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/4.0/
23:02:2024 08:54
FlyBase miscellaneous CV
2024-02-23
definition
preferred_root
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
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
id
in_subset
shorthand
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
http://www.obofoundry.org/ro/#OBO_REL:part_of
https://wiki.geneontology.org/Part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
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
preceded by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
precedes
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
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
https://wiki.geneontology.org/Occurs_in
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity.
derives from part of
has_age
A relation between a developmental stage and another, larger developmental stage during which it happens.
relationship
FBdv:00018001
Creating this relation as a temporary fix, pending adding the axiom occurrent_part_of subproperty of happens_during to RO.
substage of
A relation between a developmental stage and another, larger developmental stage during which it happens.
FBC:DPG
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
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
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
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
disposition of
X outer_layer_of Y iff:
. X :continuant that bearer_of some PATO:laminar
. X part_of Y
. exists Z :surface
. X has_boundary Z
. Z boundary_of Y
has_boundary: http://purl.obolibrary.org/obo/RO_0002002
boundary_of: http://purl.obolibrary.org/obo/RO_0002000
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
bounding layer of
A part of relation that applies only between occurrents.
occurrent 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.
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.
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.
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
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.
2017-05-24T09:49:21Z
has component process
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.
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.
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.
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.
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.
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.
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.
David Osumi-Sutherland
<=
Primitive instance level timing relation between events
before or simultaneous with
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
di
Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
encompasses
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
David Osumi-Sutherland
starts_at_end_of
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
David Osumi-Sutherland
Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which starts
David Osumi-Sutherland
ends_at_start_of
meets
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
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
https://wiki.geneontology.org/Happens_during
David Osumi-Sutherland
o
overlaps
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
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
true
A is spatially_disjoint_from B if and only if they have no parts in common
There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
spatially disjoint from
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
connected to
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
attached to part of (anatomical structure to anatomical structure)
attached to part of
true
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
This is the transitive form of the develops from relation
develops from
inverse of develops from
develops into
'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
expressed in
p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
regulates
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
negatively regulates (process to process)
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
positively regulates (process to process)
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.
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)".
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.
has function in
capable of part of
true
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
surrounded by
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
adjacent to
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
inverse of surrounded by
surrounds
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
consumes
has input
https://wiki.geneontology.org/Has_input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
produces
has output
https://wiki.geneontology.org/Has_output
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
has developmental contribution from
inverse of has developmental contribution from
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
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
https://wiki.geneontology.org/Acts_upstream_of_or_within
Inverse of developmentally preceded by
developmentally succeeded by
y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.
expresses
p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
results in developmental progression of
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
GOC:mtg_berkeley_2013
results in formation of anatomical entity
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
causally upstream of, positive effect
p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
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
inheres in part of
characteristic of part of
true
A mereological relationship or a topological relationship
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)
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
a particular instances of akt-2 enables some instance of protein kinase activity
c enables p iff c is capable of p and c acts to execute p.
catalyzes
executes
has
is catalyzing
is executing
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
enables
https://wiki.geneontology.org/Enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
false
part of structure that is capable of
true
holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism
genomically related to
c involved_in p if and only if c enables some process p', and p' is part of p
actively involved in
enables part of
involved in
https://wiki.geneontology.org/Involved_in
inverse of enables
enabled by
https://wiki.geneontology.org/Enabled_by
inverse of regulates
regulated by (processual)
regulated by
inverse of negatively regulates
negatively regulated by
inverse of positively regulates
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
member of
has member is a mereological relation between a collection and an item.
SIO
has member
inverse of has input
input of
inverse of has output
output of
formed as result of
a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
attached to (anatomical structure to anatomical structure)
attached to
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).
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
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
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
has potential to directly develop into
inverse of upstream of
causally downstream of
immediately causally downstream of
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
indirectly activates
indirectly positively regulates
https://wiki.geneontology.org/Indirectly_positively_regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly inhibits
indirectly negatively regulates
https://wiki.geneontology.org/Indirectly_negatively_regulates
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative?
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
https://en.wikipedia.org/wiki/Causality
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
causally upstream of
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
immediately causally upstream of
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
influences (processual)
affects
causally upstream of or within
inverse of causally upstream of or within
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
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
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.
executes activity in
enables activity in
is active in
https://wiki.geneontology.org/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.
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
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.
Considering relabeling as 'pairwise interacts with'
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
http://purl.obolibrary.org/obo/MI_0914
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
Axiomatization to GO to be added later
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.
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.
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.
directly activates
molecularly increases activity of
directly positively regulates activity of
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)
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
composed primarily of
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.
has part that occurs in
true
is kinase activity
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
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
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.
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
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between entities
A coral reef environment is determined by a particular coral reef
s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
determined by (system to material entity)
determined by
inverse of determined by
determines (material entity to system)
determines
s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
determined by part of
true
causally influenced by (entity-centric)
causally influenced by
interaction relation helper property
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
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).
causally influences (entity-centric)
causally influences
A relation that holds between elements of a musculoskeletal system or its analogs.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
biomechanically related to
A relation that holds between an attribute or a qualifier and another attribute.
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
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
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
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.
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
A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
Groups both positive and negative correlation
correlated with
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
directly positively regulates
https://wiki.geneontology.org/Directly_positively_regulates
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
directly negatively regulates
https://wiki.geneontology.org/Directly_negatively_regulates
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
a produced_by b iff some process that occurs_in b has_output a.
produced by
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
2018-01-25T23:20:13Z
enables subfunction
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect
2018-01-26T23:49:51Z
acts upstream of or within, negative effect
https://wiki.geneontology.org/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
2018-01-26T23:53:14Z
acts upstream of, positive effect
https://wiki.geneontology.org/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
2018-01-26T23:53:22Z
acts upstream of, negative effect
https://wiki.geneontology.org/Acts_upstream_of,_negative_effect
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect
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.
regulates activity of
p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
2022-09-26T06:07:17Z
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
2022-09-26T06:08:01Z
indirectly regulates
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.
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.
https://orcid.org/0000-0002-6601-2165
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.
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.
https://orcid.org/0000-0002-6601-2165
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.
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.
https://orcid.org/0000-0002-6601-2165
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.
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.
https://orcid.org/0000-0002-6601-2165
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
2021-11-08T12:00:00Z
utilizes
device utilizes material
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
positively regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
negatively regulates characteristic
in_response_to
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.
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
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
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.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
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]
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
(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]
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 (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]
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
specifically dependent continuant
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
per discussion with Barry Smith
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
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]
fiat-object-part
FiatObjectPart
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object part
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
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]
object
Object
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
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.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
generically dependent continuant
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
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]
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.
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: 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.
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
9/18/11
organism or virus or viroid
organism
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.
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. 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
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
Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.
-1
0.000548579903
0.0
KEGG:C05359
PMID:21614077
Wikipedia:Electron
electron
chebi_ontology
Elektron
beta
beta(-)
beta-particle
e
e(-)
e-
negatron
CHEBI:10545
electron
PMID:21614077
Europe PMC
electron
ChEBI
electron
IUPAC
electron
KEGG_COMPOUND
Elektron
ChEBI
beta
IUPAC
beta(-)
ChEBI
beta-particle
IUPAC
e
IUPAC
e(-)
UniProt
e-
KEGG_COMPOUND
negatron
IUPAC
Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).
Wikipedia:https://en.wikipedia.org/wiki/Gas
chebi_ontology
gas molecular entities
gaseous molecular entities
gaseous molecular entity
CHEBI:138675
gas molecular entity
gas molecular entities
ChEBI
gaseous molecular entities
ChEBI
gaseous molecular entity
ChEBI
A molecular entity that can transfer an electron to another molecular entity.
electron donor
chebi_ontology
Elektronendonator
donneur d'electron
CHEBI:15022
electron donor
electron donor
IUPAC
Elektronendonator
ChEBI
donneur d'electron
IUPAC
A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
CHEBI:13699
CHEBI:2377
KEGG:C00028
KEGG:C16722
Acceptor
chebi_ontology
A
Akzeptor
Hydrogen-acceptor
Oxidized donor
accepteur
CHEBI:15339
acceptor
Acceptor
KEGG_COMPOUND
A
KEGG_COMPOUND
Akzeptor
ChEBI
Hydrogen-acceptor
KEGG_COMPOUND
Oxidized donor
KEGG_COMPOUND
accepteur
ChEBI
An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms
0
H2O
InChI=1S/H2O/h1H2
XLYOFNOQVPJJNP-UHFFFAOYSA-N
18.01530
18.01056
[H]O[H]
CHEBI:10743
CHEBI:13352
CHEBI:27313
CHEBI:42043
CHEBI:42857
CHEBI:43228
CHEBI:44292
CHEBI:44701
CHEBI:44819
CHEBI:5585
Beilstein:3587155
CAS:7732-18-5
Gmelin:117
HMDB:HMDB0002111
KEGG:C00001
KEGG:D00001
MetaCyc:WATER
MolBase:1
PDBeChem:HOH
Reaxys:3587155
Wikipedia:Water
WATER
Water
oxidane
water
chebi_ontology
BOUND WATER
H2O
HOH
Wasser
[OH2]
acqua
agua
aqua
dihydridooxygen
dihydrogen oxide
eau
hydrogen hydroxide
CHEBI:15377
water
Beilstein:3587155
Beilstein
CAS:7732-18-5
ChemIDplus
CAS:7732-18-5
KEGG COMPOUND
CAS:7732-18-5
NIST Chemistry WebBook
Gmelin:117
Gmelin
Reaxys:3587155
Reaxys
WATER
PDBeChem
Water
KEGG_COMPOUND
oxidane
IUPAC
water
IUPAC
BOUND WATER
PDBeChem
H2O
KEGG_COMPOUND
H2O
UniProt
HOH
ChEBI
Wasser
ChEBI
[OH2]
IUPAC
acqua
ChEBI
agua
ChEBI
aqua
ChEBI
dihydridooxygen
IUPAC
dihydrogen oxide
IUPAC
eau
ChEBI
hydrogen hydroxide
ChEBI
0
O2
InChI=1S/O2/c1-2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
31.998
31.98983
O=O
CHEBI:10745
CHEBI:13416
CHEBI:23833
CHEBI:25366
CHEBI:30491
CHEBI:44742
CHEBI:7860
CAS:7782-44-7
Gmelin:485
HMDB:HMDB0001377
KEGG:C00007
KEGG:D00003
MetaCyc:OXYGEN-MOLECULE
MolBase:750
PDBeChem:OXY
PMID:10906528
PMID:16977326
PMID:18210929
PMID:18638417
PMID:19840863
PMID:7710549
PMID:9463773
Wikipedia:Oxygen
dioxygen
chebi_ontology
Disauerstoff
E 948
E-948
E948
O2
OXYGEN MOLECULE
Oxygen
[OO]
dioxygene
molecular oxygen
CHEBI:15379
dioxygen
CAS:7782-44-7
ChemIDplus
CAS:7782-44-7
KEGG COMPOUND
CAS:7782-44-7
NIST Chemistry WebBook
Gmelin:485
Gmelin
PMID:10906528
Europe PMC
PMID:16977326
Europe PMC
PMID:18210929
Europe PMC
PMID:18638417
Europe PMC
PMID:19840863
Europe PMC
PMID:7710549
Europe PMC
PMID:9463773
Europe PMC
dioxygen
IUPAC
Disauerstoff
ChEBI
E 948
ChEBI
E-948
ChEBI
E948
ChEBI
O2
IUPAC
O2
KEGG_COMPOUND
O2
UniProt
OXYGEN MOLECULE
PDBeChem
Oxygen
KEGG_COMPOUND
[OO]
MolBase
dioxygene
ChEBI
molecular oxygen
ChEBI
-1
HO
InChI=1S/H2O/h1H2/p-1
XLYOFNOQVPJJNP-UHFFFAOYSA-M
17.00734
17.00329
[O-][H]
CHEBI:13365
CHEBI:13419
CHEBI:44641
CHEBI:5594
CAS:14280-30-9
Gmelin:24714
KEGG:C01328
PDBeChem:OH
hydridooxygenate(1-)
hydroxide
oxidanide
chebi_ontology
HO-
HYDROXIDE ION
Hydroxide ion
OH(-)
OH-
CHEBI:16234
hydroxide
CAS:14280-30-9
ChemIDplus
CAS:14280-30-9
NIST Chemistry WebBook
Gmelin:24714
Gmelin
hydridooxygenate(1-)
IUPAC
hydroxide
IUPAC
oxidanide
IUPAC
HO-
KEGG_COMPOUND
HYDROXIDE ION
PDBeChem
Hydroxide ion
KEGG_COMPOUND
OH(-)
IUPAC
OH-
KEGG_COMPOUND
A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food.
0
CO2
InChI=1S/CO2/c2-1-3
CURLTUGMZLYLDI-UHFFFAOYSA-N
44.010
43.98983
O=C=O
CHEBI:13282
CHEBI:13283
CHEBI:13284
CHEBI:13285
CHEBI:23011
CHEBI:3283
CHEBI:48829
Beilstein:1900390
CAS:124-38-9
Drug_Central:4256
Gmelin:989
HMDB:HMDB0001967
KEGG:C00011
KEGG:D00004
MetaCyc:CARBON-DIOXIDE
MolBase:752
PDBeChem:CO2
PMID:10826146
PMID:11094503
PMID:11584085
PMID:11802652
PMID:14639145
PMID:15050588
PMID:16591971
PMID:16656478
PMID:16659660
PMID:17190796
PMID:17448243
PMID:17878298
PMID:17884085
PMID:19043767
PMID:19259576
PMID:19854893
PMID:23384758
PMID:23828359
PMID:24258718
PMID:8482095
PMID:8818713
PMID:8869828
PMID:9611769
PMID:9730350
PPDB:119
Reaxys:1900390
UM-BBD_compID:c0131
Wikipedia:Carbon_dioxide
CARBON DIOXIDE
Carbon dioxide
carbon dioxide
dioxidocarbon
methanedione
chebi_ontology
CO2
E 290
E-290
E290
R-744
[CO2]
carbonic anhydride
CHEBI:16526
carbon dioxide
Beilstein:1900390
Beilstein
CAS:124-38-9
ChemIDplus
CAS:124-38-9
KEGG COMPOUND
CAS:124-38-9
NIST Chemistry WebBook
Drug_Central:4256
DrugCentral
Gmelin:989
Gmelin
PMID:10826146
Europe PMC
PMID:11094503
Europe PMC
PMID:11584085
Europe PMC
PMID:11802652
Europe PMC
PMID:14639145
Europe PMC
PMID:15050588
Europe PMC
PMID:16591971
Europe PMC
PMID:16656478
Europe PMC
PMID:16659660
Europe PMC
PMID:17190796
Europe PMC
PMID:17448243
Europe PMC
PMID:17878298
Europe PMC
PMID:17884085
Europe PMC
PMID:19043767
Europe PMC
PMID:19259576
Europe PMC
PMID:19854893
Europe PMC
PMID:23384758
Europe PMC
PMID:23828359
Europe PMC
PMID:24258718
Europe PMC
PMID:8482095
Europe PMC
PMID:8818713
Europe PMC
PMID:8869828
Europe PMC
PMID:9611769
Europe PMC
PMID:9730350
Europe PMC
Reaxys:1900390
Reaxys
UM-BBD_compID:c0131
UM-BBD
CARBON DIOXIDE
PDBeChem
Carbon dioxide
KEGG_COMPOUND
carbon dioxide
IUPAC
dioxidocarbon
IUPAC
methanedione
IUPAC
CO2
KEGG_COMPOUND
CO2
UniProt
E 290
ChEBI
E-290
ChEBI
E290
ChEBI
R-744
ChEBI
[CO2]
MolBase
carbonic anhydride
UM-BBD
A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
CHEBI:14202
CHEBI:4697
KEGG:C01351
Donor
chebi_ontology
Donator
donneur
CHEBI:17891
donor
Donor
KEGG_COMPOUND
Donator
ChEBI
donneur
ChEBI
An elemental molecule consisting of two trivalently-bonded nitrogen atoms.
0
N2
InChI=1S/N2/c1-2
IJGRMHOSHXDMSA-UHFFFAOYSA-N
28.01348
28.00615
N#N
CHEBI:13388
CHEBI:14660
CHEBI:25365
CHEBI:43128
CHEBI:7593
CAS:7727-37-9
Drug_Central:4251
Gmelin:150
HMDB:HMDB0001371
KEGG:C00697
KEGG:D00083
MetaCyc:NITROGEN-MOLECULE
PDBeChem:HDZ
PMID:18334638
PMID:22237545
Reaxys:15940095
Wikipedia:Nitrogen
dinitrogen
chebi_ontology
N#N
N2
Nitrogen
molecular nitrogen
CHEBI:17997
dinitrogen
CAS:7727-37-9
ChemIDplus
CAS:7727-37-9
KEGG COMPOUND
CAS:7727-37-9
NIST Chemistry WebBook
Drug_Central:4251
DrugCentral
Gmelin:150
Gmelin
PMID:18334638
Europe PMC
PMID:22237545
Europe PMC
Reaxys:15940095
Reaxys
dinitrogen
IUPAC
N#N
ChEBI
N2
IUPAC
N2
KEGG_COMPOUND
N2
UniProt
Nitrogen
KEGG_COMPOUND
molecular nitrogen
ChEBI
A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base).
KEGG:C00701
Base
base
chebi_ontology
Base1
Base2
Basen
Nucleobase
bases
CHEBI:22695
base
Base
ChEBI
base
ChEBI
base
IUPAC
Base1
KEGG_COMPOUND
Base2
KEGG_COMPOUND
Basen
ChEBI
Nucleobase
KEGG_COMPOUND
bases
ChEBI
chebi_ontology
carbon oxides
oxides of carbon
CHEBI:23014
carbon oxide
carbon oxides
ChEBI
oxides of carbon
ChEBI
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
molecular entity
chebi_ontology
entidad molecular
entidades moleculares
entite moleculaire
molecular entities
molekulare Entitaet
CHEBI:23367
molecular entity
molecular entity
IUPAC
entidad molecular
IUPAC
entidades moleculares
IUPAC
entite moleculaire
IUPAC
molecular entities
IUPAC
molekulare Entitaet
ChEBI
Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances.
chebi_ontology
drugs
medicine
CHEBI:23888
drug
drugs
ChEBI
medicine
ChEBI
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
chemical entity
chebi_ontology
CHEBI:24431
chemical entity
chemical entity
UniProt
A role played by the molecular entity or part thereof within a biological context.
chebi_ontology
biological function
CHEBI:24432
biological role
biological function
ChEBI
A defined linked collection of atoms or a single atom within a molecular entity.
group
chebi_ontology
Gruppe
Rest
groupe
grupo
grupos
CHEBI:24433
group
group
IUPAC
Gruppe
ChEBI
Rest
ChEBI
groupe
IUPAC
grupo
IUPAC
grupos
IUPAC
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
chebi_ontology
CHEBI:24651
hydroxides
A molecular entity that contains no carbon.
chebi_ontology
anorganische Verbindungen
inorganic compounds
inorganic entity
inorganic molecular entities
inorganics
CHEBI:24835
inorganic molecular entity
anorganische Verbindungen
ChEBI
inorganic compounds
ChEBI
inorganic entity
ChEBI
inorganic molecular entities
ChEBI
inorganics
ChEBI
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
CHEBI:26619
CHEBI:35220
metabolite
chebi_ontology
metabolites
primary metabolites
secondary metabolites
CHEBI:25212
metabolite
metabolite
IUPAC
metabolites
ChEBI
primary metabolites
ChEBI
secondary metabolites
ChEBI
A molecule all atoms of which have the same atomic number.
chebi_ontology
homoatomic molecule
homoatomic molecules
CHEBI:25362
elemental molecule
homoatomic molecule
ChEBI
homoatomic molecules
ChEBI
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
molecule
chebi_ontology
Molekuel
molecula
molecules
neutral molecular compounds
CHEBI:25367
molecule
molecule
IUPAC
Molekuel
ChEBI
molecula
IUPAC
molecules
IUPAC
neutral molecular compounds
IUPAC
0
N
14.007
14.00307
WebElements:N
nitrogen
chebi_ontology
7N
N
Stickstoff
azote
nitrogen
nitrogeno
CHEBI:25555
nitrogen atom
nitrogen
IUPAC
7N
IUPAC
N
IUPAC
Stickstoff
ChEBI
azote
IUPAC
nitrogen
ChEBI
nitrogeno
ChEBI
nonmetal
chebi_ontology
Nichtmetall
Nichtmetalle
no metal
no metales
non-metal
non-metaux
nonmetal
nonmetals
CHEBI:25585
nonmetal atom
nonmetal
IUPAC
Nichtmetall
ChEBI
Nichtmetalle
ChEBI
no metal
ChEBI
no metales
ChEBI
non-metal
ChEBI
non-metaux
ChEBI
nonmetal
ChEBI
nonmetals
ChEBI
An oxide in which the oxygen atom is bonded to a carbon atom.
chebi_ontology
organic oxides
CHEBI:25701
organic oxide
organic oxides
ChEBI
An oxide is a chemical compound of oxygen with other chemical elements.
oxide
chebi_ontology
oxides
CHEBI:25741
oxide
oxide
ChEBI
oxides
ChEBI
0
O
InChI=1S/O
QVGXLLKOCUKJST-UHFFFAOYSA-N
15.99940
15.99491
[O]
KEGG:C00007
WebElements:O
oxygen
chebi_ontology
8O
O
Sauerstoff
oxigeno
oxygen
oxygene
CHEBI:25805
oxygen atom
oxygen
IUPAC
8O
IUPAC
O
IUPAC
Sauerstoff
ChEBI
oxigeno
ChEBI
oxygen
ChEBI
oxygene
ChEBI
oxygen molecular entity
chebi_ontology
oxygen molecular entities
CHEBI:25806
oxygen molecular entity
oxygen molecular entity
ChEBI
oxygen molecular entities
ChEBI
Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions.
Wikipedia:Micronutrient
chebi_ontology
micronutrients
trace elements
CHEBI:27027
micronutrient
micronutrients
ChEBI
trace elements
ChEBI
0
C
InChI=1S/C
OKTJSMMVPCPJKN-UHFFFAOYSA-N
12.01070
12.00000
[C]
CHEBI:23009
CHEBI:3399
CAS:7440-44-0
KEGG:C06265
WebElements:C
carbon
chebi_ontology
6C
C
Carbon
Kohlenstoff
carbon
carbone
carbonium
carbono
CHEBI:27594
carbon atom
CAS:7440-44-0
ChemIDplus
CAS:7440-44-0
KEGG COMPOUND
carbon
IUPAC
6C
IUPAC
C
IUPAC
C
KEGG_COMPOUND
Carbon
KEGG_COMPOUND
Kohlenstoff
ChEBI
carbon
ChEBI
carbone
ChEBI
carbonium
ChEBI
carbono
ChEBI
+1
H3O
InChI=1S/H2O/h1H2/p+1
XLYOFNOQVPJJNP-UHFFFAOYSA-O
19.02322
19.01784
[H][O+]([H])[H]
CAS:13968-08-6
Gmelin:141
MolBase:1646
aquahydrogen(1+)
oxidanium
oxonium
trihydridooxygen(1+)
chebi_ontology
H3O(+)
Hydronium cation
Hydronium ion
[OH3](+)
CHEBI:29412
oxonium
CAS:13968-08-6
ChemIDplus
CAS:13968-08-6
NIST Chemistry WebBook
Gmelin:141
Gmelin
aquahydrogen(1+)
IUPAC
oxidanium
IUPAC
oxonium
IUPAC
trihydridooxygen(1+)
IUPAC
H3O(+)
IUPAC
Hydronium cation
NIST_Chemistry_WebBook
Hydronium ion
ChemIDplus
[OH3](+)
MolBase
+1
HO2
InChI=1S/O2/c1-2/p+1
MYMOFIZGZYHOMD-UHFFFAOYSA-O
33.00674
32.99711
[H][O+]=O
Gmelin:508
dioxidenium
hydridodioxygen(1+)
chebi_ontology
HO2(+)
HOO(+)
[HO2](+)
CHEBI:29793
hydridodioxygen(1+)
Gmelin:508
Gmelin
dioxidenium
IUPAC
hydridodioxygen(1+)
IUPAC
HO2(+)
IUPAC
HOO(+)
ChEBI
[HO2](+)
ChEBI
+2
H2N2
InChI=1S/H2N2/c1-2/h1-2H/q+2
DIDSLFHMVHAEHA-UHFFFAOYSA-N
30.02936
30.02070
[H][N+]#[N+][H]
diazynediium
chebi_ontology
HNNH(2+)
[HNNH](2+)
CHEBI:30099
diazynediium
diazynediium
IUPAC
HNNH(2+)
IUPAC
[HNNH](2+)
ChEBI
+1
HN2
InChI=1S/N2/c1-2/p+1
IJGRMHOSHXDMSA-UHFFFAOYSA-O
29.02142
29.01342
[H][N+]#N
CAS:12357-66-3
diazynium
chebi_ontology
HN2+
N#NH(+)
CHEBI:30102
diazynium
CAS:12357-66-3
NIST Chemistry WebBook
diazynium
IUPAC
HN2+
NIST_Chemistry_WebBook
N#NH(+)
IUPAC
0
He
InChI=1S/He
SWQJXJOGLNCZEY-UHFFFAOYSA-N
4.00260
4.00260
[He]
CAS:7440-59-7
Drug_Central:4262
Gmelin:16294
WebElements:He
helium
chebi_ontology
2He
He
Helium
helio
helium
CHEBI:30217
helium atom
CAS:7440-59-7
NIST Chemistry WebBook
Drug_Central:4262
DrugCentral
Gmelin:16294
Gmelin
helium
IUPAC
2He
IUPAC
He
IUPAC
Helium
ChEBI
helio
ChEBI
helium
ChEBI
Intended use of the molecular entity or part thereof by humans.
chebi_ontology
CHEBI:33232
application
A particle not known to have substructure.
elementary particle
chebi_ontology
elementary particles
CHEBI:33233
fundamental particle
elementary particle
IUPAC
elementary particles
ChEBI
chebi_ontology
inorganic hydrides
CHEBI:33242
inorganic hydride
inorganic hydrides
ChEBI
Any substituent group which does not contain carbon.
chebi_ontology
inorganic groups
CHEBI:33246
inorganic group
inorganic groups
ChEBI
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
CHEBI:22671
CHEBI:23907
atom
chebi_ontology
atome
atomo
atoms
atomus
element
elements
CHEBI:33250
atom
atom
IUPAC
atome
IUPAC
atomo
IUPAC
atoms
ChEBI
atomus
ChEBI
element
ChEBI
elements
ChEBI
A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
nucleus
chebi_ontology
Atomkern
Kern
noyau
noyau atomique
nuclei
nucleo
nucleo atomico
nucleus atomi
CHEBI:33252
atomic nucleus
nucleus
IUPAC
Atomkern
ChEBI
Kern
ChEBI
noyau
IUPAC
noyau atomique
ChEBI
nuclei
ChEBI
nucleo
IUPAC
nucleo atomico
ChEBI
nucleus atomi
ChEBI
Heavy nuclear particle: proton or neutron.
nucleon
chebi_ontology
Nukleon
Nukleonen
nucleons
CHEBI:33253
nucleon
nucleon
IUPAC
nucleon
IUPAC
Nukleon
ChEBI
Nukleonen
ChEBI
nucleons
ChEBI
A molecular entity all atoms of which have the same atomic number.
chebi_ontology
homoatomic entity
homoatomic molecular entities
homoatomic molecular entity
CHEBI:33259
elemental molecular entity
homoatomic entity
ChEBI
homoatomic molecular entities
ChEBI
homoatomic molecular entity
ChEBI
chebi_ontology
CHEBI:33262
elemental oxygen
0
O2
31.999
31.98983
chebi_ontology
CHEBI:33263
diatomic oxygen
0
N2
28.013
28.00615
chebi_ontology
CHEBI:33266
diatomic nitrogen
chebi_ontology
CHEBI:33267
elemental nitrogen
A nutrient is a food component that an organism uses to survive and grow.
chebi_ontology
nutrients
CHEBI:33284
nutrient
nutrients
ChEBI
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
chebi_ontology
heteroorganic entities
organoelement compounds
CHEBI:33285
heteroorganic entity
heteroorganic entities
ChEBI
organoelement compounds
ChEBI
Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
pnictogens
chebi_ontology
group 15 elements
group V elements
nitrogenoideos
nitrogenoides
pnictogene
pnictogenes
CHEBI:33300
pnictogen
pnictogens
IUPAC
group 15 elements
ChEBI
group V elements
ChEBI
nitrogenoideos
ChEBI
nitrogenoides
ChEBI
pnictogene
ChEBI
pnictogenes
ChEBI
A p-block molecular entity containing any pnictogen.
pnictogen molecular entity
chebi_ontology
pnictogen molecular entities
CHEBI:33302
pnictogen molecular entity
pnictogen molecular entity
ChEBI
pnictogen molecular entities
ChEBI
Any p-block element belonging to the group 16 family of the periodic table.
PMID:17084588
chalcogen
chalcogens
chebi_ontology
Chalkogen
Chalkogene
anfigeno
anfigenos
calcogeno
calcogenos
chalcogene
chalcogenes
group 16 elements
group VI elements
CHEBI:33303
chalcogen
PMID:17084588
Europe PMC
chalcogen
IUPAC
chalcogens
IUPAC
Chalkogen
ChEBI
Chalkogene
ChEBI
anfigeno
ChEBI
anfigenos
ChEBI
calcogeno
ChEBI
calcogenos
ChEBI
chalcogene
ChEBI
chalcogenes
ChEBI
group 16 elements
ChEBI
group VI elements
ChEBI
Any p-block molecular entity containing a chalcogen.
chalcogen molecular entity
chebi_ontology
chalcogen compounds
chalcogen molecular entities
CHEBI:33304
chalcogen molecular entity
chalcogen molecular entity
ChEBI
chalcogen compounds
ChEBI
chalcogen molecular entities
ChEBI
group 14 elements
chebi_ontology
carbon group element
carbon group elements
carbonoides
cristallogene
cristallogenes
group IV elements
CHEBI:33306
carbon group element atom
group 14 elements
IUPAC
carbon group element
ChEBI
carbon group elements
ChEBI
carbonoides
ChEBI
cristallogene
ChEBI
cristallogenes
ChEBI
group IV elements
ChEBI
noble gas
noble gases
chebi_ontology
Edelgas
Edelgase
gas noble
gases nobles
gaz noble
gaz nobles
group 18 elements
group VIII elements
inert gases
noble gas
rare gases
CHEBI:33309
noble gas atom
noble gas
IUPAC
noble gases
IUPAC
Edelgas
ChEBI
Edelgase
ChEBI
gas noble
ChEBI
gases nobles
ChEBI
gaz noble
ChEBI
gaz nobles
ChEBI
group 18 elements
IUPAC
group VIII elements
ChEBI
inert gases
ChEBI
noble gas
ChEBI
rare gases
ChEBI
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
main group elements
chebi_ontology
Hauptgruppenelement
Hauptgruppenelemente
main group element
CHEBI:33318
main group element atom
main group elements
IUPAC
Hauptgruppenelement
ChEBI
Hauptgruppenelemente
ChEBI
main group element
ChEBI
elemental pnictogen
chebi_ontology
elemental pnictogens
CHEBI:33465
elemental pnictogen
elemental pnictogen
ChEBI
elemental pnictogens
ChEBI
An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity.
CHEBI:25217
CHEBI:6788
KEGG:C00050
PMID:21784043
Wikipedia:Metal
chebi_ontology
elemental metal
elemental metals
metal element
metal elements
metals
CHEBI:33521
metal atom
PMID:21784043
Europe PMC
elemental metal
ChEBI
elemental metals
ChEBI
metal element
ChEBI
metal elements
ChEBI
metals
ChEBI
chebi_ontology
s-block element
s-block elements
CHEBI:33559
s-block element atom
s-block element
ChEBI
s-block elements
ChEBI
Any main group element atom belonging to the p-block of the periodic table.
chebi_ontology
p-block element
p-block elements
CHEBI:33560
p-block element atom
p-block element
ChEBI
p-block elements
ChEBI
A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
chebi_ontology
main group compounds
main group molecular entities
CHEBI:33579
main group molecular entity
main group compounds
ChEBI
main group molecular entities
ChEBI
carbon group molecular entity
chebi_ontology
carbon group molecular entities
CHEBI:33582
carbon group molecular entity
carbon group molecular entity
ChEBI
carbon group molecular entities
ChEBI
A main group molecular entity containing one or more atoms of any noble gas.
noble gas molecular entity
chebi_ontology
noble gas compounds
noble gas molecular entities
CHEBI:33583
noble gas molecular entity
noble gas molecular entity
ChEBI
noble gas compounds
ChEBI
noble gas molecular entities
ChEBI
chebi_ontology
hydrogen compounds
hydrogen molecular entities
CHEBI:33608
hydrogen molecular entity
hydrogen compounds
ChEBI
hydrogen molecular entities
ChEBI
An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.
s-block molecular entity
chebi_ontology
s-block compounds
s-block molecular entities
CHEBI:33674
s-block molecular entity
s-block molecular entity
ChEBI
s-block compounds
ChEBI
s-block molecular entities
ChEBI
A main group molecular entity that contains one or more atoms of a p-block element.
chebi_ontology
p-block compounds
p-block molecular entities
p-block molecular entitiy
CHEBI:33675
p-block molecular entity
p-block compounds
ChEBI
p-block molecular entities
ChEBI
p-block molecular entitiy
ChEBI
helium molecular entity
chebi_ontology
helium compounds
helium molecular entities
CHEBI:33679
helium molecular entity
helium molecular entity
ChEBI
helium compounds
ChEBI
helium molecular entities
ChEBI
Hydrides are chemical compounds of hydrogen with other chemical elements.
chebi_ontology
CHEBI:33692
hydrides
oxygen hydride
chebi_ontology
hydrides of oxygen
oxygen hydrides
CHEBI:33693
oxygen hydride
oxygen hydride
ChEBI
hydrides of oxygen
ChEBI
oxygen hydrides
ChEBI
A macromolecule formed by a living organism.
biopolymer
chebi_ontology
Biopolymere
biomacromolecules
biopolymers
CHEBI:33694
biomacromolecule
biopolymer
IUPAC
Biopolymere
ChEBI
biomacromolecules
ChEBI
biopolymers
ChEBI
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
Wikipedia:Macromolecule
macromolecule
chebi_ontology
macromolecules
polymer
polymer molecule
polymers
CHEBI:33839
macromolecule
macromolecule
IUPAC
macromolecules
ChEBI
polymer
ChEBI
polymer molecule
IUPAC
polymers
ChEBI
A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
reagent
chebi_ontology
reactif
reactivo
reagents
CHEBI:33893
reagent
reagent
IUPAC
reactif
IUPAC
reactivo
IUPAC
reagents
ChEBI
Any nutrient required in large quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Macronutrients are usually chemical elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur) that humans consume in the largest quantities. Calcium, sodium, magnesium and potassium are sometimes included as macronutrients because they are required in relatively large quantities compared with other vitamins and minerals.
chebi_ontology
macronutrients
CHEBI:33937
macronutrient
macronutrients
ChEBI
chebi_ontology
nitrogen hydrides
CHEBI:35106
nitrogen hydride
nitrogen hydrides
ChEBI
A substance that reduces or suppresses inflammation.
chebi_ontology
anti-inflammatory drugs
antiinflammatory agent
antiinflammatory drug
antiinflammatory drugs
CHEBI:35472
anti-inflammatory drug
anti-inflammatory drugs
ChEBI
antiinflammatory agent
ChEBI
antiinflammatory drug
ChEBI
antiinflammatory drugs
ChEBI
A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume.
chebi_ontology
cardiovascular agent
cardiovascular drugs
CHEBI:35554
cardiovascular drug
cardiovascular agent
ChEBI
cardiovascular drugs
ChEBI
A drug used to cause dilation of the blood vessels.
chebi_ontology
vasodilator
vasodilator agents
CHEBI:35620
vasodilator agent
vasodilator
ChEBI
vasodilator agents
ChEBI
pnictogen hydride
chebi_ontology
pnictogen hydrides
CHEBI:35881
pnictogen hydride
pnictogen hydride
ChEBI
pnictogen hydrides
ChEBI
Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).
chebi_ontology
leptons
CHEBI:36338
lepton
leptons
ChEBI
Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).
chebi_ontology
baryons
CHEBI:36339
baryon
baryons
ChEBI
Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.
fermion
chebi_ontology
fermions
CHEBI:36340
fermion
fermion
IUPAC
fermions
ChEBI
A particle smaller than an atom.
Wikipedia:Subatomic_particle
chebi_ontology
subatomic particles
CHEBI:36342
subatomic particle
subatomic particles
ChEBI
A subatomic particle known to have substructure (i.e. consisting of smaller particles).
chebi_ontology
composite particles
CHEBI:36343
composite particle
composite particles
ChEBI
Hadron is a subatomic particle which experiences the strong force.
chebi_ontology
hadrons
CHEBI:36344
hadron
hadrons
ChEBI
A nucleus or any of its constituents in any of their energy states.
nuclear particle
chebi_ontology
CHEBI:36347
nuclear particle
nuclear particle
IUPAC
Any molecular entity consisting of more than one atom.
chebi_ontology
polyatomic entities
CHEBI:36357
polyatomic entity
polyatomic entities
ChEBI
chalcogen hydride
chebi_ontology
chalcogen hydrides
CHEBI:36902
chalcogen hydride
chalcogen hydride
ChEBI
chalcogen hydrides
ChEBI
argon molecular entity
chebi_ontology
argon compounds
argon molecular entities
CHEBI:36908
argon molecular entity
argon molecular entity
ChEBI
argon compounds
ChEBI
argon molecular entities
ChEBI
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
organochalcogen compound
chebi_ontology
organochalcogen compounds
CHEBI:36962
organochalcogen compound
organochalcogen compound
ChEBI
organochalcogen compounds
ChEBI
An organochalcogen compound containing at least one carbon-oxygen bond.
PMID:17586126
organooxygen compound
chebi_ontology
organooxygen compounds
CHEBI:36963
organooxygen compound
PMID:17586126
Europe PMC
organooxygen compound
ChEBI
organooxygen compounds
ChEBI
mononuclear parent hydrides
chebi_ontology
mononuclear hydride
mononuclear hydrides
CHEBI:37176
mononuclear parent hydride
mononuclear parent hydrides
IUPAC
mononuclear hydride
ChEBI
mononuclear hydrides
IUPAC
An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid).
CHEBI:13800
CHEBI:13801
CHEBI:22209
CHEBI:2426
KEGG:C00174
Acid
acid
chebi_ontology
Saeure
Saeuren
acide
acido
acids
CHEBI:37527
acid
Acid
KEGG_COMPOUND
acid
IUPAC
Saeure
ChEBI
Saeuren
ChEBI
acide
IUPAC
acido
ChEBI
acids
ChEBI
A molecular entity consisting of two or more chemical elements.
chebi_ontology
chemical compound
heteroatomic molecular entities
CHEBI:37577
heteroatomic molecular entity
chemical compound
ChEBI
heteroatomic molecular entities
ChEBI
Substance which produces loss of feeling or sensation.
anaesthetic
chebi_ontology
Anaesthetika
Anaesthetikum
anaesthetics
anesthetic agent
anesthetic drug
anesthetics
CHEBI:38867
anaesthetic
anaesthetic
IUPAC
Anaesthetika
ChEBI
Anaesthetikum
ChEBI
anaesthetics
ChEBI
anesthetic agent
ChEBI
anesthetic drug
ChEBI
anesthetics
ChEBI
A molecular entity capable of donating a hydron to an acceptor (Bronsted base).
Bronsted acid
chebi_ontology
Bronsted-Saeure
acide de Bronsted
donneur d'hydron
hydron donor
CHEBI:39141
Bronsted acid
Bronsted acid
IUPAC
Bronsted-Saeure
ChEBI
acide de Bronsted
IUPAC
donneur d'hydron
IUPAC
hydron donor
IUPAC
A molecular entity capable of accepting a hydron from a donor (Bronsted acid).
Bronsted base
chebi_ontology
Bronsted-Base
accepteur d'hydron
base de Bronsted
hydron acceptor
CHEBI:39142
Bronsted base
Bronsted base
IUPAC
Bronsted-Base
ChEBI
accepteur d'hydron
IUPAC
base de Bronsted
IUPAC
hydron acceptor
IUPAC
0
HO
17.00734
17.00274
*O[H]
CHEBI:24706
CHEBI:43171
PDBeChem:OH
HYDROXY GROUP
hydroxy
hydroxy group
chebi_ontology
-OH
hydroxyl
hydroxyl group
CHEBI:43176
hydroxy group
HYDROXY GROUP
PDBeChem
hydroxy
IUPAC
hydroxy group
UniProt
-OH
IUPAC
hydroxyl
ChEBI
hydroxyl group
ChEBI
In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals').
Wikipedia:Mineral
mineral
chebi_ontology
Minerale
minerales
minerals
mineraux
CHEBI:46662
mineral
mineral
ChEBI
Minerale
ChEBI
minerales
ChEBI
minerals
ChEBI
mineraux
ChEBI
A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
Wikipedia:Solvent
chebi_ontology
Loesungsmittel
solvant
solvents
CHEBI:46787
solvent
Loesungsmittel
ChEBI
solvant
ChEBI
solvents
ChEBI
A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds.
polar solvent
chebi_ontology
polar solvents
CHEBI:48354
polar solvent
polar solvent
IUPAC
polar solvents
ChEBI
A polar solvent that is capable of acting as a hydron (proton) donor.
protogenic solvent
chebi_ontology
CHEBI:48356
protic solvent
protogenic solvent
IUPAC
Solvent that is capable of acting as a hydron (proton) acceptor.
protophilic solvent
chebi_ontology
HBA solvent
hydrogen bond acceptor solvent
CHEBI:48359
protophilic solvent
protophilic solvent
IUPAC
HBA solvent
ChEBI
hydrogen bond acceptor solvent
ChEBI
Self-ionizing solvent possessing both characteristics of Bronsted acids and bases.
amphiprotic solvent
chebi_ontology
CHEBI:48360
amphiprotic solvent
amphiprotic solvent
IUPAC
Substance that attaches to and blocks cell receptors that normally bind naturally occurring substances.
antagonist
chebi_ontology
antagonista
antagoniste
antagonists
CHEBI:48706
antagonist
antagonist
IUPAC
antagonista
ChEBI
antagoniste
ChEBI
antagonists
ChEBI
0
Ar
InChI=1S/Ar
XKRFYHLGVUSROY-UHFFFAOYSA-N
39.94800
39.96238
[Ar]
CHEBI:33311
CAS:7440-37-1
WebElements:Ar
argon
chebi_ontology
18Ar
Ar
argon
CHEBI:49475
argon atom
CAS:7440-37-1
ChemIDplus
argon
IUPAC
18Ar
IUPAC
Ar
IUPAC
argon
ChEBI
0
H
InChI=1S/H
YZCKVEUIGOORGS-UHFFFAOYSA-N
1.00794
1.00783
[H]
CHEBI:24634
CHEBI:49636
WebElements:H
hydrogen
chebi_ontology
1H
H
Wasserstoff
hidrogeno
hydrogen
hydrogene
CHEBI:49637
hydrogen atom
hydrogen
IUPAC
1H
IUPAC
H
IUPAC
Wasserstoff
ChEBI
hidrogeno
ChEBI
hydrogen
ChEBI
hydrogene
ChEBI
chebi_ontology
CHEBI:50312
onium compound
Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families.
onium cations
chebi_ontology
onium cations
onium ion
onium ions
CHEBI:50313
onium cation
onium cations
IUPAC
onium cations
ChEBI
onium ion
ChEBI
onium ions
ChEBI
Any molecular entity that contains carbon.
CHEBI:25700
CHEBI:33244
chebi_ontology
organic compounds
organic entity
organic molecular entities
CHEBI:50860
organic molecular entity
organic compounds
ChEBI
organic entity
ChEBI
organic molecular entities
ChEBI
A role is particular behaviour which a material entity may exhibit.
chebi_ontology
CHEBI:50906
role
A role played by the molecular entity or part thereof within a chemical context.
chebi_ontology
CHEBI:51086
chemical role
CHEBI:25556
CHEBI:7594
KEGG:C06061
chebi_ontology
Nitrogenous compounds
nitrogen compounds
nitrogen molecular entities
CHEBI:51143
nitrogen molecular entity
Nitrogenous compounds
KEGG_COMPOUND
nitrogen compounds
ChEBI
nitrogen molecular entities
ChEBI
A biological role played by the molecular entity or part thereof within a biochemical context.
chebi_ontology
CHEBI:52206
biochemical role
A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties.
chebi_ontology
CHEBI:52210
pharmacological role
chebi_ontology
CHEBI:52211
physiological role
Any substance introduced into a living organism with therapeutic or diagnostic purpose.
CHEBI:33293
CHEBI:33294
chebi_ontology
farmaco
medicament
pharmaceuticals
CHEBI:52217
pharmaceutical
farmaco
ChEBI
medicament
ChEBI
pharmaceuticals
ChEBI
chebi_ontology
inorganic hydroxides
CHEBI:52625
inorganic hydroxy compound
inorganic hydroxides
ChEBI
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
chebi_ontology
Chemische Substanz
CHEBI:59999
chemical substance
Chemische Substanz
ChEBI
A substance that removes electrons from another reactant in a redox reaction.
chebi_ontology
oxidant
oxidants
oxidiser
oxidisers
oxidising agents
oxidizer
oxidizers
oxidizing agent
oxidizing agents
CHEBI:63248
oxidising agent
oxidant
ChEBI
oxidants
ChEBI
oxidiser
ChEBI
oxidisers
ChEBI
oxidising agents
ChEBI
oxidizer
ChEBI
oxidizers
ChEBI
oxidizing agent
ChEBI
oxidizing agents
ChEBI
Any substance which is added to food to preserve or enhance its flavour and/or appearance.
Wikipedia:Food_additive
chebi_ontology
food additives
CHEBI:64047
food additive
food additives
ChEBI
An organic molecular entity containing a single carbon atom (C1).
chebi_ontology
one-carbon compounds
CHEBI:64708
one-carbon compound
one-carbon compounds
ChEBI
Any compound that has anti-inflammatory effects.
chebi_ontology
anti-inflammatory agents
antiinflammatory agent
antiinflammatory agents
CHEBI:67079
anti-inflammatory agent
anti-inflammatory agents
ChEBI
antiinflammatory agent
ChEBI
antiinflammatory agents
ChEBI
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
chebi_ontology
organic compound
organic compounds
organic molecules
CHEBI:72695
organic molecule
organic compound
ChEBI
organic compounds
ChEBI
organic molecules
ChEBI
Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms.
chebi_ontology
eukaryotic metabolites
CHEBI:75763
eukaryotic metabolite
eukaryotic metabolites
ChEBI
Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals.
CHEBI:77721
CHEBI:77743
chebi_ontology
animal metabolites
CHEBI:75767
animal metabolite
animal metabolites
ChEBI
Any animal metabolite produced during a metabolic reaction in mammals.
CHEBI:77464
CHEBI:77744
chebi_ontology
mammalian metabolites
CHEBI:75768
mammalian metabolite
mammalian metabolites
ChEBI
Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus).
chebi_ontology
Mus musculus metabolite
Mus musculus metabolites
mouse metabolites
CHEBI:75771
mouse metabolite
Mus musculus metabolite
ChEBI
Mus musculus metabolites
ChEBI
mouse metabolites
ChEBI
Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae).
CHEBI:76949
CHEBI:76951
chebi_ontology
S. cerevisiae metabolite
S. cerevisiae metabolites
S. cerevisiae secondary metabolite
S. cerevisiae secondary metabolites
Saccharomyces cerevisiae metabolites
Saccharomyces cerevisiae secondary metabolites
baker's yeast metabolite
baker's yeast metabolites
baker's yeast secondary metabolite
baker's yeast secondary metabolites
CHEBI:75772
Saccharomyces cerevisiae metabolite
S. cerevisiae metabolite
ChEBI
S. cerevisiae metabolites
ChEBI
S. cerevisiae secondary metabolite
ChEBI
S. cerevisiae secondary metabolites
ChEBI
Saccharomyces cerevisiae metabolites
ChEBI
Saccharomyces cerevisiae secondary metabolites
ChEBI
baker's yeast metabolite
ChEBI
baker's yeast metabolites
ChEBI
baker's yeast secondary metabolite
ChEBI
baker's yeast secondary metabolites
ChEBI
Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea.
chebi_ontology
prokaryotic metabolites
CHEBI:75787
prokaryotic metabolite
prokaryotic metabolites
ChEBI
A gas in an atmosphere that absorbs and emits radiation within the thermal infrared range, so contributing to the 'greenhouse effect'.
Wikipedia:Greenhouse_gas
chebi_ontology
greenhouse gases
CHEBI:76413
greenhouse gas
greenhouse gases
ChEBI
A compressed gas or liquid with a boiling point lower than room temperature which to used to propel and dispense liquids such as deodorants, insecticides, paints, etc. from aerosol cans.
PMID:22519407
PMID:24001847
chebi_ontology
propellants
CHEBI:76414
propellant
PMID:22519407
Europe PMC
PMID:24001847
Europe PMC
propellants
ChEBI
Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds.
CHEBI:75765
CHEBI:76947
chebi_ontology
fungal metabolites
CHEBI:76946
fungal metabolite
fungal metabolites
ChEBI
Any prokaryotic metabolite produced during a metabolic reaction in bacteria.
CHEBI:75760
CHEBI:76970
chebi_ontology
CHEBI:76969
bacterial metabolite
Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.
chebi_ontology
E.coli metabolite
E.coli metabolites
Escherichia coli metabolites
CHEBI:76971
Escherichia coli metabolite
E.coli metabolite
ChEBI
E.coli metabolites
ChEBI
Escherichia coli metabolites
ChEBI
Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).
CHEBI:75770
CHEBI:77123
chebi_ontology
H. sapiens metabolite
H. sapiens metabolites
Homo sapiens metabolite
Homo sapiens metabolites
CHEBI:77746
human metabolite
H. sapiens metabolite
ChEBI
H. sapiens metabolites
ChEBI
Homo sapiens metabolite
ChEBI
Homo sapiens metabolites
ChEBI
A food additive that is a (generally inert) gas which is used to envelop foodstuffs during packing and so protect them from unwanted chemical reactions such as food spoilage or oxidation during subsequent transport and storage. The term includes propellant gases, used to expel foods from a container.
Wikipedia:Packaging_gas
chebi_ontology
food packaging gases
CHEBI:77974
food packaging gas
food packaging gases
ChEBI
A propellant that is used to expel foods from an aerosol container.
chebi_ontology
food propellants
CHEBI:78017
food propellant
food propellants
ChEBI
A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants.
chebi_ontology
dietary component
dietary components
food components
CHEBI:78295
food component
dietary component
ChEBI
dietary components
ChEBI
food components
ChEBI
A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a "R" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure.
Wikipedia:Refrigerant
chebi_ontology
refrigerants
CHEBI:78433
refrigerant
refrigerants
ChEBI
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CALOHA:TS-2035
FBbt:00007002
FMA:68646
GO:0005623
KUPO:0000002
MESH:D002477
VHOG:0001533
WBbt:0004017
XAO:0003012
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
cell
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CARO:mah
A cell that moves by its own activities.
motile cell
A cell that moves by its own activities.
FB:ma
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
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
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 region rendered barren or partially barren by environmental extremes, especially by low rainfall.
EcoLexicon:desert
FTT:1
FTT:188
Geonames:T.DSRT
LTER:147
SWEETRealm:Desert
TGN:21201
https://en.wikipedia.org/wiki/Desert
arid region
envoPolar
desert area
A region rendered barren or partially barren by environmental extremes, especially by low rainfall.
USGS:SDTS
arid region
ADL:FTT
An environmental material which is 1) composed primarily of soil or rock and included ice or organic material and 2) at or below the freezing point of water for two or more years.
LTER:408
https://en.wikipedia.org/wiki/Permafrost
envoPolar
Ice is not always present, as may be in the case of nonporous bedrock, but it frequently occurs and it may be in amounts exceeding the potential hydraulic saturation of the ground material.
permafrost
An environmental material which is 1) composed primarily of soil or rock and included ice or organic material and 2) at or below the freezing point of water for two or more years.
https://en.wikipedia.org/wiki/Permafrost
A part of an astronomical body which is primarily composed of solid material.
EcoLexicon:landform
EcoLexicon:landforms
FTT:754
FTT:96
SWEETRealm:Landform
TGN:21400
TGN:21401
geological feature
landform
physiographic feature
solid astronomical body part
A part of an astronomical body which is primarily composed of solid material.
https://en.wikipedia.org/wiki/Landform
geological feature
ADL:FTT
A mass of solid material which is composed primarily of rock.
FTT:1010
FTT:145
Geonames:T.RK
Geonames:T.RKS
TGN:21444
piece of rock
A particle which 1) is composed primarily of and derived from rock or mineral sources and 2) is or was part of a portion of sand.
grain of sand
granule of sand
sand granule
In general, sand grains are larger than those of silt, but finer than those of gravel.
particle of sand
A particle which 1) is composed primarily of and derived from rock or mineral sources and 2) is or was part of a portion of sand.
A particle which 1) is primarily composed of quartz or feldspar and 2) is or was part of a portion of silt.
grain of silt
granule of silt
The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam.
particle of silt
The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam.
grain of desert sand
A biome is an ecosystem which is undergoing climactic ecological succession.
EcoLexicon:biome
LTER:809
major habitat type
EcosytemType
In this definition, there is an assumption that no major perturbations are occurring or have occurred in a time frame affects the successional dynamics of the ecosystem. A "major" perturbation is one which disrupts the community's ability to restore its (near) equilibrium. Usually, pioneer or early secondary successional processes would be in effect in such scenarios.
biome
A biome is an ecosystem which is undergoing climactic ecological succession.
DOI:10.1186/2041-1480-4-43
https://en.wikipedia.org/wiki/Biome
LTER:809
https://vocab.lternet.edu/vocab/vocab/index.php?tema=809&/biomes
major habitat type
WWF:Biome
EcosytemType
NASA:earthrealm
A biome which is primarily or completely situated on a landmass.
LTER:798
SPIRE:Terrestrial
terrestrial realm
terrestrial biome
A biome which is primarily or completely situated on a landmass.
https://en.wikipedia.org/wiki/Biome#Terrestrial_biomes
A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids.
EcoLexicon:rock
FTT:1010
FTT:145
Geonames:T.RK
Geonames:T.RKS
SWEETRealm:Rock
TGN:21444
https://en.wikipedia.org/wiki/Rock
From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.
rock
A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids.
MA:ma
https://en.wikipedia.org/wiki/Rock_(geology)
An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms.
The various 'has part' and 'has quality' relations may not hold true for all soils; however, I have yet to find counter examples. Require input from a pedologist or similar. [pbuttigieg]
regolith
LTER:535
SPIRE:Soil
SWEETRealm:Soil
https://en.wikipedia.org/wiki/Soil
'In engineering terms, soil is referred to as regolith, or loose rock material that lies above the 'solid geology'. Soil is commonly referred to as "earth" or "dirt"; technically, the term "dirt" should be restricted to displaced soil.' https://en.wikipedia.org/wiki/Soil
" The upper limit of soil is the boundary between soil and air, shallow water, live plants, or plant materials that have not begun to decompose. Areas are not considered to have soil if the surface is permanently covered by water too deep (typically more than 2.5 meters) for the growth of rooted plants.
The lower boundary that separates soil from the nonsoil underneath is most difficult to define. Soil consists of horizons near the Earth's surface that, in contrast to the underlying parent material, have been altered by the interactions of climate, relief, and living organisms over time. Commonly, soil grades at its lower boundary to hard rock or to earthy materials virtually devoid of animals, roots, or other marks of biological activity. For purposes of classification, the lower boundary of soil is arbitrarily set at 200 cm." Soil taxonomy, 2nd Ed., quoted in http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280
soil
An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms.
https://en.wikipedia.org/wiki/Soil
The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth.
EcoLexicon:air
LTER:18
SWEETRealm:Air
https://en.wikipedia.org/wiki/Air
envoPolar
air
The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth.
https://en.wikipedia.org/wiki/Air
An environmental material primarily composed of dihydrogen oxide in its liquid form.
water
EcoLexicon:water
LTER:617
https://en.wikipedia.org/wiki/Water
liquid water
An environmental material primarily composed of dihydrogen oxide in its liquid form.
MA:ma
Particulate environmental material which is formed as a result of the transport and deposition of particles by flowing liquid.
EcoLexicon:sediment
EcoLexicon:sedimentation
LTER:492
LTER:493
SWEETRealm:Sediment
https://en.wikipedia.org/wiki/Sediment
envoPolar
Sediment is typically deposited on the bed or bottom of a body of water or other liquid.
sediment
Particulate environmental material which is formed as a result of the transport and deposition of particles by flowing liquid.
https://en.wikipedia.org/wiki/Sediment
Particulate environmental material which 1) is composed primarily of clay particles, with only minor proportions of other materials, 2) demonstrates plasticity when wet, and 3) is capable of hardening when dried or fired.
Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.
EcoLexicon:clay
SWEETRealm:Clay
This definition is intentionally ambiguous to support the multiple thresholds set by different authorities.The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam. Similar mixtures with greater than 40% clay are often considered clay soils.
clay
Particulate environmental material which 1) is composed primarily of clay particles, with only minor proportions of other materials, 2) demonstrates plasticity when wet, and 3) is capable of hardening when dried or fired.
https://en.wikipedia.org/wiki/Clay
This definition is intentionally ambiguous to support the multiple thresholds set by different authorities.The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam. Similar mixtures with greater than 40% clay are often considered clay soils.
A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
manufactured good
manufactured product
A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
https://en.wikipedia.org/wiki/Manufactured_product
Sand which is part of a desert.
desert sand
A material entity which other material entities in an environmental system are primarily or partially composed of.
portion of environmental material
Everything under this parent must be a mass noun (i.e. not countable). All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water".
Instances of this class are portions of environmental materials, such as seawater in bucket, a water parcel in the photic zone of a lake, or the concrete that composes a building part. Instances of these portions may have fiat or non-fiat boundaries. For example, a water parcel has not physical boundaries, while the seawater in a bucket is bounded by the internal surfaces of the bucket.
environmental material
A material entity which other material entities in an environmental system are primarily or partially composed of.
A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings.
EcoLexicon:surface
http://sweetontology.net/reprSpaceGeometry/Surface
https://en.wikipedia.org/wiki/Surface
This class is distinct from a geometric surface, which is two-dimensional. The idea of "uppermost" may be problematic. Further, the definition of layer (the superclass of surface in rev 133) references surface. This may be another issue. Perhaps this can be made into an inferred class using 'bounding layer of' some material entity, note that 'bounding layer' implies containment, which may not be valid here.
surface layer
A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings.
URL:http://www.merriam-webster.com/dictionary/surface
Anthropogenic material in or on which organisms may live.
ENVO
ENVO:0010001
anthropogenic environmental material
Anthropogenic material in or on which organisms may live.
MA:ma
Particulate environmental material which is primarily composed of silt particles.
Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.
EcoLexicon:silt
SWEETRealm:Silt
https://en.wikipedia.org/wiki/Silt
This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider this soil material that contains 80% or more silt and less than 12% clay. In the Udden-Wentworth scale (due to Krumbein), silt particles range between 0.0039 to 0.0625 mm, larger than clay but smaller than sand particles. ISO 14688 grades silts between 0.002 mm and 0.063 mm. In actuality, silt is chemically distinct from clay, and unlike clay, grains of silt are approximately the same size in all dimensions; furthermore, their size ranges overlap. Clays are formed from thin plate-shaped particles held together by electrostatic forces, so present a cohesion. According to the U.S. Department of Agriculture Soil Texture Classification system, the sand-silt distinction is made at the 0.05 mm particle size. The USDA system has been adopted by the Food and Agriculture Organization (FAO). In the Unified Soil Classification System (USCS) and the AASHTO Soil Classification system, the sand-silt distinction is made at the 0.075 mm particle size (i.e., material passing the #200 sieve). Silts and clays are distinguished mechanically by their plasticity.
silt
Particulate environmental material which is primarily composed of silt particles.
This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider this soil material that contains 80% or more silt and less than 12% clay. In the Udden-Wentworth scale (due to Krumbein), silt particles range between 0.0039 to 0.0625 mm, larger than clay but smaller than sand particles. ISO 14688 grades silts between 0.002 mm and 0.063 mm. In actuality, silt is chemically distinct from clay, and unlike clay, grains of silt are approximately the same size in all dimensions; furthermore, their size ranges overlap. Clays are formed from thin plate-shaped particles held together by electrostatic forces, so present a cohesion. According to the U.S. Department of Agriculture Soil Texture Classification system, the sand-silt distinction is made at the 0.05 mm particle size. The USDA system has been adopted by the Food and Agriculture Organization (FAO). In the Unified Soil Classification System (USCS) and the AASHTO Soil Classification system, the sand-silt distinction is made at the 0.075 mm particle size (i.e., material passing the #200 sieve). Silts and clays are distinguished mechanically by their plasticity.
Particulate environmental material which is composed primarily of particles of sand with only minor proportions of other substances.
Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.
EcoLexicon:sand
LTER:484
SWEETRealm:Sand
https://en.wikipedia.org/wiki/Sand
This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider as sands soil material that contains 85% or more sand; the percentage of silt plus 1.5 times the percentage of clay does not exceed 15. coarse sand (sable grossier) 25% or more very coarse and coarse sand, and less than 50% any other one grade of sand.
sand
Particulate environmental material which is composed primarily of particles of sand with only minor proportions of other substances.
https://en.wikipedia.org/wiki/Sand
This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider as sands soil material that contains 85% or more sand; the percentage of silt plus 1.5 times the percentage of clay does not exceed 15. coarse sand (sable grossier) 25% or more very coarse and coarse sand, and less than 50% any other one grade of sand.
https://sis.agr.gc.ca/cansis/glossary/t/index.html
An environmental material which is composed primarily of particles.
Do not oversimplify this branch with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.
particulate matter
envoAtmo
envoPolar
particulate environmental material
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
ORCID:0000-0002-4366-3088
2010-03-20T08:40:04Z
EcoLexicon:organic_material
biomass
organic material
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
ISBN:978-0-618-45504-1
ORCID:0000-0002-4366-3088
A desert ecosystem which is undergoing climactic ecological succession.
ORCID:0000-0002-4366-3088
2013-04-07T14:26:46Z
SPIRE:Desert_or_dune
wwfBiome
desert biome
An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system.
ORCID:0000-0002-4366-3088
2013-04-07T14:35:18Z
envoPolar
A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional.
environmental condition
An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system.
DOI:10.1186/2041-1480-4-43
An anthropogenic terrestrial biome is a terrestrial biome which has community structures determined by human activity.
ORCID:0000-0002-4366-3088
2013-04-07T14:45:22Z
anthrome
human biome
Preliminary definition.
anthropogenic terrestrial biome
An anthropogenic terrestrial biome is a terrestrial biome which has community structures determined by human activity.
http://www.eoearth.org/view/article/150128/
An environmental condition in which annual precipitation is less than half of annual potential evapotranspiration.
ORCID:0000-0002-4366-3088
2013-04-24T13:28:18Z
EcoLexicon:aridity
envoPolar
arid
A system which has the disposition to environ one or more material entities.
2013-09-23T16:04:08Z
EcoLexicon:environment
environment
In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.
environmental system
A system which has the disposition to environ one or more material entities.
DOI:10.1186/2041-1480-4-43
A mineral material is an environmental material which is primarily composed of some substance that is naturally occurring, solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and that has an ordered atomic structure.
Look for "mineral" in a chemical or geochemical ontology to formalise the composed primarily of link.
From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.
ORCID:0000-0002-4366-3088
2013-10-05T12:37:41Z
LTER:341
mineral material
A mineral material is an environmental material which is primarily composed of some substance that is naturally occurring, solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and that has an ordered atomic structure.
https://en.wikipedia.org/wiki/Mineral
Water vapour is a vapour which is the gas phase of water.
ORCID:0000-0002-4366-3088
2013-10-10T07:58:18Z
aqueous vapor
aqueous vapour
water vapor
Perhaps a better relation between water vapour and water can be found in or added to RO?
water vapour
Water vapour is a vapour which is the gas phase of water.
https://en.wikipedia.org/wiki/Water_vapor
aqueous vapor
https://en.wikipedia.org/wiki/Water_vapor
aqueous vapour
https://en.wikipedia.org/wiki/Water_vapor
water vapor
https://en.wikipedia.org/wiki/Water_vapor
An atmosphere is a layer of gases surrounding a material body of sufficient mass that is held in place by the gravity of the body.
ORCID:0000-0002-4366-3088
2013-10-10T08:14:50Z
LTER:48
atmosphere
An atmosphere is a layer of gases surrounding a material body of sufficient mass that is held in place by the gravity of the body.
https://en.wikipedia.org/wiki/Atmosphere
https://en.wikipedia.org/wiki/Physical_geography
Atmospheric water vapour is water vapour that is part of an atmosphere.
ORCID:0000-0002-4366-3088
2013-10-10T08:22:07Z
atmospheric water vapor
ENVO
ENVO:01000268
envoPolar
atmospheric water vapour
Atmospheric water vapour is water vapour that is part of an atmosphere.
https://en.wikipedia.org/wiki/Water_vapor
atmospheric water vapor
https://en.wikipedia.org/wiki/Water_vapor
A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
ORCID:0000-0002-4366-3088
2013-10-12T17:21:09Z
envoPolar
Unlike biomes, ecoregions are geographically defined entities. ENVO's sister project, GAZ, contains terms for instances of ecoregions (e.g. Beringia lowland tundra). Requests for new terms should be directed to GAZ. ENVO will only contain this top-level class. The class' definition is preliminary and will be aligned to BFO.
ecoregion
A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
DOI:10.1641/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2
URL:http://worldwildlife.org/biomes
Ice which is formed from water.
2013-10-13T12:01:28Z
LTER:262
ice
envoPolar
Water ice can appear transparent or opaque bluish-white color, depending on the presence of impurities or air inclusions. The addition of other materials such as soil may further alter its appearance.
When speaking about ice on Earth, usually water ice is meant - the solid, crystalline form of water found in the atmosphere as snow crystals, hail, ice pellets, etc., and on the earth's surface in forms such as hoarfrost, rime, glaze, sea ice, glacier ice, ground ice, frazil, anchor ice, etc.
This form of water is, strictly speaking, called ice Ih, the Roman numeral I distinguishing it from more than a dozen other phases and the letter h distinguishing it from the metastable cubic phase ice Ic. Ice Ih is the only one of the several known phases of water ice that is stable at commonly occurring temperatures and pressures. (Some of the other forms have very unusual properties, ice VII, for example, being stable only at pressures above 22 400 kg/cm^2, but then existing at temperatures up to about 100C.)
It has an open structure with a specific gravity of 0.9166 which is slightly less than water; because the water molecules bond to their neighbors covalently only in four directions; it therefore floats on higher density water, where broken molecular bonds permit closer packing. All commonly occurring forms of ice are crystalline, although large single crystals are relatively rare except in glaciers. The ice crystal lattice possesses hexagonal symmetry that manifests itself in the gross forms of such single crystals as are sometimes found in snow. At an air pressure of one atmosphere, ice melts at 0 C by definition of the Celsius temperature scale. (Strictly speaking the equilibrium point among water, ice, and vapor occurs at +0.01C, the triple point.) On the other hand, ice does not invariably form in liquid water cooled below this temperature; it has a tendency to supercool, more so in the absence of ice nuclei.
In permafrost regions, ice may occupy voids in soils and rocks and may develop in a variety of forms. Ice may be colourless to pale blue or greenish-blue. It may appear white due to included gas bubbles; in exposures, ground ice may also appear black.
In nature ice is formed either by: (a) the freezing of water, (b) the condensation of atmospheric water vapour direct into ice crystals, (c) the compaction of snow with or without the motion of a glacier, or (d) the impregnation of porous snow masses with water which subsequently freeze.
water ice
Ice which is formed from water.
https://en.wikipedia.org/wiki/Ice
ice
http://www.eionet.europa.eu/gemet/concept/4131
Ecozones delineate large areas of a planetary surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, or high mountain ranges, that constitute barriers to migration.
ORCID:0000-0002-4366-3088
2013-10-13T18:32:46Z
envoPolar
ENVO contains this top-level class, but all instances will be in GAZ. The definition is preliminary and will be aligned to BFO.
https://en.wikipedia.org/wiki/ Ecozones correspond to the floristic kingdoms of botany or zoogeographic regions of zoology. Ecozones are characterized by the evolutionary history of the organisms they contain. They are distinct from biomes, also known as major habitat types, which are divisions of the Earth's surface based on life form, or the adaptation of plants and animals to climatic, soil, and other conditions. Biomes are characterized by similar climax vegetation. Each ecozone may include a number of different biomes. A tropical moist broadleaf forest in Central America, for example, may be similar to one in New Guinea in its vegetation type and structure, climate, soils, etc., but these forests are inhabited by plants and animals with very different evolutionary histories.
ecozone
Ecozones delineate large areas of a planetary surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, or high mountain ranges, that constitute barriers to migration.
https://en.wikipedia.org/wiki/ecozone
A material entity which 1) is spatially continuous, 2) is composed of material of comparable thickness, composition, and physical properties, and 3) is physically distinct from adjacent portions of environmental material.
2013-10-15T16:42:02Z
envoPolar
layer
A material entity which 1) is spatially continuous, 2) is composed of material of comparable thickness, composition, and physical properties, and 3) is physically distinct from adjacent portions of environmental material.
A mass of water ice.
Class should be populated by inference and asserted subclasses redistributed.
ORCID:0000-0002-4366-3088
2013-10-15T19:49:11Z
accumulation of ice
ice accumulation
http://sweetontology.net/phenCryo/Accumulation
envoPolar
ice mass
An endolithic environment is an environment that exists within solid rock.
endolithic environment
A high temperature environment is an environment in which material entities are exposed to increased levels of heat radiation or which have molecules or atoms moving randomly with increased levels of average kinietic energy.
high temperature environment
An environment which has a lower temperature than some local or global average.
envoPolar
The definition of the deprecated 'cold temperature habitat' class, which this class was derived from, quotes an upper threshold of 15 degrees Celsius for 'coldness'.
cold environment
An anthropogenic environment is an environmental system which is the product of human activity.
Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic.
anthropogenic environment
An environment whose dynamics are strongly influenced by water.
aquatic environment
The atmospheric boundary layer is the lowest layer of an atmosphere which is strongly influenced by its contact with a planetary surface with strong vertical mixing and in which physical quantities such as flow velocity, temperature, and moisture display rapid fluctuations (turbulence).
planetary boundary layer
envoPolar
atmospheric boundary layer
A planetary surface is a surface layer where the solid or liquid material of a planet comes into contact with an atmosphere or outer space.
a useful class: this can be used to define sub-terrestrial and sub-marine entities
planetary surface
A layer in a water mass, itself composed primarily of water.
envoPolar
This class will eventually be populated by inference, and its asserted subclasses removed.
aquatic layer
Snow is an environmental material which is primarily composed of flakes of crystalline water ice.
envoPolar
snow
Snow is an environmental material which is primarily composed of flakes of crystalline water ice.
http://www.eionet.europa.eu/gemet/concept/7769
https://en.wikipedia.org/wiki/Snow
A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein.
environmental area
envoPolar
Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition.
environmental zone
A layer that is part of the atmosphere.
ORCID:0000-0002-4366-3088
atmospheric layering
envoPolar
This could be made into an inferred class, rather than having asserted subclasses.
atmospheric layer
atmospheric layering
GEMET:http://www.eionet.europa.eu/gemet/concept/627
A boundary layer is a layer of fluid in the immediate vicinity of a bounding surface where the effects of viscosity are significant enough to distort the surrounding non-viscous flow.
ORCID:0000-0002-4366-3088
boundary layer
boundary layer
A boundary layer is a layer of fluid in the immediate vicinity of a bounding surface where the effects of viscosity are significant enough to distort the surrounding non-viscous flow.
https://en.wikipedia.org/wiki/Boundary_layer
boundary layer
http://www.eionet.europa.eu/gemet/concept/976
Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase.
condensation
envoAtmo
envoPolar
"process" is included in the label to make it clear that we are not referring to the condensed material (e.g. water droplets, window fog)
hydrological condensation process
Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase.
https://en.wikipedia.org/wiki/Condensation
A landmass which is part of a planet.
land
ground
planetary landmass
A landmass which is part of a planet.
Adpated from https://en.wikipedia.org/wiki/Planetary_surface
Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies.
space
envoAstro
outer space
Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies.
https://en.wikipedia.org/wiki/Outer_space
A planetary crust is the outermost solid shell of a rocky planet or natural satellite, which is chemically distinct from the underlying mantle.
crust
This class is meant to be applicable accross planets. Earth's crust would be an instance.
planetary crust
A planetary crust is the outermost solid shell of a rocky planet or natural satellite, which is chemically distinct from the underlying mantle.
https://en.wikipedia.org/wiki/Crust_(geology)
A planetary structural layer is laminar part of a terrestrial planet or other rocky body large enough to have differentiation by density. Planetary layers have differing physicochemical properties and composition.
Label should be improved to match definition.
planetary structural layer
A planetary mantle is a planetary layer which is an interior part of a terrestrial planet or other rocky body large enough to have differentiation by density.
mantle
This class is meant to be applicable accross planets. Earth's mantle would be an instance.
planetary mantle
A planetary mantle is a planetary layer which is an interior part of a terrestrial planet or other rocky body large enough to have differentiation by density.
https://en.wikipedia.org/wiki/Mantle_(geology)
A lithosphere is the outermost shell of a terrestrial-type planet or natural satellite that is defined by its rigid mechanical properties.
Earth's lithosphere includes the crust and uppermost mantle.
lithosphere
A lithosphere is the outermost shell of a terrestrial-type planet or natural satellite that is defined by its rigid mechanical properties.
https://en.wikipedia.org/wiki/Lithosphere
Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity.
precipitation
"process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet)
hydrological precipitation process
Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity.
https://en.wikipedia.org/wiki/Precipitation
Condensation is a process during which a gas undergoes a phase transition into a liquid.
condensation process
Condensation is a process during which a gas undergoes a phase transition into a liquid.
https://en.wikipedia.org/wiki/Condensation
Desublimation is a process in which a portion of some gas undergoes a phase transition into a portion of some solid.
deposition
desublimation process
Desublimation is a process in which a portion of some gas undergoes a phase transition into a portion of some solid.
https://en.wikipedia.org/wiki/Deposition_(phase_transition)
An area of a planet's surface which is primarily composed of bedrock, desert pavement, scarp rock, talus, material exposed by slides, volcanic material, glacial debris, sand, material exposed during strip mining, gravel, and other accumulations of earthen material in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
The range of entities that are considered "barren land" are not exhaustive, making axiomatisation risky at this stage.
Barren Land (Rock/Sand/Clay)
NLCD:31
envoPolar
nlcd2011
According to the NLCD 2011, areas of barren land generally have less than 15% cover of vegetation. A specific threshold is not asserted in this definition.
area of barren land
An area of a planet's surface which is primarily composed of bedrock, desert pavement, scarp rock, talus, material exposed by slides, volcanic material, glacial debris, sand, material exposed during strip mining, gravel, and other accumulations of earthen material in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
https://en.wikipedia.org/wiki/Exosphere
https://en.wikipedia.org/wiki/Planetary_surface
https://www.mrlc.gov/nlcd11_leg.php
A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely.
This class is to be populated by inference.
gas
gaseous environmental material
A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely.
http://www.merriam-webster.com/dictionary/gas
A material entity which is composed of a volume of unbound positive and negative particles in roughly equal numbers, conducts electricity, and possesses internal magnetic fields.
An NTR for `quality of a plasma` has been posted on the PATO tracker: https://github.com/pato-ontology/pato/issues/88
plasma
A material entity which is composed of a volume of unbound positive and negative particles in roughly equal numbers, conducts electricity, and possesses internal magnetic fields.
http://www.merriam-webster.com/dictionary/plasma
https://en.wikipedia.org/wiki/Plasma_%28physics%29
An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space.
celestial body
envoAstro
Astronomical bodies are usually cohesive, thus the use of the term 'object' sensu BFO 'object'.
astronomical body
An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space.
https://en.wikipedia.org/wiki/Astronomical_object
A planet is an astronomical body orbiting a star or stellar remnant that is massive enough to be rounded by its own gravity, is not massive enough to cause thermonuclear fusion, and has cleared its neighbouring region of planetesimals.
envoAstro
envoPolar
Considerable debate on the definition of planet exists.
planet
A planet is an astronomical body orbiting a star or stellar remnant that is massive enough to be rounded by its own gravity, is not massive enough to cause thermonuclear fusion, and has cleared its neighbouring region of planetesimals.
http://solarsystem.nasa.gov/planets/whatisaplanet
https://en.wikipedia.org/wiki/Planet
An astronomical object which is composed primarily of luminous plasma held in a spherical form by gravitational forces.
Add qualities such as spherical. Request NTRs if not available in PATO.
envoAstro
envoPolar
star
An astronomical object which is composed primarily of luminous plasma held in a spherical form by gravitational forces.
https://en.wikipedia.org/wiki/Star
An object which is composed of one or more gravitationally bound structures that are associated with a position in space.
celestial object
envoAstro
If there is only one astronomical body involved, this class is equivalent to ENVO:01000799. This may be problematic with reasoning, but it seems to be true to the rather fuzzy definitions found thus far.
astronomical object
An object which is composed of one or more gravitationally bound structures that are associated with a position in space.
https://en.wikipedia.org/wiki/Astronomical_object
A material part of an astronomical body.
Also note that some astronomical body parts (ABPs) may have fiat boundaries: if there's strong debate about where an ABP begins or ends (over and above fuzzy boundaries), with different official classifications setting different thresholds or limits, axiomatise the class with fiat boundaries of the appropriate dimension.
Note that material entities may have immaterial entities (e.g. sites) as parts.
This class includes material parts of astronomical bodies. Immaterial parts, such as magnetospheres, are represented as sites under the influence of magnetic fields.Please post countercases in the ENVO tracker for revision of this hierarchy if needed.
envoAstro
envoPolar
Material parts of astronomical bodies generally have boundaries formed by discontinuities in qualities, composition, or other physical characterisitcs. These boundaries are sometimes sharp, and sometimes diffuse, with different classification systems and communities declaring varying thresholds (e.g. for where a shoreline, forest, or other entity begins and ends). However, some boundaries are declared by fiat - that is, by arbitrary human convention or decree - particularly by regulatory or other authorities and communities of practice. The classes in this hierarchy attempt to offer generalisable definitions that allow multiple classfiication systems to map to and interoperate through. If desired, we can create classes that declare thresholds used by a given authority or community under the more generic ones, annotated with source information.
astronomical body part
An environmental material which is in a solid state.
This is a defined class: its subclasses will not be asserted, but filled by inference.
solid environmental material
An environmental material which is in a liquid state.
envoPolar
This is a defined class: most of its subclasses will not be asserted, but filled by inference.
liquid environmental material
An astronomical body part which includes all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact.
Whether this class should be grouped with classes such as "hydrosphere" and "cryosphere" requires some discussion.
envoAstro
envoPolar
The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations.
biosphere
An astronomical body part which includes all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact.
http://www.biology-online.org/dictionary/Biosphere
https://en.wikipedia.org/wiki/Biosphere
An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet.
envoAstro
envoPolar
This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class.
hydrosphere
An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet.
https://en.wikipedia.org/wiki/Hydrosphere
An astronomical body part which is composed of soil, subject to soil formation processes, and found on the surface of a lithosphere.
envoAstro
This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class.
pedosphere
An astronomical body part which is composed of soil, subject to soil formation processes, and found on the surface of a lithosphere.
https://en.wikipedia.org/wiki/Pedosphere
A solid material whose constituents, such as atoms, molecules or ions, are arranged in a highly ordered microscopic structure, forming a crystal lattice that extends in all directions.
This class refers to a portion of crystal and not an individual crystal.
crystal
A solid material whose constituents, such as atoms, molecules or ions, are arranged in a highly ordered microscopic structure, forming a crystal lattice that extends in all directions.
https://en.wikipedia.org/wiki/Crystal
A crystal which is primarily composed of water ice.
ice crystal
envoPolar
Any one of a number of macroscopic, crystalline forms in which ice appears, including hexagonal columns, hexagonal platelets, dendritic crystals, ice needles, and combinations of these forms. The crystal lattice of ice is hexagonal in its symmetry under most atmospheric conditions.
water ice crystal
Any one of a number of macroscopic, crystalline forms in which ice appears, including hexagonal columns, hexagonal platelets, dendritic crystals, ice needles, and combinations of these forms. The crystal lattice of ice is hexagonal in its symmetry under most atmospheric conditions.
A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force.
precipitation process
A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force.
https://en.wikipedia.org/wiki/Precipitation_%28chemistry%29
https://en.wikipedia.org/wiki/Precipitation
A hydrological process in which irregular aggregates of snow fall to the surface of an astronomical body.
This is currently bound to water-based snow on Earth, may need revisions for interplanetary applications
2021-04-14T18:57:18.275Z
snow fall
environmental_hazards
envoCryo
envoPolar
snowfall
An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.
non-anthropised environment
non-anthropized environment
In most contexts, 'natural' is defined by the lack of intervention or influence by humans and their activities. On Earth, most environments fall on a scale between completely natural and anthropised.
natural environment
An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.
https://en.wikipedia.org/wiki/Anthropization
https://en.wikipedia.org/wiki/Natural_environment
A process during which a natural environmental system is altered by human action.
anthropization
An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action.
anthropisation
A process during which a natural environmental system is altered by human action.
https://en.wikipedia.org/wiki/Anthropization
An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action.
https://en.wikipedia.org/wiki/Anthropization
A planet that is composed primarily of silicate rocks or metals.
rocky planet
telluric planet
Earth-like planet
envoAstro
terrestrial planet
A planet that is composed primarily of silicate rocks or metals.
https://en.wikipedia.org/wiki/Terrestrial_planet
A material transport process during which a volume of liquid water is transported due to a disequilibria in physical forces.
environmental_hazards
water flow process
A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation.
The term may refer to a range of human activity, from handicraft to high tech, but is most commonly applied to industrial production, in which raw materials are transformed into finished goods on a large scale.
manufacturing process
A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation.
https://en.wikipedia.org/wiki/Manufacturing
The term may refer to a range of human activity, from handicraft to high tech, but is most commonly applied to industrial production, in which raw materials are transformed into finished goods on a large scale.
https://en.wikipedia.org/wiki/Manufacturing
An environmental system which is determined by materials bearing roughly homogeneous qualities.
Organisational class. Not intended for annotation.
environmental system determined by a quality
An environmental system within which an environmental material strongly influences the system's composition and properties.
Organisational class. Not intended for annotation. Subclasses describe environments which are usually permeated by an environmental material. They may also describe environments which are sufficiently close to a material, that their dynamics are strongly influenced by it (e.g. a patch of forest ecosystem neighbouring a uranium dump).
environmental system determined by a material
A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium.
Requires addition of waves for full axiomatisation. This should be linked to "subatomic particle" with an "or". Note that ENVO represents space as an environmental material (a hard vacuum with sparse material inclusions).
environmental_hazards
envoAstro
radiation
A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium.
https://en.wikipedia.org/wiki/Radiation
A radiation process during which waves (or their quanta, photons) of the electromagnetic field propagate (radiate) through space carrying electromagnetic energy.
EM radiation
environmental_hazards
envoAstro
Note that this class is concerned only with active radiative processes: static electric and magnetic fields are not inlcuded. All electromagnetic radiation carries radiant energy.
electromagnetic radiation
A radiation process during which waves (or their quanta, photons) of the electromagnetic field propagate (radiate) through space carrying electromagnetic energy.
https://en.wikipedia.org/wiki/Electromagnetic_radiation
An environmental system which has its properties and dynamics determined by soil.
Soil (non-saline)
envoEmpo
envoOmics
soil environment
Soil (non-saline)
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
An environmental system which has its properties and dynamics determined by sediment.
envoEmpo
envoOmics
sediment environment
A material which is composed primarily of one or more pure metals and which shows their properties.
Far more axiomatisation can be done should the qualities of metals be added to PATO or a similar quality ontology. However, note that there are many exceptions to the typical qualities of the majority of metals.
metal
While this class allows for some degree of contamination by non-metal substances, the material represented should show at least some of the typical features of a pure metal: hardness (except for liquid metals), opacity, lustre, malleability, fusibility, ductile and good electrical and thermal conductivity.
metallic material
A material which is composed primarily of one or more pure metals and which shows their properties.
https://en.wikipedia.org/wiki/Metal
An environmental system which includes both living and non-living components.
LTER:173
This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.
ecosystem
An environmental system which includes both living and non-living components.
https://en.wikipedia.org/wiki/Ecosystem
LTER:173
https://vocab.lternet.edu/vocab/vocab/index.php?tema=173&/ecosystems
A planet which is primarily composed of hydrogen and helium.
envoAstro
Gas giants are composed of about 90% hydrogen and helium. Jupiter and Saturn are examples of gas giants.
gas planet
A planet which is primarily composed of hydrogen and helium.
http://solarsystem.nasa.gov/planets/whatisaplanet
https://en.wikipedia.org/wiki/List_of_planet_types
https://en.wikipedia.org/wiki/Planet
An ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure.
Note that ice may be formed at very high temperatures, due to gravitational effects and/or pressure.
ice
A terrestrial planet which has a surface dominated by hot deserts.
dry planet
envoAstro
This class of planet is still mostly theoretical.
desert planet
A planet which has a surface layer that nearly completely or completely covered by water, and which has a substantial portion of its mass composed of water.
An axiom to express that the planet has a 'substantial' proportion of its mass in the form of water wound enhance this class.
aquaplanet
panthalassic planet
water world
envoAstro
While this planetary form is still mostly theoretical, strong candidates exist such as the extrasolar planet GJ 1214 b and ocean planet candidate Kepler-22b.
ocean planet
A planet which has a surface layer that nearly completely or completely covered by water, and which has a substantial portion of its mass composed of water.
https://en.wikipedia.org/wiki/Ocean_planet
A planet which has a surface layer that nearly completely or completely covered by ice, and which has a substantial portion of its mass composed of ice.
cryoplanet
envoAstro
While this planetary form is still mostly theoretical, strong candidates exist such as OGLE-2005-BLG-390Lb, OGLE-2013-BLG-0341L b and MOA-2007-BLG-192Lb. Pluto was considered an ice planet until its reclassification in 2006 CE. Surface temperatures of ice planets would have to be below 260 K (−13°C) if composed primarily of water, below 180 K (−93°C) if primarily composed of CO2 and ammonia, and below 80 K (−193°C) if composed primarily of methane.
ice planet
A planet which has a surface layer that nearly completely or completely covered by ice, and which has a substantial portion of its mass composed of ice.
https://en.wikipedia.org/wiki/Ice_planet
While this planetary form is still mostly theoretical, strong candidates exist such as OGLE-2005-BLG-390Lb, OGLE-2013-BLG-0341L b and MOA-2007-BLG-192Lb. Pluto was considered an ice planet until its reclassification in 2006 CE. Surface temperatures of ice planets would have to be below 260 K (−13°C) if composed primarily of water, below 180 K (−93°C) if primarily composed of CO2 and ammonia, and below 80 K (−193°C) if composed primarily of methane.
https://en.wikipedia.org/wiki/Ice_planet
Ice which is primarily composed of carbon dioxide.
dry ice
envoAstro
carbon dioxide ice
Ice which is primarily composed of carbon dioxide.
https://en.wikipedia.org/wiki/Ice
A gas planet which has an atmosphere composed primarily of helium.
The placement of this class assumes that some traces of hydrogen are left in the atmosphere. If this is not the case, the axiom on gas planet must be updated.
envoAstro
A helium planet might form via hydrogen evaporation from a gaseous planet orbiting close to a star. Low-mass white dwarfs may transition into objects which are essentially helium planets by hydrogen depletion through mass transfer to a massive object such as a neutron star. Gliese 436 b is a candidate helium planet.
helium planet
A gas planet which has an atmosphere composed primarily of helium.
https://en.wikipedia.org/wiki/Helium_planet
A helium planet might form via hydrogen evaporation from a gaseous planet orbiting close to a star. Low-mass white dwarfs may transition into objects which are essentially helium planets by hydrogen depletion through mass transfer to a massive object such as a neutron star. Gliese 436 b is a candidate helium planet.
https://en.wikipedia.org/wiki/Helium_planet
A material which is composed primarily of chemical elements and compounds with relatively low boiling points, equilibrium condensation temperatures below 1300 Kelvin, and which are part of the crust or atmosphere of a moon or planet.
Add and axiomatise with moon and lunar crust
volatile
envoAstro
Examples include nitrogen, water, carbon dioxide, ammonia, hydrogen, methane and sulfur dioxide. In astrogeology, these compounds, in their solid state, often comprise large proportions of the crusts of moons and dwarf planets.
volatile astrogeological material
A material which is composed primarily of chemical elements and compounds with relatively low boiling points, equilibrium condensation temperatures below 1300 Kelvin, and which are part of the crust or atmosphere of a moon or planet.
https://en.wikipedia.org/wiki/Volatiles
Examples include nitrogen, water, carbon dioxide, ammonia, hydrogen, methane and sulfur dioxide. In astrogeology, these compounds, in their solid state, often comprise large proportions of the crusts of moons and dwarf planets.
https://en.wikipedia.org/wiki/Volatiles
An astrogeological volatile which is composed primarily of chemical compounds with boiling points around those of hydrogen and helium.
gas
envoAstro
This is a term native to the fields of planetary science and astrophysics. Hydrogen has a boiling point of 20.271 Kelvin and a melting point of 13.99 Kelvin. Helium has a boiling point of 4.222 Kelvin and a melting point of 0.95 Kelvin.
astrogeological gas
An astrogeological volatile which is composed primarily of chemical compounds with boiling points around those of hydrogen and helium.
https://en.wikipedia.org/wiki/Volatiles
A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms.
Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities.
geodiversity
A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms.
https://en.wikipedia.org/wiki/Geodiversity
Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities.
The surface layer of a volume of water.
EcoLexicon:surface_water
SWEETRealm:SurfaceWater
https://en.wikipedia.org/wiki/Surface_water
surface of a body of water
water body surface
water surface
The surface layer of a mass of sediment.
surface of a sedimentary mass
surface sediment
sediment surface
An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it.
terrestrial environmental zone
A terrestrial zone which is bounded by constructed, manufactured, or other anthropogenic material entities.
anthropised terrestrial environmental zone
An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a star.
NCIT:C44445
solar radiation
environmental_hazards
envoAstro
stellar radiation
An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a star.
https://en.wikipedia.org/wiki/Electromagnetic_radiation
https://en.wikipedia.org/wiki/Solar_irradiance
solar radiation
NCIT:C44445
A natural environment which is located on a land mass.
terrestrial natural environment
A layer which is primarily composed of some liquid material.
liquid layer
A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid.
solid layer
A solid layer which is primarily composed of some water-based ice.
water ice layer
An environmental zone which is part of an atmosphere.
atmospheric area
atmospheric zone
A liquid surface layer which is in contact with air.
liquid air-water interface layer
A surface layer which is composed primarily of some liquid.
liquid surface layer
A surface layer which is composed primarily of solid environmental material.
solid surface layer
A landform which has been rendered barren or partially barren by environmental extremes, especially by low rainfall, and which loses more liquid water by evapotranspiration than is supplied by precipitation.
desert
A process during which an ecosystem - natural or anthropised - is changed by the actions of humans.
anthropogenic ecosystem conversion process
A part of an astronomical body which is primarily composed of liquid material.
liquid astronomical body part
A part of an astronomical body which is primarily composed of gaseous material.
gaseous astronomical body part
A part of an astronomical body which is primarily composed of fluid.
2018-10-04T13:59:22Z
fluid astronomical body part
A part of an astronomical body which is primarily composed of fluid.
A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space.
2018-10-04T16:55:57Z
land surface
a useful class: this can be used to define sub-terrestrial and sub-marine entities
surface of an astronomical body
An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a manufactured product.
2019-01-09T09:07:24Z
anthropogenic radiation
artificial radiation
environmental_hazards
envoAstro
radiation from a manufactured product
An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a manufactured product.
https://en.wikipedia.org/wiki/Electromagnetic_radiation
https://en.wikipedia.org/wiki/Solar_irradiance
A material transformation process during which a material's viscosity increase either through a reduction in temperature, through chemical reactions, or other physical effects.
2019-01-14T18:47:32Z
congelation
congelation process
Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question.
material congelation process
A material transformation process during which a material's viscosity increase either through a reduction in temperature, through chemical reactions, or other physical effects.
https://en.wikipedia.org/wiki/Congelation
Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question.
https://en.wikipedia.org/wiki/Congelation
Land which is below the freezing point of water.
2019-01-14T21:18:19Z
http://sweetontology.net/realmCryo/FrozenGround
frozen ground
Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load.
frozen land
Land which is below the freezing point of water.
https://orcid.org/0000-0003-4808-4736
Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load.
https://orcid.org/0000-0003-4808-4736
Soil which is below the freezing point of water.
2019-01-14T21:26:59Z
frozen soil
A material congelation process during which a liquid turns into a solid when its temperature is lowered below its melting point.
2019-01-31T21:13:16Z
envoCryo
envoPolar
freezing
A material congelation process during which a liquid turns into a solid when its temperature is lowered below its melting point.
https://en.wikipedia.org/wiki/Freezing
A freezing process during which liquid water is transformed into water ice.
2019-01-31T21:16:46Z
freezing of water into water ice
An ecoregion which is located on a landmass.
2019-03-05T17:40:44Z
https://www.worldwildlife.org/biome-categories/terrestrial-ecoregions
terrestrial ecoregion
A layer which is part of a cryosphere.
2019-04-09T13:05:25Z
envoPolar
cryospheric layer
Permafrost which contains inclusions of water-based ice.
2019-04-09T13:45:40Z
ice-bearing permafrost
A material accumulation process during which the mass of snow on a surface increases.
2019-04-24T18:29:18Z
http://sweetontology.net/phenCryo/Accumulation
This term is used both as a process and as an amount of mass added. Semantically speaking these are two distinct concepts (e.g., accumulation results in accumulation_amount of ice or snow gain), though accumulation_amount would more likely be an attribute.
The scope of this term varies depending on the definition. Some definitions constrain themselves snow or ice added to glaciers; while others also include ice fields, snow cover, and/or floating ice. How to resolve this depends on the scope desired.
Some definitions include additional discussion of the the physics involved which would be useful for connecting glacier ontologies to atmospheric, hydrologic, etc. ontologies. This information should be captured no matter how the inconsistencies above are resolved.
snow accumulation process
A material accumulation process during which the mass of snow on a surface increases.
A material accumulation process during which ice forms in an environmental material or an existing accumulation of ice increases in mass.
2019-04-24T18:48:53Z
http://sweetontology.net/phenCryo/Accumulation
ice accumulation process
A material accumulation process during which ice forms in an environmental material or an existing accumulation of ice increases in mass.
A material accumulation process during which a accumulation of snow and ice forms or increases in mass.
2019-04-24T18:59:45Z
http://sweetontology.net/phenCryo/Accumulation
snow and ice accumulation process
A material accumulation process during which a accumulation of snow and ice forms or increases in mass.
A object which is composed primarily of water-based snow and ice.
2019-04-24T19:08:03Z
http://sweetontology.net/phenCryo/Accumulation
mass of ice and snow
That part of an atmosphere which is composed of gaseous material.
2019-06-02T07:52:47Z
gaseous part of an atmosphere
A surface layer which is composed primarily of some liquid or gas.
2019-08-20T08:28:42Z
fluid surface layer
A surface layer which separates two portions of fluid with respect to either 1) a discontinuity of some fluid property or 2) some derivative of one of these properties in a direction normal to the interface.
2019-07-22T17:29:44Z
fluid interface layer
A surface layer which separates two portions of fluid with respect to either 1) a discontinuity of some fluid property or 2) some derivative of one of these properties in a direction normal to the interface.
A layer which is composed primarily of some fluid.
2019-07-22T17:35:08Z
fluid layer
A fluid interface which separates two fluid masses with differing properties.
2019-07-22T17:43:32Z
fluid front
A fluid interface which separates two fluid masses with differing properties.
A fluid front which is composed primarily of gaseous material and separates at least two gaseous masses.
2019-07-22T17:50:08Z
gaseous front
2
A gaseous front which separates two masses of air with different densities and is a principal cause of meteorological phenomena.
2019-07-22T17:57:21Z
meteorological front
envoAtmo
This class refers to Earth's weather fronts. Other forms, not composed of air, are present on other planets and can be created on request. Note: "Since the temperature distribution is the most important regulator of atmospheric density, a front almost invariably separates air masses of different temperature. Along with the basic density criterion and the common temperature criterion, many other features may distinguish a front, such as a pressure trough, a change in wind direction, a moisture discontinuity, and certain characteristic cloud and precipitation forms."
weather front
A gaseous front which separates two masses of air with different densities and is a principal cause of meteorological phenomena.
This class refers to Earth's weather fronts. Other forms, not composed of air, are present on other planets and can be created on request. Note: "Since the temperature distribution is the most important regulator of atmospheric density, a front almost invariably separates air masses of different temperature. Along with the basic density criterion and the common temperature criterion, many other features may distinguish a front, such as a pressure trough, a change in wind direction, a moisture discontinuity, and certain characteristic cloud and precipitation forms."
An object which is composed of a continuous mass of air.
2019-08-20T07:54:32Z
envoAtmo
air mass
A fluid surface layer which is composed primarily of some gaseous material.
2019-08-20T08:30:01Z
gaseous surface layer
A layer which separates two portions of environmental material which possess 1) differing compositions, 2) a discontinuity of some property, or 3) some derivative of some property in a direction normal to the interface.
2019-08-20T09:28:10Z
interface layer
An object which is composed primarily of an environmental material
2019-08-20T09:38:29Z
This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types.
mass of environmental material
An mass of environmental material which is composed primarily of a solid environmental material
2019-08-20T09:41:27Z
This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types.
mass of solid material
An object which is composed primarily of a fluid.
2019-08-20T09:42:35Z
fluid mass
This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types.
mass of fluid
An object which is composed primarily of a gas.
2019-08-20T09:44:01Z
gaseous mass
This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types.
mass of gas
An object which is composed primarily of a liquid.
2019-08-20T09:45:03Z
liquid mass
This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types.
mass of liquid
2
An mass of environmental materials which has appreciable quantities of several individual materials, such that the removal of one would convert the mass into a different entity.
2019-08-20T09:47:10Z
mass of compounded environmental materials
A weather front which separates air masses of tropical and polar origin.
2019-08-20T13:46:42Z
envoAtmo
envoPolar
polar front
A weather front which separates air masses of tropical and polar origin.
An ecosystem in which the composition, structure, and function of resident ecological assemblages are primarily determined by a desert.
2019-10-17T08:21:08Z
desert ecosystem
A solid astronomical body part which is part of the landmass of that body.
2019-10-17T08:27:17Z
part of a landmass
A large continuous area of land, either surrounded by sea or contiguous with another landmass.
2019-10-17T08:31:26Z
landmass
A large continuous area of land, either surrounded by sea or contiguous with another landmass.
A part of an astronomical body which is composed of a continuous medium bearing liquid, gaseous, and solid material in variable quantities.
2019-10-17T08:36:00Z
compound astronomical body part
A part of an astronomical body which is composed of a continuous medium bearing liquid, gaseous, and solid material in variable quantities.
https://en.wikipedia.org/wiki/Landform
A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water.
2019-10-21T10:42:26Z
land
A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water.
An ecosystem which primarily occurs on land.
2019-10-21T11:09:58Z
terrestrial ecosystem
An environmental process either driven by or primarily impacting the parts or emergent properties of an ecosystem.
2019-10-21T11:52:55Z
ecosystem process
An object which is formed as a result of one or more biological processes and is composed primarily of organic material.
2019-10-29T15:02:58Z
organic object
An ecosystem process during which the species composition of an ecosystem gradually changes as species which are more adapted to the prevailing conditions in the ecosystem replace those which are less adapted.
2023-09-07T13:10:32Z
ecological succession
An ecosystem process during which the species composition of an ecosystem gradually changes as species which are more adapted to the prevailing conditions in the ecosystem replace those which are less adapted.
An ecological succession process during which 1) organisms in ecological communities possess high adaptation to the conditions in the ecosystem, 2) participant communities largely fill available niches, 3) individual organisms are typically replaced by others of the same species, 4) a near equilibrium is maintained between gross primary production and total respiration and across biogeochemical cycles.
2023-09-07T13:35:09Z
climactic ecological succession
An ecological succession process during which 1) organisms in ecological communities possess high adaptation to the conditions in the ecosystem, 2) participant communities largely fill available niches, 3) individual organisms are typically replaced by others of the same species, 4) a near equilibrium is maintained between gross primary production and total respiration and across biogeochemical cycles.
An ecosystem which is formed as a result of human activity or impact.
2023-09-07T16:56:05Z
anthropised ecosystem
A biome which is subject to arid environmental conditions.
2019-11-06T16:06:47Z
arid biome
A process during which one entity loses energy to another entity.
2020-02-13T13:34:28Z
energy transfer process
A material accumulation process during which the volume of liquid entity increases.
2020-05-18T14:39:20Z
liquid accumulation process
A landform which occurs on the surface of an astronomical body.
2021-05-15T09:16:23Z
geographic feature
The usage of "surface" here aligns with that of planetary surface: in contact with the atmosphere or space. The extent of the "surface" can vary. For rocky planets like Earth, astrogeologists consider the crust as the surface.
surface landform
A solid astronomical body part which has been formed from and is composed primarily of the matter of that astronomical body.
2021-05-15T09:40:37Z
Landforms may be natural or anthropogenic. This term has often has loose usage when referencing entities which are either subterranean or submerged below water bodies. In some cases, oceans themselves are considered landforms. Here, we have provided subclasses to resolve this ambiguity, but place oceans and other water bodies elsewhere.In later revisions, this hiearchy is likely to be reordered based on the formation processes of the entities within it.
landform
A solid astronomical body part which has been formed from and is composed primarily of the matter of that astronomical body.
A disposition of a material entity which is realised when it is saturated with liquid water.
water-holding capacity
A mass of solid material which is either 1) a minute fragment of a larger mass or 2) one of a collection of small masses composing an aggregate.
grain
particle
A mass of solid material which is either 1) a minute fragment of a larger mass or 2) one of a collection of small masses composing an aggregate.
A particle which 1) is composed primarily of hydrous aluminium phyllosilicate minerals, in turn composed of aluminium and silicon ions bonded into tiny, thin plates by interconnecting oxygen and hydroxide ions, and 2) is or was part of a portion of clay.
clay particle
The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam.
particle of clay
A particle which 1) is composed primarily of hydrous aluminium phyllosilicate minerals, in turn composed of aluminium and silicon ions bonded into tiny, thin plates by interconnecting oxygen and hydroxide ions, and 2) is or was part of a portion of clay.
The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam.
An environmental material which is unable to resist shear forces and continuously deforms when subject to them.
fluid
fluid environmental material
An environmental material which is unable to resist shear forces and continuously deforms when subject to them.
https://github.com/EnvironmentOntology/envo/issues/940
A process in which includes the components of an environmental system as participants.
This is a convenience class for organisation and should not be used for annotation.
environmental system process
A process which occurs within an atmosphere.
This class will be populated by inference and is primarily organisational.
atmospheric process
An environmental process which is driven by the action of humans.
anthropogenic environmental process
An environmental process which has water - in any of its states - as a participant.
This classes asserted subclasses will be moved away as it should be an inferred class.
hydrological process
A physical process during which atoms, molecules, or other consituents of a material entity are forced closer together.
http://orcid.org/0000-0002-3410-4655
envoPolar
compaction process
A physical process during which atoms, molecules, or other consituents of a material entity are forced closer together.
https://en.wikipedia.org/wiki/Compaction
A process during which the mass of one or more materials, present within a given site, increases.
http://orcid.org/0000-0002-3410-4655
envoPolar
Experimental class for structural purposes not recommended for annotation. A material accumulation process ends a material transport process.
material accumulation process
A process during which material is displaced from its original location and transported either to a new location or back to the original location.
http://orcid.org/0000-0002-3410-4655
envoPolar
Experimental class for structural purposes not recommended for annotation.
material transport process
A process during which a portion of some environmental material is converted into a different material or a collection of materials.
A different material transformation process class (or similarly named class) pertaining to the conversion of a specific chemical into another belongs in CHEBI and or REX ontologies.
http://orcid.org/0000-0002-3410-4655
envoPolar
Experimental class for structural purposes not recommended for annotation. A material transformation process only refers to ENVO:environmental material classes (e.g. bulk and typically impure substances), rather than transformations converting a specific chemical into another.
material transformation process
A desublimation process during which water vapour is frozen into water ice.
http://orcid.org/0000-0002-3410-4655
envoPolar
desublimation of water vapour into ice
A solid astronomical body part which is primarily composed of a continuous mass of snow and/or ice.
Place holder class. Also the axiom should be changed to something along the lines of 'primairly composed of’ some ‘environmental material’ and ‘has quality’ frozen once PATO:frozen is imported.
http://orcid.org/0000-0002-3410-4655
envoPolar
cryoform
A mass of snow.
http://orcid.org/0000-0002-3410-4655
accumulation of snow
snow accumulation
http://sweetontology.net/phenCryo/Accumulation
envoPolar
snow mass
An astronomical body part which is composed primarily of environmental materials in their frozen form.
For the moment the definition links to liquid water but in the future we might need to link to other materials for other planets, e.g., Mars. Need to make this planet agnostic. Might want to not have the definition link to years as some astronomical body parts might not be in systems with years.
Note that in a strict sense, rocks are also frozen but in a practical sense we use terms like "solidified". This maybe something to revist if we add more astrogelogical content.
2021-04-14T18:57:18.275Z
envoCryo
envoPolar
The term generally refers to the portions of the Earth where water is in solid form, including snow cover, floating ice, glaciers, ice caps, ice sheets, seasonally frozen ground and perennially frozen ground (permafrost). The Cryosphere may be divided into the cryoatmosphere, the cryohydrosphere (snow cover, glaciers, and river, lake and sea Ice) and the cryolithosphere (perennially and seasonally cryotic ground, rock glacier). Some definitions consider the cryosphere to include any area of Earth which is sufficiently cold for pure water to freeze for at least a part of each year. It should be noted that "Some authorities exclude the earth's atmosphere from the Earth's Cryosphere; others restrict the term Cryosphere to the regions of the earth's crust where Permafrost exists."
Definitions of Cryosphere come from several glossaries including:
- PhysicalGeography.net http://physicalgeography.net/
- van Everdingen, Robert, ed., 2005 (1998 revised May 2005). Multi-language glossary of permafrost and related ground-ice terms. Boulder, CO: National Snow and Ice Data Center/World Data Center for Glaciology. [https://globalcryospherewatch.org/reference/glossary_docs/Glossary_of_Permafrost_and_Ground-Ice_IPA_2005.pdf]
- American Meteorological Society, 2015. Glossary of Meteorology [online], Available at: http://glossary.ametsoc.org/wiki/Main_Page. [Accessed 27/01/2017].
- EU Climate-ADAPT (The European Climate Adaptation Platform), no date, Glossary, Available from: http://climate-adapt.eea.europa.eu/glossary
- IPCC, 2014: Annex II: Glossary [Agard, J., Schipper, E. L. F., (ed.)]. In: Climate Change 2014: Impacts, Adaptation, and Vulnerability. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change [Birkmann, J., Campos, M., Dubeux, C., Nojiri, Y., Olsson, L., Osman-Elasha, B., Pelling, M., Prather, M. J., Rivera-Ferre M. G., Ruppel, O. C., Sallenger, A., Smith, K. R., St. Clair, A. L.,]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA. [Link]
- NSIDC, The National Snow and Ice Data Center glossary is available at https://nsidc.org/cryosphere/glossary, Last accessed [26/01/2016].
- Trombotto, D., P. Wainstein & L. Arenson, 2014, Guía Terminológica de la Geocriología Sudamericana” / “Terminological Guide of the South American Geocryology, 1a ed. 128 pp. [Link]
- UNESCO-WMO, 2012, International Glossary of Hydrology, 3rd edition, WMO-No. 385. [Link]
cryosphere
An astronomical body part which is composed primarily of environmental materials in their frozen form.
The term generally refers to the portions of the Earth where water is in solid form, including snow cover, floating ice, glaciers, ice caps, ice sheets, seasonally frozen ground and perennially frozen ground (permafrost). The Cryosphere may be divided into the cryoatmosphere, the cryohydrosphere (snow cover, glaciers, and river, lake and sea Ice) and the cryolithosphere (perennially and seasonally cryotic ground, rock glacier). Some definitions consider the cryosphere to include any area of Earth which is sufficiently cold for pure water to freeze for at least a part of each year. It should be noted that "Some authorities exclude the earth's atmosphere from the Earth's Cryosphere; others restrict the term Cryosphere to the regions of the earth's crust where Permafrost exists."
Definitions of Cryosphere come from several glossaries including:
- PhysicalGeography.net http://physicalgeography.net/
- van Everdingen, Robert, ed., 2005 (1998 revised May 2005). Multi-language glossary of permafrost and related ground-ice terms. Boulder, CO: National Snow and Ice Data Center/World Data Center for Glaciology. [https://globalcryospherewatch.org/reference/glossary_docs/Glossary_of_Permafrost_and_Ground-Ice_IPA_2005.pdf]
- American Meteorological Society, 2015. Glossary of Meteorology [online], Available at: http://glossary.ametsoc.org/wiki/Main_Page. [Accessed 27/01/2017].
- EU Climate-ADAPT (The European Climate Adaptation Platform), no date, Glossary, Available from: http://climate-adapt.eea.europa.eu/glossary
- IPCC, 2014: Annex II: Glossary [Agard, J., Schipper, E. L. F., (ed.)]. In: Climate Change 2014: Impacts, Adaptation, and Vulnerability. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change [Birkmann, J., Campos, M., Dubeux, C., Nojiri, Y., Olsson, L., Osman-Elasha, B., Pelling, M., Prather, M. J., Rivera-Ferre M. G., Ruppel, O. C., Sallenger, A., Smith, K. R., St. Clair, A. L.,]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA. [Link]
- NSIDC, The National Snow and Ice Data Center glossary is available at https://nsidc.org/cryosphere/glossary, Last accessed [26/01/2016].
- Trombotto, D., P. Wainstein & L. Arenson, 2014, Guía Terminológica de la Geocriología Sudamericana” / “Terminological Guide of the South American Geocryology, 1a ed. 128 pp. [Link]
- UNESCO-WMO, 2012, International Glossary of Hydrology, 3rd edition, WMO-No. 385. [Link]
Snowfall which has an increased rate.
2021-04-14T18:57:18.275Z
intense snowfall
heavy snow
intense snow
envoCryo
envoPolar
This generally means snowfall accumulating to 4 inches or more in depth in 12 hours or less; or snowfall accumulating to 6 inches or more in depth in 24 hours or less. In forecasts, snowfall amounts are expressed as a range of values, e.g., "8 to 12 inches." However, in heavy snow situations where there is considerable uncertainty concerning the range of values, more appropriate phrases are used, such as "...up to 12 inches..." or alternatively "...8 inches or more...".
heavy snowfall
Snowfall which has an increased rate.
This generally means snowfall accumulating to 4 inches or more in depth in 12 hours or less; or snowfall accumulating to 6 inches or more in depth in 24 hours or less. In forecasts, snowfall amounts are expressed as a range of values, e.g., "8 to 12 inches." However, in heavy snow situations where there is considerable uncertainty concerning the range of values, more appropriate phrases are used, such as "...up to 12 inches..." or alternatively "...8 inches or more...".
A water ice crystal which is constituted by water molecules aligned in a hexagonal array.
snowflake
snow crystal
A water ice crystal which is constituted by water molecules aligned in a hexagonal array.
snowflake
Snow crystals and snowflakes are often noted as synonyms, however, the term "snowflake" is generally used more loosely. Some sites mention that snow crystals refer to individual crystals of ice, while the term "snowflake" can refer both to an individual crystal of ice and to a bundle of snow crystals. Please see here [https://github.com/EnvironmentOntology/envo/issues/998#issuecomment-685649444]
A surface layer which is composed primarily of soil.
2019-04-12T17:35:13Z
envoNceas
soil surface layer
A soil which has a high bulk density and/or a low porosity. A compacted soil has a reduced rate of both water infiltration and drainage
compacted soil
A soil which has a high bulk density and/or a low porosity. A compacted soil has a reduced rate of both water infiltration and drainage
A layer that is composed primarily of soil.
soil layer
Texture which inheres in soil.
2021-12-26T21:49:12Z
soil texture
Water-holding capacity which inheres in some soil.
soil water-holding capacity
water-holding capacity of soil
Water-holding capacity which inheres in some soil.
The amount of a carbon atom when measured in environmental material.
environmental material carbon atom amount
amount of carbon atom in environmental material
The amount of a carbon atom when measured in soil.
soil carbon atom amount
amount of carbon atom in soil
The amount of a carbon atom when measured in water.
water carbon atom amount
amount of carbon atom in water
The amount of a nitrogen atom when measured in environmental material.
environmental material nitrogen atom amount
amount of nitrogen atom in environmental material
The amount of a nitrogen atom when measured in soil.
soil nitrogen atom amount
amount of nitrogen atom in soil
The amount of a nitrogen atom when measured in water.
water nitrogen atom amount
amount of nitrogen atom in water
The temperature of some environmental material.
environmental material temperature
temperature of environmental material
The temperature of some air.
air temperature
temperature of air
The quality of a environmental system process.
quality of environmental system process
environmental system process quality
The porosity of some soil.
soil porosity
porosity of soil
The composition of some soil.
soil composition
composition of soil
The structure of some soil.
soil structure
structure of soil
The temperature of some soil.
soil temperature
temperature of soil
The temperature of some water.
water temperature
temperature of water
The composition of some water.
water composition
composition of water
The color of some soil.
soil color
color of soil
The porosity of some snow.
snow porosity
porosity of snow
The porosity of some water ice.
water ice porosity
porosity of water ice
Any anatomical entity (FBbt:10000000) that develops from some germ layer (FBbt:00000110).
fly_anatomy.ontology
FBbt:00000000
germ layer derivative
Any anatomical entity (FBbt:10000000) that develops from some germ layer (FBbt:00000110).
FlyBase:FBrf0043441
FlyBase:FBrf0053832
An individual member of the species Drosophila melanogaster.
CARO:0000012
NCBITaxon:7227
UBERON:0000468
fly_anatomy.ontology
Drosophila
whole organism
FBbt:00000001
organism
An individual member of the species Drosophila melanogaster.
https://orcid.org/0000-0002-7073-9172
One of the three main divisions of the whole organism formed from groups of segments.
UBERON:6000002
fly_anatomy.ontology
FBbt:00000002
tagma
One of the three main divisions of the whole organism formed from groups of segments.
FBC:GG
One of the repeated divisions of the whole organism.
UBERON:0000914
fly_anatomy.ontology
FBbt:00000003
segment
One of the repeated divisions of the whole organism.
FBC:GG
Anterior part of the organism, including mouthparts, some sensory structures and the brain.
UBERON:6000004
fly_anatomy.ontology
FBbt:00000004
head
Anterior part of the organism, including mouthparts, some sensory structures and the brain.
https://orcid.org/0000-0002-1373-1705
Head segment derived from the second embryonic segment (between the labral and antennal segments). In the larva, this segment includes Bolwig's organ.
UBERON:6000005
fly_anatomy.ontology
acron
FBbt:00000005
While classically this structure is not considered to be a segment, but rather to be the non-segmental acron - anterior to the first segment, this ontology follows Schmidt-Ott and colleagues (Schmidt-Ott et al., 1994, and Schmidt-Ott and Technau, 1992) in considering it to be the second segment (posterior to the labral segment in the segmenting embryo). This is based on relating gene expression in the early segmenting embryo to the effects of loss of function mutations of these genes on formation of larval head structures.
ocular segment
Head segment derived from the second embryonic segment (between the labral and antennal segments). In the larva, this segment includes Bolwig's organ.
FlyBase:FBrf0055841
FlyBase:FBrf0075072
Any segment (FBbt:00000003) that is part of some head (FBbt:00000004).
UBERON:6000006
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.
UBERON:6000007
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
Anteriormost procephalic segment, anterior to the ocular segment. In the adult it bears the clypeo-labrum.
UBERON:6000008
fly_anatomy.ontology
clypeo-labrum
FBbt:00000008
labral segment
Anteriormost procephalic segment, anterior to the ocular segment. In the adult it bears the clypeo-labrum.
FlyBase:FBrf0055841
FlyBase:FBrf0075072
FlyBase:FBrf0089570
Segment anterior to the intercalary segment. In the adult it bears the antennae.
UBERON:6000009
fly_anatomy.ontology
FBbt:00000009
antennal segment
Segment anterior to the intercalary segment. In the adult it bears the antennae.
https://orcid.org/0000-0002-7073-9172
.
UBERON:0000922
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.
https://orcid.org/0000-0002-7073-9172
Complex primordium that is formed during gastrulation (stage 6-7), when anlagen invaginate from the monolayer of the cellular blastoderm (Campos-Ortega and Hartenstein, 1997; Hartenstein, 2004). The invaginated anlagen become organized into the middle two layers of a three-layered tube structure (Campos-Ortega and Hartenstein, 1997). These three layers correspond to the three germ layers of the endoderm, mesoderm and ectoderm (from inner to outer, respectively), with each layer having distinct cell division patterns and cell fates (Campos-Ortega and Hartenstein, 1997).
UBERON:0000923
fly_anatomy.ontology
FBbt:00000110
germ layer
Complex primordium that is formed during gastrulation (stage 6-7), when anlagen invaginate from the monolayer of the cellular blastoderm (Campos-Ortega and Hartenstein, 1997; Hartenstein, 2004). The invaginated anlagen become organized into the middle two layers of a three-layered tube structure (Campos-Ortega and Hartenstein, 1997). These three layers correspond to the three germ layers of the endoderm, mesoderm and ectoderm (from inner to outer, respectively), with each layer having distinct cell division patterns and cell fates (Campos-Ortega and Hartenstein, 1997).
FlyBase:FBrf0089570
FlyBase:FBrf0155831
FlyBase:FBrf0178740
Outermost germ layer of the embryo (Campos-Ortega and Hartenstein, 1997). It is formed from the ectoderm anlage, which includes the cells of the cellular blastoderm monolayer that do not invaginate during gastrulation (Campos-Ortega and Hartenstein, 1997).
UBERON:0000924
fly_anatomy.ontology
FBbt:00000111
ectoderm
Outermost germ layer of the embryo (Campos-Ortega and Hartenstein, 1997). It is formed from the ectoderm anlage, which includes the cells of the cellular blastoderm monolayer that do not invaginate during gastrulation (Campos-Ortega and Hartenstein, 1997).
FlyBase:FBrf0089570
FlyBase:FBrf0155831
FlyBase:FBrf0244630
The region of the ectoderm anterior to the cephalic furrow.
UBERON:6000119
fly_anatomy.ontology
FBbt:00000119
anterior ectoderm
The region of the ectoderm anterior to the cephalic furrow.
https://orcid.org/0000-0002-7073-9172
Any tagma (FBbt:00000002) that is part of some embryo (FBbt:00000052).
UBERON:6000137
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).
UBERON:6000154
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).
UBERON:0008816
fly_anatomy.ontology
FBbt:00000155
embryonic head
Any head (FBbt:00000004) that is part of some embryo (FBbt:00000052).
FBC:Autogenerated
Any ocular segment (FBbt:00000005) that is part of some embryo (FBbt:00000052).
fly_anatomy.ontology
embryonic acron
FBbt:00000156
embryonic ocular segment
Any ocular segment (FBbt:00000005) that is part of some embryo (FBbt:00000052).
FBC:Autogenerated
Any segment (FBbt:00000003) that is part of some embryonic head (FBbt:00000155).
UBERON:6000157
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 embryo (FBbt:00000052).
UBERON:6000158
fly_anatomy.ontology
FBbt:00000158
embryonic procephalic segment
Any procephalic segment (FBbt:00000007) that is part of some embryo (FBbt:00000052).
FBC:Autogenerated
Any labral segment (FBbt:00000008) that is part of some embryo (FBbt:00000052).
fly_anatomy.ontology
FBbt:00000159
embryonic labral segment
Any labral segment (FBbt:00000008) that is part of some embryo (FBbt:00000052).
FBC:Autogenerated
Any antennal segment (FBbt:00000009) that is part of some embryo (FBbt:00000052).
UBERON:6000160
fly_anatomy.ontology
FBbt:00000160
embryonic antennal segment
Any antennal segment (FBbt:00000009) that is part of some embryo (FBbt:00000052).
FBC:Autogenerated
Primordium of the late extended germ band and closure embryo that gives rise to the embryonic/larval optic anlage. It corresponds to the middle region that develops from the visual primordium.
UBERON:6000186
fly_anatomy.ontology
FBbt:00000186
embryonic optic lobe primordium
Primordium of the late extended germ band and closure embryo that gives rise to the embryonic/larval optic anlage. It corresponds to the middle region that develops from the visual primordium.
FBC:VH
FlyBase:FBrf0089570
FlyBase:FBrf0151275
https://orcid.org/0000-0002-7073-9172
Apodeme that is part of the embryo/larva. Apodemes are not a continuous structure, but are split into two halves. In the embryo, this break is visible laterally. In the larva, the dorsal and ventral halves in the thoracic and abdominal segments are staggered, with the dorsal part being posterior to the ventral one.
larval apodeme
fly_anatomy.ontology
FBbt:00001005
embryonic/larval apodeme
Apodeme that is part of the embryo/larva. Apodemes are not a continuous structure, but are split into two halves. In the embryo, this break is visible laterally. In the larva, the dorsal and ventral halves in the thoracic and abdominal segments are staggered, with the dorsal part being posterior to the ventral one.
FBC:SPR
FlyBase:FBrf0089570
The sum of all the structures in the embryo that will develop into the embryonic/larval nervous system.
UBERON:6001055
fly_anatomy.ontology
embryonic nervous system
FBbt:00001055
presumptive embryonic/larval nervous system
The sum of all the structures in the embryo that will develop into the embryonic/larval nervous system.
FlyBase:FBrf0031012
embryonic nervous system
https://orcid.org/0000-0002-7073-9172
The sum of all the structures in the embryo that will develop into the embryonic/larval central nervous system.
UBERON:6001056
fly_anatomy.ontology
embryonic central nervous system
FBbt:00001056
presumptive embryonic/larval central nervous system
The sum of all the structures in the embryo that will develop into the embryonic/larval central nervous system.
FlyBase:FBrf0031012
embryonic central nervous system
https://orcid.org/0000-0002-7073-9172
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).
UBERON:0002346
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
Tissue which becomes morphologically distinct shortly after cephalic furrow formation as two strips of about 80 enlarged cells which extend dorso-ventrally on either side of the developing head. It gives rise to neuroblasts of the brain.
pregnathal neuroectoderm
procephalic neuroectoderm
fly_anatomy.ontology
FBbt:00001058
procephalic neurogenic region
Tissue which becomes morphologically distinct shortly after cephalic furrow formation as two strips of about 80 enlarged cells which extend dorso-ventrally on either side of the developing head. It gives rise to neuroblasts of the brain.
FlyBase:FBrf0089570
FlyBase:FBrf0090460
pregnathal neuroectoderm
FlyBase:FBrf0161020
procephalic neuroectoderm
FlyBase:FBrf0161020
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.
UBERON:6001059
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
https://orcid.org/0000-0002-7073-9172
Brain of the embryo, consisting of the protocerebrum, deutocerebrum and tritocerebrum (Urbach and Technau, 2003; Crews, 2019). It develops from the procephalic neurogenic region (Urbach and Technau, 2003).
UBERON:6001060
VFB:FBbt_00001060
fly_anatomy.ontology
FBbt:00001060
embryonic brain
Brain of the embryo, consisting of the protocerebrum, deutocerebrum and tritocerebrum (Urbach and Technau, 2003; Crews, 2019). It develops from the procephalic neurogenic region (Urbach and Technau, 2003).
FlyBase:FBrf0161020
FlyBase:FBrf0244240
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
Neuromere of the embryonic supraesophageal ganglion, anterior to the subesophageal ganglion.
VFB:FBbt_00001062
fly_anatomy.ontology
FBbt:00001062
embryonic supraesophageal neuromere
Neuromere of the embryonic supraesophageal ganglion, anterior to the subesophageal ganglion.
https://orcid.org/0000-0002-1373-1705
Protocerebrum of the embryo. It is the most anterior of the supraesophageal neuromeres, located anterior to the deutocerebral neuromere. It is derived from the labral and ocular segments.
FBbt:00001926
VFB:FBbt_00001066
neuromere b1
fly_anatomy.ontology
procephalic lobe
FBbt:00001066
embryonic protocerebrum
Protocerebrum of the embryo. It is the most anterior of the supraesophageal neuromeres, located anterior to the deutocerebral neuromere. It is derived from the labral and ocular segments.
FlyBase:FBrf0089570
neuromere b1
FlyBase:FBrf0084032
procephalic lobe
FlyBase:FBrf0045366
Deutocerebrum of the embryo. It is the middle one of the three supraesophageal neuromeres, posterior to the protocerebrum and anterior to the tritocerebrum. It is part of the antennal segment.
FBbt:00001958
VFB:FBbt_00001067
embryonic deuterocerebral neuromere
embryonic deuterocerebrum
embryonic deutocerebral neuromere
neuromere b2
fly_anatomy.ontology
FBbt:00001067
embryonic deutocerebrum
Deutocerebrum of the embryo. It is the middle one of the three supraesophageal neuromeres, posterior to the protocerebrum and anterior to the tritocerebrum. It is part of the antennal segment.
FlyBase:FBrf0089570
FlyBase:FBrf0161020
neuromere b2
FlyBase:FBrf0084032
Embryonic structure that will develop into a larval imaginal tissue, which will later form an adult structure (Cohen, 1993).
UBERON:6001648
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).
UBERON:6001649
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.
UBERON:6001652
fly_anatomy.ontology
eye-antennal disc specific anlage
FBbt:00001652
eye-antennal disc primordium
Primordium from which the eye-antennal disc develops.
FBC:SPR
UBERON:0002548
fly_anatomy.ontology
FBbt:00001727
larva
Any tagma (FBbt:00000002) that is part of some larva (FBbt:00001727).
UBERON:6001728
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).
UBERON:6001729
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).
UBERON:6001730
fly_anatomy.ontology
FBbt:00001730
larval head
Any head (FBbt:00000004) that is part of some larva (FBbt:00001727).
FBC:Autogenerated
Any ocular segment (FBbt:00000005) that is part of some larva (FBbt:00001727).
UBERON:6001731
fly_anatomy.ontology
larval acron
FBbt:00001731
larval ocular segment
Any ocular segment (FBbt:00000005) that is part of some larva (FBbt:00001727).
FBC:Autogenerated
Any segment (FBbt:00000003) that is part of some larval head (FBbt:00001730).
UBERON:6001732
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 larva (FBbt:00001727).
UBERON:6001733
fly_anatomy.ontology
FBbt:00001733
larval procephalic segment
Any procephalic segment (FBbt:00000007) that is part of some larva (FBbt:00001727).
FBC:Autogenerated
Any labral segment (FBbt:00000008) that is part of some larva (FBbt:00001727).
UBERON:6001734
fly_anatomy.ontology
FBbt:00001734
larval labral segment
Any labral segment (FBbt:00000008) that is part of some larva (FBbt:00001727).
FBC:Autogenerated
Any antennal segment (FBbt:00000009) that is part of some larva (FBbt:00001727).
UBERON:6001735
fly_anatomy.ontology
FBbt:00001735
larval antennal segment
Any antennal segment (FBbt:00000009) that is part of some larva (FBbt:00001727).
FBC:Autogenerated
Imaginal tissue that is found in the larva and will develop into an adult structure during metamorphosis.
UBERON:6001760
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.
UBERON:0000939
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).
UBERON:6001766
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
UBERON:6001911
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
Neuromere of the larval nervous system.
VFB:FBbt_00001912
fly_anatomy.ontology
FBbt:00001912
larval neuromere
Neuromere of the larval nervous system.
FlyBase:FBrf0047815
FlyBase:FBrf0084032
FlyBase:FBrf0089217
FlyBase:FBrf0105282
Central nervous system of the embryo/larva.
UBERON:6001919
VFB:FBbt_00001919
embryonic/larval CNS
larval central nervous system
fly_anatomy.ontology
FBbt:00001919
embryonic/larval central nervous system
Central nervous system of the embryo/larva.
FBC:SPR
Supraesophageal ganglion of the late embryo or larva, consisting of the protocerebrum, deutocerebrum and tritocerebrum (Urbach and Technau, 2003; Li et al., 2014; Crews, 2019).
UBERON:6001920
VFB:FBbt_00001920
embryonic/larval SPG
embryonic/larval supraesophageal complex
embryonic/larval supraesophageal ganglion
larval SPG
larval brain
larval cerebral ganglion
larval supraesophageal ganglion
fly_anatomy.ontology
FBbt:00001920
embryonic/larval brain
Supraesophageal ganglion of the late embryo or larva, consisting of the protocerebrum, deutocerebrum and tritocerebrum (Urbach and Technau, 2003; Li et al., 2014; Crews, 2019).
FlyBase:FBrf0161020
FlyBase:FBrf0225812
FlyBase:FBrf0244240
embryonic/larval supraesophageal complex
FlyBase:FBrf0225812
Protocerebrum of the embryo/larva.
UBERON:6001925
VFB:FBbt_00001925
larvalbrain_neuropil:392
larvalbrain_neuropil:570
embryonic/larval protocerebrum
fly_anatomy.ontology
FBbt:00001925
larval protocerebrum
Protocerebrum of the embryo/larva.
FBC:SPR
Region of the embryonic or larval brain that contains the neuroepithelial cells that will give rise to the adult optic lobe, and the larval optic neuropil that processes visual information in the larva.
VFB:FBbt_00001930
larvalbrain_neuropil:391
larvalbrain_neuropil:569
larval optic lobe
fly_anatomy.ontology
FBbt:00001930
embryonic/larval optic lobe
Region of the embryonic or larval brain that contains the neuroepithelial cells that will give rise to the adult optic lobe, and the larval optic neuropil that processes visual information in the larva.
FlyBase:FBrf0052913
FlyBase:FBrf0064800
FlyBase:FBrf0215208
Deutocerebrum of the embryo/larva.
VFB:FBbt_00001957
larvalbrain_neuropil:337
larvalbrain_neuropil:515
embryonic/larval deuterocerebrum
embryonic/larval deutocerebrum
larval deuterocerebrum
fly_anatomy.ontology
FBbt:00001957
larval deutocerebrum
Deutocerebrum of the embryo/larva.
FBC:SPR
Any sense organ (FBbt:00005155) that is part of some larva (FBbt:00001727).
UBERON:6002639
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 embryonic/larval sense organ (FBbt:00002639) that is part of some ocular segment (FBbt:00000005).
UBERON:6002642
VFB:FBbt_00002642
embryonic/larval ocular segment sensillum
fly_anatomy.ontology
FBbt:00002642
larval ocular segment sense organ
Any embryonic/larval sense organ (FBbt:00002639) that is part of some ocular segment (FBbt:00000005).
FBC:Autogenerated
Any embryonic/larval sense organ (FBbt:00002639) that is part of some labral segment (FBbt:00000008).
FBbt:00002650
VFB:FBbt_00002649
larval labral segment sense organ
fly_anatomy.ontology
FBbt:00002649
embryonic/larval labral segment sense organ
Any embryonic/larval sense organ (FBbt:00002639) that is part of some labral segment (FBbt:00000008).
FBC:Autogenerated
Any embryonic/larval sense organ (FBbt:00002639) that is part of some antennal segment (FBbt:00000009).
VFB:FBbt_00002654
embryonic/larval antennal segment sensillum
fly_anatomy.ontology
FBbt:00002654
larval antennal segment sense organ
Any embryonic/larval sense organ (FBbt:00002639) that is part of some antennal segment (FBbt:00000009).
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.
UBERON:0003142
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.
UBERON:0003143
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
.
UBERON:0007023
fly_anatomy.ontology
imago
FBbt:00003004
adult
.
FlyBase:FBrf0036849
Any tagma (FBbt:00000002) that is part of some adult (FBbt:00003004).
UBERON:6003005
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.
UBERON:6003006
fly_anatomy.ontology
FBbt:00003006
adult segment
Segment of the adult.
FBC:SPR
Head of the adult organism.
UBERON:6003007
fly_anatomy.ontology
FBbt:00003007
adult head
Head of the adult organism.
FBC:SPR
Any ocular segment (FBbt:00000005) that is part of some adult (FBbt:00003004).
fly_anatomy.ontology
adult acron
FBbt:00003008
adult ocular segment
Any ocular segment (FBbt:00000005) that is part of some adult (FBbt:00003004).
FBC:Autogenerated
Segment of the adult head.
UBERON:6003009
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 (FBbt:00003004).
UBERON:6003010
fly_anatomy.ontology
FBbt:00003010
adult procephalic segment
Any procephalic segment (FBbt:00000007) that is part of some adult (FBbt:00003004).
FBC:Autogenerated
Any labral segment (FBbt:00000008) that is part of some adult (FBbt:00003004).
UBERON:6003011
fly_anatomy.ontology
FBbt:00003011
adult labral segment
Any labral segment (FBbt:00000008) that is part of some adult (FBbt:00003004).
FBC:Autogenerated
Any antennal segment (FBbt:00000009) that is part of some adult (FBbt:00003004).
FBbt:00004512
UBERON:6003012
adult antennal structure
fly_anatomy.ontology
FBbt:00003012
adult antennal segment
Any antennal segment (FBbt:00000009) that is part of some adult (FBbt:00003004).
FBC:Autogenerated
Digestive system of the pupa or adult.
fly_anatomy.ontology
FBbt:00003123
pupal/adult digestive system
Digestive system of the pupa or adult.
FlyBase:FBrf0007735
The entire anatomical structure through which food and its digestion products are ingested, digested and excreted. At its anterior and posterior ends this includes structures that are not foregut or hindgut.
UBERON:0001555
fly_anatomy.ontology
FBbt:00003125
alimentary canal
The entire anatomical structure through which food and its digestion products are ingested, digested and excreted. At its anterior and posterior ends this includes structures that are not foregut or hindgut.
https://orcid.org/0000-0002-7073-9172
Muscle system of the adult.
fly_anatomy.ontology
FBbt:00003218
adult muscle system
Muscle system of the adult.
FlyBase:FBrf0007735
Any muscle cell (FBbt:00005074) that is part of some adult somatic muscle (FBbt:00058784).
UBERON:6003259
adult skeletal muscle cell
fly_anatomy.ontology
FBbt:00003259
adult somatic muscle cell
Any muscle cell (FBbt:00005074) that is part of some adult somatic muscle (FBbt:00058784).
FBC:Autogenerated
Any muscle cell (FBbt:00005074) that is part of some adult somatic muscle of head (FBbt:00058785).
skeletal muscle cell of head
fly_anatomy.ontology
FBbt:00003260
adult somatic muscle cell of head
Any muscle cell (FBbt:00005074) that is part of some adult somatic muscle of head (FBbt:00058785).
FBC:Autogenerated
Apodeme that is part of an adult.
fly_anatomy.ontology
FBbt:00003516
adult apodeme
Apodeme that is part of an adult.
FBC:SPR
Any nervous system (FBbt:00005093) that is part of some adult (FBbt:00003004).
UBERON:6003559
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
Central nervous system of the adult.
UBERON:6003623
VFB:FBbt_00003623
adult CNS
fly_anatomy.ontology
FBbt:00003623
adult central nervous system
Central nervous system of the adult.
FBC:SPR
Portion of the adult central nervous system found in the head, consisting of the cerebral and gnathal ganglia (Ito et al., 2014).
UBERON:6003624
VFB:FBbt_00003624
fly_anatomy.ontology
FBbt:00003624
adult brain
Portion of the adult central nervous system found in the head, consisting of the cerebral and gnathal ganglia (Ito et al., 2014).
FlyBase:FBrf0224194
The pre-oral neuropils of the brain located above and some of it below the esophagus, comprising three fused ganglia (protocerebrum, deutocerebrum, and tritocerebrum) in the head.
UBERON:6003626
VFB:FBbt_00003626
fly_anatomy.ontology
SPG
FBbt:00003626
In the adult, this region is referred to as cerebral ganglia (Ito et al., 2014).
supraesophageal ganglion
The pre-oral neuropils of the brain located above and some of it below the esophagus, comprising three fused ganglia (protocerebrum, deutocerebrum, and tritocerebrum) in the head.
FlyBase:FBrf0224194
The most anterior neuromere of the central nervous system, developing from neuroblasts of the labral and ocular segments (Urbach and Technau, 2003; Ito et al., 2014). The protocerebrum comprises many discrete neuropil regions including the central complex and mushroom bodies (Ito et al., 2014).
UBERON:6003627
VFB:FBbt_00003627
PR
protocerebral neuromere
fly_anatomy.ontology
FBbt:00003627
Urbach and Technau (2003) divide the protocerebrum into labral and ocular neuromeres.
protocerebrum
The most anterior neuromere of the central nervous system, developing from neuroblasts of the labral and ocular segments (Urbach and Technau, 2003; Ito et al., 2014). The protocerebrum comprises many discrete neuropil regions including the central complex and mushroom bodies (Ito et al., 2014).
FlyBase:FBrf0161020
FlyBase:FBrf0224194
PR
FlyBase:FBrf0224194
protocerebral neuromere
FlyBase:FBrf0092819
Neuromere of the antennal segment, located between the protocerebrum and tritocerebrum, connected to antennal nerve trunk (Urbach and Technau, 2003; Ito et al., 2014).
VFB:FBbt_00003923
deuterocerebral neuromere
deuterocerebrum
deutocerebral neuromere
fly_anatomy.ontology
FBbt:00003923
deutocerebrum
Neuromere of the antennal segment, located between the protocerebrum and tritocerebrum, connected to antennal nerve trunk (Urbach and Technau, 2003; Ito et al., 2014).
FlyBase:FBrf0161020
FlyBase:FBrf0224194
deuterocerebral neuromere
FlyBase:FBrf0092819
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 sensillum (FBbt:00007152) that is part of some head (FBbt:00000004).
UBERON:0000963
VFB:FBbt_00004114
fly_anatomy.ontology
FBbt:00004114
head sensillum
Any sensillum (FBbt:00007152) that is part of some head (FBbt:00000004).
FBC:Autogenerated
Anlage that develops into the ventral ectoderm. It is found in the lateroventral trunk region of the embryo at the cellular blastoderm stage, prior to gastrulation (Stathopoulos and Newcomb, 2020).
presumptive neuroectoderm
ventral/neuroectoderm anlage
fly_anatomy.ontology
Asn/A VenEc
FBbt:00004204
ventral ectoderm anlage
Anlage that develops into the ventral ectoderm. It is found in the lateroventral trunk region of the embryo at the cellular blastoderm stage, prior to gastrulation (Stathopoulos and Newcomb, 2020).
FlyBase:FBrf0244630
presumptive neuroectoderm
FlyBase:FBrf0244630
ventral/neuroectoderm anlage
FlyBase:FBrf0244630
Asn/A VenEc
https://orcid.org/0000-0002-7073-9172
Any developing material anatomical entity (FBbt:00007006) that is part of some embryo (FBbt:00000052).
UBERON:0002050
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.
https://orcid.org/0000-0002-7073-9172
A bilaterally paired compound sense organ of the adult head that functions in visual perception.
UBERON:0000018
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.
https://orcid.org/0000-0002-7073-9172
A division of the whole organism into specialized systems.
UBERON:0000467
fly_anatomy.ontology
FBbt:00004856
organ system
A division of the whole organism into specialized systems.
FBC:GG
The organ system that forms the covering layer of the animal.
UBERON:0002416
fly_anatomy.ontology
FBbt:00004969
integumentary system
The organ system that forms the covering layer of the animal.
FBC:GG
The outer non-living layer of the integumentary system that is secreted by the underlying epidermis.
UBERON:0001001
fly_anatomy.ontology
FBbt:00004970
cuticle
The outer non-living layer of the integumentary system that is secreted by the underlying epidermis.
FlyBase:FBrf0064790
The middle layer of the procuticle of the pupa, that forms after the pupal molt. It is composed of chitin, and it has a lighter pigmentation and less dense structure than the exocuticle. This layer is only found in pupa.
UBERON:0003202
fly_anatomy.ontology
FBbt:00004974
pupal endocuticle
The middle layer of the procuticle of the pupa, that forms after the pupal molt. It is composed of chitin, and it has a lighter pigmentation and less dense structure than the exocuticle. This layer is only found in pupa.
FlyBase:FBrf0064790
FlyBase:FBrf0111704
Lamellate innermost layer of cuticle between the epicuticle and the epidermis. It consists largely of protein and chitin. Within each lamella layer, chitin-protein fibers are arranged parallel to each other and to the surface of the underlying epidermis. The lamellae themselves are arranged in a helicoid fashion.
fly_anatomy.ontology
FBbt:00004975
procuticle
Lamellate innermost layer of cuticle between the epicuticle and the epidermis. It consists largely of protein and chitin. Within each lamella layer, chitin-protein fibers are arranged parallel to each other and to the surface of the underlying epidermis. The lamellae themselves are arranged in a helicoid fashion.
FlyBase:FBrf0064790
Non-innervated projection of the cuticle around an actin-rich cellular process of an underlying epidermal cell.
UBERON:6004979
fly_anatomy.ontology
cell hair
FBbt:00004979
trichome
Non-innervated projection of the cuticle around an actin-rich cellular process of an underlying epidermal cell.
https://orcid.org/0000-0002-7073-9172
Cuticle of the late embryo or larva.
UBERON:6004983
larval cuticle
fly_anatomy.ontology
FBbt:00004983
embryonic/larval cuticle
Cuticle of the late embryo or larva.
FlyBase:FBrf0234504
Cuticle of the pupal stage.
fly_anatomy.ontology
FBbt:00004991
pupal cuticle
Cuticle of the pupal stage.
https://orcid.org/0000-0001-5948-3092
Tissue composed of epithelial cells. It secretes and underlies the cuticle.
UBERON:0007376
fly_anatomy.ontology
hypoderm
hypodermis
FBbt:00004993
epidermis
Tissue composed of epithelial cells. It secretes and underlies the cuticle.
FlyBase:FBrf0064790
The organ system involved in the absorption of nutrients.
UBERON:0001007
fly_anatomy.ontology
FBbt:00005055
digestive system
The organ system involved in the absorption of nutrients.
FBC:GG
Comprising somatic and visceral muscles, the muscle system consist of a multitude of contractile fibers arranged in groups and layers.
fly_anatomy.ontology
FBbt:00005069
muscle system
Comprising somatic and visceral muscles, the muscle system consist of a multitude of contractile fibers arranged in groups and layers.
FlyBase:FBrf0007735
FlyBase:FBrf0031016
FlyBase:FBrf0041814
FlyBase:FBrf0044229
FlyBase:FBrf0064793
Muscle cell of the body, excluding the muscles associated with the intestinal tract. It is attached at either end to the cuticle. Fibers of somatic muscles are multinucleate, with the contractile material grouped into fibrils. Somatic muscles appear striated.
CL:0008004
skeletal muscle cell
fly_anatomy.ontology
FBbt:00005073
somatic muscle cell
Muscle cell of the body, excluding the muscles associated with the intestinal tract. It is attached at either end to the cuticle. Fibers of somatic muscles are multinucleate, with the contractile material grouped into fibrils. Somatic muscles appear striated.
FlyBase:FBrf0239227
FlyBase:FBrf0239342
Somatic, contractile cell that makes up a muscle. It is formed by several fusion events between fusion competent myoblasts and one founder cell.
CL:0000187
fly_anatomy.ontology
muscle fiber
myofiber
myofibril
FBbt:00005074
In contrast to vertebrates, in Drosophila embryos and larva, each muscle is a single myotube (Maqbool and Jagla, 2007).
muscle cell
Somatic, contractile cell that makes up a muscle. It is formed by several fusion events between fusion competent myoblasts and one founder cell.
FlyBase:FBrf0051585
FlyBase:FBrf0205186
FlyBase:FBrf0217289
muscle fiber
FlyBase:FBrf0217289
myofiber
FlyBase:FBrf0217289
myofibril
FlyBase:FBrf0212347
The place where the muscle system attaches to the cuticle.
fly_anatomy.ontology
FBbt:00005089
muscle attachment site
The place where the muscle system attaches to the cuticle.
FBC:GG
A cuticular ingrowth of the exoskeleton, sometimes only a peg, frequently ridge-like, and often serving as a muscle attachment site. Does not generally correspond to superficial invaginations.
fly_anatomy.ontology
FBbt:00005091
apodeme
A cuticular ingrowth of the exoskeleton, sometimes only a peg, frequently ridge-like, and often serving as a muscle attachment site. Does not generally correspond to superficial invaginations.
FlyBase:FBrf0111704
FlyBase:FBrf0166419
All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems.
UBERON:0001016
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
Collective name for all the nerve centers and their connective in the insect's body. In the context of Drosophila refers to the part of the nervous system consisting of the brain and ventral ganglia.
UBERON:0001017
VFB:FBbt_00005094
fly_anatomy.ontology
CNS
FBbt:00005094
central nervous system
Collective name for all the nerve centers and their connective in the insect's body. In the context of Drosophila refers to the part of the nervous system consisting of the brain and ventral ganglia.
FBC:GG
FlyBase:FBrf0166419
Anterodorsal portion of the central nervous system. The neuromeres considered to be part of the brain vary by stage. In the larva, the cerebral (supraesophageal) neuromeres, which form a bilateral pair of lobes, constitute the brain (Urbach and Technau, 2003; Li et al., 2014; Crews, 2019). During metamorphosis, the gnathal ganglion separates from the prothoracic neuromere and fuses with the supraesophageal ganglion, to become the ventral part of the adult brain (Ito et al., 2014; Hartenstein et al., 2018; Kendroud et al., 2018).
UBERON:0000955
VFB:FBbt_00005095
fly_anatomy.ontology
FBbt:00005095
brain
Anterodorsal portion of the central nervous system. The neuromeres considered to be part of the brain vary by stage. In the larva, the cerebral (supraesophageal) neuromeres, which form a bilateral pair of lobes, constitute the brain (Urbach and Technau, 2003; Li et al., 2014; Crews, 2019). During metamorphosis, the gnathal ganglion separates from the prothoracic neuromere and fuses with the supraesophageal ganglion, to become the ventral part of the adult brain (Ito et al., 2014; Hartenstein et al., 2018; Kendroud et al., 2018).
FlyBase:FBrf0161020
FlyBase:FBrf0224194
FlyBase:FBrf0225812
FlyBase:FBrf0237251
FlyBase:FBrf0237252
FlyBase:FBrf0244240
Any of a number of aggregations of neurons, glial cells and their processes, and surrounded by a glial cell and connective tissue sheath (plural: ganglia).
VFB:FBbt_00005137
fly_anatomy.ontology
FBbt:00005137
ganglion
A segmental subdivision of the nervous system.
VFB:FBbt_00005140
fly_anatomy.ontology
ganglion
FBbt:00005140
neuromere
A segmental subdivision of the nervous system.
https://orcid.org/0000-0002-7073-9172
Multicellular anatomical structure with largely bona fide boundary that transduces some sensory stimulus to the nervous system.
UBERON:0000020
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.
https://orcid.org/0000-0002-7073-9172
A light sensitive sense organ.
UBERON:0000970
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
Sensory organ that has external structures that detect mechanical or chemical stimuli.
UBERON:6005168
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.
https://orcid.org/0000-0002-7073-9172
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:GG
https://orcid.org/0000-0002-7073-9172
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:MA
FlyBase:FBrf0089570
https://orcid.org/0000-0002-7073-9172
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.
UBERON:0004734
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:GG
https://orcid.org/0000-0002-7073-9172
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.
https://orcid.org/0000-0002-7073-9172
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.
https://orcid.org/0000-0002-7073-9172
A collective term for stages 16 and 17.
UBERON:0000323
fly_anatomy.ontology
FBbt:00005333
DEPRECATION WARNING.
late embryo
A collective term for stages 16 and 17.
https://orcid.org/0000-0002-7073-9172
A posterior part of the alimentary canal derived from the ectoderm. It extends anteriorly from close to the point of attachment of the Malpighian tubules to the anus. It is lined on its luminal side by an impermeable cuticle (Skaer, 1993).
UBERON:0001046
fly_anatomy.ontology
FBbt:00005384
Adult and larval hindguts express the transcription factor brachyenteron (Sawyer et al., 2017).
hindgut
A posterior part of the alimentary canal derived from the ectoderm. It extends anteriorly from close to the point of attachment of the Malpighian tubules to the anus. It is lined on its luminal side by an impermeable cuticle (Skaer, 1993).
FBC:GG
FlyBase:FBrf0064792
The sum of all the structures in the embryo that will develop into the embryonic/larval integumentary system.
fly_anatomy.ontology
embryonic integumentary system
FBbt:00005392
presumptive embryonic/larval integumentary system
The sum of all the structures in the embryo that will develop into the embryonic/larval integumentary system.
https://orcid.org/0000-0002-7073-9172
embryonic integumentary system
https://orcid.org/0000-0002-7073-9172
Integumentary system of the late embryo or larva.
UBERON:6005393
larval integumentary system
fly_anatomy.ontology
FBbt:00005393
embryonic/larval integumentary system
Integumentary system of the late embryo or larva.
https://orcid.org/0000-0001-5948-3092
Integumentary system of the prepupa.
fly_anatomy.ontology
FBbt:00005394
prepupal integumentary system
Integumentary system of the prepupa.
https://orcid.org/0000-0001-5948-3092
Epidermis of the embryo.
fly_anatomy.ontology
FBbt:00005397
embryonic epidermis
Epidermis of the embryo.
https://orcid.org/0000-0001-5948-3092
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 embryonic central brain in a stage 5 embryo. It will give rise to the central brain anlage.
Asn CenBr
fly_anatomy.ontology
A0ProcEC
procephalic ectoderm anlage in statu nascendi
FBbt:00005415
central brain anlage in statu nascendi
Anlage in statu nascendi of the embryonic central brain in a stage 5 embryo. It will give rise to the central brain anlage.
FBC:VH
Asn CenBr
https://orcid.org/0000-0002-7073-9172
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
https://orcid.org/0000-0002-7073-9172
Population of contiguous cells, typically arranged in one plane, that is morphologically indistinct from surrounding cells, but already corresponds to a later organ/tissue and can be identified based on gene expression or lineage tracing (Tomancak et al., 2002; Hartenstein, 2004).
UBERON:0007688
fly_anatomy.ontology
FBbt:00005426
anlage
Population of contiguous cells, typically arranged in one plane, that is morphologically indistinct from surrounding cells, but already corresponds to a later organ/tissue and can be identified based on gene expression or lineage tracing (Tomancak et al., 2002; Hartenstein, 2004).
FlyBase:FBrf0089570
FlyBase:FBrf0155831
FlyBase:FBrf0178740
Cells of the early embryo that will become the ectoderm following gastrulation (Campos-Ortega and Hartenstein, 1997). It remains at the surface of the embryo as the endodermal and mesodermal anlagen invaginate (Campos-Ortega and Hartenstein, 1997).
UBERON:6005427
fly_anatomy.ontology
FBbt:00005427
ectoderm anlage
Cells of the early embryo that will become the ectoderm following gastrulation (Campos-Ortega and Hartenstein, 1997). It remains at the surface of the embryo as the endodermal and mesodermal anlagen invaginate (Campos-Ortega and Hartenstein, 1997).
FlyBase:FBrf0089570
FlyBase:FBrf0155831
FlyBase:FBrf0244630
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
https://orcid.org/0000-0002-7073-9172
Precursor structure that can be recognised based on its distinct morphology and will give rise to one or more differentiated structures (Tomancak et al., 2002; Hartenstein, 2004). It develops from an anlage and may contain smaller anlage and primordia that will produce substructures (Tomancak et al., 2002).
UBERON:0001048
fly_anatomy.ontology
P
placode
FBbt:00005495
primordium
Precursor structure that can be recognised based on its distinct morphology and will give rise to one or more differentiated structures (Tomancak et al., 2002; Hartenstein, 2004). It develops from an anlage and may contain smaller anlage and primordia that will produce substructures (Tomancak et al., 2002).
FlyBase:FBrf0089570
FlyBase:FBrf0155831
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:VH
FlyBase:FBrf0089570
FlyBase:FBrf0151275
https://orcid.org/0000-0002-7073-9172
A(n) primordium that develops into some denticle field anlage and some anal pad primordium and some embryonic ventral epidermis and some imaginal disc primordium and some ventral apodeme anlage and some ventral trunk epidermis primordium. It develops from some ventral neurectoderm.
UBERON:6005533
fly_anatomy.ontology
P2 iVenEp
venEpiP2
FBbt:00005533
ventral epidermis primordium
A(n) primordium that develops into some denticle field anlage and some anal pad primordium and some embryonic ventral epidermis and some imaginal disc primordium and some ventral apodeme anlage and some ventral trunk epidermis primordium. It develops from some ventral neurectoderm.
FBC:Autogenerated
P2 iVenEp
https://orcid.org/0000-0002-7073-9172
Primordium of the embryonic central brain in the extended germ band and dorsal closure embryo.
P1 Cen Br
P3 CenBr
fly_anatomy.ontology
ProcEcP2
procephalic ectoderm primordium
FBbt:00005542
central brain primordium
Primordium of the embryonic central brain in the extended germ band and dorsal closure embryo.
FBC:VH
https://orcid.org/0000-0002-7073-9172
P1 Cen Br
https://orcid.org/0000-0002-7073-9172
P3 CenBr
https://orcid.org/0000-0002-7073-9172
Primordium that develops into a region of head epidermis.
fly_anatomy.ontology
HeadEpiP3
FBbt:00005547
head epidermis primordium
A(n) primordium that develops into some embryonic protocerebrum.
VFB:FBbt_00005549
fly_anatomy.ontology
ProtP3
FBbt:00005549
protocerebrum primordium
A(n) primordium that develops into some embryonic protocerebrum.
FBC:Autogenerated
Ventral region of the trunk ectoderm, which gives rise to the ventral epidermis and the central nervous system (Stathopoulos and Newcomb, 2020).
UBERON:6005558
neuroectoderm
neurogenic ectoderm
fly_anatomy.ontology
P2 VenEc
venEc
FBbt:00005558
ventral ectoderm
Ventral region of the trunk ectoderm, which gives rise to the ventral epidermis and the central nervous system (Stathopoulos and Newcomb, 2020).
FlyBase:FBrf0244630
FlyBase:FBrf0246683
neuroectoderm
FlyBase:FBrf0244630
neurogenic ectoderm
FlyBase:FBrf0246683
P2 VenEc
https://orcid.org/0000-0002-7073-9172
Brain of the embryo that excludes the optic lobes. It includes the protocerebrum, deutocerebrum and tritocerebrum.
VFB:FBbt_00005662
fly_anatomy.ontology
FBbt:00005662
embryonic central brain
Brain of the embryo that excludes the optic lobes. It includes the protocerebrum, deutocerebrum and tritocerebrum.
https://orcid.org/0000-0001-5948-3092
Epidermis of the embryonic head.
fly_anatomy.ontology
FBbt:00005741
embryonic head epidermis
Epidermis of the embryonic head.
https://orcid.org/0000-0001-5948-3092
Epidermal pouch in the embryonic head that incorporates the acron and dorsal regions of the head segments. It forms following the movement of the dorsal fold over the clypeolabrum and procephalic lobe.
fly_anatomy.ontology
FBbt:00005743
Note - possible redundancy between primordium term and embryonic term. ds060616.
embryonic dorsal pouch
Epidermal pouch in the embryonic head that incorporates the acron and dorsal regions of the head segments. It forms following the movement of the dorsal fold over the clypeolabrum and procephalic lobe.
FlyBase:FBrf0041814
Epidermis of the ventral region of the embryo.
fly_anatomy.ontology
FBbt:00005747
embryonic ventral epidermis
Epidermis of the ventral region of the embryo.
https://orcid.org/0000-0001-5948-3092
Anal pad of the embryo.
fly_anatomy.ontology
FBbt:00005748
embryonic anal pad
Anal pad of the embryo.
https://orcid.org/0000-0001-5948-3092
Ventral halve of an embryonic apodeme. The discontinuity between dorsal and ventral halves is visible on a lateral view.
fly_anatomy.ontology
FBbt:00005749
embryonic ventral apodeme
Ventral halve of an embryonic apodeme. The discontinuity between dorsal and ventral halves is visible on a lateral view.
FlyBase:FBrf0089570
Plate or plates that surrounds the anus.
fly_anatomy.ontology
FBbt:00005785
anal pad
Plate or plates that surrounds the anus.
https://orcid.org/0000-0001-5948-3092
Visual organ of the larva. It consists of a dense cluster of 12 ciliated photoreceptor neurons located on either side of the midline in a dorsomedial position in the anterior region of the larva.
FBbt:00002643
FBbt:00005742
FBbt:00015250
UBERON:6005805
VFB:FBbt_00005805
Bolwig's organ
embryonic Bolwig's organ
embryonic visual system
larval Bolwig's organ
larval eye
stemmata organ
fly_anatomy.ontology
dorsocaudal pharyngeal sense organ
FBbt:00005805
Location in ocular segment on basis of FBrf0075072.
Bolwig organ
Visual organ of the larva. It consists of a dense cluster of 12 ciliated photoreceptor neurons located on either side of the midline in a dorsomedial position in the anterior region of the larva.
FlyBase:FBrf0089570
larval eye
FlyBase:FBrf0213587
stemmata organ
FlyBase:FBrf0047902
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
Epidermal pouch in the head of the embryo or larva.
fly_anatomy.ontology
FBbt:00005807
dorsal pouch
Epidermal pouch in the head of the embryo or larva.
https://orcid.org/0000-0001-5948-3092
Primordium of the late extended and dorsal closure embryo that gives rise to the larval Bolwig organ. It corresponds to the most posterior region that develops from the visual primordium.
UBERON:6005830
Bolwig's organ primordium
P1 BolOrg
fly_anatomy.ontology
FBbt:00005830
Bolwig organ primordium
Primordium of the late extended and dorsal closure embryo that gives rise to the larval Bolwig organ. It corresponds to the most posterior region that develops from the visual primordium.
FBC:VH
FlyBase:FBrf0089570
FlyBase:FBrf0151275
https://orcid.org/0000-0002-7073-9172
P1 BolOrg
https://orcid.org/0000-0002-7073-9172
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.
UBERON:6006011
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
UBERON:0000061
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.
https://orcid.org/0000-0001-9114-8737
https://orcid.org/0000-0002-7073-9172
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.
https://orcid.org/0000-0001-9114-8737
Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships.
CARO:0000043
UBERON:0000479
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.
https://orcid.org/0000-0001-9114-8737
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
UBERON:0000483
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.
https://orcid.org/0000-0001-9114-8737
UBERON:0005423
fly_anatomy.ontology
FBbt:00007006
developing material anatomical entity
Anatomical structure that is a primary subdivision of whole organism. The mereological sum of these is the whole organism.
CARO:0000032
UBERON:0000475
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.
https://orcid.org/0000-0001-9114-8737
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
UBERON:0000481
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.
https://orcid.org/0000-0001-9114-8737
CARO:0000040
UBERON:0000476
fly_anatomy.ontology
FBbt:00007013
acellular anatomical structure
CARO:0000006
UBERON:0000465
fly_anatomy.ontology
FBbt:00007016
material anatomical entity
An epithelium consisting of columnar shaped cells.
UBERON:0000485
fly_anatomy.ontology
FBbt:00007027
cuboidal/columnar epithelium
An epithelium consisting of columnar shaped cells.
FlyBase:FBrf0239342
The region of the ectoderm posterior to the cephalic furrow.
UBERON:6007045
fly_anatomy.ontology
FBbt:00007045
trunk ectoderm
The region of the ectoderm posterior to the cephalic furrow.
https://orcid.org/0000-0002-7073-9172
The cerebral ganglion, minus the optic lobes. It includes part of the protocerebrum (without the optic lobes), the deutocerebrum and the tritocerebrum.
VFB:FBbt_00007050
fly_anatomy.ontology
FBbt:00007050
adult cerebrum
The cerebral ganglion, minus the optic lobes. It includes part of the protocerebrum (without the optic lobes), the deutocerebrum and the tritocerebrum.
FlyBase:FBrf0224194
The sum of all the developing presumptive components of a specific embryonic/larval system in an embryo.
UBERON:6007116
fly_anatomy.ontology
FBbt:00007116
presumptive embryonic/larval system
The sum of all the developing presumptive components of a specific embryonic/larval system in an embryo.
https://orcid.org/0000-0002-7073-9172
Protocerebrum of the adult brain.
2008-06-13T10:49:41Z
UBERON:6007145
VFB:FBbt_00007145
fly_anatomy.ontology
FBbt:00007145
adult protocerebrum
Protocerebrum of the adult brain.
FlyBase:FBrf0224194
Deutocerebrum of the adult brain. Substantial portions are below the level of the esophagus (Ito et al., 2014).
2008-06-13T10:52:46Z
VFB:FBbt_00007146
adult deuterocerebrum
fly_anatomy.ontology
FBbt:00007146
adult deutocerebrum
Deutocerebrum of the adult brain. Substantial portions are below the level of the esophagus (Ito et al., 2014).
FlyBase:FBrf0224194
adult deuterocerebrum
FlyBase:FBrf0224194
A sense organ embedded in the integument and consisting of one or a cluster of sensory neurons and associated sensory structures, support cells and glial cells forming a single organized unit with a largely bona fide boundary.
UBERON:0002536
VFB:FBbt_00007152
fly_anatomy.ontology
FBbt:00007152
sensillum
A sense organ embedded in the integument and consisting of one or a cluster of sensory neurons and associated sensory structures, support cells and glial cells forming a single organized unit with a largely bona fide boundary.
FlyBase:FBrf0111704
A cluster of cells of various types which form a discrete structure with a largely bona fide boundary.
2008-10-21T12:18:17Z
UBERON:0010001
fly_anatomy.ontology
FBbt:00007229
cell cluster organ
A cluster of cells of various types which form a discrete structure with a largely bona fide boundary.
https://orcid.org/0000-0002-7073-9172
An anatomical structure consisting of multiple cell cluster organs and which does not contain portions of tissue.
2008-10-21T12:20:23Z
UBERON:0014732
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.
https://orcid.org/0000-0002-7073-9172
Sensillum that is internal to the animal - i.e. having no part that is part of the cuticle.
2008-10-21T02:04:23Z
UBERON:6007233
VFB:FBbt_00007233
fly_anatomy.ontology
FBbt:00007233
internal sensillum
Sensillum that is internal to the animal - i.e. having no part that is part of the cuticle.
https://orcid.org/0000-0002-7073-9172
Any compound cell cluster organ (FBbt:00007230) that is capable of some detection of stimulus involved in sensory perception (GO:0050906).
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 is capable of some detection of stimulus involved in sensory perception (GO:0050906).
FBC:Autogenerated
Compound sense organ that is located within the epidermis.
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
Any sensillum (FBbt:00007152) that is part of some adult (FBbt:00003004).
2008-10-22T09:42:58Z
VFB:FBbt_00007239
fly_anatomy.ontology
FBbt:00007239
adult sensillum
Any sensillum (FBbt:00007152) that is part of some adult (FBbt:00003004).
FBC:Autogenerated
Any sensillum (FBbt:00007152) that is part of some larva (FBbt:00001727).
2008-10-22T09:42:58Z
UBERON:6007240
VFB:FBbt_00007240
larval sensillum
fly_anatomy.ontology
FBbt:00007240
embryonic/larval sensillum
Any sensillum (FBbt:00007152) that is part of some larva (FBbt:00001727).
FBC:Autogenerated
Any sensillum (FBbt:00007152) that is part of some adult head (FBbt:00003007).
2008-10-22T09:42:58Z
VFB:FBbt_00007241
fly_anatomy.ontology
FBbt:00007241
adult head sensillum
Any sensillum (FBbt:00007152) that is part of some adult head (FBbt:00003007).
FBC:Autogenerated
Any sensillum (FBbt:00007152) that is part of some larval head (FBbt:00001730).
2008-10-22T09:42:58Z
UBERON:6007242
VFB:FBbt_00007242
larval head sensillum
fly_anatomy.ontology
FBbt:00007242
embryonic/larval head sensillum
Any sensillum (FBbt:00007152) that is part of some larval head (FBbt:00001730).
FBC:Autogenerated
Specialized structure that is found on the cuticle.
2008-10-22T02:20:05Z
UBERON:6007245
fly_anatomy.ontology
FBbt:00007245
cuticular specialization
Specialized structure that is found on the cuticle.
https://orcid.org/0000-0001-5948-3092
A layer of the cuticle.
2008-10-22T02:24:54Z
fly_anatomy.ontology
FBbt:00007246
cuticle layer
A layer of the cuticle.
https://orcid.org/0000-0001-5948-3092
Material anatomical entity generated by coordinated expression of the organism's own genome and whose component parts are not all continuous with each other.
2008-11-04T03:09:28Z
UBERON:0034923
fly_anatomy.ontology
FBbt:00007276
disconnected anatomical group
Material anatomical entity generated by coordinated expression of the organism's own genome and whose component parts are not all continuous with each other.
https://orcid.org/0000-0002-7073-9172
Anatomical group whose component anatomical structures lie in close proximity to each other.
2008-11-04T03:13:41Z
UBERON:0000477
fly_anatomy.ontology
FBbt:00007277
anatomical cluster
Anatomical group whose component anatomical structures lie in close proximity to each other.
https://orcid.org/0000-0002-7073-9172
An anatomical group whose component structures share a common function.
2008-11-04T03:18:01Z
UBERON:0015203
fly_anatomy.ontology
FBbt:00007278
non-connected functional system
An anatomical group whose component structures share a common function.
https://orcid.org/0000-0002-7073-9172
Any sense organ (FBbt:00005155) that is part of some larval head (FBbt:00001730).
2008-11-05T10:34:14Z
UBERON:6007280
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
A region of cuticle and its underlying epidermis.
2008-11-06T02:05:25Z
UBERON:6007284
fly_anatomy.ontology
FBbt:00007284
region of integument
A region of cuticle and its underlying epidermis.
https://orcid.org/0000-0002-7073-9172
Specialized structure that is found on the integument.
2008-11-06T03:13:52Z
UBERON:6007288
integumentary specialisation
fly_anatomy.ontology
FBbt:00007288
integumentary specialization
Specialized structure that is found on the integument.
https://orcid.org/0000-0001-5948-3092
A multi-nucleate cell having no internal boundaries between nuclei.
2008-11-06T05:12:28Z
fly_anatomy.ontology
FBbt:00007290
syncytium
A multi-nucleate cell having no internal boundaries between nuclei.
https://orcid.org/0000-0002-7073-9172
2008-12-12T07:22:29Z
UBERON:0011216
fly_anatomy.ontology
FBbt:00007330
organ system subdivision
The part of some organism that is part of some specified segment.
2008-12-12T07:22:57Z
UBERON:6007331
fly_anatomy.ontology
FBbt:00007331
segmental subdivision of organ system
The part of some organism that is part of some specified segment.
https://orcid.org/0000-0002-7073-9172
Sense organ that is internal to the animal - i.e. having no part that is part of the cuticle.
2009-10-19T02:27:41Z
UBERON:6007373
VFB:FBbt_00007373
fly_anatomy.ontology
FBbt:00007373
internal sense organ
Sense organ that is internal to the animal - i.e. having no part that is part of the cuticle.
https://orcid.org/0000-0002-7073-9172
Structure consisting of a simple epithelium surrounded by visceral muscles, nerves and tracheae. The adult gut is divided into the adult foregut, midgut and hindgut regions, based on developmental origin.
2010-10-04T11:02:39Z
fly_anatomy.ontology
FBbt:00007513
adult gut
Structure consisting of a simple epithelium surrounded by visceral muscles, nerves and tracheae. The adult gut is divided into the adult foregut, midgut and hindgut regions, based on developmental origin.
FlyBase:FBrf0223413
https://orcid.org/0000-0002-7073-9172
A group of trichomes covering a region of integument.
fly_anatomy.ontology
FBbt:00007658
trichome field
A group of trichomes covering a region of integument.
https://orcid.org/0000-0002-7073-9172
An anlage that is a precursor of some part of the adult optic lobe in the larva. It develops from the embryonic optic lobe primordium.
2013-03-13T02:59:16Z
VFB:FBbt_00007676
fly_anatomy.ontology
FBbt:00007676
larval optic anlage
An anlage that is a precursor of some part of the adult optic lobe in the larva. It develops from the embryonic optic lobe primordium.
FlyBase:FBrf0089570
https://orcid.org/0000-0002-7073-9172
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.
https://orcid.org/0000-0002-7073-9172
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.
https://orcid.org/0000-0002-7073-9172
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.
https://orcid.org/0000-0002-7073-9172
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.
https://orcid.org/0000-0002-7073-9172
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.
https://orcid.org/0000-0002-7073-9172
An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception.
UBERON:0001032
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.
https://orcid.org/0000-0002-7073-9172
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.
https://orcid.org/0000-0002-7073-9172
A(n) primordium that develops into some lateral head epidermis. It develops from some central brain anlage.
P1 HeadEpL
P2 HeadEpL
fly_anatomy.ontology
FBbt:00014203
lateral head epidermis primordium
A(n) primordium that develops into some lateral head epidermis. It develops from some central brain anlage.
FBC:Autogenerated
P1 HeadEpL
https://orcid.org/0000-0002-7073-9172
P2 HeadEpL
https://orcid.org/0000-0002-7073-9172
Anlage of the embryonic central brain in the gastrula embryo that will give rise to the central brain primordium.
A CenBr
fly_anatomy.ontology
AProcEC
procephalic ectoderm anlage
FBbt:00015256
central brain anlage
Anlage of the embryonic central brain in the gastrula embryo that will give rise to the central brain primordium.
FBC:VH
https://orcid.org/0000-0001-5948-3092
A CenBr
https://orcid.org/0000-0002-7073-9172
Primordium of the ventral trunk epidermis of the late extended germ band and dorsal closure embryo that will give rise to the embryonic ventral trunk epidermis.
P1 VenEp
fly_anatomy.ontology
FBbt:00016007
ventral trunk epidermis primordium
Primordium of the ventral trunk epidermis of the late extended germ band and dorsal closure embryo that will give rise to the embryonic ventral trunk epidermis.
FBC:VH
P1 VenEp
https://orcid.org/0000-0002-7073-9172
Primordium of the anal pad of the late extended germ band and dorsal closure embryo that will give rise to the embryonic anal pads.
fly_anatomy.ontology
A/P1 AnPd
anal pad specific anlage
FBbt:00016008
anal pad primordium
Primordium of the anal pad of the late extended germ band and dorsal closure embryo that will give rise to the embryonic anal pads.
FBC:VH
A/P1 AnPd
https://orcid.org/0000-0002-7073-9172
Anlage of the ventral apodeme of the late extended germ band embryo that will give rise to the ventral apodeme primordium.
A venApo
fly_anatomy.ontology
FBbt:00016009
ventral apodeme anlage
Anlage of the ventral apodeme of the late extended germ band embryo that will give rise to the ventral apodeme primordium.
FBC:VH
A venApo
https://orcid.org/0000-0002-7073-9172
Primordium of the ventral apodeme of the dorsal closure embryo that will give rise to the ventral apodemes.
P1 venApo
fly_anatomy.ontology
ventral apodeme specific primordium
FBbt:00016010
ventral apodeme primordium
Primordium of the ventral apodeme of the dorsal closure embryo that will give rise to the ventral apodemes.
FBC:VH
P1 venApo
https://orcid.org/0000-0002-7073-9172
Primordium of the denticle field of the dorsal closure embryo that will give rise to the larval denticle fields.
P DenBl
fly_anatomy.ontology
FBbt:00016011
denticle field primordium
Primordium of the denticle field of the dorsal closure embryo that will give rise to the larval denticle fields.
FBC:VH
P DenBl
https://orcid.org/0000-0002-7073-9172
Region of embryonic and larval ventral cuticle that displays denticle belts. It develops from the denticle field primordium.
fly_anatomy.ontology
FBbt:00016012
denticle field
Region of embryonic and larval ventral cuticle that displays denticle belts. It develops from the denticle field primordium.
FBC:VH
FlyBase:FBrf0089570
Any anatomical entity (FBbt:10000000) that develops from some ectoderm (FBbt:00000111).
FBbt:00005253
fly_anatomy.ontology
FBbt:00025990
ectodermal derivative
Any anatomical entity (FBbt:10000000) that develops from some ectoderm (FBbt:00000111).
FlyBase:FBrf0043441
FlyBase:FBrf0053832
Any anatomical entity (FBbt:10000000) that develops from some anterior ectoderm (FBbt:00000119).
fly_anatomy.ontology
FBbt:00025991
anterior ectoderm derivative
Any anatomical entity (FBbt:10000000) that develops from some anterior ectoderm (FBbt:00000119).
https://orcid.org/0000-0002-7073-9172
Any anatomical entity (FBbt:10000000) that develops from some ventral ectoderm (FBbt:00005558).
fly_anatomy.ontology
FBbt:00025993
ventral ectoderm derivative
Any anatomical entity (FBbt:10000000) that develops from some ventral ectoderm (FBbt:00005558).
https://orcid.org/0000-0002-7073-9172
The sum of all the anlagen and primordia that will develop into a single system.
2010-04-29T07:57:11Z
UBERON:6040003
fly_anatomy.ontology
FBbt:00040003
Note - this may be the precursor of a connected system that starts out non-connected, such as the tracheal system, or of a system that remains disconnected, e.g. functionally defined systems such as the endocrine system.
non-connected developing system
The sum of all the anlagen and primordia that will develop into a single system.
https://orcid.org/0000-0002-7073-9172
Structure consisting of a simple epithelium surrounded by visceral muscles, nerves and tracheae. The gut is divided into foregut, midgut and hindgut regions, based on developmental origin.
fly_anatomy.ontology
FBbt:00047143
gut
Structure consisting of a simple epithelium surrounded by visceral muscles, nerves and tracheae. The gut is divided into foregut, midgut and hindgut regions, based on developmental origin.
FlyBase:FBrf0223413
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.
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.
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.
https://orcid.org/0000-0002-1373-1705
Adult brain excluding the optic lobes. This consists of the cerebrum and the gnathal ganglion.
2018-10-24T14:35:45Z
VFB:FBbt_00047887
midbrain
fly_anatomy.ontology
FBbt:00047887
adult central brain
Adult brain excluding the optic lobes. This consists of the cerebrum and the gnathal ganglion.
FlyBase:FBrf0224194
midbrain
FlyBase:FBrf0224194
Brain excluding the optic lobes.
2018-10-24T15:11:55Z
VFB:FBbt_00047888
fly_anatomy.ontology
FBbt:00047888
central brain
Brain excluding the optic lobes.
FlyBase:FBrf0224194
https://orcid.org/0000-0002-1373-1705
Larval brain excluding the optic lobes.
2018-10-24T15:12:43Z
VFB:FBbt_00047889
fly_anatomy.ontology
FBbt:00047889
larval central brain
Larval brain excluding the optic lobes.
https://orcid.org/0000-0002-1373-1705
Neuropil mass below the larval esophagus consisting of the gnathal ganglion and part of the tritocerebrum.
2021-02-26T11:25:02Z
VFB:FBbt_00051067
larval SEZ
fly_anatomy.ontology
larval subesophageal ganglion
FBbt:00051067
This is analogous to the adult term based on Ito et al. (2014), reflecting location relative to the esophagus, rather than segmental identity.
larval subesophageal zone
Neuropil mass below the larval esophagus consisting of the gnathal ganglion and part of the tritocerebrum.
FlyBase:FBrf0224194
FlyBase:FBrf0229672
FlyBase:FBrf0237252
larval SEZ
FlyBase:FBrf0237252
Neuropil mass below the esophagus encompassing the three gnathal neuromeres and any regions of the cephalic (supraesophageal) neuromeres situated below the esophagus (Ito et al., 2014).
2021-02-26T11:59:59Z
VFB:FBbt_00051068
SEZ
fly_anatomy.ontology
subesophageal ganglion
FBbt:00051068
subesophageal zone
Neuropil mass below the esophagus encompassing the three gnathal neuromeres and any regions of the cephalic (supraesophageal) neuromeres situated below the esophagus (Ito et al., 2014).
FlyBase:FBrf0224194
SEZ
FlyBase:FBrf0224194
Neuropil mass above the esophagus (Ito et al., 2014). It is part of the cerebral (supraesophageal) ganglion (Ito et al., 2014).
2021-02-26T13:05:56Z
supraesophageal ganglion
VFB:FBbt_00051069
SPZ
fly_anatomy.ontology
FBbt:00051069
supraesophageal zone
Neuropil mass above the esophagus (Ito et al., 2014). It is part of the cerebral (supraesophageal) ganglion (Ito et al., 2014).
FlyBase:FBrf0224194
SPZ
FlyBase:FBrf0224194
Neuropil mass above the larval esophagus consisting of the protocerebral and deutocerebral neuromeres and part of the tritocerebrum.
2021-02-26T13:07:57Z
larval supraesophageal ganglion
VFB:FBbt_00051070
larval SPZ
fly_anatomy.ontology
FBbt:00051070
This is analogous to the adult term based on Ito et al. (2014), reflecting location relative to the esophagus, rather than segmental identity.
larval supraesophageal zone
Neuropil mass above the larval esophagus consisting of the protocerebral and deutocerebral neuromeres and part of the tritocerebrum.
FlyBase:FBrf0224194
Procuticle of the pupa, it is composed of three distinct layers: exocuticle, endocuticle and assembly zone (Fristrom and Fristrom, 1993).
2021-12-20T14:18:25Z
fly_anatomy.ontology
FBbt:00052034
pupal procuticle
Procuticle of the pupa, it is composed of three distinct layers: exocuticle, endocuticle and assembly zone (Fristrom and Fristrom, 1993).
FlyBase:FBrf0064790
Procuticle of the adult. It does not have distinct exo- and endocuticle layers (Fristrom and Fristrom, 1993).
2021-12-20T14:18:48Z
fly_anatomy.ontology
FBbt:00052035
adult procuticle
Procuticle of the adult. It does not have distinct exo- and endocuticle layers (Fristrom and Fristrom, 1993).
FlyBase:FBrf0064790
Procuticle of the larva. Its lamellae have a wavy morphology, which becomes more distinct throughout development, and are thicker in the basal region than the apical region (Tajiri et al., 2017).
2021-12-20T14:27:53Z
fly_anatomy.ontology
FBbt:00052036
larval procuticle
Procuticle of the larva. Its lamellae have a wavy morphology, which becomes more distinct throughout development, and are thicker in the basal region than the apical region (Tajiri et al., 2017).
FlyBase:FBrf0234504
Any neuromere (FBbt:00005140) that is part of some embryo (FBbt:00000052).
2024-01-12T15:01:48Z
fly_anatomy.ontology
FBbt:00052717
embryonic neuromere
Any neuromere (FBbt:00005140) that is part of some embryo (FBbt:00000052).
FBC:Autogenerated
Any neuromere (FBbt:00005140) that is part of some adult (FBbt:00003004).
2024-01-12T15:15:54Z
fly_anatomy.ontology
FBbt:00052718
adult neuromere
Any neuromere (FBbt:00005140) that is part of some adult (FBbt:00003004).
FBC:Autogenerated
2008-06-30T04:15:23Z
UBERON:6057001
fly_anatomy.ontology
FBbt:00057001
anterior-posterior subdivision of organism
A multicellular structure made of one or several myofibers associated with tendon cells that attach the myofiber(s) to the exoskeleton or other organs.
2022-06-23T16:54:03Z
fly_anatomy.ontology
FBbt:00058111
somatic muscle
A multicellular structure made of one or several myofibers associated with tendon cells that attach the myofiber(s) to the exoskeleton or other organs.
FlyBase:FBrf0211520
Any muscle cell (FBbt:00005074) that is part of some adult muscle system (FBbt:00003218).
2021-09-06T09:13:41Z
fly_anatomy.ontology
FBbt:00058230
adult muscle cell
Any muscle cell (FBbt:00005074) that is part of some adult muscle system (FBbt:00003218).
FBC:Autogenerated
A muscle attached to the inner surface of the adult body wall, extending between articulated or flexibly joined areas, that serves to move the parts of the exoskeleton.
2022-07-05T13:30:44Z
adult skeletal muscle
fly_anatomy.ontology
FBbt:00058784
adult somatic muscle
A muscle attached to the inner surface of the adult body wall, extending between articulated or flexibly joined areas, that serves to move the parts of the exoskeleton.
FlyBase:FBrf0007735
Somatic muscle that is part of the adult head.
2022-07-05T13:30:44Z
skeletal muscle of head
fly_anatomy.ontology
FBbt:00058785
adult somatic muscle of head
Somatic muscle that is part of the adult head.
FBC:SPR
Specialized structure that is found on the endocuticle.
2010-09-29T04:14:31Z
fly_anatomy.ontology
FBbt:00100290
endocuticular specialization
Specialized structure that is found on the endocuticle.
https://orcid.org/0000-0001-5948-3092
Anatomical structure that has multiple cells as parts.
2010-11-02T02:25:04Z
UBERON:0010000
fly_anatomy.ontology
FBbt:00100313
multicellular structure
Anatomical structure that has multiple cells as parts.
https://orcid.org/0000-0002-7073-9172
A subdivision of the gut along its long axis.
2010-11-02T05:21:35Z
UBERON:0004921
fly_anatomy.ontology
FBbt:00100315
gut section
A subdivision of the gut along its long axis.
https://orcid.org/0000-0002-7073-9172
2010-11-04T08:35:02Z
fly_anatomy.ontology
FBbt:00100318
somatic cell
The entire adult anatomical structure through which food and its digestion products are ingested, digested and excreted. At its anterior and posterior ends this includes structures that are not foregut or hindgut.
fly_anatomy.ontology
FBbt:00100322
adult alimentary canal
The entire adult anatomical structure through which food and its digestion products are ingested, digested and excreted. At its anterior and posterior ends this includes structures that are not foregut or hindgut.
https://orcid.org/0000-0002-7073-9172
.
fly_anatomy.ontology
FBbt:00105220
lateral head epidermis
.
FBC:VH
https://orcid.org/0000-0002-7073-9172
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:VH
FlyBase:FBrf0089570
FlyBase:FBrf0151275
https://orcid.org/0000-0002-7073-9172
Nervous system of the pupa.
2013-01-04T10:01:28Z
VFB:FBbt_00110192
fly_anatomy.ontology
FBbt:00110192
pupal nervous system
Nervous system of the pupa.
https://orcid.org/0000-0001-5948-3092
The supraesophageal neuropils of the adult brain located above, around and partially below the esophagus, including the optic lobes. It excludes the gnathal ganglion. Developmentally, it comprises three fused neuromeres: protocerebrum, deutocerebrum, and tritocerebrum.
2013-10-08T17:05:57Z
UBERON:6110636
VFB:FBbt_00110636
CRG
fly_anatomy.ontology
SPG
adult supraesophageal ganglion
brain
cerebrum
FBbt:00110636
This term is related to what used to be called supraesophageal ganglion, and is now referred to as supraesophageal zone. The adult cerebral ganglion, together with the gnathal ganglia (GNG), denote regions that follow the segmental neuromeres of the brain (the 3 rostral and 3 caudal, respectively). These are distinguishable from supra- and subesophageal zones, as these refer to the neuropil masses above and below the esophagus and do not respect neuromere boundaries (Ito et al., 2014).
adult cerebral ganglion
The supraesophageal neuropils of the adult brain located above, around and partially below the esophagus, including the optic lobes. It excludes the gnathal ganglion. Developmentally, it comprises three fused neuromeres: protocerebrum, deutocerebrum, and tritocerebrum.
FlyBase:FBrf0224194
CRG
FlyBase:FBrf0224194
Neuropil mass above the esophagus in the adult brain. It is part of the cerebral ganglion.
2013-10-08T17:07:47Z
VFB:FBbt_00110638
SPZ
adult supraesophageal ganglion
fly_anatomy.ontology
FBbt:00110638
This term refers to what used to be called supraesophageal ganglion. The new name, together with subesophageal zone, refer to the neuropil masses above and below the esophagus and do not respect neuromere boundaries. The terms cerebral ganglia (CRG) and gnathal ganglia (GNG), denote regions that follow the segmental neuromeres of the brain (the 3 rostral and 3 caudal, respectively) (Ito et al., 2014).
adult supraesophageal zone
Neuropil mass above the esophagus in the adult brain. It is part of the cerebral ganglion.
FlyBase:FBrf0224194
SPZ
FlyBase:FBrf0224194
Neuropil mass below the esophagus in the adult brain. It encompasses the gnathal ganglion, the prow and the saddle.
2013-10-08T17:53:57Z
VFB:FBbt_00110639
SEZ
SEG
SOG
adult subesophageal ganglion
adult suboesophageal ganglion
fly_anatomy.ontology
FBbt:00110639
This term refers to what used to be called subesophageal ganglion. The new name, together with supraesophageal zone, refer to the brain tissue below and above the esophagus and do not respect neuromere boundaries. The terms cerebral ganglia (CRG) and gnathal ganglia (GNG), denote the segmental neuromeres of the brain (the 3 rostral and 3 caudal, respectively) (Ito et al., 2014). Sterne et al. (2021) - FBrf0251280 define the SEZ as comprising GNG + TR.
adult subesophageal zone
Neuropil mass below the esophagus in the adult brain. It encompasses the gnathal ganglion, the prow and the saddle.
FlyBase:FBrf0224194
SEZ
FlyBase:FBrf0224194
Anlage that develops into the anterior ectoderm. It is found anterior to the dorsal, lateral and ventral regions of the ectoderm anlage and posterior to the anterior endoderm anlage at the cellular blastoderm stage, prior to gastrulation (Stathopoulos and Newcomb, 2020).
fly_anatomy.ontology
FBbt:01000119
anterior ectoderm anlage
Anlage that develops into the anterior ectoderm. It is found anterior to the dorsal, lateral and ventral regions of the ectoderm anlage and posterior to the anterior endoderm anlage at the cellular blastoderm stage, prior to gastrulation (Stathopoulos and Newcomb, 2020).
FlyBase:FBrf0244630
The epidermis of the embryonic ventral trunk.
fly_anatomy.ontology
FBbt:01005747
embryonic ventral trunk epidermis
The epidermis of the embryonic ventral trunk.
https://orcid.org/0000-0001-5948-3092
Anatomical entity which is part_of Drosophila melanogaster.
FBbt_root:00000000
UBERON:0001062
fly_anatomy.ontology
Drosophila
FBbt:10000000
anatomical entity
Anatomical entity which is part_of Drosophila melanogaster.
https://orcid.org/0000-0001-9114-8737
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
https://orcid.org/0000-0002-7073-9172
A(n) anlage that develops into some denticle field primordium. It develops from some ventral epidermis primordium.
fly_anatomy.ontology
A DenBl
FBbt:10005326
denticle field anlage
A(n) anlage that develops into some denticle field primordium. It develops from some ventral epidermis primordium.
FBC:Autogenerated
A DenBl
https://orcid.org/0000-0002-7073-9172
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.
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.
reduced body size
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.
aging defective
phenotypic_class
FBcv:0000384
abnormal aging
Phenotype that is any abnormality in aging.
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 an decrease in any kind of rate (e.g. speed, frequency) of `multicellular organismal movement` (GO:0050879) compared to wild-type.
hypoactive
reduced rate of movement
phenotypic_class
FBcv:0000390
decreased rate of movement
A phenotype consisting of an decrease in any kind of rate (e.g. speed, 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 an increase in any kind of rate (e.g. speed, frequency) of `multicellular organismal movement` (GO:0050879) compared to wild-type.
hyperactive
phenotypic_class
FBcv:0000392
increased rate of movement
A phenotype consisting of an increase in any kind of rate (e.g. speed, 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.'.
abnormal chemosensitive behavior
chemosensitive behavior defective
chemosensitive behaviour defective
phenotypic_class
FBcv:0000403
abnormal chemosensory 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.
reduced cell death
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
FBcv:0000430
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
obsolete 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 the number of cells in a tissue or organ, usually associated with an increase in size, where the affected tissue or organ maintains its normal form.
hyperplastic
phenotypic_class
FBcv:0000444
hyperplasia
Phenotype that is an increase in the number of cells in a tissue or organ, usually associated with an increase in size, where the affected tissue or organ maintains its normal form.
ISBN:978-0-19-850673-7
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.
obsolete 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 any kind of rate (e.g. speed, frequency) of any 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 any kind of rate (e.g. speed, frequency) of any 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.'
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.'
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.'
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.'
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.'
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.'
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.'
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.
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 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.'
FBC:DOS
GOC:cjm
GOC:dph
GOC:ems
GOC:pf
Wikipedia:Cell_migration
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) 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 rate
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) 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 any kind of rate (e.g. speed, frequency) of cell growth (GO:0016049) in a whole animal or in some specific organ tissue or clone of cells compared to wild-type.
reduced cell growth rate
phenotypic_class
FBcv:0000718
decreased cell growth rate
Phenotype that is an decrease in any kind of rate (e.g. speed, frequency) 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.
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.
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.
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 is slower than in wild-type.
reduced speed of aging
phenotypic_class
delayed aging
FBcv:0000791
decreased speed of aging
A phenotype in which the aging process is slower than in wild-type.
FBC:DOC
A phenotype in which the aging process is accelerated compared to wild-type.
phenotypic_class
premature aging
FBcv:0000792
increased speed of aging
A phenotype in which the aging process 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].
obsolete 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].
obsolete 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
FBcv:0002000
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
FBcv:0002001
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
FBcv:0002002
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
FBcv:0002003
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
FBcv:0002004
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
FBcv:0002005
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
FBcv:0002006
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
FBcv:0002007
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
FBcv:0002008
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
FBcv:0002009
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
FBcv:0002010
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
FBcv:0002011
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
FBcv:0002012
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
FBcv:0002013
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
FBcv:0002014
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
FBcv:0002015
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
FBcv:0002019
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
FBcv:0002020
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
FBcv:0002021
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
FBcv:0002022
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
FBcv:0002023
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
FBcv:0002024
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
FBcv:0002025
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
FBcv:0002026
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
FBcv:0002027
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
FBcv:0002030
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
FBcv:0002031
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'.
obsolete 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
A phenotype of a population that is the death of all animals in that population during the embryonic stage.
embryonic lethal
phenotypic_class
FBcv:0002033
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
FBcv:0002034
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
FBcv:0002035
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
FBcv:0002036
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
FBcv:0002037
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
FBcv:0002038
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
FBcv:0002039
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
FBcv:0002040
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
FBcv:0002041
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
FBcv:0002042
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
FBcv:0002050
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
FBcv:0002051
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.
reduced fecundity
phenotypic_class
FBcv:0006002
decreased fecundity
Phenotype that is a decrease in the number of gametes produced.
FBC:TEMJ
FlyBase miscellaneous CV
FBcv:0006003
population of Drosophila
Phenotype that is any abnormality in oviposition (GO:0018991) despite production of eggs. 'oviposition' is defined as: 'A reproductive behavior that results in 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. It is not possible to observe an oviposition abnormality if eggs are not being produced. 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:0018991) despite production of eggs. 'oviposition' is defined as: 'A reproductive behavior that results in the deposition of eggs (either fertilized or not) upon a surface or into a medium such as water.'.
FBC:TEMJ
GOC:ems
PMID:18050396
PMID:31164023
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.'.
reduced occurrence of cell division
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
FlyBase miscellaneous CV
FBcv:0006007
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
reduced body weight
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
reduced size
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 any kind of rate (e.g. speed, frequency) 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 any kind of rate (e.g. speed, frequency) 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 any kind of rate (e.g. speed, frequency) 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
reduced rate of phototaxis
phenotypic_class
FBcv:0007510
decreased rate of phototaxis
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) 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 any kind of rate (e.g. speed, frequency) 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 any kind of rate (e.g. speed, frequency) 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 any kind of rate (e.g. speed, frequency) 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
reduced rate of cell adhesion
phenotypic_class
FBcv:0007512
decreased rate of cell adhesion
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) 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
reduced sleep
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 rate of 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
reduced rate of feeding behavior
phenotypic_class
FBcv:0007516
decreased rate of 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
improved memory
phenotypic_class
FBcv:0007517
This will usually be measured as an increased magnitude/rate of a behavioral output associated with memory formation.
increased efficacy of 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
impaired memory
reduced efficacy of memory
phenotypic_class
FBcv:0007518
This will usually be measured as a decreased magnitude/rate of a behavioral output associated with memory formation.
decreased efficacy of 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 efficacy of 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
reduced efficacy of short-term memory
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 efficacy of 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 efficacy of 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
reduced efficacy of long-term memory
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 efficacy of 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 efficacy of 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
reduced efficacy of anesthesia-resistant memory
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 efficacy of 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 efficacy of 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
reduced efficacy of medium-term memory
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 efficacy of 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
Any abnormality in adult walking behavior (GO:0007628), which is defined as 'The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.'.
2022-08-12T08:45:06Z
phenotypic_class
FBcv:0007527
abnormal adult walking behavior
Any abnormality in adult walking behavior (GO:0007628), which is defined as 'The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.'.
GO:0007628
GOC:jid
GOC:pr
ISBN:0198606907
Any abnormality in larval locomotory behavior (GO:0008345), which is defined as 'Locomotory behavior in a larval (immature) organism.'.
2022-08-12T08:46:33Z
phenotypic_class
FBcv:0007528
abnormal larval locomotory behavior
Any abnormality in larval locomotory behavior (GO:0008345), which is defined as 'Locomotory behavior in a larval (immature) organism.'.
GO:0008345
GOC:ai
Any abnormality in adult locomotory behavior (GO:0008344), which is defined as 'Locomotory behavior in a fully developed and mature organism.'.
2022-08-12T08:50:44Z
phenotypic_class
FBcv:0007529
abnormal adult locomotory behavior
Any abnormality in adult locomotory behavior (GO:0008344), which is defined as 'Locomotory behavior in a fully developed and mature organism.'.
GO:0008344
GOC:ai
Phenotype that is an increase in the efficacy of learning (GO:0007612), relative to controls. 'learning' is defined as: 'Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.'
2022-08-12T08:57:36Z
improved learning
phenotypic_class
FBcv:0007530
increased efficacy of learning
Phenotype that is an increase in the efficacy of learning (GO:0007612), relative to controls. 'learning' is defined as: 'Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.'
ISBN:0582227089
ISBN:0721662544
Phenotype that is a decrease in the efficacy of learning (GO:0007612), relative to controls. 'learning' is defined as: 'Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.'
2022-08-12T09:06:29Z
impaired learning
reduced efficacy of learning
phenotypic_class
FBcv:0007531
decreased efficacy of learning
Phenotype that is a decrease in the efficacy of learning (GO:0007612), relative to controls. 'learning' is defined as: 'Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.'
ISBN:0582227089
ISBN:0721662544
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of chemosensory behavior (GO:0007635). 'chemosensory behavior' is defined as: 'Behavior that is dependent upon the sensation of chemicals.'.
2022-08-12T10:04:22Z
increased rate of chemosensitive behavior
phenotypic_class
FBcv:0007532
increased rate of chemosensory behavior
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of chemosensory behavior (GO:0007635). 'chemosensory behavior' is defined as: 'Behavior that is dependent upon the sensation of chemicals.'.
GO:0007635
GOC:go_curators
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of 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.'.
2022-08-12T10:14:45Z
phenotypic_class
FBcv:0007533
increased rate of proboscis extension reflex
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of 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
GO:0007637
GOC:jid
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of 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.'.
2022-08-12T10:16:08Z
phenotypic_class
FBcv:0007534
increased rate of grooming behavior
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of 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.'.
GO:0007625
GOC:jl
GOC:pr
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of 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.'.
2022-08-12T10:19:14Z
phenotypic_class
FBcv:0007535
increased rate of locomotory behavior
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of 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.'.
GO:0007626
GOC:dph
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of adult walking behavior (GO:0007628). 'adult walking behavior' is defined as: 'The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.'.
2022-08-12T10:20:31Z
phenotypic_class
FBcv:0007536
increased rate of adult walking behavior
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of adult walking behavior (GO:0007628). 'adult walking behavior' is defined as: 'The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.'.
GO:0007628
GOC:jid
GOC:pr
ISBN:0198606907
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of larval locomotory behavior (GO:0008345). 'larval locomotory behavior' is defined as: 'Locomotory behavior in a larval (immature) organism.'.
2022-08-12T10:21:27Z
phenotypic_class
FBcv:0007537
increased rate of larval locomotory behavior
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of larval locomotory behavior (GO:0008345). 'larval locomotory behavior' is defined as: 'Locomotory behavior in a larval (immature) organism.'.
GO:0008345
GOC:ai
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of adult locomotory behavior (GO:0008344). 'adult locomotory behavior' is defined as: 'Locomotory behavior in a fully developed and mature organism.'.
2022-08-12T10:22:30Z
phenotypic_class
FBcv:0007538
increased rate of adult locomotory behavior
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of adult locomotory behavior (GO:0008344). 'adult locomotory behavior' is defined as: 'Locomotory behavior in a fully developed and mature organism.'.
GO:0008344
GOC:ai
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of 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.'.
2022-08-12T10:23:15Z
phenotypic_class
FBcv:0007539
increased rate of mating behavior
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of 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.'.
GO:0007617
GOC:ai
GOC:dph
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of courtship behavior (GO:0007619). 'courtship behavior' is defined as: 'The behavior of an organism for the purpose of attracting sexual partners.'.
2022-08-12T10:23:56Z
phenotypic_class
FBcv:0007540
increased rate of courtship behavior
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of courtship behavior (GO:0007619). 'courtship behavior' is defined as: 'The behavior of an organism for the purpose of attracting sexual partners.'.
GO:0007619
GOC:ai
GOC:dph
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of flight behavior (GO:0007629). 'flight behavior' is defined as: 'The response to external or internal stimuli that results in the locomotory process of flight. Flight is the self-propelled movement of an organism through the air.'.
2022-08-12T10:25:01Z
phenotypic_class
FBcv:0007541
increased rate of flight behavior
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of flight behavior (GO:0007629). 'flight behavior' is defined as: 'The response to external or internal stimuli that results in the locomotory process of flight. Flight is the self-propelled movement of an organism through the air.'.
GO:0007629
GOC:jid
ISBN:0198606907
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of jump response (GO:0007630). 'jump response' is defined as: 'The sudden, usually upward, movement off the ground or other surface through sudden muscular effort in the legs, following exposure to an external stimulus.'.
2022-08-12T10:25:43Z
phenotypic_class
FBcv:0007542
increased rate of jump response
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of jump response (GO:0007630). 'jump response' is defined as: 'The sudden, usually upward, movement off the ground or other surface through sudden muscular effort in the legs, following exposure to an external stimulus.'.
GO:0007630
GOC:jid
ISBN:0198606907
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of copulation (GO:0007620). 'copulation' is defined as: 'The act of sexual union between male and female, involving the transfer of sperm.'.
2022-08-12T10:26:28Z
phenotypic_class
FBcv:0007543
increased rate of copulation
Phenotype that is an increase in any kind of rate (e.g. speed, frequency) of copulation (GO:0007620). 'copulation' is defined as: 'The act of sexual union between male and female, involving the transfer of sperm.'.
GO:0007620
ISBN:0721662544
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of chemosensory behavior (GO:0007635). 'chemosensory behavior' is defined as: 'Behavior that is dependent upon the sensation of chemicals.'.
2022-08-12T10:30:08Z
decreased rate of chemosensitive behavior
reduced rate of chemosensory behavior
phenotypic_class
FBcv:0007544
decreased rate of chemosensory behavior
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of chemosensory behavior (GO:0007635). 'chemosensory behavior' is defined as: 'Behavior that is dependent upon the sensation of chemicals.'.
GO:0007635
GOC:go_curators
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of 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.'.
2022-08-12T10:30:42Z
reduced rate of proboscis extension reflex
phenotypic_class
FBcv:0007545
decreased rate of proboscis extension reflex
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of 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
GO:0007637
GOC:jid
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of 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.'.
2022-08-12T10:31:07Z
reduced rate of grooming behavior
phenotypic_class
FBcv:0007546
decreased rate of grooming behavior
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of 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.'.
GO:0007625
GOC:jl
GOC:pr
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of 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.'.
2022-08-12T10:31:37Z
reduced rate of locomotory behavior
phenotypic_class
FBcv:0007547
decreased rate of locomotory behavior
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of 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.'.
GO:0007626
GOC:dph
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of adult walking behavior (GO:0007628). 'adult walking behavior' is defined as: 'The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.'.
2022-08-12T10:31:54Z
reduced rate of adult walking behavior
phenotypic_class
FBcv:0007548
decreased rate of adult walking behavior
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of adult walking behavior (GO:0007628). 'adult walking behavior' is defined as: 'The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.'.
GO:0007628
GOC:jid
GOC:pr
ISBN:0198606907
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of larval locomotory behavior (GO:0008345). 'larval locomotory behavior' is defined as: 'Locomotory behavior in a larval (immature) organism.'.
2022-08-12T10:32:11Z
reduced rate of larval locomotory behavior
phenotypic_class
FBcv:0007549
decreased rate of larval locomotory behavior
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of larval locomotory behavior (GO:0008345). 'larval locomotory behavior' is defined as: 'Locomotory behavior in a larval (immature) organism.'.
GO:0008345
GOC:ai
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of adult locomotory behavior (GO:0008344). 'adult locomotory behavior' is defined as: 'Locomotory behavior in a fully developed and mature organism.'.
2022-08-12T10:32:30Z
reduced rate of adult locomotory behavior
phenotypic_class
FBcv:0007550
decreased rate of adult locomotory behavior
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of adult locomotory behavior (GO:0008344). 'adult locomotory behavior' is defined as: 'Locomotory behavior in a fully developed and mature organism.'.
GO:0008344
GOC:ai
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of 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.'.
2022-08-12T10:32:56Z
reduced rate of mating behavior
phenotypic_class
FBcv:0007551
decreased rate of mating behavior
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of 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.'.
GO:0007617
GOC:ai
GOC:dph
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of courtship behavior (GO:0007619). 'courtship behavior' is defined as: 'The behavior of an organism for the purpose of attracting sexual partners.'.
2022-08-12T10:33:17Z
reduced rate of courtship behavior
phenotypic_class
FBcv:0007552
decreased rate of courtship behavior
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of courtship behavior (GO:0007619). 'courtship behavior' is defined as: 'The behavior of an organism for the purpose of attracting sexual partners.'.
GO:0007619
GOC:ai
GOC:dph
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of flight behavior (GO:0007629). 'flight behavior' is defined as: 'The response to external or internal stimuli that results in the locomotory process of flight. Flight is the self-propelled movement of an organism through the air.'.
2022-08-12T10:33:37Z
reduced rate of flight behavior
phenotypic_class
FBcv:0007553
decreased rate of flight behavior
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of flight behavior (GO:0007629). 'flight behavior' is defined as: 'The response to external or internal stimuli that results in the locomotory process of flight. Flight is the self-propelled movement of an organism through the air.'.
GO:0007629
GOC:jid
ISBN:0198606907
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of jump response (GO:0007630). 'jump response' is defined as: 'The sudden, usually upward, movement off the ground or other surface through sudden muscular effort in the legs, following exposure to an external stimulus.'.
2022-08-12T10:33:59Z
reduced rate of jump response
phenotypic_class
FBcv:0007554
decreased rate of jump response
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of jump response (GO:0007630). 'jump response' is defined as: 'The sudden, usually upward, movement off the ground or other surface through sudden muscular effort in the legs, following exposure to an external stimulus.'.
GO:0007630
GOC:jid
ISBN:0198606907
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of copulation (GO:0007620). 'copulation' is defined as: 'The act of sexual union between male and female, involving the transfer of sperm.'.
2022-08-12T10:34:20Z
reduced rate of copulation
phenotypic_class
FBcv:0007555
decreased rate of copulation
Phenotype that is a decrease in any kind of rate (e.g. speed, frequency) of copulation (GO:0007620). 'copulation' is defined as: 'The act of sexual union between male and female, involving the transfer of sperm.'.
GO:0007620
ISBN:0721662544
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
The complete process of formation and maturation of an ovum or female gemate from a primordial female germ cell.
GO:0048477
oogenesis stage
FlyBase_development_CV
FBdv:00004886
Temporal ordering number - 10000.
oogenesis
The complete process of formation and maturation of an ovum or female gemate from a primordial female germ cell.
GO:0048477
A temporal subdivision of a developmental process.
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
Developmental stage that starts with ovulation, at the end of oogenesis, until the egg is fertilized by a sperm.
FlyBase_development_CV
FBdv:00005287
Temporal ordering number - 10300.
unfertilized egg stage
Developmental stage that starts with ovulation, at the end of oogenesis, until the egg is fertilized by a sperm.
FlyBase:FBrf0158848
Developmental stage that starts with sperm entry until the first mitotic division of the zygote.
FlyBase_development_CV
FBdv:00005288
Temporal ordering number - 10.
fertilized egg stage
Developmental stage that starts with sperm entry until the first mitotic division of the zygote.
FlyBase:FBrf0229233
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.).
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.
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.
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.
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
A biological process whose specific outcome is the progression of an integrated living unit (an anatomical structure or an entire organism) over time from an initial condition to a later condition.
2009-10-01T05:56:42Z
GO:0032502
FlyBase_development_CV
FBdv:00007009
developmental process
A biological process whose specific outcome is the progression of an integrated living unit (an anatomical structure or an entire organism) over time from an initial condition to a later condition.
GO:0032502
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.
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.
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.
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.
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).
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).
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).
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).
2011-04-26T12:03:14Z
FlyBase_development_CV
FBdv:00007018
Temporal ordering number - 394. Should not be used to stage embryos whose development is at temperatures other than 25'C.
embryonic stage 17(iv)
Hours 6-8 (the last two hours) of embryonic stage 17 at 25'C. (Approximately 22-24 hours at 25'C after egg laying).
FBC:DOS
The substage of the wandering third instar larval stage, prior to the beginning of clearance of the gut.
FlyBase_development_CV
FBdv:00007019
Temporal ordering number - 462. This is commonly assayed by adding 0.5% bromophenol blue to the food and looking for wandering third instar larvae with the same color guts (dark blue) as feeding larvae (Andres and Thummel, 1994). Larvae at this stage are in chromosomal puff stage 1 (Andres and Thummel, 1994).
third instar - uncleared gut stage
The substage of the wandering third instar larval stage, prior to the beginning of clearance of the gut.
FlyBase:FBrf0076598
The substage of the wandering third instar larval stage when the larva has partially cleared its gut contents.
FlyBase_development_CV
FBdv:00007020
Temporal ordering number - 465. This is commonly assayed by adding 0.5% bromophenol blue to the food and looking for wandering third instar larvae with lighter colored guts (light blue) than feeding larvae (Andres and Thummel, 1994). Larvae at this stage are mainly in chromosomal puff stages 2-7 (Andres and Thummel, 1994).
third instar - partially cleared gut stage
The substage of the wandering third instar larval stage when the larva has partially cleared its gut contents.
FlyBase:FBrf0076598
The substage of the wandering third instar larval stage when the larva has cleared its gut contents.
FlyBase_development_CV
FBdv:00007021
Temporal ordering number - 467. This is commonly assayed by adding 0.5% bromophenol blue to the food and looking for wandering third instar larvae with guts lacking any blue stain (Andres and Thummel, 1994). Larvae at this stage are mainly in chromosomal puff stages 7-9 and pupate within 1-6 hours (Andres and Thummel, 1994.
third instar - cleared gut stage
The substage of the wandering third instar larval stage when the larva has cleared its gut contents.
FlyBase:FBrf0076598
The execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module.
GO:0008150
FlyBase_development_CV
FBdv:00007024
biological process
The execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module.
GO:0008150
The developmental stage that lasts from eclosion of the adult from the pupal case until tanning is complete (the end of adult stage A3).
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.
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
Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates.
establishment of planar cell polarity
biological_process
GO:0001736
establishment of planar polarity
Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates.
GOC:dph
The morphogenetic process in which the anatomical structures of a polarized epithelium are generated and organized. A polarized epithelium is an epithelium where the epithelial sheet is oriented with respect to the planar axis.
epithelial polarization
biological_process
GO:0001738
morphogenesis of a polarized epithelium
The morphogenetic process in which the anatomical structures of a polarized epithelium are generated and organized. A polarized epithelium is an epithelium where the epithelial sheet is oriented with respect to the planar axis.
GOC:dph
epithelial polarization
GOC:dph
The 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
Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process.
down regulation of immune system process
down-regulation of immune system process
downregulation of immune system process
inhibition of immune system process
biological_process
GO:0002683
negative regulation of immune system process
Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process.
GOC:add
Any process that activates or increases the frequency, rate, or extent of an immune system process.
up regulation of immune system process
up-regulation of immune system process
upregulation of immune system process
activation of immune system process
stimulation of immune system process
biological_process
GO:0002684
positive regulation of immune system process
Any process that activates or increases 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.
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 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.
GOC:pdt
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Wikipedia:Enzyme
enzyme activity
molecular_function
GO:0003824
catalytic activity
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GOC:vw
ISBN:0198506732
enzyme activity
GOC:dph
GOC:tb
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 the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).
phosphorus metabolism
biological_process
GO:0006793
phosphorus metabolic process
The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).
GOC:ai
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
phosphate metabolism
biological_process
phosphate metabolic process
GO:0006796
phosphate-containing compound metabolic process
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
GOC:ai
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
https://github.com/geneontology/go-ontology/issues/26424
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
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.
https://github.com/geneontology/go-ontology/issues/24775
GO:0034984
response to DNA damage stimulus
cellular DNA damage response
cellular response to DNA damage stimulus
response to genotoxic stress
biological_process
GO:0006974
DNA damage response
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
Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
down regulation of cell adhesion
down-regulation of cell adhesion
downregulation of cell adhesion
inhibition of cell adhesion
biological_process
cell adhesion receptor inhibitor activity
GO:0007162
negative regulation of cell adhesion
Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
GOC:go_curators
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
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
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
OBSOLETE. 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).
https://github.com/geneontology/go-ontology/issues/24930
GO:0016280
ageing
biological_process
GO:0007568
The reason for obsoletion is that this represents a phenotype.
obsolete aging
true
OBSOLETE. 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 behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.
adult walking behaviour
biological_process
GO:0007628
adult walking behavior
The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.
GOC:jid
GOC:pr
ISBN:0198606907
The response to external or internal stimuli that results in the locomotory process of flight. Flight is the self-propelled movement of an organism through the air.
flight behaviour
fly
biological_process
GO:0007629
flight behavior
The response to external or internal stimuli that results in the locomotory process of flight. Flight is the self-propelled movement of an organism through the air.
GOC:jid
ISBN:0198606907
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 is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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.
https://github.com/geneontology/go-ontology/issues/24968
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 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 is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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).
https://github.com/geneontology/go-ontology/issues/24680
biological_process
accidental cell death
necrosis
GO:0008219
This term should not be used for direct annotation, it is currently kept in GO as a placeholder for describing cell death phenotypes in uPHENO. When information is provided on a programmed 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'). Unintentional cell death, i.e. cell death caused by injury, ageing, or cell phenotypes observed as a result of a pathological mutation in an essential gene should NOT be annotated using GO terms.
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
Locomotory behavior in a larval (immature) organism.
larval locomotory behaviour
biological_process
GO:0008345
See also the biological process term 'locomotory behavior ; GO:0007626'.
larval locomotory behavior
Locomotory behavior in a larval (immature) 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
Any process that modulates the frequency, rate or extent of replication and segregation of genetic material in the embryo.
embryonic mitotic cell cycle modulation
embryonic mitotic cell cycle regulation
modulation of embryonic mitotic cell cycle progression
regulation of embryonic mitotic cell cycle
regulation of embryonic mitotic cell cycle progression
regulation of progression through embryonic mitotic cell cycle
biological_process
embryonic mitotic cell cycle regulator
GO:0009794
regulation of mitotic cell cycle, embryonic
Any process that modulates the frequency, rate or extent of replication and segregation of genetic material in the embryo.
GOC:dph
GOC:go_curators
GOC:tb
regulation of embryonic mitotic cell cycle
GOC:dph
GOC:tb
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
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GO:0044252
down regulation of metabolic process
down-regulation of metabolic process
downregulation of metabolic process
negative regulation of metabolism
negative regulation of organismal metabolism
inhibition of metabolic process
inhibition of organismal metabolic process
negative regulation of multicellular organismal metabolic process
biological_process
GO:0009892
negative regulation of metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GO:0044253
positive regulation of metabolism
up regulation of metabolic process
up-regulation of metabolic process
upregulation of metabolic process
activation of metabolic process
positive regulation of multicellular organismal metabolic process
positive regulation of organismal metabolism
stimulation of metabolic process
stimulation of organismal metabolic process
up-regulation of organismal metabolic process
biological_process
GO:0009893
positive regulation of metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GOC:go_curators
The establishment, maintenance and elaboration of the 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
This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
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 increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
biological_process
GO:0010562
positive regulation of phosphorus metabolic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
GOC:dph
GOC:tb
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
biological_process
GO:0010563
negative regulation of phosphorus metabolic process
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
GOC:dph
GOC:tb
Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
biological_process
GO:0010564
regulation of cell cycle process
Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
GOC:dph
GOC:tb
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
biological_process
GO:0010604
positive regulation of macromolecule metabolic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GOC:dph
GOC:tb
Any process that decreases 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:0010605
negative regulation of macromolecule metabolic process
Any process that decreases 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 increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
positive regulation of organelle organisation
biological_process
positive regulation of organelle organization and biogenesis
GO:0010638
positive regulation of organelle organization
Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
GOC:dph
GOC:tb
positive regulation of organelle organisation
GOC:mah
positive regulation of organelle organization and biogenesis
GOC:mah
Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
negative regulation of organelle organisation
biological_process
negative regulation of organelle organization and biogenesis
GO:0010639
negative regulation of organelle organization
Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
GOC:dph
GOC:tb
negative regulation of organelle organisation
GOC:mah
negative regulation of organelle organization and biogenesis
GOC:mah
Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
tb
2009-04-27T09:53:22Z
biological_process
GO:0010948
negative regulation of cell cycle process
Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
GOC:dph
GOC:tb
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
GO:0044235
GO:0071842
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
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Reactome:R-HSA-6788855
Reactome:R-HSA-6788867
phosphokinase activity
molecular_function
GO:0016301
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
kinase activity
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
ISBN:0198506732
Reactome:R-HSA-6788855
FN3KRP phosphorylates PsiAm, RibAm
Reactome:R-HSA-6788867
FN3K phosphorylates ketosamines
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
Wikipedia:Phosphorylation
biological_process
GO:0016310
phosphorylation
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
ISBN:0198506732
The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues.
https://github.com/geneontology/go-ontology/issues/24787
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.
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
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
EC:2.-.-.-
Reactome:R-HSA-1483089
Reactome:R-HSA-1483186
Reactome:R-HSA-5668414
Reactome:R-HSA-8868783
molecular_function
GO:0016740
transferase activity
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
ISBN:0198506732
Reactome:R-HSA-1483089
PE is converted to PS by PTDSS2
Reactome:R-HSA-1483186
PC is converted to PS by PTDSS1
Reactome:R-HSA-5668414
TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK
Reactome:R-HSA-8868783
TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
EC:2.7.-.-
molecular_function
GO:0016772
Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
transferase activity, transferring phosphorus-containing groups
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
GOC:jl
ISBN:0198506732
A reproductive behavior that results in the deposition of eggs (either fertilized or not) upon a surface or into a medium such as water.
https://github.com/geneontology/go-ontology/issues/24955
GO:0060403
egg laying
egg-laying
Wikipedia:Oviposition
oviposition
post-mating oviposition
biological_process
GO:0018991
egg-laying behavior
A reproductive behavior that results in the deposition of eggs (either fertilized or not) upon a surface or into a medium such as water.
GOC:ems
PMID:18050396
PMID:31164023
The specific behavior of an organism that is associated with reproduction.
https://github.com/geneontology/go-ontology/issues/23491
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 involving phosphates.
regulation of phosphate metabolism
biological_process
GO:0019220
regulation of phosphate metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
GOC:go_curators
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GO:0044246
regulation of metabolism
regulation of multicellular organismal metabolic process
regulation of organismal metabolic process
biological_process
GO:0019222
regulation of metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GOC:go_curators
regulation of organismal metabolic process
GOC:tb
A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid).
https://github.com/geneontology/go-ontology/issues/22929
Wikipedia:Sexual_reproduction
biological_process
GO:0019953
Note that gametes 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. Note also that 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 type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid).
Wikipedia:Sexual_reproduction
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
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 activates or increases the frequency, rate, extent or direction of cell growth.
up regulation of cell growth
up-regulation of cell growth
upregulation of cell growth
activation of cell growth
stimulation of cell growth
biological_process
GO:0030307
positive regulation of cell growth
Any process that activates or increases the frequency, rate, extent or direction of cell growth.
GOC:go_curators
Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
down regulation of cell growth
down-regulation of cell growth
downregulation of cell growth
inhibition of cell growth
biological_process
GO:0030308
negative regulation of cell growth
Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
GOC:go_curators
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 that activates or increases the frequency, rate or extent of cell migration.
up regulation of cell migration
up-regulation of cell migration
upregulation of cell migration
activation of cell migration
stimulation of cell migration
biological_process
GO:0030335
positive regulation of cell migration
Any process that activates or increases the frequency, rate or extent of cell migration.
GOC:go_curators
Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
down regulation of cell migration
down-regulation of cell migration
downregulation of cell migration
inhibition of cell migration
biological_process
GO:0030336
negative regulation of cell migration
Any process that stops, prevents, or reduces 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
Behavior in a larval form of an organism, an immature organism that must undergo metamorphosis to assume adult characteristics.
GO:0017037
larval behaviour
biological_process
GO:0030537
See also the biological process term 'behavior ; GO:0007610'.
larval behavior
Behavior in a larval form of an organism, an immature organism that must undergo metamorphosis to assume adult characteristics.
GOC:mah
ISBN:0877797099
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 stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
down regulation of cellular metabolic process
down-regulation of cellular metabolic process
downregulation of cellular metabolic process
negative regulation of cellular metabolism
inhibition of cellular metabolic process
biological_process
GO:0031324
negative regulation of cellular metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
GOC:mah
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
positive regulation of cellular metabolism
up regulation of cellular metabolic process
up-regulation of cellular metabolic process
upregulation of cellular metabolic process
activation of cellular metabolic process
stimulation of cellular metabolic process
biological_process
GO:0031325
positive regulation of cellular metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
GOC:mah
Any process that 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
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 process that stops, prevents, or reduces the frequency, rate or extent of the division of the cytoplasm of a cell, and its separation into two daughter cells.
GO:0071776
down regulation of cytokinesis
down-regulation of cytokinesis
downregulation of cytokinesis
inhibition of cytokinesis
biological_process
negative regulation of cell cycle cytokinesis
GO:0032466
negative regulation of cytokinesis
Any process that stops, prevents, or reduces the frequency, rate or extent of the division of the cytoplasm of a cell, and its separation into two daughter cells.
GOC:mah
Any process that activates or increases the frequency, rate or extent of the division of the cytoplasm of a cell, and its separation into two daughter cells.
GO:0071777
up regulation of cytokinesis
up-regulation of cytokinesis
upregulation of cytokinesis
activation of cytokinesis
stimulation of cytokinesis
biological_process
positive regulation of cell cycle cytokinesis
GO:0032467
positive regulation of cytokinesis
Any process that activates or increases 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 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
Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
down regulation of kinase activity
down-regulation of kinase activity
downregulation of kinase activity
inhibition of kinase activity
kinase inhibitor
biological_process
GO:0033673
negative regulation of kinase activity
Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GOC:mah
Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
up regulation of kinase activity
up-regulation of kinase activity
upregulation of kinase activity
kinase activator
stimulation of kinase activity
biological_process
GO:0033674
positive regulation of kinase activity
Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GOC:mah
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
https://github.com/geneontology/go-ontology/issues/26424
cellular nitrogen compound metabolism
biological_process
GO:0034641
cellular nitrogen compound metabolic process
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
GOC:mah
The 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 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
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 activates or increases the frequency, rate or extent of embryonic development.
up regulation of embryonic development
up-regulation of embryonic development
upregulation of embryonic development
activation of embryonic development
stimulation of embryonic development
biological_process
GO:0040019
positive regulation of embryonic development
Any process that activates or increases the frequency, rate or extent of embryonic development.
GOC:go_curators
Any process that modulates the frequency, rate or extent of 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
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
Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
biological_process
GO:0042325
regulation of phosphorylation
Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
GOC:jl
Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
down regulation of phosphorylation
down-regulation of phosphorylation
downregulation of phosphorylation
inhibition of phosphorylation
biological_process
GO:0042326
negative regulation of phosphorylation
Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
GOC:jl
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
up regulation of phosphorylation
up-regulation of phosphorylation
upregulation of phosphorylation
activation of phosphorylation
stimulation of phosphorylation
biological_process
GO:0042327
positive regulation of phosphorylation
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
GOC:jl
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
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
Any process that activates or increases the activity of an enzyme.
GO:0048554
positive regulation of enzyme activity
up regulation of enzyme activity
up-regulation of enzyme activity
upregulation of enzyme activity
activation of enzyme activity
activation of metalloenzyme activity
positive regulation of metalloenzyme activity
stimulation of enzyme activity
stimulation of metalloenzyme activity
up regulation of metalloenzyme activity
up-regulation of metalloenzyme activity
upregulation of metalloenzyme activity
biological_process
GO:0043085
positive regulation of catalytic activity
Any process that activates or increases the activity of an enzyme.
GOC:ebc
GOC:jl
GOC:tb
GOC:vw
positive regulation of enzyme activity
GOC:tb
Any process that stops or reduces the activity of an enzyme.
GO:0048553
down regulation of enzyme activity
down-regulation of enzyme activity
down-regulation of metalloenzyme activity
downregulation of enzyme activity
negative regulation of enzyme activity
down regulation of metalloenzyme activity
downregulation of metalloenzyme activity
inhibition of enzyme activity
inhibition of metalloenzyme activity
negative regulation of metalloenzyme activity
biological_process
GO:0043086
negative regulation of catalytic activity
Any process that stops or reduces the activity of an enzyme.
GOC:ebc
GOC:jl
GOC:tb
GOC:vw
negative regulation of enzyme activity
GOC:tb
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.
https://github.com/geneontology/go-ontology/issues/26424
GO:0034960
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
Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
biological_process
GO:0043549
regulation of kinase activity
Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GOC:bf
Any process that 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
Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
jl
2009-04-21T04:07:27Z
biological_process
GO:0044092
negative regulation of molecular function
Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
GO:jl
Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
jl
2009-04-21T04:11:06Z
biological_process
GO:0044093
positive regulation of molecular function
Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
GO:jl
The chemical reactions and pathways by which individual cells transform chemical substances.
cellular metabolism
biological_process
intermediary metabolism
GO:0044237
This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
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.
https://github.com/geneontology/go-ontology/issues/26424
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
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 DNA repair.
down regulation of DNA repair
down-regulation of DNA repair
downregulation of DNA repair
inhibition of DNA repair
biological_process
GO:0045738
negative regulation of DNA repair
Any process that stops, prevents, or reduces the frequency, rate or extent of DNA repair.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of DNA repair.
up regulation of DNA repair
up-regulation of DNA repair
upregulation of DNA repair
activation of DNA repair
stimulation of DNA repair
biological_process
GO:0045739
positive regulation of DNA repair
Any process that activates or increases the frequency, rate or extent of DNA repair.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of cell adhesion.
up regulation of cell adhesion
up-regulation of cell adhesion
upregulation of cell adhesion
activation of cell adhesion
stimulation of cell adhesion
biological_process
GO:0045785
positive regulation of cell adhesion
Any process that activates or increases the frequency, rate or extent of cell adhesion.
GOC:go_curators
Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
down regulation of progression through cell cycle
down-regulation of progression through cell cycle
downregulation of progression through cell cycle
negative regulation of cell cycle progression
negative regulation of progression through cell cycle
inhibition of progression through cell cycle
biological_process
GO:0045786
negative regulation of cell cycle
Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
GOC:dph
GOC:go_curators
GOC:tb
Any process that activates or increases the rate or extent of progression through the cell cycle.
positive regulation of cell cycle progression
positive regulation of progression through cell cycle
up regulation of progression through cell cycle
up-regulation of progression through cell cycle
upregulation of progression through cell cycle
activation of progression through cell cycle
stimulation of progression through cell cycle
biological_process
GO:0045787
positive regulation of cell cycle
Any process that activates or increases the rate or extent of progression through the cell cycle.
GOC:go_curators
positive regulation of progression through cell cycle
GOC:dph
GOC:tb
Any process that stops, prevents, or reduces the 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
Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis.
down regulation of meiosis
down-regulation of meiosis
downregulation of meiosis
negative regulation of meiosis
inhibition of meiosis
biological_process
GO:0045835
negative regulation of meiotic nuclear division
Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of meiosis.
positive regulation of meiosis
up regulation of meiosis
up-regulation of meiosis
upregulation of meiosis
activation of meiosis
stimulation of meiosis
biological_process
GO:0045836
positive regulation of meiotic nuclear division
Any process that activates or increases the frequency, rate or extent of meiosis.
GOC:go_curators
Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother.
down regulation of mitosis
down-regulation of mitosis
downregulation of mitosis
negative regulation of mitosis
inhibition of mitosis
biological_process
GO:0045839
negative regulation of mitotic nuclear division
Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother.
GOC:dph
GOC:go_curators
GOC:tb
Any process that activates or increases the frequency, rate or extent of mitosis.
positive regulation of mitosis
up regulation of mitosis
up-regulation of mitosis
upregulation of mitosis
activation of mitosis
mitogenic activity
stimulation of mitosis
biological_process
GO:0045840
positive regulation of mitotic nuclear division
Any process that activates or increases the frequency, rate or extent of mitosis.
GOC:go_curators
Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism.
down regulation of growth
down-regulation of growth
downregulation of growth
inhibition of growth
biological_process
GO:0045926
negative regulation of growth
Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism.
GOC:go_curators
Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism.
up regulation of growth
up-regulation of growth
upregulation of growth
activation of growth
stimulation of growth
biological_process
GO:0045927
positive regulation of growth
Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism.
GOC:go_curators
Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle.
down regulation of progression through mitotic cell cycle
down-regulation of progression through mitotic cell cycle
downregulation of progression through mitotic cell cycle
negative regulation of mitotic cell cycle progression
negative regulation of progression through mitotic cell cycle
inhibition of progression through mitotic cell cycle
biological_process
GO:0045930
negative regulation of mitotic cell cycle
Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle.
GOC:dph
GOC:go_curators
GOC:tb
negative regulation of progression through mitotic cell cycle
GOC:dph
GOC:tb
Any process that activates or increases the rate or extent of progression through the mitotic cell cycle.
positive regulation of mitotic cell cycle progression
positive regulation of progression through mitotic cell cycle
up regulation of progression through mitotic cell cycle
up-regulation of progression through mitotic cell cycle
upregulation of progression through mitotic cell cycle
activation of progression through mitotic cell cycle
stimulation of progression through mitotic cell cycle
biological_process
GO:0045931
positive regulation of mitotic cell cycle
Any process that activates or increases the rate or extent of progression through the mitotic cell cycle.
GOC:dph
GOC:go_curators
GOC:tb
positive regulation of progression through mitotic cell cycle
GOC:dph
GOC:tb
Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
inhibition of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
biological_process
negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
GO:0045934
negative regulation of nucleobase-containing compound metabolic process
Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
GOC:go_curators
negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
GOC:dph
GOC:tb
Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
biological_process
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
GO:0045935
positive regulation of nucleobase-containing compound metabolic process
Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
GOC:go_curators
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
GOC:dph
GOC:tb
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
down regulation of phosphate metabolic process
down-regulation of phosphate metabolic process
downregulation of phosphate metabolic process
negative regulation of phosphate metabolism
inhibition of phosphate metabolic process
biological_process
GO:0045936
negative regulation of phosphate metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
positive regulation of phosphate metabolism
up regulation of phosphate metabolic process
up-regulation of phosphate metabolic process
upregulation of phosphate metabolic process
activation of phosphate metabolic process
stimulation of phosphate metabolic process
biological_process
GO:0045937
positive regulation of phosphate metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
GOC:go_curators
Any process that stops, prevents or reduces the rate or extent of progression through the embryonic mitotic cell cycle.
down regulation of progression through embryonic mitotic cell cycle
down-regulation of progression through embryonic mitotic cell cycle
downregulation of progression through embryonic mitotic cell cycle
negative regulation of embryonic mitotic cell cycle
negative regulation of embryonic mitotic cell cycle progression
negative regulation of progression through embryonic mitotic cell cycle
inhibition of progression through embryonic mitotic cell cycle
biological_process
GO:0045976
negative regulation of mitotic cell cycle, embryonic
Any process that stops, prevents or reduces the rate or extent of progression through the embryonic mitotic cell cycle.
GOC:dph
GOC:go_curators
GOC:tb
negative regulation of embryonic mitotic cell cycle
GOC:dph
GOC:tb
negative regulation of progression through embryonic mitotic cell cycle
GOC:dph
GOC:tb
Any process that activates or increases the frequency, rate or extent of progression through the embryonic mitotic cell cycle.
positive regulation of embryonic mitotic cell cycle
positive regulation of embryonic mitotic cell cycle progression
positive regulation of progression through embryonic mitotic cell cycle
up regulation of mitotic cell cycle, embryonic
up-regulation of mitotic cell cycle, embryonic
upregulation of mitotic cell cycle, embryonic
activation of mitotic cell cycle, embryonic
stimulation of mitotic cell cycle, embryonic
biological_process
GO:0045977
positive regulation of mitotic cell cycle, embryonic
Any process that activates or increases the frequency, rate or extent of progression through the embryonic mitotic cell cycle.
GOC:dph
GOC:go_curators
GOC:tb
positive regulation of embryonic mitotic cell cycle
GOC:dph
GOC:tb
positive regulation of progression through embryonic mitotic cell cycle
GOC:dph
GOC:tb
Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development.
down regulation of embryonic development
down-regulation of embryonic development
downregulation of embryonic development
inhibition of embryonic development
biological_process
GO:0045992
negative regulation of embryonic development
Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development.
GOC:go_curators
Any process that modulates the frequency, rate or extent of embryonic development.
biological_process
GO:0045995
regulation of embryonic development
Any process that modulates the frequency, rate or extent of embryonic development.
GOC:go_curators
The 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 oviposition
regulation of post-mating oviposition
biological_process
GO:0046662
regulation of egg-laying behavior
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
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.
https://github.com/geneontology/go-ontology/issues/25943
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 activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GO:0051242
positive regulation of cellular physiological process
up regulation of cellular process
up-regulation of cellular process
upregulation of cellular process
activation of cellular process
stimulation of cellular process
biological_process
GO:0048522
positive regulation of cellular process
Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:jid
Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GO:0051243
down regulation of cellular process
down-regulation of cellular process
downregulation of cellular process
negative regulation of cellular physiological process
inhibition of cellular process
biological_process
GO:0048523
negative regulation of cellular process
Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:jid
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
biological_process
GO:0048583
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
regulation of response to stimulus
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
GOC:jid
Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
up regulation of response to stimulus
up-regulation of response to stimulus
upregulation of response to stimulus
activation of response to stimulus
stimulation of response to stimulus
biological_process
GO:0048584
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
positive regulation of response to stimulus
Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
GOC:jid
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
down regulation of response to stimulus
down-regulation of response to stimulus
downregulation of response to stimulus
inhibition of response to stimulus
biological_process
GO:0048585
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
negative regulation of response to stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
GOC:jid
The 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
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
Any process that activates, maintains or increases the rate of developmental growth.
up regulation of developmental growth
up-regulation of developmental growth
upregulation of developmental growth
activation of developmental growth
stimulation of developmental growth
biological_process
GO:0048639
positive regulation of developmental growth
Any process that activates, maintains or increases the rate of developmental growth.
GOC:go_curators
Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth.
down regulation of developmental growth
down-regulation of developmental growth
downregulation of developmental growth
inhibition of developmental growth
biological_process
GO:0048640
negative regulation of developmental growth
Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth.
GOC:go_curators
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 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.
https://github.com/geneontology/go-ontology/issues/26424
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.
https://github.com/geneontology/go-ontology/issues/19809
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 stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
down regulation of immune response
down-regulation of immune response
downregulation of immune response
inhibition of immune response
biological_process
GO:0050777
negative regulation of immune response
Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
GOC:ai
Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
up regulation of immune response
up-regulation of immune response
upregulation of immune response
stimulation of immune response
biological_process
GO:0050778
positive regulation of immune response
Any process that activates or increases 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 activity of an enzyme.
GO:0048552
regulation of enzyme activity
regulation of metalloenzyme activity
biological_process
GO:0050790
regulation of catalytic activity
Any process that modulates the activity of an enzyme.
GOC:ai
GOC:ebc
GOC:vw
Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
biological_process
GO:0050793
regulation of developmental process
Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
GOC:go_curators
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GO:0051244
regulation of cellular physiological process
biological_process
GO:0050794
regulation of cellular process
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:go_curators
Any process that 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 frequency, rate or extent of the chemical reactions and pathways involving DNA.
down regulation of DNA metabolic process
down-regulation of DNA metabolic process
downregulation of DNA metabolic process
negative regulation of DNA metabolism
inhibition of DNA metabolic process
biological_process
GO:0051053
negative regulation of DNA metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA.
GOC:ai
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA.
positive regulation of DNA metabolism
up regulation of DNA metabolic process
up-regulation of DNA metabolic process
upregulation of DNA metabolic process
activation of DNA metabolic process
stimulation of DNA metabolic process
biological_process
GO:0051054
positive regulation of DNA metabolic process
Any process that activates or increases 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 stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
down regulation of cell organization
down-regulation of cell organization
downregulation of cell organization
inhibition of cell organization
biological_process
negative regulation of cell organisation
negative regulation of cellular component organization and biogenesis
GO:0051129
negative regulation of cellular component organization
Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
GOC:ai
negative regulation of cell organisation
GOC:mah
negative regulation of cellular component organization and biogenesis
GOC:mah
Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
positive regulation of cell organisation
up regulation of cell organization
up-regulation of cell organization
upregulation of cell organization
activation of cell organization
stimulation of cell organization
biological_process
positive regulation of cellular component organization and biogenesis
GO:0051130
positive regulation of cellular component organization
Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
GOC:ai
positive regulation of cellular component organization and biogenesis
GOC:mah
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving 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 that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
down regulation of nitrogen metabolic process
down-regulation of nitrogen metabolic process
downregulation of nitrogen metabolic process
negative regulation of nitrogen metabolic process
negative regulation of nitrogen metabolism
inhibition of nitrogen metabolic process
biological_process
GO:0051172
negative regulation of nitrogen compound metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
GOC:ai
GOC:tb
negative regulation of nitrogen metabolic process
GOC:tb
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
positive regulation of nitrogen metabolic process
positive regulation of nitrogen metabolism
up regulation of nitrogen metabolic process
up-regulation of nitrogen metabolic process
upregulation of nitrogen metabolic process
activation of nitrogen metabolic process
stimulation of nitrogen metabolic process
biological_process
GO:0051173
positive regulation of nitrogen compound metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
GOC:ai
GOC:tb
positive regulation of nitrogen metabolic process
GOC:tb
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
regulation of phosphorus metabolism
biological_process
GO:0051174
regulation of phosphorus metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
GOC:ai
Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.
biological_process
GO:0051239
regulation of multicellular organismal process
Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.
GOC:ai
GOC:dph
GOC:tb
Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
up regulation of multicellular organismal process
up-regulation of multicellular organismal process
upregulation of multicellular organismal process
activation of multicellular organismal process
stimulation of multicellular organismal process
biological_process
GO:0051240
positive regulation of multicellular organismal process
Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
GOC:ai
Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
down regulation of multicellular organismal process
down-regulation of multicellular organismal process
downregulation of multicellular organismal process
inhibition of multicellular organismal process
biological_process
GO:0051241
negative regulation of multicellular organismal process
Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
GOC:ai
The 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.
https://github.com/geneontology/go-ontology/issues/24599
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 frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
transferase regulator
biological_process
GO:0051338
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
regulation of transferase activity
Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
GOC:ai
Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
transferase activator
up regulation of transferase activity
up-regulation of transferase activity
upregulation of transferase activity
activation of transferase activity
stimulation of transferase activity
biological_process
GO:0051347
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
positive regulation of transferase activity
Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
GOC:ai
Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
down regulation of transferase activity
down-regulation of transferase activity
downregulation of transferase activity
transferase inhibitor
inhibition of transferase activity
biological_process
GO:0051348
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
negative regulation of transferase activity
Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
GOC:ai
Any process that 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
Any process that activates or increases the frequency, rate or extent of progression through the meiotic cell cycle.
positive regulation of meiotic cell cycle progression
positive regulation of progression through meiotic cell cycle
up regulation of progression through meiotic cell cycle
up-regulation of progression through meiotic cell cycle
upregulation of progression through meiotic cell cycle
activation of progression through meiotic cell cycle
stimulation of progression through meiotic cell cycle
biological_process
GO:0051446
positive regulation of meiotic cell cycle
Any process that activates or increases the frequency, rate or extent of progression through the meiotic cell cycle.
GOC:ai
GOC:dph
GOC:tb
positive regulation of progression through meiotic cell cycle
GOC:dph
GOC:tb
Any process that stops, prevents or reduces the rate or extent of progression through the meiotic cell cycle.
down regulation of progression through meiotic cell cycle
down-regulation of progression through meiotic cell cycle
downregulation of progression through meiotic cell cycle
negative regulation of meiotic cell cycle progression
negative regulation of progression through meiotic cell cycle
inhibition of progression through meiotic cell cycle
biological_process
GO:0051447
negative regulation of meiotic cell cycle
Any process that stops, prevents or reduces the rate or extent of progression through the meiotic cell cycle.
GOC:ai
GOC:dph
GOC:tb
negative 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 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 activates or increases the frequency, rate or extent of cell division.
up regulation of cell division
up-regulation of cell division
upregulation of cell division
activation of cell division
stimulation of cell division
biological_process
GO:0051781
positive regulation of cell division
Any process that activates or increases the frequency, rate or extent of cell division.
GOC:ai
Any process that stops, prevents, or reduces the frequency, rate or extent of cell division.
down regulation of cell division
down-regulation of cell division
downregulation of cell division
inhibition of cell division
biological_process
GO:0051782
negative regulation of cell division
Any process that stops, prevents, or reduces the frequency, rate or extent of cell division.
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 stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
down regulation of nuclear division
down-regulation of nuclear division
downregulation of nuclear division
inhibition of nuclear division
biological_process
GO:0051784
negative regulation of nuclear division
Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
GOC:ai
Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
up regulation of nuclear division
up-regulation of nuclear division
upregulation of nuclear division
activation of nuclear division
stimulation of nuclear division
biological_process
GO:0051785
positive regulation of nuclear division
Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
GOC:ai
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
Self-propelled movement of an organism from one location to another through the air that is part of the organism's response to external or internal stimuli resulting in flight.
biological_process
GO:0060362
flight involved in flight behavior
Self-propelled movement of an organism from one location to another through the air that is part of the organism's response to external or internal stimuli resulting in flight.
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
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 decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
dph
2010-02-25T10:33:30Z
biological_process
GO:0061045
negative regulation of wound healing
Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
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 stops, prevents, or reduces the frequency, 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
2018-02-05T15:04:33Z
biological_process
GO:0061964
negative regulation of entry into reproductive diapause
Any process that stops, prevents, or reduces the frequency, 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 activates or increases 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
2018-02-05T15:06:51Z
biological_process
GO:0061965
positive regulation of entry into reproductive diapause
Any process that activates or increases 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
Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
regulation of a molecular function
biological_process
GO:0065009
regulation of molecular function
Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
GOC:isa_complete
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.
https://github.com/geneontology/go-ontology/issues/26424
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 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
Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
tb
2009-09-09T11:39:52Z
biological_process
GO:0090068
positive regulation of cell cycle process
Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
GOC:dph
GOC:tb
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 process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
tb
2010-03-22T02:12:03Z
biological_process
GO:0090303
positive regulation of wound healing
Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
GOC:BHF
Any cellular metabolic process involving nucleic acids.
https://github.com/geneontology/go-ontology/issues/26133
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
The behavior of an organism relating to the progression of that organism along the ground by the process of lifting and setting down each leg.
tb
2015-08-27T16:34:28Z
locomotor gait pattern
biological_process
GO:0090659
walking behavior
The behavior of an organism relating to the progression of that organism along the ground by the process of lifting and setting down each leg.
GOC:tb
Any process that activates or increases the frequency, rate or extent of animal organ morphogenesis.
kmv
2018-07-05T14:10:14Z
biological_process
GO:0110110
positive regulation of animal organ morphogenesis
Any process that activates or increases the frequency, rate or extent of animal organ morphogenesis.
GOC:kmv
Any process that stops, prevents, or reduces the frequency, rate or extent of animal organ morphogenesis.
kmv
2018-07-05T14:25:21Z
biological_process
GO:0110111
negative regulation of animal organ morphogenesis
Any process that stops, prevents, or reduces the frequency, rate or extent of animal organ morphogenesis.
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
negative regulation of oviposition
inhibition of oviposition
biological_process
GO:1901045
negative regulation of egg-laying behavior
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
positive regulation of oviposition
up regulation of oviposition
up-regulation of oviposition
upregulation of oviposition
activation of oviposition
biological_process
GO:1901046
positive regulation of egg-laying behavior
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 stops, prevents or reduces the frequency, rate or extent of response to oxidative stress.
kmv
2014-04-03T20:30:20Z
down regulation of response to oxidative stress
down-regulation of response to oxidative stress
downregulation of response to oxidative stress
inhibition of response to oxidative stress
biological_process
GO:1902883
negative regulation of response to oxidative stress
Any process that stops, prevents or reduces the frequency, rate or extent of response to oxidative stress.
GOC:TermGenie
GOC:kmv
GO_REF:0000058
PMID:16899554
down regulation of response to oxidative stress
GOC:TermGenie
down-regulation of response to oxidative stress
GOC:TermGenie
downregulation of response to oxidative stress
GOC:TermGenie
inhibition of response to oxidative stress
GOC:TermGenie
Any process that activates or increases the frequency, rate or extent of response to oxidative stress.
kmv
2014-04-03T20:30:47Z
up regulation of response to oxidative stress
up-regulation of response to oxidative stress
upregulation of response to oxidative stress
activation of response to oxidative stress
biological_process
GO:1902884
positive regulation of response to oxidative stress
Any process that activates or increases the frequency, rate or extent of response to oxidative stress.
GOC:TermGenie
GOC:kmv
GO_REF:0000058
PMID:16899554
up regulation of response to oxidative stress
GOC:TermGenie
up-regulation of response to oxidative stress
GOC:TermGenie
upregulation of response to oxidative stress
GOC:TermGenie
activation of response to oxidative stress
GOC:TermGenie
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
Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding.
kmv
2014-05-18T01:28:52Z
down regulation of physiological response to wounding
down regulation of response to wounding
down-regulation of physiological response to wounding
down-regulation of response to wounding
downregulation of physiological response to wounding
downregulation of response to wounding
negative regulation of physiological response to wounding
inhibition of physiological response to wounding
inhibition of response to wounding
biological_process
GO:1903035
negative regulation of response to wounding
Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding.
GOC:TermGenie
GOC:kmv
GO_REF:0000058
PMID:19164535
down regulation of physiological response to wounding
GOC:TermGenie
down regulation of response to wounding
GOC:TermGenie
down-regulation of physiological response to wounding
GOC:TermGenie
down-regulation of response to wounding
GOC:TermGenie
downregulation of physiological response to wounding
GOC:TermGenie
downregulation of response to wounding
GOC:TermGenie
negative regulation of physiological response to wounding
GOC:TermGenie
inhibition of physiological response to wounding
GOC:TermGenie
inhibition of response to wounding
GOC:TermGenie
Any process that activates or increases the frequency, rate or extent of response to wounding.
kmv
2014-05-18T01:28:58Z
positive regulation of physiological response to wounding
up regulation of physiological response to wounding
up regulation of response to wounding
up-regulation of physiological response to wounding
up-regulation of response to wounding
upregulation of physiological response to wounding
upregulation of response to wounding
activation of physiological response to wounding
activation of response to wounding
biological_process
GO:1903036
positive regulation of response to wounding
Any process that activates or increases the frequency, rate or extent of response to wounding.
GOC:TermGenie
GOC:kmv
GO_REF:0000058
PMID:19164535
positive regulation of physiological response to wounding
GOC:TermGenie
up regulation of physiological response to wounding
GOC:TermGenie
up regulation of response to wounding
GOC:TermGenie
up-regulation of physiological response to wounding
GOC:TermGenie
up-regulation of response to wounding
GOC:TermGenie
upregulation of physiological response to wounding
GOC:TermGenie
upregulation of response to wounding
GOC:TermGenie
activation of physiological response to wounding
GOC:TermGenie
activation of 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 stops, prevents or reduces the frequency, rate or extent of locomotor rhythm.
sl
2015-03-18T20:38:58Z
down regulation of locomotor rhythm
down-regulation of locomotor rhythm
downregulation of locomotor rhythm
down regulation of circadian locomotor activity rhythm
down-regulation of circadian locomotor activity rhythm
downregulation of circadian locomotor activity rhythm
inhibition of circadian locomotor activity rhythm
inhibition of locomotor rhythm
negative regulation of circadian locomotor activity rhythm
biological_process
GO:1904060
negative regulation of locomotor rhythm
Any process that stops, prevents or reduces the frequency, rate or extent of locomotor rhythm.
GOC:TermGenie
GO_REF:0000058
PMID:16310969
down regulation of locomotor rhythm
GOC:TermGenie
down-regulation of locomotor rhythm
GOC:TermGenie
downregulation of locomotor rhythm
GOC:TermGenie
down regulation of circadian locomotor activity rhythm
GOC:TermGenie
down-regulation of circadian locomotor activity rhythm
GOC:TermGenie
downregulation of circadian locomotor activity rhythm
GOC:TermGenie
inhibition of circadian locomotor activity rhythm
GOC:TermGenie
inhibition of locomotor rhythm
GOC:TermGenie
negative regulation of circadian locomotor activity rhythm
GOC:TermGenie
Any process that activates or increases the frequency, rate or extent of locomotor rhythm.
sl
2015-03-18T20:39:03Z
up regulation of locomotor rhythm
up-regulation of locomotor rhythm
upregulation of locomotor rhythm
activation of circadian locomotor activity rhythm
activation of locomotor rhythm
positive regulation of circadian locomotor activity rhythm
up regulation of circadian locomotor activity rhythm
up-regulation of circadian locomotor activity rhythm
upregulation of circadian locomotor activity rhythm
biological_process
GO:1904061
positive regulation of locomotor rhythm
Any process that activates or increases the frequency, rate or extent of locomotor rhythm.
GOC:TermGenie
GO_REF:0000058
PMID:16310969
up regulation of locomotor rhythm
GOC:TermGenie
up-regulation of locomotor rhythm
GOC:TermGenie
upregulation of locomotor rhythm
GOC:TermGenie
activation of circadian locomotor activity rhythm
GOC:TermGenie
activation of locomotor rhythm
GOC:TermGenie
positive regulation of circadian locomotor activity rhythm
GOC:TermGenie
up regulation of circadian locomotor activity rhythm
GOC:TermGenie
up-regulation of circadian locomotor activity rhythm
GOC:TermGenie
upregulation 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 stops, prevents or reduces the frequency, rate or extent of morphogenesis of an epithelium.
bhm
2016-07-22T07:13:57Z
down regulation of epithelium morphogenesis
down regulation of morphogenesis of an epithelium
down-regulation of epithelium morphogenesis
down-regulation of morphogenesis of an epithelium
downregulation of epithelium morphogenesis
downregulation of morphogenesis of an epithelium
negative regulation of epithelium morphogenesis
inhibition of epithelium morphogenesis
inhibition of morphogenesis of an epithelium
biological_process
GO:1905331
An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay).
negative regulation of morphogenesis of an epithelium
Any process that stops, prevents or reduces the frequency, rate or extent of morphogenesis of an epithelium.
GOC:TermGenie
GOC:bhm
GO_REF:0000058
PMID:25745997
down regulation of epithelium morphogenesis
GOC:TermGenie
down regulation of morphogenesis of an epithelium
GOC:TermGenie
down-regulation of epithelium morphogenesis
GOC:TermGenie
down-regulation of morphogenesis of an epithelium
GOC:TermGenie
downregulation of epithelium morphogenesis
GOC:TermGenie
downregulation of morphogenesis of an epithelium
GOC:TermGenie
negative regulation of epithelium morphogenesis
GOC:TermGenie
inhibition of epithelium morphogenesis
GOC:TermGenie
inhibition of morphogenesis of an epithelium
GOC:TermGenie
Any process that activates or increases the frequency, rate or extent of morphogenesis of an epithelium.
bhm
2016-07-22T07:14:05Z
positive regulation of epithelium morphogenesis
up regulation of epithelium morphogenesis
up regulation of morphogenesis of an epithelium
up-regulation of epithelium morphogenesis
up-regulation of morphogenesis of an epithelium
upregulation of epithelium morphogenesis
upregulation of morphogenesis of an epithelium
activation of epithelium morphogenesis
activation of morphogenesis of an epithelium
biological_process
GO:1905332
An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay).
positive regulation of morphogenesis of an epithelium
Any process that activates or increases the frequency, rate or extent of morphogenesis of an epithelium.
GOC:TermGenie
GOC:bhm
GO_REF:0000058
PMID:25745997
positive regulation of epithelium morphogenesis
GOC:TermGenie
up regulation of epithelium morphogenesis
GOC:TermGenie
up regulation of morphogenesis of an epithelium
GOC:TermGenie
up-regulation of epithelium morphogenesis
GOC:TermGenie
up-regulation of morphogenesis of an epithelium
GOC:TermGenie
upregulation of epithelium morphogenesis
GOC:TermGenie
upregulation of morphogenesis of an epithelium
GOC:TermGenie
activation of epithelium morphogenesis
GOC:TermGenie
activation of morphogenesis of an epithelium
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 stops, prevents, or reduces the frequency, rate or extent of cell motility.
mah
2010-10-01T09:41:26Z
negative regulation of cell locomotion
negative regulation of movement of a cell
biological_process
negative regulation of cell movement
GO:2000146
negative regulation of cell motility
negative regulation of movement of a cell
GOC:obol
negative regulation of cell movement
GOC:obol
Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility.
GOC:mah
negative regulation of cell locomotion
GOC:obol
Any process that activates or increases the frequency, rate or extent of cell motility.
mah
2010-10-01T09:41:30Z
positive regulation of cell locomotion
positive regulation of movement of a cell
biological_process
positive regulation of cell movement
GO:2000147
positive regulation of cell motility
Any process that activates or increases the frequency, rate or extent of cell motility.
GOC:mah
positive regulation of cell locomotion
GOC:obol
positive regulation of movement of a cell
GOC:obol
positive 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
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.
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
Cognitive perception of a sensation by any of the five senses -- vision, touch, smell, taste, and hearing.
NBO:GVG
"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 visual stimulus." [GO:0007632]
2011-04-05T10:36:24Z
George Gkoutos
behavioral response to visual stimulus
behavioural response to visual stimulus
visual behaviour
behavior_ontology
visual behavior
"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.
2011-04-05T10:40:36Z
George Gkoutos
proprioception
behavior_ontology
vestibular behavior
Behavior related to the awareness of body balance and movement.
MBP:GVG
Behavior related to the sensations arising from the skin and from the muscles, tendons, and joints.
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
Behavior related to the sensations arising from the skin and from the muscles, tendons, and joints.
OBP:GVG
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.
2011-04-06T09:44:37Z
George Gkoutos
behavior_ontology
terrestrial locomotory behavior
Behavior associated with surface locomotion.
NBO:GVG
Behaviour related to cognitive processes.
2011-04-14T03:51:13Z
George Gkoutos
behavior_ontology
cognitive behavior
Behaviour related to cognitive processes.
NBO:JH
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
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATO:0000072
quality
PATO:0000001
quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATOC:GVG
A 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 single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.
PATO:0002015
composed of
compositionality
content
structure, composition
quality
PATO:0000025
For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood).
composition
A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.
PATOC:GVG
A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced
quality
impenetrability
toughness
PATO:0000048
hardness
A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced
merriam-webster:merriam-webster
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 physical quality of the thermal energy of a system.
quality
PATO:0000146
temperature
A physical quality of the thermal energy of a system.
PATOC:GVG
A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics.
quality
PATO:0000150
texture
A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics.
PATOC:GVG
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 hardness quality of being rigid and resistant to pressure.
quality
firm
impenetrable
tough
PATO:0000386
hard
A hardness quality of being rigid and resistant to pressure.
PATOC:GVG
A hardness quality of giving little resistance to pressure.
quality
PATO:0000387
soft
A hardness quality of giving little resistance to pressure.
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
We recommend using the new absent terms (physical absence, absent anatomical entity, or absent process) instead of this class. This is a legacy term and will ultimately be obsoleted.
See https://github.com/pato-ontology/pato/issues/331.
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 physical quality inhering in an organ or tissue by virtue of the bearer's exhibiting an increased number of cells, typically associated with an increase in size.
PATO:0000943
hyperplasia
quality
overdeveloped
PATO:0000644
hyperplastic
A physical quality inhering in an organ or tissue by virtue of the bearer's exhibiting an increased number of cells, typically associated with an increase in size.
Wikipedia:Hyperplasia
A physical quality inhering in an organ or tissue by virtue of the bearer's exhibiting a decreased number of cells, typically associated with a decrease in size.
PATO:0000942
hypoplasia
quality
underdeveloped
PATO:0000645
hypoplastic
A physical quality inhering in an organ or tissue by virtue of the bearer's exhibiting a decreased number of cells, typically associated with a decrease in size.
PATOC:GVG
Wikipedia:Hypoplasia
A quality of a single process inhering in a bearer by virtue of the bearer's being uninterrupted in time, sequence, substance, or extent.
PATO:0000429
uninterrupted
quality
PATO:0000689
continuous
A quality of a single process inhering in a bearer by virtue of the bearer's being uninterrupted in time, sequence, substance, or extent.
thefreedictionary.com:thefreedictionary.com
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
An optical quality which obtains by virtue of the ability of the bearer to absorb visible light.
quality
PATO:0000957
opacity
An optical quality which obtains by virtue of the ability of the bearer to absorb visible light.
PATOC:GVG
A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy.
non-transparent
quality
clouding
cloudy
PATO:0000963
opaque
A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy.
PATOC:GVG
A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices.
quality
PATO:0000973
porosity
A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices.
PATOC:GVG
A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices.
quality
PATO:0000984
porous
A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices.
PATOC:GVG
A physical quality of a fluid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow.
quality
PATO:0000992
viscosity
A physical quality of a fluid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow.
PATOC:GVG
A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity.
quality
PATO:0000998
viscous
A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity.
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
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
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 temperature which is relatively high.
PATO:0000678
high temperature
hot
quality
PATO:0001305
increased temperature
A temperature which is relatively high.
PATOC:GVG
A temperature which is relatively low.
PATO:0000677
cold
low temperature
quality
PATO:0001306
decreased temperature
A temperature which is relatively low.
PATOC:GVG
A structural quality inhering in a bearer by virtue of the bearer's having distinct structure.
quality
PATO:0001411
structured
A structural quality inhering in a bearer by virtue of the bearer's having distinct structure.
PATOC:GVG
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
A structural quality inhering in a bearer by virtue of the bearer's being thicker or more closely packed together; pressed tightly together.
PATO:0001840
compact
compressed
squashed
quality
dense
PATO:0001485
condensed
A structural quality inhering in a bearer by virtue of the bearer's being thicker or more closely packed together; pressed tightly together.
PATOC:GVG
A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking.
quality
PATO:0001543
flexibility
A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking.
merriam-webster:merriam-webster
A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking.
stiff
quality
stiffness
PATO:0001545
inflexible
A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking.
merriam-webster:merriam-webster
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
solidity
quality
PATO:0001546
quality of a solid
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
Chemistry:http://chemistry.about.com/od/chemistryglossary/a/soliddefinition.htm
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape.
gaseous
quality
PATO:0001547
quality of a gas
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape.
Chemistry:http://chemistry.about.com/od/chemistryglossary/a/gasdefinition.htm
PATOC:GVG
A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.
liquidity
quality
PATO:0001548
quality of a liquid
A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.
url:http://www.chemistry-dictionary.com/definition/liquid.php
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 viscosity which relatively high.
high viscosity
quality
PATO:0001693
increased viscosity
A viscosity which relatively high.
PATOC:GVG
A viscosity which relatively low.
low viscosity
quality
PATO:0001694
decreased viscosity
A viscosity which 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 composition quality inhering in a bearer by virtue of the bearer's containing granules.
quality
PATO:0001759
granular
A composition quality inhering in a bearer by virtue of the bearer's containing granules.
thefreedictionary.com:thefreedictionary.com
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 quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
quality
PATO:0001985
frozen
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
OBI:OBI
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.
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.
2009-03-26T11:12:35Z
decreased incidence
quality
PATO:0002052
decreased occurrence
An occurrence which is relatively low.
PATOC:GVG
2009-06-05T09:16:46Z
quality
PATO:0002062
physical quality of a process
Having extra or fewer parts.
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 processing the form of a thin plate sheet or layer.
2009-10-06T04:37:14Z
quality
PATO:0002124
laminar
A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
PATOC:GVG
A positional quality inhering in a bearer by virtue the bearer's being changed in position.
2010-03-01T02:56:33Z
quality
PATO:0002181
displaced
A positional quality inhering in a bearer by virtue the bearer's being changed in position.
PATOC:GVG
A quality inhering in a bearer by virtue of its constitution.
2010-03-15T04:35:27Z
quality
PATO:0002198
quality of a substance
A quality inhering in a bearer by virtue of its constitution.
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.
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
A shape that inheres in a 3 dimensional entity.
2010-10-05T12:31:16Z
quality
PATO:0002266
3-D shape
A shape that inheres in a 3 dimensional entity.
PATOC:OREGON
2011-04-18T05:11:33Z
quality
PATO:0002290
aplastic/hypoplastic
A quality that has a value that is increased compared to normal or average.
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.
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.
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.
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.
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.
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.
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 structural quality inhering in the bearer by virtue of the bearer consisting of a single, maximally connected structure.
2014-12-12T08:41:11Z
quality
PATO:0010000
What counts as maximally connected may be relative to some specification of granularity.
maximally connected
A structural quality inhering in the bearer by virtue of the bearer consisting of a single, maximally connected structure.
GOC:dos
A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other.
2014-12-12T08:43:17Z
quality
PATO:0010001
disconnected
A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other.
GOC:dos
The ability of a process to produce its output.
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.
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.
quality
PATO:0015004
increased efficacy
A increase in the ability of a process to produce its output.
PATOC:PortlandMeetingFeb2015
An increase in porosity.
quality
PATO:0015024
increased porosity
An increase in porosity.
https://github.com/pato-ontology/pato/issues/110
An decrease in porosity.
quality
PATO:0015025
decreased porosity
An decrease in porosity.
https://github.com/pato-ontology/pato/issues/110
The rate of output of a continuous process. Example include: growth rate, cell migration rate, enzyme reaction rate.
quality
PATO:0050001
rate of continuous process
The rate of output of a continuous process. Example include: growth rate, cell migration rate, enzyme reaction rate.
https://orcid.org/0000-0002-9943-9018
A rate of output of a continuous process that is relatively high.
2020-08-19T09:24:56Z
quality
PATO:0055005
increased rate of continuous process
A rate of output of a continuous process that is relatively high.
https://orcid.org/0000-0003-4148-4606
A rate of output of a continuous process that is relatively low.
2020-08-19T09:25:07Z
quality
PATO:0055006
decreased rate of continuous process
A rate of output of a continuous process that is relatively low.
https://orcid.org/0000-0003-4148-4606
A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength.
quality
PATO:0070060
quality of interaction of a substance with electromagnetic radiation
A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength.
https://orcid.org/0000-0002-5111-7263
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
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
http://www.jbiomedsem.com/content/4/1/43
system
2019-03-05T17:25:21Z
Western Australia Ecoregion
WWF:AA1310
https://www.worldwildlife.org/ecoregions/aa1310
Western Australian Mulga Shrublands Ecoregion
2019-03-05T17:51:32Z
https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands
Australasia Ecoregion
2019-03-05T17:52:41Z
Southern central Australia Ecoregion
WWF:AA1309
https://www.worldwildlife.org/ecoregions/aa1309
Tirari-Sturt Stony Desert Ecoregion
2019-03-05T17:54:35Z
Eastern central Australia Ecoregion
WWF:AA1308
https://www.worldwildlife.org/ecoregions/aa1308
Simpson Desert Region
2019-03-05T17:56:13Z
Western Australia Ecoregion
WWF:AA1307
https://www.worldwildlife.org/ecoregions/aa1307
Pilbara Shrublands Ecoregion
2019-03-05T18:10:52Z
Western coast of Australia Ecoregion
WWF:AA1301
https://www.worldwildlife.org/ecoregions/aa1301
Carnarvon Xeric Shrublands Ecoregion
2019-03-05T18:12:28Z
Central Australia Ecoregion
WWF:AA1302
https://www.worldwildlife.org/ecoregions/aa1302
Central Ranges Xeric Shrub Ecoregion
2019-03-05T18:15:11Z
Western central Australia
WWF:AA1303
https://www.worldwildlife.org/ecoregions/aa1303
Gibson Desert Ecoregion
2019-03-05T18:17:15Z
Northwestern Australia
WWF:AA1304
https://www.worldwildlife.org/ecoregions/aa1304
The Great Sandy-Tanami Desert Ecoregion
2019-03-05T18:24:06Z
Southern Australia Ecoregion
WWF:AA1305
https://www.worldwildlife.org/ecoregions/aa1305
Great Victoria Desert Ecoregion
2019-03-05T18:26:16Z
Southern Australia Ecoregion
WWF:AA1306
https://www.worldwildlife.org/ecoregions/aa1306
Nullarbor Plains Xeric Shrubland Ecoregion
2019-03-06T22:01:41Z
https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands
Afrotropical Ecoregion
2019-03-06T22:02:37Z
Southern Africa: Southern Namibia into South Africa
WWF:AT1322
https://www.worldwildlife.org/ecoregions/at1322
Succulent Karoo Ecoregion
2019-03-06T22:07:38Z
WWF:AT1321
https://www.worldwildlife.org/ecoregions/at1321
Arabian Peninsula: Yemen and Saudi Arabia
Yemen and Saudi Arabia Ecoregion
2019-03-06T22:11:38Z
WWF:AT1320
https://www.worldwildlife.org/ecoregions/at1320
Arabian Peninsula: Yemen, Saudi Arabia, and Oman
Yemen, Saudi Arabia, and Oman Ecoregion
2019-03-06T22:13:00Z
WWF:AT1319
https://www.worldwildlife.org/ecoregions/at1319
Somali montane xeric woodlands ecoregion
Somali Montane Xeric Woodland Ecoregion
2019-03-06T22:15:07Z
Islands east of the Horn of Africa and south of Yemen Ecoregion
WWF:AT1318
https://www.worldwildlife.org/ecoregions/at1318
Socotran Archipelago Ecoregion
2019-03-06T22:18:55Z
WWF:AT1317
https://www.worldwildlife.org/ecoregions/at1317
Red Sea Coastal Desert Ecoregion
2019-03-06T22:20:56Z
WWF:AT1316
https://www.worldwildlife.org/ecoregions/at1316
Namibian Savanna Woodland Ecoregion
2019-03-06T22:24:28Z
Africa: Namibia Ecoregion
WWF:AT1315
https://www.worldwildlife.org/ecoregions/at1315
Namib Desert Ecoregion
2019-03-06T22:26:15Z
WWF:AT1314
https://www.worldwildlife.org/ecoregions/at1314
Nama Karoo Ecoregion
2019-03-06T22:28:43Z
WWF:AT1313
https://www.worldwildlife.org/ecoregions/at1313
Masai Xeric Grasslands and Shrublands Ecoregion
2019-03-06T22:30:23Z
WWF:AT1312
https://www.worldwildlife.org/ecoregions/at1312
Madagascar Succulent Woodlands Ecoregion
2019-03-06T22:31:29Z
WWF:AT1311
https://www.worldwildlife.org/ecoregions/at1311
Madagascar spiny desert ecoregion
Madagascar Spiny Thickets Ecoregion
2019-03-06T22:39:32Z
WWF:AT1310
https://www.worldwildlife.org/ecoregions/at1310
Africa: Coastal Namibia and Angola Ecoregion
Kaokoveld Desert Ecoregion
2019-03-06T22:42:47Z
WWF:AT1309
https://www.worldwildlife.org/ecoregions/at1309
Kalahari Xeric Savanna Ecoregion
2019-03-06T22:44:54Z
WWF:AT1308
https://www.worldwildlife.org/ecoregions/at1308
Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion
Ile Europa and Bassas da India Ecoregion
2019-03-06T22:46:58Z
Eastern Africa: Somalia
WWF:AT1307
https://www.worldwildlife.org/ecoregions/at1307
Hobyo Grassland and Shrubland Ecoregion
2019-03-06T22:54:57Z
WWF:AT1306
https://www.worldwildlife.org/ecoregions/at1306
Arabian Peninsula: Oman and United Arab Emirates Ecoregion
Oman and United Arab Emirates Ecoregion
2019-03-07T00:08:06Z
WWF:AT1305
https://www.worldwildlife.org/ecoregions/at1305
Ethiopian Xeric Grasslands and Shrublands Ecoregion
2019-03-07T00:11:29Z
WWF:AT1304
https://www.worldwildlife.org/ecoregions/at1304
Eritrean Coastal Desert Ecoregion
2019-03-07T00:13:33Z
WWF:AT1303
https://www.worldwildlife.org/ecoregions/at1303
North central Africa: Eastern Chad and small area of western Sudan
East Saharan Montane Xeric Woodland Ecoregion
2019-03-07T00:16:12Z
WWF:AT1302
https://www.worldwildlife.org/ecoregions/at1302
Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion
Oman, Yemen, and Saudi Arabia Ecoregion
2019-03-07T00:18:09Z
WWF:AT1301
https://www.worldwildlife.org/ecoregions/at1301
Aldabra Island Xeric Scrub Ecoregion
2019-04-26T23:38:50Z
Indo-Malay Ecoregion
2019-04-26T23:40:13Z
WWF:IM1304
Southern Asia: Western India into Pakistan
Thar Desert
2019-04-27T00:12:51Z
WWF:IM1303
Southern Asia: Eastern India and western Pakistan
Northwestern Thorn Scrub Forests
A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth.
2019-08-20T13:47:18Z
envoAtmo
envoPolar
Arctic front
A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth.
A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth.
2019-08-20T13:48:44Z
envoAtmo
envoPolar
Antarctic front
A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth.
Stellar radiation emitted from Sol.
2020-05-19T22:27:44Z
Solar radiation
subset_oio
true
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
infer input from direct reg
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
enabling an MF enables its parts
true
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
involved in BP
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).