, veined wing vibration
biological_process
male courtship behavior, wing vibration
male courtship behaviour, wing vibration
GO:0016545
male courtship behavior, veined wing vibration
The process during courtship where the male insect vibrates his wings. An example of this is found in Drosophila melanogaster.
GOC:mtg_sensu
PMID:11092827
transferase activity
transferase activity, transferring phosphorus-containing groups
The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water.
GO:0060403
egg laying
egg-laying
Wikipedia:Oviposition
post-mating oviposition
biological_process
GO:0018991
oviposition
The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water.
GOC:ems
The specific behavior of an organism that is associated with reproduction.
jl
2012-09-19T16:01:37Z
GO:0033057
GO:0044704
GO:0044705
reproductive behavior in a multicellular organism
reproductive behaviour
multi-organism reproductive behavior
multicellular organism reproductive behavior
biological_process
single-organism reproductive behavior
GO:0019098
reproductive behavior
The specific behavior of an organism that is associated with reproduction.
GOC:jl
GOC:pr
Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
biological_process
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
GO:0019219
regulation of nucleobase-containing compound metabolic process
Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
GOC:go_curators
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
GOC:dph
GOC:tb
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
A reproduction process that creates a new organism by combining the genetic material of two gametes, which may come from two organisms or from a single organism, in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two gametes join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny.
Wikipedia:Sexual_reproduction
biological_process
GO:0019953
Sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.
sexual reproduction
A reproduction process that creates a new organism by combining the genetic material of two gametes, which may come from two organisms or from a single organism, in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two gametes join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny.
GOC:jl
GOC:kmv
GOC:krc
GOC:tb
ISBN:0387520546
Wikipedia:Sexual_reproduction
neural tube development
The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.
biological_process
GO:0022402
cell cycle process
The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.
GOC:isa_complete
GOC:mtg_cell_cycle
A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism.
reproductive cellular process in multicellular organism
biological_process
GO:0022412
cellular process involved in reproduction in multicellular organism
A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism.
GOC:isa_complete
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
jl
2012-09-19T15:56:06Z
GO:0044702
biological_process
single organism reproductive process
GO:0022414
reproductive process
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
GOC:dph
GOC:isa_complete
Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis.
regulation of morphogenesis
biological_process
GO:0022603
regulation of anatomical structure morphogenesis
Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis.
GOC:mah
The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions.
biological_process
GO:0022610
biological adhesion
The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions.
GOC:isa_complete
A developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated.
multicellular organism dormancy process
spore dormancy process
biological_process
GO:0022611
In plants and animals, dormancy may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. In plants, dormancy may involve the formation of dormant buds, and may be preceded by the senescence of plant parts such as leaves in woody plants or most of the shoot system in herbaceous perennials. The exit from dormancy in vascular plants is marked by resumed growth of buds and/or growth of vascular cambium.
dormancy process
A developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated.
GOC:PO_curators
GOC:isa_complete
PO_REF:00009
spore dormancy process
GOC:PO_curators
Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
biological_process
cell adhesion receptor regulator activity
GO:0030155
regulation of cell adhesion
Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
GOC:mah
Any process that modulates the frequency, rate or extent of cell migration.
biological_process
GO:0030334
regulation of cell migration
Any process that modulates the frequency, rate or extent of cell migration.
GOC:go_curators
Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain.
Wikipedia:Sleep
biological_process
diapause
dormancy
lethargus
GO:0030431
sleep
Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain.
ISBN:0192800981
Behavior in a fully developed and mature organism.
adult behavioral response to stimulus
adult behaviour
adult behavioural response to stimulus
biological_process
GO:0030534
See also the biological process term 'behavior ; GO:0007610'.
adult behavior
Behavior in a fully developed and mature organism.
GOC:mah
ISBN:0877797099
A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
NIF_Subcellular:sao830981606
cellular_component
intracellular membrane
GO:0031090
organelle membrane
A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
GOC:dos
GOC:mah
intracellular membrane
NIF_Subcellular:sao830981606
The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass).
Wikipedia:Regeneration_(biology)
biological_process
GO:0031099
regeneration
The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass).
GOC:mah
GOC:pr
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 modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system.
regulation of neurological process
regulation of neurological system process
regulation of neurophysiological process
biological_process
GO:0031644
regulation of nervous system process
Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system.
GOC:dph
GOC:mah
GOC:tb
regulation of neurological process
GOC:dph
GOC:tb
Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process.
down regulation of neurological process
down-regulation of neurological process
downregulation of neurological process
negative regulation of neurological process
negative regulation of neurological system process
negative regulation of neurophysiological process
inhibition of neurological process
biological_process
GO:0031645
negative regulation of nervous system process
Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process.
GOC:dph
GOC:mah
GOC:tb
negative regulation of neurological process
GOC:dph
GOC:tb
Any process that activates or increases the frequency, rate or extent of a neurophysiological process.
positive regulation of neurological process
positive regulation of neurological system process
positive regulation of neurophysiological process
up regulation of neurological process
up-regulation of neurological process
upregulation of neurological process
activation of neurological process
stimulation of neurological process
biological_process
GO:0031646
positive regulation of nervous system process
Any process that activates or increases the frequency, rate or extent of a neurophysiological process.
GOC:dph
GOC:mah
GOC:tb
positive regulation of neurological process
GOC:dph
GOC:tb
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 reflecting the presence, absence, or concentration of nutrients.
biological_process
GO:0031667
response to nutrient levels
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 reflecting the presence, absence, or concentration of nutrients.
GOC:mah
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
NIF_Subcellular:sao1687101204
cellular_component
GO:0031965
nuclear membrane
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
GOC:mah
GOC:pz
A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes.
cellular_component
GO:0031967
organelle envelope
A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes.
GOC:mah
GOC:pz
A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers.
cellular_component
GO:0031975
envelope
A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers.
GOC:mah
GOC:pz
Self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.
locomotion during locomotory behaviour
biological_process
GO:0031987
locomotion involved in locomotory behavior
Self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.
GOC:mah
Any process that modulates the frequency, rate or extent of a response to an external stimulus.
biological_process
GO:0032101
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
regulation of response to external stimulus
Any process that modulates the frequency, rate or extent of a response to an external stimulus.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus.
down regulation of response to external stimulus
down-regulation of response to external stimulus
downregulation of response to external stimulus
inhibition of response to external stimulus
biological_process
GO:0032102
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
negative regulation of response to external stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus.
GOC:mah
Any process that activates, maintains or increases the rate of a response to an external stimulus.
up regulation of response to external stimulus
up-regulation of response to external stimulus
upregulation of response to external stimulus
activation of response to external stimulus
stimulation of response to external stimulus
biological_process
GO:0032103
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
positive regulation of response to external stimulus
Any process that activates, maintains or increases the rate of a response to an external stimulus.
GOC:mah
Any process that modulates the frequency, rate or extent of a response to an extracellular stimulus.
biological_process
GO:0032104
regulation of response to extracellular stimulus
Any process that modulates the frequency, rate or extent of a response to an extracellular stimulus.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an extracellular stimulus.
down regulation of response to extracellular stimulus
down-regulation of response to extracellular stimulus
downregulation of response to extracellular stimulus
inhibition of response to extracellular stimulus
biological_process
GO:0032105
negative regulation of response to extracellular stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an extracellular stimulus.
GOC:mah
Any process that activates, maintains or increases the rate of a response to an extracellular stimulus.
up regulation of response to extracellular stimulus
up-regulation of response to extracellular stimulus
upregulation of response to extracellular stimulus
activation of response to extracellular stimulus
stimulation of response to extracellular stimulus
biological_process
GO:0032106
positive regulation of response to extracellular stimulus
Any process that activates, maintains or increases the rate of a response to an extracellular stimulus.
GOC:mah
Any process that modulates the frequency, rate or extent of a response to nutrient levels.
biological_process
GO:0032107
regulation of response to nutrient levels
Any process that modulates the frequency, rate or extent of a response to nutrient levels.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to nutrient levels.
down regulation of response to nutrient levels
down-regulation of response to nutrient levels
downregulation of response to nutrient levels
inhibition of response to nutrient levels
biological_process
GO:0032108
negative regulation of response to nutrient levels
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to nutrient levels.
GOC:mah
Any process that activates or increases the frequency, rate or extent of a response to nutrient levels.
up regulation of response to nutrient levels
up-regulation of response to nutrient levels
upregulation of response to nutrient levels
activation of response to nutrient levels
stimulation of response to nutrient levels
biological_process
GO:0032109
positive regulation of response to nutrient levels
Any process that activates or increases the frequency, rate or extent of a response to nutrient levels.
GOC:mah
Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells.
GO:0071775
regulation of cell cycle cytokinesis
biological_process
GO:0032465
regulation of cytokinesis
Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells.
GOC:mah
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
jl
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.
jl
2012-12-19T12:21:31Z
GO:0044767
development
biological_process
single-organism developmental process
GO:0032502
developmental process
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
GOC:isa_complete
The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
biological_process
GO:0032504
multicellular organism reproduction
The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
GOC:isa_complete
GOC:jid
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
regulation of localisation
biological_process
GO:0032879
regulation of localization
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
GOC:mah
regulation of localisation
GOC:mah
Any process that modulates the frequency, rate or extent of 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 results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
biological_process
GO:0033554
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
cellular response to stress
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
GOC:mah
Any process that results in a change in state or activity of a multicellular organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
biological_process
GO:0033555
multicellular organismal response to stress
Any process that results in a change in state or activity of a multicellular organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
GOC:mah
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
cellular nitrogen compound metabolism
biological_process
GO:0034641
cellular nitrogen compound metabolic process
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
GOC:mah
tube formation
The specific behavior of an organism during the emergence from an egg shell. In Drosophila for example, the larva swings its head reiteratively through a semicircular arc, using its mouth hooks to tear apart the chorion in front of it and thus free itself from within the egg shell.
hatching behaviour
biological_process
GO:0035187
hatching behavior
The specific behavior of an organism during the emergence from an egg shell. In Drosophila for example, the larva swings its head reiteratively through a semicircular arc, using its mouth hooks to tear apart the chorion in front of it and thus free itself from within the egg shell.
GOC:pr
PMID:10436051
The emergence of an immature organism from a protective structure.
biological_process
GO:0035188
hatching
The emergence of an immature organism from a protective structure.
GOC:dgh
GOC:isa_complete
ISBN:0198612001
The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
biological_process
GO:0035239
tube morphogenesis
The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
GOC:bf
PMID:14624839
The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts.
biological_process
GO:0035295
tube development
The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts.
PMID:12526790
The fluctuation in mating behavior that occurs over an approximately 24 hour cycle.
bf
2011-01-25T10:20:05Z
circadian mating behaviour
circadian mating rhythm
biological_process
GO:0035648
circadian mating behavior
The fluctuation in mating behavior that occurs over an approximately 24 hour cycle.
GOC:bf
GOC:dos
PMID:11470898
PMID:17276917
circadian mating behaviour
GOC:bf
circadian mating rhythm
GOC:dos
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO:0048590
biological_process
growth pattern
non-developmental growth
GO:0040007
See also the biological process term 'cell growth ; GO:0016049'.
growth
The increase in size or mass of an entire organism, a part of an organism or a cell.
GOC:bf
GOC:ma
non-developmental growth
GOC:mah
Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
biological_process
GO:0040008
regulation of growth
Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
GOC:ems
GOC:mah
Self-propelled movement of a cell or organism from one location to another.
biological_process
GO:0040011
locomotion
Self-propelled movement of a cell or organism from one location to another.
GOC:dgh
Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.
biological_process
GO:0040012
regulation of locomotion
Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.
GOC:ems
Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism.
down regulation of locomotion
down-regulation of locomotion
downregulation of locomotion
inhibition of locomotion
biological_process
GO:0040013
negative regulation of locomotion
Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism.
GOC:go_curators
embryonic cleavage
Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism.
up regulation of locomotion
up-regulation of locomotion
upregulation of locomotion
activation of locomotion
stimulation of locomotion
biological_process
GO:0040017
positive regulation of locomotion
Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism.
GOC:go_curators
Any process that modulates the frequency, rate or extent of meiotic nuclear division, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes.
regulation of meiosis
biological_process
GO:0040020
regulation of meiotic nuclear division
Any process that modulates the frequency, rate or extent of meiotic nuclear division, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes.
GOC:ems
GOC:ma
regulation of meiosis
GOC:vw
The series of events that restore integrity to a damaged tissue, following an injury.
Wikipedia:Wound_healing
biological_process
GO:0042060
wound healing
The series of events that restore integrity to a damaged tissue, following an injury.
GOC:bf
PMID:15269788
cell migration involved in gastrulation
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 chemical stimulus.
response to chemical stimulus
response to chemical substance
biological_process
GO:0042221
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 chemical
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 chemical stimulus.
GOC:jl
response to chemical stimulus
GOC:dos
The regrowth of lost or destroyed tissues.
biological_process
GO:0042246
tissue regeneration
The regrowth of lost or destroyed tissues.
GOC:curators
The directed movement of a motile cell or organism in response to an external stimulus.
Wikipedia:Taxis
directed movement in response to stimulus
biological_process
GO:0042330
taxis
The directed movement of a motile cell or organism in response to an external stimulus.
GOC:jl
ISBN:0192801023
The directed movement of a motile cell or organism in response to light.
GO:0046953
Wikipedia:Phototaxis
phototactic behavior
phototactic behaviour
taxis in response to light
biological_process
GO:0042331
phototaxis
The directed movement of a motile cell or organism in response to light.
GOC:jl
ISBN:0192800981
The directed movement of a motile cell or organism in response to gravity.
GO:0048062
geotactic behavior
geotactic behaviour
geotaxis
gravitactic behavior
gravitactic behaviour
taxis in response to gravitational stimulus
taxis in response to gravity
biological_process
GO:0042332
gravitaxis
The directed movement of a motile cell or organism in response to gravity.
GOC:jid
GOC:jl
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.
biological_process
GO:0042594
response to starvation
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 starvation stimulus, deprivation of nourishment.
GOC:go_curators
Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.
biological_process
GO:0042752
regulation of circadian rhythm
Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.
GOC:dph
GOC:jl
GOC:tb
Any process that activates or increases the frequency, rate or extent of a circadian rhythm behavior.
up regulation of circadian rhythm
up-regulation of circadian rhythm
upregulation of circadian rhythm
activation of circadian rhythm
stimulation of circadian rhythm
biological_process
GO:0042753
positive regulation of circadian rhythm
Any process that activates or increases the frequency, rate or extent of a circadian rhythm behavior.
GOC:go_curators
Any process that stops, prevents, or reduces the frequency, rate or extent of a circadian rhythm behavior.
down regulation of circadian rhythm
down-regulation of circadian rhythm
downregulation of circadian rhythm
inhibition of circadian rhythm
biological_process
GO:0042754
negative regulation of circadian rhythm
Any process that stops, prevents, or reduces the frequency, rate or extent of a circadian rhythm behavior.
GOC:go_curators
chordate embryonic development
The directed movement of a motile cell or organism in response to a temperature gradient. Movement may be towards either a higher or lower temperature.
Wikipedia:Thermotaxis
taxis in response to temperature stimulus
biological_process
GO:0043052
thermotaxis
The directed movement of a motile cell or organism in response to a temperature gradient. Movement may be towards either a higher or lower temperature.
GOC:cab1
WB_REF:cgc467
The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night).
photoentrainment of circadian clock
biological_process
GO:0043153
entrainment of circadian clock by photoperiod
The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night).
GOC:jl
photoentrainment of circadian clock
PMID:10217146
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GO:0043283
GO:0044259
biopolymer metabolic process
macromolecule metabolism
organismal macromolecule metabolism
multicellular organismal macromolecule metabolic process
biological_process
GO:0043170
macromolecule metabolic process
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GOC:mah
biopolymer metabolic process
GOC:mtg_chebi_dec09
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
NIF_Subcellular:sao1539965131
Wikipedia:Organelle
cellular_component
GO:0043226
organelle
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
NIF_Subcellular:sao414196390
membrane-enclosed organelle
cellular_component
GO:0043227
membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
cellular_component
GO:0043229
intracellular organelle
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
intracellular membrane-enclosed organelle
cellular_component
GO:0043231
intracellular membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
GOC:go_curators
Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system.
biological_process
GO:0044057
regulation of system process
Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system.
GOC:jl
The chemical reactions and pathways by which individual cells transform chemical substances.
cellular metabolism
biological_process
intermediary metabolism
GO:0044237
cellular metabolic process
The chemical reactions and pathways by which individual cells transform chemical substances.
GOC:go_curators
intermediary metabolism
GOC:mah
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
primary metabolism
biological_process
GO:0044238
primary metabolic process
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
GOC:go_curators
http://www.metacyc.org
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
GO:0034960
cellular biopolymer metabolic process
cellular macromolecule metabolism
biological_process
GO:0044260
cellular macromolecule metabolic process
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
GOC:mah
cellular biopolymer metabolic process
GOC:mtg_chebi_dec09
obsolete cell part
A biological process that directly contributes to the process of producing new individuals, involving another organism.
jl
2012-09-19T15:56:30Z
biological_process
GO:0044703
multi-organism reproductive process
A biological process that directly contributes to the process of producing new individuals, involving another organism.
GOC:jl
The process during wing vibration where the male insect produces a species-specific acoustic signal called a love song.
male courtship behavior, song production
male courtship behaviour, song production
male courtship behaviour, veined wing generated song production
biological_process
GO:0045433
male courtship behavior, veined wing generated song production
The process during wing vibration where the male insect produces a species-specific acoustic signal called a love song.
GOC:mtg_sensu
PMID:11092827
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
The rhythm of the locomotor activity of an organism during its 24 hour activity cycle.
circadian locomotor activity rhythm
biological_process
GO:0045475
locomotor rhythm
The rhythm of the locomotor activity of an organism during its 24 hour activity cycle.
GOC:go_curators
Any process that stops, prevents, or reduces the frequency, rate or extent of eclosion.
down regulation of eclosion
down-regulation of eclosion
downregulation of eclosion
inhibition of eclosion
biological_process
GO:0045804
negative regulation of eclosion
Any process that stops, prevents, or reduces the frequency, rate or extent of eclosion.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of eclosion.
up regulation of eclosion
up-regulation of eclosion
upregulation of eclosion
activation of eclosion
stimulation of eclosion
biological_process
GO:0045805
positive regulation of eclosion
Any process that activates or increases the frequency, rate or extent of eclosion.
GOC:go_curators
The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
heterocycle metabolism
biological_process
GO:0046483
heterocycle metabolic process
The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
ISBN:0198506732
Any process that modulates the frequency, rate or extent of the deposition of eggs, either fertilized or not, upon a surface or into a medium.
GO:0048042
regulation of post-mating oviposition
biological_process
GO:0046662
regulation of oviposition
Any process that modulates the frequency, rate or extent of the deposition of eggs, either fertilized or not, upon a surface or into a medium.
GOC:dph
GOC:tb
PMID:11932766
Any process that modulates the rate or extent of the response to osmotic stress.
biological_process
GO:0047484
regulation of response to osmotic stress
Any process that modulates the rate or extent of the response to osmotic stress.
GOC:ai
The directed movement of a motile cell or organism away from the source of gravity.
GO:0048063
negative geotactic behavior
negative geotactic behaviour
negative gravitactic behavior
negative gravitactic behaviour
negative taxis in response to gravity
negative taxis in response to gravitytaxis in response to gravitational stimulus
biological_process
GO:0048060
negative gravitaxis
The directed movement of a motile cell or organism away from the source of gravity.
GOC:jid
The process during courtship where the male insect extends his wings. An example of this process is found in Drosophila melanogaster.
male courtship behavior, wing extension
male courtship behaviour, wing extension
male courtship behaviour, veined wing extension
biological_process
GO:0048065
male courtship behavior, veined wing extension
The process during courtship where the male insect extends his wings. An example of this process is found in Drosophila melanogaster.
GOC:jid
GOC:mtg_sensu
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 pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.
GO:0048267
physiological response to pain
biological_process
GO:0048265
response to pain
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 pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.
GOC:jid
PMID:10203867
PMID:12723742
PMID:12843304
Wikipedia:Pain
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
mesoderm morphogenesis
Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
biological_process
rhythm
GO:0048511
rhythmic process
Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
GOC:jid
The specific behavior of an organism that recurs with a regularity of approximately 24 hours.
circadian rhythm behavior
biological_process
GO:0048512
circadian behavior
The specific behavior of an organism that recurs with a regularity of approximately 24 hours.
GOC:bf
GOC:go_curators
GOC:pr
Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
Wikipedia:Organogenesis
development of an organ
organogenesis
biological_process
GO:0048513
animal organ development
Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
GOC:dph
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 behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
up regulation of behavior
up-regulation of behavior
upregulation of behavior
activation of behavior
stimulation of behavior
biological_process
GO:0048520
positive regulation of behavior
Any process that activates or increases the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
GOC:jid
GOC:pr
Any process that stops, prevents, or reduces the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
down regulation of behavior
down-regulation of behavior
downregulation of behavior
inhibition of behavior
biological_process
GO:0048521
negative regulation of behavior
Any process that stops, prevents, or reduces the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
GOC:jid
GOC:pr
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 increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
biological_process
GO:0048589
developmental growth
The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
GOC:go_curators
embryonic morphogenesis
The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.
organismal reproductive process
reproductive process in a multicellular organism
biological_process
GO:0048609
multicellular organismal reproductive process
The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.
GOC:dph
GOC:jid
GOC:tb
Any process that modulates the frequency, rate or extent of developmental growth.
biological_process
GO:0048638
regulation of developmental growth
Any process that modulates the frequency, rate or extent of developmental growth.
GOC:go_curators
The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. 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.
formation of an anatomical structure involved in morphogenesis
biological_process
GO:0048646
Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense.
anatomical structure formation involved in morphogenesis
The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. 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.
GOC:dph
GOC:jid
GOC:tb
formation of an anatomical structure involved in morphogenesis
GOC:dph
GOC:tb
The process in which the anatomical structures of a tissue are generated and organized.
biological_process
GO:0048729
tissue morphogenesis
The process in which the anatomical structures of a tissue are generated and organized.
GOC:dph
GOC:jid
The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process.
biological_process
GO:0048731
system development
The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process.
GOC:dph
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 involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
cell locomotion
movement of a cell
biological_process
cell movement
GO:0048870
cell motility
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
GOC:dgh
GOC:dph
GOC:isa_complete
GOC:mlg
Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
biological_process
GO:0050776
regulation of immune response
Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
GOC:ai
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 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 modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
regulation of behaviour
biological_process
GO:0050795
regulation of behavior
Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
GOC:go_curators
GOC:pr
A organ system process carried out by any of the organs or tissues of neurological system.
https://github.com/geneontology/go-ontology/issues/13824
neurological system process
neurophysiological process
biological_process
pan-neural process
GO:0050877
nervous system process
A organ system process carried out by any of the organs or tissues of neurological system.
GOC:ai
GOC:mtg_cardio
Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism.
biological_process
GO:0050879
multicellular organismal movement
Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism.
GOC:dph
GOC:mtg_muscle
GOC:tb
The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
Wikipedia:Cognition
biological_process
GO:0050890
cognition
The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
ISBN:0721619908
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
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
The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal.
Wikipedia:Transduction_(physiology)
sensory detection of stimulus
sensory perception, sensory transduction of stimulus
sensory perception, stimulus detection
sensory transduction
biological_process
GO:0050906
detection of stimulus involved in sensory perception
The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal.
GOC:ai
GOC:dos
GOC:dph
The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal.
sensory detection of light during visual perception
sensory detection of light stimulus during visual perception
sensory transduction of light during visual perception
sensory transduction of light stimulus during visual perception
visual perception, detection of light stimulus
visual perception, sensory transduction during perception of light
visual perception, sensory transduction of light stimulus
biological_process
GO:0050908
detection of light stimulus involved in visual perception
The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal.
GOC:ai
GOC:dos
The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process.
Wikipedia:Taste
gustation
sense of taste
taste
taste perception
biological_process
GO:0050909
sensory perception of taste
The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process.
GOC:ai
The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
biological_process
GO:0050953
sensory perception of light stimulus
The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
GOC:ai
The series of events required for an organism to receive a sensory mechanical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
mechanosensory perception
perception of mechanical stimulus
biological_process
chemi-mechanical coupling
GO:0050954
sensory perception of mechanical stimulus
The series of events required for an organism to receive a sensory mechanical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
GOC:ai
The series of events in which a light stimulus is received by a cell and converted into a molecular signal as part of the sensory perception of light.
sensory detection of light stimulus
sensory detection of light stimulus during sensory perception
sensory perception, sensory detection of light stimulus
sensory perception, sensory transduction of light stimulus
sensory transduction of light stimulus
sensory transduction of light stimulus during sensory perception
biological_process
GO:0050962
detection of light stimulus involved in sensory perception
The series of events in which a light stimulus is received by a cell and converted into a molecular signal as part of the sensory perception of light.
GOC:ai
GOC:dos
The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach).
Wikipedia:Touch
perception of touch
tactile sense
taction
tactition
biological_process
GO:0050975
sensory perception of touch
The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach).
GOC:ai
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA.
regulation of DNA metabolism
biological_process
GO:0051052
regulation of DNA metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA.
GOC:ai
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 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 modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
regulation of nitrogen metabolic process
regulation of nitrogen metabolism
biological_process
GO:0051171
regulation of nitrogen compound metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
GOC:ai
GOC:tb
regulation of nitrogen metabolic process
GOC:tb
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
jl
2013-12-18T13:51:04Z
GO:1902578
establishment and maintenance of localization
establishment and maintenance of position
localisation
establishment and maintenance of cellular component location
establishment and maintenance of substance location
establishment and maintenance of substrate location
biological_process
single organism localization
single-organism localization
GO:0051179
localization
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
GOC:ai
GOC:dos
localisation
GOC:mah
single organism localization
GOC:TermGenie
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
Any process that modulates the frequency, rate or extent of the movement of a cellular component.
regulation of cellular component motion
biological_process
regulation of cell movement
GO:0051270
regulation of cellular component movement
Any process that modulates the frequency, rate or extent of the movement of a cellular component.
GOC:ai
GOC:dph
GOC:jl
regulation of cellular component motion
GOC:mah
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
Wikipedia:Cell_division
biological_process
GO:0051301
Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.
cell division
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
GOC:di
GOC:go_curators
GOC:pr
Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells.
biological_process
GO:0051302
regulation of cell division
Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells.
GOC:go_curators
Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
GO:0007126
Wikipedia:Meiosis
biological_process
meiosis
GO:0051321
Note that this term should not be confused with 'GO:0140013 ; meiotic nuclear division'. 'GO:0051321 ; meiotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140013 meiotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.
meiotic cell cycle
Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
GOC:ai
Any process that modulates the rate or extent of progression through the meiotic cell cycle.
meiotic cell cycle modulation
meiotic cell cycle regulation
modulation of meiotic cell cycle progression
regulation of meiotic cell cycle progression
regulation of progression through meiotic cell cycle
biological_process
meiotic cell cycle regulator
GO:0051445
regulation of meiotic cell cycle
Any process that modulates the rate or extent of progression through the meiotic cell cycle.
GOC:ai
GOC:dph
GOC:tb
regulation of progression through meiotic cell cycle
GOC:dph
GOC:tb
The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
stimulus detection
biological_process
perception of stimulus
stimulus sensing
GO:0051606
detection of stimulus
The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
GOC:add
GOC:ai
GOC:dph
GOC:mah
Any process in which a cell is transported to, and/or maintained in, a specific location.
cell localization
establishment and maintenance of cell localization
establishment and maintenance of localization of cell
localisation of cell
biological_process
GO:0051674
localization of cell
Any process in which a cell is transported to, and/or maintained in, a specific location.
GOC:ai
localisation of cell
GOC:mah
A biological process which involves another organism of the same or different species.
GO:0051706
interaction between organisms
physiological interaction between organisms
physiological interaction with other organism
biological_process
GO:0051704
multi-organism process
A biological process which involves another organism of the same or different species.
GOC:jl
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
GO:0007050
GO:0071156
GO:0071157
GO:0071158
GO:0071850
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
arrest of mitotic cell cycle progression
cell cycle arrest
mitotic cell cycle arrest
negative regulation of cell cycle arrest
positive regulation of cell cycle arrest
regulation of cell cycle arrest
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
arrest of mitotic cell cycle progression
GOC:mah
Any process that results in a change in the behavior of an organism as a result of a nutrient stimulus.
behavioural response to nutrient
biological_process
GO:0051780
behavioral response to nutrient
Any process that results in a change in the behavior of an organism as a result of a nutrient stimulus.
GOC:ai
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 modulates the frequency, rate or extent of sensory perception, the series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal.
biological_process
GO:0051931
regulation of sensory perception
Any process that modulates the frequency, rate or extent of sensory perception, the series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal.
GOC:ai
The dormancy process that results in entry into diapause. Diapause is a neurohormonally mediated, dynamic state of low metabolic activity. Associated characteristics of this form of dormancy include reduced morphogenesis, increased resistance to environmental extremes, and altered or reduced behavioral activity. Full expression develops in a species-specific manner, usually in response to a number of environmental stimuli that precede unfavorable conditions. Once diapause has begun, metabolic activity is suppressed even if conditions favorable for development prevail. Once initiated, only certain stimuli are capable of releasing the organism from this state, and this characteristic is essential in distinguishing diapause from hibernation.
Wikipedia:Diapause
biological_process
GO:0055115
entry into diapause
The dormancy process that results in entry into diapause. Diapause is a neurohormonally mediated, dynamic state of low metabolic activity. Associated characteristics of this form of dormancy include reduced morphogenesis, increased resistance to environmental extremes, and altered or reduced behavioral activity. Full expression develops in a species-specific manner, usually in response to a number of environmental stimuli that precede unfavorable conditions. Once diapause has begun, metabolic activity is suppressed even if conditions favorable for development prevail. Once initiated, only certain stimuli are capable of releasing the organism from this state, and this characteristic is essential in distinguishing diapause from hibernation.
GOC:ds
GOC:jid
GOC:mah
The dormancy process that results in entry into reproductive diapause. Reproductive diapause is a form of diapause where the organism itself will remain fully active, including feeding and other routine activities, but the reproductive organs experience a tissue-specific reduction in metabolism, with characteristic triggering and releasing stimuli.
biological_process
GO:0055116
entry into reproductive diapause
The dormancy process that results in entry into reproductive diapause. Reproductive diapause is a form of diapause where the organism itself will remain fully active, including feeding and other routine activities, but the reproductive organs experience a tissue-specific reduction in metabolism, with characteristic triggering and releasing stimuli.
GOC:ds
GOC:jid
GOC:mah
An automatic response to a stimulus beginning with a nerve impulse from a receptor and ending with the action of an effector such as a gland or a muscle. Signaling never reaches a level of consciousness.
Wikipedia:Reflex
biological_process
GO:0060004
reflex
An automatic response to a stimulus beginning with a nerve impulse from a receptor and ending with the action of an effector such as a gland or a muscle. Signaling never reaches a level of consciousness.
GOC:dph
ISBN:0877797099
The specific behavior of a male organism that is associated with reproduction.
biological_process
GO:0060179
male mating behavior
The specific behavior of a male organism that is associated with reproduction.
GOC:dph
GOC:pr
GOC:tb
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
biological_process
GO:0060255
regulation of macromolecule metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GOC:dph
GOC:tb
Any process that modulates the rate, frequency or extent of the behavior associated with the intake of food.
regulation of feeding behaviour
biological_process
GO:0060259
regulation of feeding behavior
Any process that modulates the rate, frequency or extent of the behavior associated with the intake of food.
GOC:BHF
GOC:dph
GOC:tb
regulation of feeding behaviour
GOC:dph
GOC:tb
Self-propelled movement of an organism from one location to another through the air, usually by means of active wing movement.
biological_process
GO:0060361
flight
Self-propelled movement of an organism from one location to another through the air, usually by means of active wing movement.
GOC:dph
The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.
biological_process
GO:0060429
epithelium development
The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.
GOC:dph
GOC:mtg_lung
The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape.
dph
2009-04-28T08:42:53Z
differential growth
biological_process
GO:0060560
developmental growth involved in morphogenesis
The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape.
GOC:dph
differential growth
GOC:dph
epithelial tube morphogenesis
A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
jl
2010-02-08T02:43:11Z
GO:0016044
GO:0044802
cellular membrane organisation
cellular membrane organization
membrane organisation
biological_process
membrane organization and biogenesis
single-organism membrane organization
GO:0061024
membrane organization
A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
GOC:dph
GOC:tb
membrane organisation
GOC:mah
membrane organization and biogenesis
GOC:mah
Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
dph
2010-02-25T10:14:37Z
biological_process
GO:0061041
regulation of wound healing
Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
GOC:BHF
GOC:dph
Any process that modulates the rate or extent of the dormancy process that results in entry into reproductive diapause. Reproductive diapause is a form of diapause where the organism itself will remain fully active, including feeding and other routine activities, but the reproductive organs experience a tissue-specific reduction in metabolism, with characteristic triggering and releasing stimuli.
dph
2018-02-05T15:02:16Z
biological_process
GO:0061963
regulation of entry into reproductive diapause
Any process that modulates the rate or extent of the dormancy process that results in entry into reproductive diapause. Reproductive diapause is a form of diapause where the organism itself will remain fully active, including feeding and other routine activities, but the reproductive organs experience a tissue-specific reduction in metabolism, with characteristic triggering and releasing stimuli.
GOC:ha
PMID:27689881
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
The developmental process in which an organism emerges from a surrounding protective structure such as an egg or pupa case.
mah
2010-02-19T04:23:55Z
biological_process
GO:0071684
organism emergence from protective structure
The developmental process in which an organism emerges from a surrounding protective structure such as an egg or pupa case.
GOC:mah
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
mah
2010-03-08T03:32:18Z
organic molecular entity metabolic process
organic molecular entity metabolism
organic substance metabolism
biological_process
GO:0071704
organic substance metabolic process
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
GOC:mah
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
mah
2010-09-10T01:39:16Z
GO:0071841
cellular component organisation or biogenesis
cellular component organisation or biogenesis at cellular level
cellular component organization or biogenesis at cellular level
biological_process
GO:0071840
cellular component organization or biogenesis
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
GOC:mah
cellular component organisation or biogenesis
GOC:mah
cellular component organisation or biogenesis at cellular level
GOC:mah
The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
mah
2010-10-04T01:51:47Z
cellular_component
GO:0071944
cell periphery
The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
GOC:mah
epithelial tube formation
The memory process that deals with the storage, retrieval and modification of information received at a time ago that is intermediate between that of short and long term memory (30min - 7hrs in Drosophila melanogaster).
mah
2010-11-22T11:26:54Z
middle-term memory
MTM
biological_process
GO:0072375
medium-term memory
The memory process that deals with the storage, retrieval and modification of information received at a time ago that is intermediate between that of short and long term memory (30min - 7hrs in Drosophila melanogaster).
GOC:sart
PMID:14659098
PMID:7923375
middle-term memory
GOC:sart
MTM
GOC:sart
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
dhl
2009-04-22T04:30:52Z
biological_process
GO:0080090
regulation of primary metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
PMID:19211694
Any process that modulates the frequency, rate or extent of a response to stress. Response to stress 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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
dhl
2009-05-06T04:51:28Z
biological_process
GO:0080134
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 stress
Any process that modulates the frequency, rate or extent of a response to stress. Response to stress 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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
GOC:dhl
Any process that modulates the frequency, rate or extent of a cellular response to stress. Cellular response to stress is a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
dhl
2009-05-06T05:02:52Z
biological_process
GO:0080135
regulation of cellular response to stress
Any process that modulates the frequency, rate or extent of a cellular response to stress. Cellular response to stress is a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
GOC:dhl
A process that is carried out at the cellular level which results in the separation of a single continuous membrane into two membranes.
tb
2009-12-08T03:06:36Z
membrane scission
biological_process
GO:0090148
membrane fission
A process that is carried out at the cellular level which results in the separation of a single continuous membrane into two membranes.
GOC:ascb_2009
GOC:dph
GOC:tb
Any process that modulates the rate, frequency or extent of the establishment of planar polarity, the coordinated organization of groups of cells in a tissue, such that they all orient to similar coordinates.
tb
2009-12-14T10:29:41Z
biological_process
GO:0090175
regulation of establishment of planar polarity
Any process that modulates the rate, frequency or extent of the establishment of planar polarity, the coordinated organization of groups of cells in a tissue, such that they all orient to similar coordinates.
GOC:ascb_2009
GOC:dph
GOC:tb
Any cellular metabolic process involving nucleic acids.
tb
2010-04-07T10:18:47Z
biological_process
GO:0090304
nucleic acid metabolic process
Any cellular metabolic process involving nucleic acids.
GOC:dph
GOC:tb
Any process that modulates the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.
tb
2010-05-14T10:24:29Z
biological_process
GO:0090325
regulation of locomotion involved in locomotory behavior
Any process that modulates the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.
GOC:dph
GOC:kmv
GOC:tb
Any process that increases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.
tb
2010-05-14T10:26:58Z
biological_process
GO:0090326
positive regulation of locomotion involved in locomotory behavior
Any process that increases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.
GOC:dph
GOC:kmv
GOC:tb
Any process that decreases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.
tb
2010-05-14T10:26:58Z
biological_process
GO:0090327
negative regulation of locomotion involved in locomotory behavior
Any process that decreases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.
GOC:dph
GOC:kmv
GOC:tb
A membrane that is a (regional) part of the plasma membrane.
dos
2014-03-06T11:55:32Z
region of plasma membrane
cellular_component
GO:0098590
Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass.
plasma membrane region
A membrane that is a (regional) part of the plasma membrane.
GOC:dos
Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.
cellular_component
GO:0099568
cytoplasmic region
Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.
GOC:dos
The complete extent of cell cortex that underlies some some region of the plasma membrane.
perimembrane region
cellular_component
GO:0099738
cell cortex region
The complete extent of cell cortex that underlies some some region of the plasma membrane.
GOC:dos
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
kmv
2019-08-12T18:01:37Z
cellular_component
GO:0110165
cellular anatomical entity
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
GOC:kmv
One of the two nuclear divisions that occur as part of the meiotic cell cycle.
https://github.com/geneontology/go-ontology/issues/19910
pg
2017-03-23T09:40:00Z
meiosis
biological_process
GO:0140013
meiotic nuclear division
One of the two nuclear divisions that occur as part of the meiotic cell cycle.
PMID:9334324
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.
https://github.com/geneontology/go-ontology/issues/19910
pg
2017-03-23T14:44:23Z
mitosis
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 stops, prevents or reduces the frequency, rate or extent of oviposition.
kmv
2012-06-27T06:19:58Z
down regulation of egg laying
down regulation of egg-laying
down-regulation of egg laying
down-regulation of egg-laying
downregulation of egg laying
downregulation of egg-laying
inhibition of egg laying
inhibition of egg-laying
negative regulation of egg laying
negative regulation of egg-laying
down regulation of oviposition
down-regulation of oviposition
downregulation of oviposition
inhibition of oviposition
biological_process
GO:1901045
negative regulation of oviposition
Any process that stops, prevents or reduces the frequency, rate or extent of oviposition.
GOC:TermGenie
GOC:kmv
down regulation of egg laying
GOC:TermGenie
down regulation of egg-laying
GOC:TermGenie
down-regulation of egg laying
GOC:TermGenie
down-regulation of egg-laying
GOC:TermGenie
downregulation of egg laying
GOC:TermGenie
downregulation of egg-laying
GOC:TermGenie
inhibition of egg laying
GOC:TermGenie
inhibition of egg-laying
GOC:TermGenie
negative regulation of egg laying
GOC:TermGenie
negative regulation of egg-laying
GOC:TermGenie
down regulation of oviposition
GOC:TermGenie
down-regulation of oviposition
GOC:TermGenie
downregulation of oviposition
GOC:TermGenie
inhibition of oviposition
GOC:TermGenie
Any process that activates or increases the frequency, rate or extent of oviposition.
kmv
2012-06-27T06:20:20Z
activation of egg laying
activation of egg-laying
positive regulation of egg laying
positive regulation of egg-laying
up regulation of egg laying
up regulation of egg-laying
up-regulation of egg laying
up-regulation of egg-laying
upregulation of egg laying
upregulation of egg-laying
up regulation of oviposition
up-regulation of oviposition
upregulation of oviposition
activation of oviposition
biological_process
GO:1901046
positive regulation of oviposition
Any process that activates or increases the frequency, rate or extent of oviposition.
GOC:TermGenie
GOC:kmv
activation of egg laying
GOC:TermGenie
activation of egg-laying
GOC:TermGenie
positive regulation of egg laying
GOC:TermGenie
positive regulation of egg-laying
GOC:TermGenie
up regulation of egg laying
GOC:TermGenie
up regulation of egg-laying
GOC:TermGenie
up-regulation of egg laying
GOC:TermGenie
up-regulation of egg-laying
GOC:TermGenie
upregulation of egg laying
GOC:TermGenie
upregulation of egg-laying
GOC:TermGenie
up regulation of oviposition
GOC:TermGenie
up-regulation of oviposition
GOC:TermGenie
upregulation of oviposition
GOC:TermGenie
activation of oviposition
GOC:TermGenie
The chemical reactions and pathways involving organic cyclic compound.
bf
2012-09-14T09:03:51Z
organic cyclic compound metabolism
biological_process
GO:1901360
organic cyclic compound metabolic process
The chemical reactions and pathways involving organic cyclic compound.
GOC:TermGenie
organic cyclic compound metabolism
GOC:TermGenie
Any process that modulates the frequency, rate or extent of male mating behavior.
mm2
2013-10-09T15:49:56Z
biological_process
GO:1902435
regulation of male mating behavior
Any process that modulates the frequency, rate or extent of male mating behavior.
GOC:TermGenie
PMID:24089208
Any process that stops, prevents or reduces the frequency, rate or extent of male mating behavior.
mm2
2013-10-09T15:50:05Z
down regulation of male mating behavior
down-regulation of male mating behavior
downregulation of male mating behavior
inhibition of male mating behavior
biological_process
GO:1902436
negative regulation of male mating behavior
Any process that stops, prevents or reduces the frequency, rate or extent of male mating behavior.
GOC:TermGenie
PMID:24089208
down regulation of male mating behavior
GOC:TermGenie
down-regulation of male mating behavior
GOC:TermGenie
downregulation of male mating behavior
GOC:TermGenie
inhibition of male mating behavior
GOC:TermGenie
Any process that activates or increases the frequency, rate or extent of male mating behavior.
mm2
2013-10-09T15:50:14Z
up regulation of male mating behavior
up-regulation of male mating behavior
upregulation of male mating behavior
activation of male mating behavior
biological_process
GO:1902437
positive regulation of male mating behavior
Any process that activates or increases the frequency, rate or extent of male mating behavior.
GOC:TermGenie
PMID:24089208
up regulation of male mating behavior
GOC:TermGenie
up-regulation of male mating behavior
GOC:TermGenie
upregulation of male mating behavior
GOC:TermGenie
activation of male mating behavior
GOC:TermGenie
Any process that modulates the frequency, rate or extent of response to oxidative stress.
kmv
2014-04-03T20:29:52Z
biological_process
GO:1902882
regulation of response to oxidative stress
Any process that modulates the frequency, rate or extent of response to oxidative stress.
GOC:TermGenie
GOC:kmv
GO_REF:0000058
PMID:16899554
Any process that modulates the frequency, rate or extent of response to wounding.
kmv
2014-05-18T01:28:46Z
regulation of physiological response to wounding
biological_process
GO:1903034
regulation of response to wounding
Any process that modulates the frequency, rate or extent of response to wounding.
GOC:TermGenie
GOC:kmv
GO_REF:0000058
pmid:19164535
regulation of physiological response to wounding
GOC:TermGenie
A process that is part of the meiotic cell cycle.
jl
2014-05-22T14:22:28Z
biological_process
GO:1903046
meiotic cell cycle process
A process that is part of the meiotic cell cycle.
GOC:TermGenie
GOC:mtg_cell_cycle
GO_REF:0000060
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 locomotor rhythm.
sl
2015-03-18T20:38:52Z
regulation of circadian locomotor activity rhythm
biological_process
GO:1904059
regulation of locomotor rhythm
Any process that modulates the frequency, rate or extent of locomotor rhythm.
GOC:TermGenie
GO_REF:0000058
PMID:16310969
regulation of circadian locomotor activity rhythm
GOC:TermGenie
Any process that modulates the frequency, rate or extent of morphogenesis of an epithelium.
bhm
2016-07-22T07:13:49Z
regulation of epithelium morphogenesis
biological_process
GO:1905330
An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay).
regulation of morphogenesis of an epithelium
Any process that modulates the frequency, rate or extent of morphogenesis of an epithelium.
GOC:TermGenie
GOC:bhm
GO_REF:0000058
PMID:25745997
regulation of epithelium morphogenesis
GOC:TermGenie
Any process that modulates the frequency, rate or extent of multicellular organismal development.
tb
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 modulates the frequency, rate or extent of animal organ morphogenesis.
tb
2010-08-05T11:26:27Z
biological_process
regulation of histogenesis and organogenesis
GO:2000027
regulation of animal organ morphogenesis
Any process that modulates the frequency, rate or extent of animal organ morphogenesis.
GOC:obol
regulation of histogenesis and organogenesis
GOC:obol
Any process that modulates the frequency, rate or extent of cell motility.
mah
2010-10-01T09:41:21Z
regulation of cell locomotion
regulation of movement of a cell
biological_process
regulation of cell movement
GO:2000145
regulation of cell motility
Any process that modulates the frequency, rate or extent of cell motility.
GOC:mah
regulation of cell locomotion
GOC:obol
regulation of movement of a cell
GOC:obol
regulation of cell movement
GOC:obol
Any process that modulates the frequency, rate or extent of reproductive process.
mah
2010-11-10T02:44:02Z
biological_process
GO:2000241
regulation of reproductive process
Any process that modulates the frequency, rate or extent of reproductive process.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process.
mah
2010-11-10T02:44:05Z
biological_process
GO:2000242
negative regulation of reproductive process
Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process.
GOC:mah
Any process that activates or increases the frequency, rate or extent of reproductive process.
mah
2010-11-10T02:44:08Z
biological_process
GO:2000243
positive regulation of reproductive process
Any process that activates or increases the frequency, rate or extent of reproductive process.
GOC:mah
Any process that stops, prevents or reduces the frequency, rate or extent of feeding behavior.
yaf
2010-11-18T11:24:14Z
negative regulation of behavioral response to food
negative regulation of behavioural response to food
negative regulation of feeding behaviour
biological_process
negative regulation of drinking
negative regulation of eating
GO:2000252
negative regulation of feeding behavior
Any process that stops, prevents or reduces the frequency, rate or extent of feeding behavior.
GOC:obol
negative regulation of behavioral response to food
GOC:obol
negative regulation of behavioural response to food
GOC:obol
negative regulation of feeding behaviour
GOC:obol
negative regulation of drinking
GOC:obol
negative regulation of eating
GOC:obol
Any process that activates or increases the frequency, rate or extent of feeding behavior.
yaf
2010-11-18T11:24:18Z
positive regulation of behavioral response to food
positive regulation of behavioural response to food
positive regulation of feeding behaviour
biological_process
positive regulation of drinking
positive regulation of eating
GO:2000253
positive regulation of feeding behavior
Any process that activates or increases the frequency, rate or extent of feeding behavior.
GOC:obol
positive regulation of behavioral response to food
GOC:obol
positive regulation of behavioural response to food
GOC:obol
positive regulation of feeding behaviour
GOC:obol
positive regulation of drinking
GOC:obol
positive regulation of eating
GOC:obol
Any process that modulates the frequency, rate or extent of grooming behavior.
rl
2011-07-14T04:48:12Z
regulation of grooming behaviour
biological_process
GO:2000821
regulation of grooming behavior
Any process that modulates the frequency, rate or extent of grooming behavior.
GOC:BHF
regulation of grooming behaviour
GOC:obol
Any process that modulates the frequency, rate or extent of response to DNA damage stimulus.
yaf
2011-08-19T10:20:25Z
regulation of DNA damage response
regulation of cellular DNA damage response
regulation of cellular response to DNA damage stimulus
regulation of response to genotoxic stress
biological_process
GO:2001020
regulation of response to DNA damage stimulus
Any process that modulates the frequency, rate or extent of response to DNA damage stimulus.
GOC:obol
regulation of DNA damage response
GOC:obol
regulation of cellular DNA damage response
GOC:obol
regulation of cellular response to DNA damage stimulus
GOC:obol
regulation of response to genotoxic stress
GOC:obol
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
information content entity
information content entity
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
obsolescence reason specification
denotator type
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
denotator type
2011-04-14T01:03:39Z
George Gkoutos
behavior_ontology
whole body movement
Movement from place to place of an organism." [GO:0007626]
2011-04-14T01:03:39Z
George Gkoutos
locomotion
behavior_ontology
GO:0007626
GO:0008344
locomotory behavior
"Behavior relate to the usually upward movement off the ground or other surface through sudden muscular effort in the legs." [GO:0007630]
2011-04-14T01:03:39Z
George Gkoutos
jump
behavior_ontology
GO:0007630
jumping behavior
"Cognitive perception of a sensation by any of the five senses -- vision, touch, smell, taste, and hearing." [NBO:GVG]
2011-04-04T10:00:45Z
George Gkoutos
NBO:0000454
behavior involving perception
perception behavior
behavior_ontology
Example: moving head to watch passing object.
sensation behavior
"The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610]
2011-04-05T09:53:10Z
George Gkoutos
NBO:0000000
behavior
behaviour
behavior_ontology
GO:0007610
behavior process
"Behavior related to the actions or reactions of an organism in response to a sound." [GO:0031223]
2011-04-05T10:38:17Z
George Gkoutos
hearing behaviour
behavior_ontology
GO:0031223
auditory behavior
"Behavior related to the awareness of body balance and movement." [MBP:GVG]
2011-04-05T10:40:36Z
George Gkoutos
proprioception
behavior_ontology
vestibular behavior
"Behavior related to the sensations arising from the skin and from the muscles, tendons, and joints." [OBP:GVG]
2011-04-05T11:01:08Z
George Gkoutos
behavior_ontology
Sensations arising from the internal organs (the viscera), such as pain or the sense of fullness of the stomach or bladder, may therefore be included, although they are usually considered separately as visceral sensations. Pain arising from the viscera is often felt as though it comes from some part of the body surface or underlying tissue.
somatic sensation related behavior
2011-04-05T11:11:48Z
George Gkoutos
behavior_ontology
cutaneous sensation behavior
2011-04-05T11:36:23Z
George Gkoutos
behavior_ontology
touch related behavior
"Movement behavior of the body or its parts."
2011-04-05T02:08:47Z
George Gkoutos
behavior_ontology
kinesthetic behavior
"The coordination of combinations of body movements created with the kinematic (such as spatial direction) and kinetic (force) parameters that result in intended actions." [wikipedia:Motor_coordination]
2011-04-05T03:32:44Z
George Gkoutos
NBO:0000340
behavior_ontology
motor coordination
"Behavior associated with surface locomotion." [NBO:GVG]
2011-04-06T09:44:37Z
George Gkoutos
behavior_ontology
terrestrial locomotory behavior
"Behaviour related to cognitive processes." [NBO:JH]
2011-04-14T03:51:13Z
George Gkoutos
behavior_ontology
cognitive behavior
2012-03-16T05:23:06Z
gkoutos
behavior_ontology
perception behavior by means
"Any process that modulates the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli." [GO:0050795]
George Gkoutos
GO:0050795
regulation of behavior
GC_ID:1
ncbi_taxonomy
all
root
all
Viruses
Viroids
GC_ID:1
ncbi_taxonomy
biota
cellular organisms
biota
Bacteria
Archaea
GC_ID:1
PMID:23020233
PMID:30257078
eucaryotes
eukaryotes
ncbi_taxonomy
Eucarya
Eucaryotae
Eukarya
Eukaryotae
euk-
eukaryotes
NCBITaxon:2759
Eukaryota
eucaryotes
eukaryotes
Eucarya
Eucaryotae
Eukarya
Eukaryotae
euk-
PRO:DAN
eukaryotes
GC_ID:1
ncbi_taxonomy
Fungi/Metazoa group
opisthokonts
NCBITaxon:33154
Opisthokonta
Fungi/Metazoa group
opisthokonts
GC_ID:1
metazoans
multicellular animals
ncbi_taxonomy
Animalia
animals
metazoan-
NCBITaxon:33208
Metazoa
metazoans
multicellular animals
Animalia
animals
metazoan-
PRO:DAN
GC_ID:1
ncbi_taxonomy
Eumetazoa
obi
OBI:0100026
Category=external.
organism
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.
quality (PATO)
PATO:0000072
trait
quality
PATO:0000001
quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.
PATOC:GVG
A composite chromatic quality composed of hue, saturation and intensity parts.
PATO:0000020
colour
relative color
quality
PATO:0000014
color
A composite chromatic quality composed of hue, saturation and intensity parts.
PATOC:GVG
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
quality
PATO:0000051
morphology
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
PATOC:GVG
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
PATO:0001647
relational shape quality
quality
PATO:0000052
Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.
shape
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
PATOC:GVG
An organismal quality inhering in a bearer by virtue of the bearer's disposition to synthesize a particular organic compound required for its growth.
quality
nutritional quality
PATO:0000056
trophic quality
An organismal quality inhering in a bearer by virtue of the bearer's disposition to synthesize a particular organic compound required for its growth.
Wikipedia:http://en.wikipedia.org/wiki/Trophic_level
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence.
PATO:0000156
PATO:0000158
temporal
incidence
quality
PATO:0000057
occurrence
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence.
PATOC:GVG
quality
PATO:0000068
TODO: define this or obsolete it and move children somewhere else.
qualitative
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
quality
PATO:0000069
deviation (from_normal)
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
PATOC:GVG
The number of entities of this type that are part of the whole organism.
PATO:0000053
PATO:0000071
PATO:0001169
PATO:0001226
presence or absence in organism
quantitative
quality
count in organism
number
presence
PATO:0000070
This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10.
amount
The number of entities of this type that are part of the whole organism.
PATOC:GVG
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
quality
PATO:0000117
size
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
WordNet:WordNet
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
quality
PATO:0000125
For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism.
mass
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
PATOC:GVG
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
PATO:0001032
PATO:0001631
location
placement
relational spatial quality
quality
PATO:0000140
position
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
PATOC:GVG
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
PATO:0001452
conformation
relational structural quality
quality
PATO:0000141
structure
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
PATOC:GVG
conformation
VT:1000738
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
quality
PATO:0000161
rate
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
PATOC:melissa
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
quality
PATO:0000169
viability
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
PATOC:GVG
A reproductive quality inhering in an organism or population by virtue of the bearer's potential reproductive capacity ad measured by the number of gametes.
quality
PATO:0000273
fecundity
A reproductive quality inhering in an organism or population by virtue of the bearer's potential reproductive capacity ad measured by the number of gametes.
Wikipedia:http://en.wikipedia.org/wiki/Fecundity
A reproductive quality inhering in a bearer by virtue of the bearer's initiating, sustaining, or supporting reproduction.
quality
PATO:0000274
fertility
A reproductive quality inhering in a bearer by virtue of the bearer's initiating, sustaining, or supporting reproduction.
PATOC:GVG
A fertility quality inhering in a female by virtue of the bearer's disposition to initiate, sustain, or support reproduction.
quality
PATO:0000277
female fertility
A fertility quality inhering in a female by virtue of the bearer's disposition to initiate, sustain, or support reproduction.
PATOC:GVG
A fertility quality of inhering in a male by virtue of the bearer's disposition to initiate, sustain, or support reproduction.
quality
PATO:0000279
male fertility
A fertility quality of inhering in a male by virtue of the bearer's disposition to initiate, sustain, or support reproduction.
PATOC:GVG
A nutritional quality inhering in a bearer by virtue of the bearer's inability to synthesize a particular organic compound required for its growth.
quality
PATO:0000422
auxotrophic
A nutritional quality inhering in a bearer by virtue of the bearer's inability to synthesize a particular organic compound required for its growth.
Wikipedia:http://en.wikipedia.org/wiki/Auxotrophic
A quality inhering in a bearer by virtue of the bearer's deviation from normal or average.
quality
aberrant
atypia
atypical
defective
PATO:0000460
abnormal
A quality inhering in a bearer by virtue of the bearer's deviation from normal or average.
PATOC:GVG
A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
quality
average
PATO:0000461
normal
A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
PATOC:GVG
A quality denoting the lack of an entity.
PATO:0001996
absence
absent from organism
quality
PATO:0000462
See documentation here: http://code.google.com/p/phenotype-ontologies/wiki/ModelingOfAbsence
absent
A quality denoting the lack of an entity.
thefreedictionary.:thefreedictionary.
A quality inhering in a bearer by virtue of the bearer's existence.
quality
present in organism
PATO:0000467
present
A quality inhering in a bearer by virtue of the bearer's existence.
PATOC:GVG
An amount which is relatively high.
PATO:0000420
PATO:0000650
increased number
present in greater numbers in organism
supernumerary
quality
accessory
increased
PATO:0000470
increased amount
An amount which is relatively high.
PATOC:GVG
A size quality which is relatively high.
PATO:0001202
quality
big
enlarged
expanded
great
large
PATO:0000586
increased size
A size quality which is relatively high.
PATOC:GVG
A size quality which is relatively low.
hypoplasia
underdeveloped
quality
reduced
small
tiny
PATO:0000587
decreased size
A size quality which is relatively low.
PATOC:GVG
A increased size quality inhering in an organ or tissue by virtue of the bearer's exhibiting increased number of cells.
PATO:0000943
hyperplasia
quality
overdeveloped
PATO:0000644
hyperplastic
A increased size quality inhering in an organ or tissue by virtue of the bearer's exhibiting increased number of cells.
Wikipedia:http://en.wikipedia.org/wiki/Hyperplastic
A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced number of cells within an organ or tissue.
PATO:0000942
hypoplasia
quality
underdeveloped
PATO:0000645
hypoplastic
A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced number of cells within an organ or tissue.
PATOC:GVG
A viability quality inhering in a population by virtue of the bearer's long term survival inability.
quality
PATO:0000718
lethal (sensu genetics)
A viability quality inhering in a population by virtue of the bearer's long term survival inability.
PATOC:GVG
A viability quality inhering in a bearer or a population by virtue of the bearer's ability to survive or the long term survival ability of a given population.
quality
PATO:0000719
viable
A viability quality inhering in a bearer or a population by virtue of the bearer's ability to survive or the long term survival ability of a given population.
PATOC:GVG
A female fertility quality inhering in a female by virtue of the bearer's disposition to initiate, sustain, or support reproduction.
quality
PATO:0000888
female fertile
A female fertility quality inhering in a female by virtue of the bearer's disposition to initiate, sustain, or support reproduction.
PATOC:GVG
A male fertility quality inhering in a male by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction.
quality
male infertile
PATO:0000890
male sterile
A male fertility quality inhering in a male by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction.
PATOC:GVG
A male fertility quality inhering in a male by virtue of the bearer's being capable of initiating, sustaining, or supporting reproduction.
quality
PATO:0000891
male fertile
A male fertility quality inhering in a male by virtue of the bearer's being capable of initiating, sustaining, or supporting reproduction.
PATOC:GVG
A female fertility quality inhering in a female by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction.
quality
female infertile
PATO:0000892
female sterile
A female fertility quality inhering in a female by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction.
PATOC:GVG
A rate which is relatively low.
slow rate
quality
PATO:0000911
decreased rate
A rate which is relatively low.
PATO:GVG
A rate which is relatively high.
fast rate
high rate
quality
PATO:0000912
increased rate
A rate which is relatively high.
PATO:GVG
A fertility quality inhering in a bearer by virtue of the bearer's being capable of initiating, sustaining, or supporting reproduction.
quality
PATO:0000955
fertile
A fertility quality inhering in a bearer by virtue of the bearer's being capable of initiating, sustaining, or supporting reproduction.
PATOC:GVG
A fertility quality inhering in a bearer by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction.
quality
PATO:0000956
sterile
A fertility quality inhering in a bearer by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction.
PATOC:GVG
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
PATO:0002079
Wikipedia:Physical_property
relational physical quality
quality
PATO:0001018
physical quality
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
PATOC:GVG
A quality inhering in a bearer by virtue of the bearer's disposition to resist to a stimulus.
resistance
quality
PATO:0001046
resistance to
A quality inhering in a bearer by virtue of the bearer's disposition to resist to a stimulus.
PATOC:GVG
A resistance quality inhering in a bearer by virtue of the bearer's resistance to a stimulus.
resistant
quality
PATO:0001178
resistant to
A resistance quality inhering in a bearer by virtue of the bearer's resistance to a stimulus.
PATOC:GVG
A quality which inheres in an process.
PATO:0001239
PATO:0001240
quality of a process
quality of occurrent
quality of process
relational quality of occurrent
quality
PATO:0001236
See comments of relational quality of a physical entity.
process quality
A quality which inheres in an process.
PATOC:GVG
A quality which inheres in a continuant.
PATO:0001237
PATO:0001238
snap:Quality
monadic quality of a continuant
multiply inhering quality of a physical entity
multiply inhering quality of a physical entity
quality of a continuant
quality of a single physical entity
quality of an object
quality of continuant
monadic quality of an object
monadic quality of continuant
quality
PATO:0001241
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
physical object quality
A quality which inheres in a continuant.
PATOC:GVG
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
quality
PATO:0001291
electromagnetic (EM) radiation quality
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
quality
PATO:0001300
optical quality
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
PATOC:GVG
A monadic quality of continuant that exists at the cellular level of organisation.
quality
PATO:0001396
cellular quality
A monadic quality of continuant that exists at the cellular level of organisation.
PATOC:GVG
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
quality
PATO:0001404
nucleate quality
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
PATOC:GVG
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
quality
PATO:0001405
anucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
Biology-online:Biology-online
A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.
quality
PATO:0001406
binucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.
Biology-online:Biology-online
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
quality
PATO:0001407
mononucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
Biology-online:Biology-online
An organismal quality inhering in a bearer by virtue of the bearer's ability to produce new life or offspring.
quality
PATO:0001434
reproductive quality
An organismal quality inhering in a bearer by virtue of the bearer's ability to produce new life or offspring.
WordNet:WordNet
A position which is relatively high.
quality
high position
PATO:0001475
increased position
A position which is relatively high.
PATOC:GVG
A positional which is relatively low.
quality
low position
PATO:0001476
decreased position
A positional which is relatively low.
PATOC:GVG
The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.
OBO_REL:has_part
extra or missing physical or functional parts
has or lacks parts of type
mereological quality
number of
quality
cardinality
number
PATO:0001555
has number of
The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.
PATOC:CJM
A quality of a process inhering in a bearer by virtue of the bearer's lacking a processual part as specified by the additional entity.
quality
PATO:0001558
lacking processual parts
A quality of a process inhering in a bearer by virtue of the bearer's lacking a processual part as specified by the additional entity.
PATOC:GVG
A mass which is lower than normal or average.
PATO:0000579
low mass
small mass
quality
PATO:0001562
decreased mass
A mass which is lower than normal or average.
PATO:GVG
A mass which is higher than normal or average.
PATO:0000578
high mass
large mass
quality
PATO:0001563
increased mass
A mass which is higher than normal or average.
PATO:GVG
A quality of a process inhering in a bearer by virtue of the bearer's processual parts.
quality
PATO:0001564
extra or missing processual parts
A quality of a process inhering in a bearer by virtue of the bearer's processual parts.
PATOC:GVG
A size quality inhering in a bearer by virtue of a part or parts of the bearer's being decreased in size due to reduction in tissue mass through wasting.
atrophic
quality
PATO:0001623
atrophied
A size quality inhering in a bearer by virtue of a part or parts of the bearer's being decreased in size due to reduction in tissue mass through wasting.
Wiikipedia:Wasting
Wikipedia:Atrophy
A resistance to a stimulus which is relatively high.
high resistance to
increased resistance
quality
PATO:0001650
increased resistance to
A resistance to a stimulus which is relatively high.
PATOC:GVG
A resistance to a stimulus which is relatively low.
decreased resistance
low resistance to
quality
PATO:0001651
decreased resistance to
A resistance to a stimulus which is relatively low.
PATOC:GVG
A fecundity which is relatively high.
high fecundity
quality
PATO:0001695
increased fecundity
A fecundity which is relatively high.
PATOC:GVG
A fecundity which is relatively low.
low fecundity
quality
PATO:0001696
decreased fecundity
A fecundity which is relatively low.
PATOC:GVG
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
quality
PATO:0001739
radiation quality
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
PATOC:GVG
quality
PATO:0001760
female semi-fertile
quality
PATO:0001761
male semi-fertile
quality
PATO:0001762
male semi-sterile
quality
PATO:0001763
female semi-sterile
quality
PATO:0001767
semi-fertile
A positional quality inhering in a bearer by virtue of the bearer's location of features or characteristics along an axis.
quality
cellular polarity
PATO:0001769
positional polarity
A positional quality inhering in a bearer by virtue of the bearer's location of features or characteristics along an axis.
PATOC:MAH
cellular polarity
PATOC:MAH
A female fertility which is relatively low.
low female fertility
quality
PATO:0001830
decreased female fertility
A female fertility which is relatively low.
PATOC:GVG
A female fertility which is relatively high.
high female fertility
quality
PATO:0001831
increased female fertility
A female fertility which is relatively high.
PATOC:GVG
A male fertility which is relatively high.
high male fertility
quality
PATO:0001832
increased male fertility
A male fertility which is relatively high.
PATOC:GVG
A male fertility which is relatively low.
low male fertility
quality
PATO:0001833
decreased male fertility
A male fertility which is relatively low.
PATOC:GVG
A fertility which is relatively low.
low fertility
quality
PATO:0001834
decreased fertility
A fertility which is relatively low.
PATOC:GVG
A fertility which is relatively high.
high fertility
quality
PATO:0001835
increased fertility
A fertility which is relatively high.
PATOC:GVG
A fertility quality inhering in a bearer by virtue of the bearer's disposition to make its offspring sterile.
quality
grandchildless
PATO:0001862
lack of fertility in offspring
A fertility quality inhering in a bearer by virtue of the bearer's disposition to make its offspring sterile.
PATOC:GVG
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
quality
PATO:0001908
multinucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
PATOC:GVG
An organismal quality inhering in a bearer by virtue of the bearer's consisting cells.
quality
PATO:0001992
cellularity
An organismal quality inhering in a bearer by virtue of the bearer's consisting cells.
PATOC:GVG
A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell.
quality
PATO:0001993
multicellular
A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell.
PATOC:GVG
A quality that inheres in an entire organism or part of an organism.
quality
PATO:0001995
organismal quality
A quality that inheres in an entire organism or part of an organism.
PATOC:CJM
An amount which is relatively low.
PATO:0000419
PATO:0000468
decreased number
present in fewer numbers in organism
quality
decreased
reduced
subnumerary
PATO:0001997
decreased amount
An amount which is relatively low.
PATOC:GVG
The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type.
loss of
quality
PATO:0001999
lacks parts or has fewer parts of type
The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type.
PATOC:CJM
A quality of physical entities inhering in a bearer by virtue of the bearer's lacking a physical part as specified by the additional entity.
PATO:0001557
OBO_REL:lacks_part
lacks all physical parts of type
quality
PATO:0002000
Example: [E=organism Q=lacks_all_parts_of_type E2=Wing] - applies to an organism. A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e that has no wings, where wings are normally present in that organism type. In OWL this is equivalent to a restriction on the OBO_REL:has_part relation with cardinality=0, i.e has_part 0 E2.
lacks all parts of type
A quality of physical entities inhering in a bearer by virtue of the bearer's lacking a physical part as specified by the additional entity.
PATOC:CJM
The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly.
PATO:0001569
decreased number of
has decreased number of
has fewer physical parts of type
quality
PATO:0002001
Example: [E=hand Q=has_fewer_parts_of_type E2=digit] - applies to an organism that has no less fingers than is normal for organisms of that type.
has fewer parts of type
The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly.
PATOC:CJM
The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part.
PATO:0001560
has extra parts of
has increased number of
having extra physical parts
having supernumerary physical parts
increased number of
quality
PATO:0002002
In polydactyly, the bearer of the quality is the hand, and the entity type being counted is 'finger'. In EQ syntax, E=hand, Q=<this> E2=finger.
has extra parts of type
The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part.
PATOC:CJM
A structural quality which is held by a bearer when the latter's disposition the presence of abnormally proliferating masses of cells.
tumorous
quality
PATO:0002011
neoplastic
A structural quality which is held by a bearer when the latter's disposition the presence of abnormally proliferating masses of cells.
PATOC:MAH
An occurrence which is relatively high.
George Gkoutos
2009-03-26T11:10:11Z
increased incidence
quality
PATO:0002051
increased occurrence
An occurrence which is relatively high.
PATOC:GVG
An occurrence which is relatively low.
George Gkoutos
2009-03-26T11:12:35Z
decreased incidence
quality
PATO:0002052
decreased occurrence
An occurrence which is relatively low.
PATOC:GVG
george
2009-06-05T09:16:46Z
quality
PATO:0002062
physical quality of a process
Having extra or fewer parts.
George Gkoutos
2009-09-21T10:41:58Z
quality
PATO:0002083
altered number of
Having extra or fewer parts.
PATOC:GVG
A quality inhering in a bearer by virtue of the bearer's having or lacking of substances produced by living organisms that have a color resulting from selective color absorption.
george
2010-08-09T04:14:00Z
quality
PATO:0002247
degree of pigmentation
A quality inhering in a bearer by virtue of the bearer's having or lacking of substances produced by living organisms that have a color resulting from selective color absorption.
url:http://en.wikipedia.org/wiki/Biological_pigment
3-D shape
George Gkoutos
2011-04-18T05:11:33Z
quality
PATO:0002290
aplastic/hypoplastic
A quality that has a value that is increased compared to normal or average.
George Gkoutos
2011-06-16T06:39:43Z
quality
PATO:0002300
increased quality
A quality that has a value that is increased compared to normal or average.
PATOC:GVG
A quality that has a value that is decreased compared to normal or average.
George Gkoutos
2011-06-16T06:40:15Z
quality
PATO:0002301
decreased quality
A quality that has a value that is decreased compared to normal or average.
PATOC:GVG
A quality of a process that has a value that is decreased compared to normal or average.
George Gkoutos
2011-06-16T06:50:59Z
quality
PATO:0002302
decreased process quality
A quality of a process that has a value that is decreased compared to normal or average.
PATOC:GVG
A quality of an object that has a value that is decreased compared to normal or average.
George Gkoutos
2011-06-16T06:51:54Z
quality
PATO:0002303
decreased object quality
A quality of an object that has a value that is decreased compared to normal or average.
PATOC:GVG
A quality of a process that has a value that is increased compared to normal or average.
George Gkoutos
2011-06-16T06:53:08Z
quality
PATO:0002304
increased process quality
A quality of a process that has a value that is increased compared to normal or average.
PATOC:GVG
A quality of an object that has a value that is increased compared to normal or average.
George Gkoutos
2011-06-16T06:54:01Z
quality
PATO:0002305
increased object quality
A quality of an object that has a value that is increased compared to normal or average.
PATOC:GVG
A temporal distribution pattern of process occurrences within a regulation/reference process.
George Gkoutos
2011-11-22T01:12:28Z
quality
PATO:0002323
temporal distribution quality
A temporal distribution pattern of process occurrences within a regulation/reference process.
PATOC:LC
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
gkoutos
2013-10-21T05:44:34Z
quality
PATO:0002505
nucleated
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
PATOC:GVG
maximally connected
disconnected
The ability of a process to produce its output.
cjm
quality
PATO:0015002
process efficacy
The ability of a process to produce its output.
PATOC:PortlandMeetingFeb2015
A decrease in the ability of a process to produce its output.
cjm
quality
PATO:0015003
decreased efficacy
A decrease in the ability of a process to produce its output.
PATOC:PortlandMeetingFeb2015
A increase in the ability of a process to produce its output.
cjm
quality
PATO:0015004
increased efficacy
A increase in the ability of a process to produce its output.
PATOC:PortlandMeetingFeb2015
2
Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
A material entity that consists of two or more organisms, viruses, or viroids.
group of organism
organism collection
May be of the same or different species.
collection of organisms
This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed.
A collection of organisms, all of the same species, that live in the same place.
ISBN:0878932739
It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms.
Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used.
population of organisms
A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members.
multispecies community
ISBN:0865423504
Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community.
ecological community
A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.
collection of organisms of the same species
single-species collection of organisms
2
A collection of organisms that consists of two or more organisms from at least two species.
Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))".
multi-species collection of organisms
A material entity that is one or more organisms, viruses or viroids.
organismal entity
2
A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other.
pair of interacting organisms
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
uberon
UBERON:0000000
processual entity
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
span:ProcessualEntity
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
PNS
AAO:0000429
BAMS:PNS
BILA:0000081
BIRNLEX:1111
BTO:0001028
CALOHA:TS-0808
EFO:0000891
EHDAA2:0001445
EHDAA:2893
EMAPA:16665
EV:0100335
FBbt:00005098
FMA:9903
GAID:715
MA:0000218
MAT:0000338
MESH:D017933
MIAA:0000338
NCIT:C12465
TAO:0000142
UMLS:C0206417
UMLS:C1305921
VHOG:0000399
XAO:0000178
ZFA:0000142
pars peripherica
systema nervosum periphericum
uberon
UBERON:0000010
peripheral nervous system
http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png
cjm
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
GO:0007422
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000142
TAO
ZFIN:curator
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
2012-06-20
AAO:0000429
AAO
AAO:BJB
The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
2012-09-17
VHOG:0000399
VHOG
DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)
PNS
UMLS:C0206417
BIRNLEX:1111
UMLS:C0206417
ncithesaurus:Peripheral_Nervous_System
UMLS:C1305921
BIRNLEX:1111
pars peripherica
FMA:9903
FMA:TA
systema nervosum periphericum
FMA:9903
FMA:TA
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
EMAPA:0
FBbt:00007001
FMA:305751
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:D000825
TAO:0000037
TGMA:0001823
VHOG:0001759
XAO:0003000
ZFA:0000037
biological structure
connected biological structure
uberon
UBERON:0000061
anatomical structure
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
CARO:0000003
connected biological structure
CARO:0000003
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
BIRNLEX:4
CARO:0020004
EFO:0000634
EMAPA:35949
ENVO:01000162
FMA:67498
MA:0003001
NCIT:C13018
OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
UMLS:C0178784
WBbt:0003760
uberon
anatomical unit
body organ
element
UBERON:0000062
organ
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
GO:0048513
UMLS:C0178784
ncithesaurus:Organ
element
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
adult stage
BTO:0001043
BilaDO:0000004
EFO:0001272
FBdv:00005369
WBls:0000041
XtroDO:0000084
fully formed animal stage
juvenile-adult stage
uberon
UBERON:0000066
fully formed stage
https://github.com/obophenotype/uberon/issues/566
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
https://orcid.org/0000-0002-6601-2165
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
BilaDO:0000002
EV:0300001
FBdv:00005289
FMA:72652
HsapDv:0000002
MmusDv:0000002
OGES:000000
OGES:000022
SCTID:296280003
WBls:0000003
WBls:0000092
WBls:0000102
XAO:1000012
embryonic stage
uberon
embryogenesis
UBERON:0000068
embryo stage
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
http://orcid.org/0000-0002-6601-2165
End of the life of an organism.
ncit:Death is an outcome
XAO:0000437
XtroDO:0000085
uberon
death
UBERON:0000071
death stage
End of the life of an organism.
XAO:0000437
ncit:Death is an outcome
ncit
stage succeeding embryo, including mature structure
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
BilaDO:0000003
OGES:000010
OGES:000014
OGES:000024
WBls:0000022
WBls:0000093
WBls:0000103
postembryonic stage
post-hatching stage
uberon
postembryonic
UBERON:0000092
post-embryonic stage
https://github.com/obophenotype/uberon/issues/344
stage succeeding embryo, including mature structure
stage succeeding embryo, including mature structure
https://orcid.org/0000-0002-6601-2165
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
FBdv:00000000
HsapDv:0000001
MmusDv:0000001
OGES:000011
ncithesaurus:Life
entire life cycle
entire lifespan
life
lifespan
uberon
UBERON:0000104
life cycle
https://github.com/obophenotype/uberon/issues/532
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
https://orcid.org/0000-0002-6601-2165
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
BILS:0000105
EFO:0000399
FBdv:00007012
FMA:24120
HsapDv:0000000
MmusDv:0000000
OlatDv:0000010
PdumDv:0000090
WBls:0000002
XAO:1000000
ZFS:0000000
ZFS:0100000
ncithesaurus:Developmental_Stage
developmental stage
stage
uberon
UBERON:0000105
life cycle stage
A spatiotemporal region encompassing some part of the life cycle of an organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
https://orcid.org/0000-0002-6601-2165
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
BILS:0000106
BilaDO:0000005
EFO:0001322
EHDAA:27
FBdv:00005288
NCIT:C12601
PdumDv:0000100
VHOG:0000745
Wikipedia:Zygote
XAO:1000001
ZFS:0000001
1-cell stage
fertilized egg stage
one cell stage
uberon
fertilized egg stage
one-cell stage
zygote
zygotum
UBERON:0000106
zygote stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
A stage at which the organism is a single cell produced by means of sexual reproduction.
Wikipedia:Zygote
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
2012-09-17
VHOG:0000745
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
2012-09-17
VHOG:0000745
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107
http://bgee.unil.ch/
fertilized egg stage
BTO:0000854
one-cell stage
VHOG:0000745
zygote
VHOG:0000745
zygotum
zygotum
Wikipedia:Zygote
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
BILS:0000107
BilaDO:0000006
EFO:0001290
FBdv:00000054
MESH:A16.254.270
MmusDv:0000004
OGES:000015
OGES:000020
PdumDv:0000200
Wikipedia:Cleavage_(embryo)
XAO:1000004
ZFS:0000046
uberon
UBERON:0000107
cleavage stage
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
GO:0040016
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
GO:0040016
Wikipedia:Cleavage_(embryo)
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
consider adding a preceding stage 'morula stage' as part of cleavage
BILS:0000108
BilaDO:0000007
EFO:0001282
HsapDv:0000006
MmusDv:0000007
OGES:000003
OGES:000016
OGES:000021
OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg
WBls:0000005
Wikipedia:Blastula
XAO:1000003
ZFS:0000045
uberon
UBERON:0000108
blastula stage
http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
Wikipedia:Blastula
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
BILS:0000109
BilaDO:0000008
EFO:0001296
FBdv:00005317
HsapDv:0000010
MmusDv:0000013
OGES:000004
OGES:000019
WBls:0000010
XAO:1000005
ZFS:0000047
uberon
blastocystis trilaminaris stage
trilaminar blastocyst stage
trilaminar blastoderm stage
trilaminar disk stage
trilaminar germ stage
trilaminar stage
UBERON:0000109
gastrula stage
BILS
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
GO:0007369
blastocystis trilaminaris stage
blastocystis trilaminaris stage
https://orcid.org/0000-0002-6601-2165
trilaminar blastocyst stage
trilaminar blastocyst stage
https://orcid.org/0000-0002-6601-2165
trilaminar blastoderm stage
trilaminar blastoderm stage
https://orcid.org/0000-0002-6601-2165
trilaminar disk stage
trilaminar disk stage
https://orcid.org/0000-0002-6601-2165
trilaminar germ stage
trilaminar germ stage
https://orcid.org/0000-0002-6601-2165
trilaminar stage
trilaminar stage
https://orcid.org/0000-0002-6601-2165
Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
BILS:0000110
BilaDO:0000009
HsapDv:0000012
MmusDv:0000017
XAO:1000006
uberon
UBERON:0000110
neurula stage
https://github.com/obophenotype/uberon/issues/343
Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
GO:0001841
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
BILS:0000111
BilaDO:0000010
HsapDv:0000015
MmusDv:0000018
OGES:000005
OGES:000032
Wikipedia:Organogenesis
uberon
segmentation stage
UBERON:0000111
organogenesis stage
https://github.com/obophenotype/uberon/issues/533
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
Wikipedia:Organogenesis
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula
UBERON:0007011
BILA:0000059
BTO:0000128
GAID:1294
MESH:A16.254.270.274
OGEM:000006
OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg
blastula embryo
uberon
blastosphere
UBERON:0000307
blastula
http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
blastula embryo
BILA:0000059
blastosphere
Anatomical entity that has mass.
AAO:0010264
AEO:0000006
BILA:0000006
CARO:0000006
EHDAA2:0003006
FBbt:00007016
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
VHOG:0001721
uberon
UBERON:0000465
material anatomical entity
Anatomical entity that has mass.
Anatomical entity that has no mass.
AAO:0010265
AEO:0000007
BILA:0000007
CARO:0000007
EHDAA2:0003007
FBbt:00007015
FMA:67112
HAO:0000007
TAO:0001835
TGMA:0001827
VHOG:0001727
immaterial physical anatomical entity
uberon
UBERON:0000466
immaterial anatomical entity
Anatomical entity that has no mass.
immaterial physical anatomical entity
FMA:67112
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
system
AAO:0000007
AEO:0000011
BILA:0000011
BIRNLEX:14
BSA:0000049
CALOHA:TS-2088
CARO:0000011
EHDAA2:0003011
EHDAA:392
EMAPA:16103
EV:0100000
FBbt:00004856
FMA:7149
HAO:0000011
MA:0000003
NCIT:C12919
OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ
TAO:0001439
TGMA:0001831
UMLS:C0460002
VHOG:0001725
WBbt:0005746
WBbt:0005763
XAO:0003002
ZFA:0001439
galen:AnatomicalSystem
body system
connected anatomical system
organ system
uberon
anatomical systems
UBERON:0000467
anatomical system
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
CARO:0000011
system
GO:0048731
UMLS:C0460002
ncithesaurus:Organ_System
body system
BIRNLEX:14
connected anatomical system
CARO:0000011
anatomical systems
ZFA:0001439
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
organismal
organism
AAO:0010026
AEO:0000191
BILA:0000012
BIRNLEX:18
BSA:0000038
BTO:0000042
CARO:0000012
EFO:0002906
EHDAA2:0003103
EHDAA2:0003191
EHDAA:1
EMAPA:25765
EV:0100016
FBbt:00000001
FMA:256135
HAO:0000012
NCIT:C13041
TADS:0000001
TAO:0001094
TGMA:0001832
VHOG:0000671
WBbt:0007833
XAO:0003004
ZFA:0001094
galen:Organism
ncithesaurus:Whole_Organism
multi-cellular organism
animal
uberon
Koerper
body
whole body
whole organism
UBERON:0000468
multicellular organism
Anatomical structure that is an individual member of a species and consists of more than one cell.
CARO:0000012
organism
FBbt:00000001
VHOG:0000671
WBbt:0007833
multi-cellular organism
CARO:0000012
animal
BTO:0000042
Koerper
BTO:0001489
body
AEO:0000103
BIRNLEX:18
FMA:256135
NCIT:C13041
whole body
BTO:0001489
whole organism
FBbt:00000001
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
AAO:0000607
AAO:0010054
AEO:0000043
BILA:0000043
BIRNLEX:19
CALOHA:TS-2090
CARO:0000043
EHDAA2:0003043
EMAPA:35868
FBbt:00007003
FMA:9637
HAO:0000043
MA:0003002
MESH:D014024
NCIT:C12801
TAO:0001477
TGMA:0001844
UMLS:C0040300
VHOG:0001757
WBbt:0005729
XAO:0003040
ZFA:0001477
galen:Tissue
portion of tissue
tissue portion
simple tissue
uberon
UBERON:0000479
tissue
CARO
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
CARO:0000043
UMLS:C0040300
ncithesaurus:Tissue
portion of tissue
CARO:0000043
simple tissue
AEO:0000043
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. 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.
embryonic
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
AAO:0011035
AEO:0000169
BILA:0000056
BSA:0000039
BTO:0000379
CALOHA:TS-0229
EFO:0001367
EHDAA2:0000002
EHDAA2_RETIRED:0003236
EHDAA:38
EMAPA:16039
FBbt:00000052
FMA:69068
GAID:963
MAT:0000226
MESH:D004622
MIAA:0000019
NCIT:C28147
OGEM:000001
OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA
UMLS:C0013935
VHOG:0001766
XAO:0000113
ZFA:0000103
embryonic organism
uberon
developing organism
developmental tissue
UBERON:0000922
embryo
https://github.com/obophenotype/uberon/issues/503
Wrinkledfrog:embryos.jpg
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. 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.
BTO:0000379
FB:FBrf0039741
FB:FBrf0041814
GO:0009790
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
ZFA
UMLS:C0013935
ncithesaurus:Embryo
embryonic organism
BILA:0000056
developing organism
BILA:0000056
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
embryonic tissue
AAO:0000480
BILA:0000035
BTO:0000556
EMAPA:36033
FBbt:00000110
FMA:69069
GAID:1303
MESH:A16.254.425
NCIT:C12950
NCIT:C54105
TAO:0001122
UMLS:C0920502
UMLS:C1708239
VHOG:0001223
XAO:0003011
ZFA:0001122
germinal layer
primary germ layer
uberon
embryonic germ layer
embryonic germ layers
UBERON:0000923
Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]
germ layer
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
2012-09-17
VHOG:0001223
VHOG
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
embryonic tissue
FMA:69069
UMLS:C0920502
ncithesaurus:Embryonic_Tissue
UMLS:C1708239
ncithesaurus:Germinal_Layer
germinal layer
ncithesaurus:Germinal_Layer
primary germ layer
GO:0001704
ZFA:0001122
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
ectodermal
AAO:0000137
BILA:0000036
BTO:0000315
CALOHA:TS-0216
EFO:0000414
EHDAA2:0000428
EMAPA:16069
EV:0100003
FBbt:00000111
FMA:69070
GAID:1304
MAT:0000155
MAT:0000173
MESH:A16.254.425.273
MIAA:0000173
NCIT:C12703
TAO:0000016
UMLS:C0013574
VHOG:0000153
XAO:0000001
ZFA:0000016
embryonic ectoderm
uberon
UBERON:0000924
ectoderm
http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png
Bgee:AN
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
2012-06-20
AAO:0000137
AAO
AAO:EJS
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
2012-09-17
VHOG:0000153
VHOG
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
UMLS:C0013574
ncithesaurus:Ectoderm
embryonic ectoderm
VHOG:0000153
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
nervous
neural
AAO:0000324
BILA:0000079
BIRNLEX:844
BTO:0001484
CALOHA:TS-1313
EFO:0000802
EHDAA2:0001246
EHDAA:826
EMAPA:16469
EV:0100162
FBbt:00005093
FMA:7157
GAID:466
MA:0000016
MAT:0000026
MESH:D009420
MIAA:0000026
NCIT:C12755
OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA
TAO:0000396
UMLS:C0027763
VHOG:0000402
WBbt:0005735
XAO:0000177
ZFA:0000396
neurological system
nerve net
uberon
systema nervosum
UBERON:0001016
nervous system
http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg
http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png
Bgee:AN
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
BIRNLEX:844
ISBN:0-14-051288-8
ISBN:3110148986
NLM:nervous+system
WB:rynl
ZFIN:curator
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
2012-08-14
TAO:0000396
TAO
ZFIN:curator
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
2012-06-20
AAO:0000324
AAO
AAO:BJB
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
2012-09-17
VHOG:0000402
VHOG
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117
UMLS:C0027763
ncithesaurus:Nervous_System
neurological system
GO:0050877
nerve net
systema nervosum
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
Part of the nervous system which includes the brain and spinal cord.[AAO]
The brain and spinal cord. Kimmel et al, 1995.[TAO]
The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
AAO:0000090
BAMS:CNS
BILA:0000080
BIRNLEX:1099
BTO:0000227
CALOHA:TS-0150
EFO:0000908
EHDAA2:0000225
EHDAA:828
EMAPA:16470
EMAPA:16754
EV:0100163
FBbt:00005094
FMA:55675
GAID:570
MA:0000167
MAT:0000457
MESH:D002490
NCIT:C12438
OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA
TAO:0000012
UMLS:C0927232
VHOG:0000293
XAO:0000215
ZFA:0000012
CNS
systema nervosum centrale
cerebrospinal axis
uberon
neuraxis
UBERON:0001017
central nervous system
FBbt
cjm
Bgee:AN
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
GO:0021551
Part of the nervous system which includes the brain and spinal cord.[AAO]
2012-06-20
AAO:0000090
AAO
AAO:BJB
The brain and spinal cord. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000012
TAO
ZFIN:curator
The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
BIRNLEX:1099
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
2012-09-17
VHOG:0000293
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)
UMLS:C0927232
BIRNLEX:1099
UMLS:C0927232
ncithesaurus:Central_Nervous_System
CNS
systema nervosum centrale
FMA:55675
FMA:TA
cerebrospinal axis
FMA:55675
neuraxis
FMA:55675
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
AAO:0000555
BAMS:SEN
BILA:0000099
EFO:0000805
EHDAA2:0003094
EMAPA:16192
FBbt:00007692
FMA:75259
MA:0002442
MAT:0000031
MIAA:0000031
NLXANAT:090816
TAO:0000282
VHOG:0001674
XAO:0003194
ZFA:0000282
organa sensuum
sense organ subsystem
sense organs
sense organs set
sensory subsystem
sensory systems
uberon
organa sensuum
sensory organ system
set of sense organs
UBERON:0001032
sensory system
http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
2012-09-17
VHOG:0001674
VHOG
DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)
organa sensuum
FMA:75259
FMA:TA
sense organs
FMA:75259
sense organs set
FMA:75259
sensory systems
TAO:0000282
organa sensuum
set of sense organs
FMA:75259
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
AAO:0010841
AEO:0000000
BILA:0000000
BIRNLEX:6
CARO:0000000
EHDAA2:0002229
FBbt:10000000
FBbt_root:00000000
FMA:62955
HAO:0000000
MA:0000001
NCIT:C12219
TAO:0100000
TGMA:0001822
UMLS:C1515976
WBbt:0000100
XAO:0000000
ZFA:0100000
uberon
UBERON:0001062
anatomical entity
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
FMA:62955
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
FMA:62955
http://orcid.org/0000-0001-9114-8737
UMLS:C1515976
ncithesaurus:Anatomic_Structure_System_or_Substance
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
in FMA embryo is_a embryonic structure
AAO:0000138
BILA:0000034
BTO:0000174
CALOHA:TS-2110
EFO:0000461
FBbt:00004208
FMA:69067
GAID:407
MESH:D004628
NCIT:C13229
RETIRED_EHDAA2:0003169
TAO:0001105
UMLS:C0013948
VSAO:0000178
XAO:0003042
ZFA:0001105
developing embryonic structure
embryonic anatomical structure
uberon
developing structure
embryonale Struktur
embryonic structures
UBERON:0002050
embryonic structure
Anatomical structure that is part of an embryo.
BTO:0000174
ZFIN:curator
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
2012-06-20
AAO:0000138
AAO
AAO:BJB
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
2012-08-14
TAO:0001105
TAO
ZFIN:curator
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
2012-08-14
VSAO:0000178
VSAO
ZFIN:curator
in FMA embryo is_a embryonic structure
FMA
UMLS:C0013948
ncithesaurus:Embryonic_Structure
developing embryonic structure
FBbt:00004208
embryonic anatomical structure
RETIRED_EHDAA2:0003169
embryonale Struktur
BTO:0000174
embryonic structures
ZFA:0001105
Sensory system responsible for the perception of spatial orientation and auditory stimuli.
The sensory system used for balance and hearing.[AAO]
AAO:0000631
EMAPA:36002
EMAPA:37985
FMA:78500
TAO:0001138
XAO:0003195
ZFA:0001138
auditory organ system
vestibuloauditory system
uberon
auditory system
auditory/vestibular system
vestibuloauditory system
UBERON:0002105
vestibulo-auditory system
http://upload.wikimedia.org/wikipedia/commons/d/d2/Anatomy_of_the_Human_Ear.svg
Sensory system responsible for the perception of spatial orientation and auditory stimuli.
ZFA:0001138
The sensory system used for balance and hearing.[AAO]
2012-06-20
AAO:0000631
AAO
AAO:EJS
EMAPA:37985
MA:th
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
BTO:0004593
FMA:296704
MAT:0000067
MIAA:0000067
VHOG:0000243
epiblast
uberon
blastocyst
ectoblast
epiblastus
primitive ectoderm
UBERON:0002532
epiblast (generic)
http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
ZFIN:curator
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
2012-09-17
VHOG:0000243
VHOG
DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)
epiblast
VHOG:0000243
ectoblast
MP:0003886
epiblastus
primitive ectoderm
VHOG:0000243
An anatomical structure that develops (entirely or partially) from the ectoderm.
Grouping term for query purposes
FBbt:00025990
ectodermal deriviative
uberon
UBERON:0004121
ectoderm-derived structure
An anatomical structure that develops (entirely or partially) from the ectoderm.
ectodermal deriviative
FBbt:00025990
An embryo at the neurula stage.
UBERON:0007013
BILA:0000061
BTO:0001766
NCIT:C34229
UMLS:C1518306
neurula
uberon
UBERON:0004455
neurula embryo
An embryo at the neurula stage.
UMLS:C1518306
ncithesaurus:Neurula
neurula
BTO:0001766
Sum of all sensory systems in an organism.
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
FMA:78499
sense organ system
uberon
UBERON:0004456
entire sense organ system
Sum of all sensory systems in an organism.
sense organ system
FMA:78499
Organism at the gastrula stage.
We explicitly merge the NCITA terms here
UBERON:0007012
BILA:0000060
BTO:0001403
FBbt:00005317
FMA:293108
GAID:1302
MESH:A16.254.412
MIAA:0000179
NCIT:C34057
NCIT:C34058
UMLS:C0017199
UMLS:C1284022
gastrula embryo
uberon
blastocystis trilaminaris
tri-laminar disc
tri-laminar disk
trilaminar blastocyst
trilaminar blastoderm
trilaminar disc
trilaminar disk
trilaminar germ
UBERON:0004734
gastrula
Organism at the gastrula stage.
We explicitly merge the NCITA terms here
NCIT
UMLS:C0017199
ncithesaurus:Gastrula
UMLS:C1284022
ncithesaurus:Trilaminar_Embryonic_Disc
gastrula embryo
BILA:0000060
blastocystis trilaminaris
tri-laminar disc
tri-laminar disk
trilaminar blastocyst
trilaminar blastoderm
trilaminar disc
trilaminar disk
trilaminar germ
A portion of tissue that is part of an embryo.
CALOHA:TS-2100
portion of embryonic tissue
uberon
developing tissue
UBERON:0005291
embryonic tissue
A portion of tissue that is part of an embryo.
OBOL:automatic
portion of embryonic tissue
OBOL:automatic
AEO:0000125
CALOHA:TS-2122
EHDAA2:0003125
FBbt:00007006
FMA:292313
MIAA:0000019
uberon
developing structure
developmental structure
developmental tissue
UBERON:0005423
developing anatomical structure
developmental tissue
MIAA:0000019
Portion of embryonic tissue determined by fate mapping to become a structure.
Consider merging with anlage
AAO:0000479
TAO:0001116
ZFA:0001116
future structure
presumptive structures
uberon
UBERON:0006598
presumptive structure
Portion of embryonic tissue determined by fate mapping to become a structure.
GOC:CVS
GOC:YMB
ZFA:0001116
presumptive structures
ZFA:0001116
Presumptive structure of the blastula that will develop into ectoderm.
AAO:0000470
EFO:0003466
TAO:0001376
XAO:0004132
ZFA:0001376
uberon
presumptive epidermis
UBERON:0006601
presumptive ectoderm
Presumptive structure of the blastula that will develop into ectoderm.
presumptive epidermis
ZFA:0001376
A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n
BILA:0000010
CARO:0001002
EHDAA2_RETIRED:0003192
FMA:24137
NCIT:C34022
UMLS:C1515977
uberon
UBERON:0006984
Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.
anatomical surface
via morphological boundary in CARO
A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n
CARO:0001002
UMLS:C1515977
ncithesaurus:Anatomic_Surface
Organism at the cleavage stage.
BILA:0000058
uberon
UBERON:0007010
cleaving embryo
Organism at the cleavage stage.
OBOL:automatic
A multicellular organism that existence_starts_with a post-embryonic stage.
MA:0002405
postnatal organism
TS28 mouse
post-hatching organism
post-natal organism
postnatal mouse
uberon
UBERON:0009953
post-embryonic organism
https://github.com/obophenotype/uberon/issues/667
A multicellular organism that existence_starts_with a post-embryonic stage.
OBOL:automatic
TS28 mouse
MA:0002405
post-hatching organism
post-natal organism
postnatal mouse
MA:0002405
An anatomical structure that has more than one cell as a part.
CARO:0010000
FBbt:00100313
multicellular structure
uberon
UBERON:0010000
multicellular anatomical structure
An anatomical structure that has more than one cell as a part.
CARO:0010000
multicellular structure
FBbt:00100313
An anatomical boundary that corresponds to some physical discontinuity.
CARO:0001004
uberon
UBERON:0010199
One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)
bona-fide anatomical boundary
CARO
An anatomical boundary that corresponds to some physical discontinuity.
CARO:0001004
uberon
UBERON:0010316
germ layer / neural crest
A subdivision of an anatomical system.
FBbt:00007330
FMA:67509
uberon
UBERON:0011216
organ system subdivision
FBbt
A subdivision of an anatomical system.
Primordium that develops into the central nervous system
UBERON:3000469
future CNS
presumptive central nervous system
uberon
UBERON:0016879
future central nervous system
Primordium that develops into the central nervous system
Primordium that develops into the nervous system
UBERON:3000477
AAO:0000477
presumptive nervous system
uberon
UBERON:0016880
future nervous system
Primordium that develops into the nervous system
presumptive nervous system
AAO:0000477
example to be eventually removed
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
Person:Alan Ruttenberg
failed exploratory term
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
ready for release
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
pending final vetting
placeholder removed
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term imported
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
term split
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
Alan Ruttenberg
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
universal
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
Alan Ruttenberg
defined class
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
Alan Ruttenberg
named class expression
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI
requires discussion
subset_oio
2
2
1
2
Should belong in BFO, but lives in caro for now.
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).