editor preferred label
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has axiom id
Person:Alan Ruttenberg
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
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
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
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/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
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
We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'.
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
preceded by
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.
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
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.
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.
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
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
x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer
x distal to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
x proximal to y iff x is closer to the point of attachment with the body than y.
x proximal_to y iff x is closer to the point of attachment with the body than y.
x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion.
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion.
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion.
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion.
X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure
X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
x immediately deep to y iff x deep_to y and x is contiguous with y.
x immediately superficial to y iff x superficial to y and x is contiguous with y.
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
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 relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
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
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
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
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
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
disposition of
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
location_of
location of
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
contained_in
contains
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
2D boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
has boundary
has_2D_boundary
has 2D boundary
innervated_by
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 relationship that holds between a process that regulates a transport process and the entity transported by that process.
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.
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.
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.
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
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
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.
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.
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.
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
Primitive instance level timing relation between events
before or simultaneous with
Relation between occurrents, shares start and end boundaries.
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
Relation between a neuron and an anatomical structure that its soma is part of.
<http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
has soma location
Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
Chris Mungall
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
has plasma membrane part
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
Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
David Osumi-Sutherland
<http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
continuous with
lactation SubClassOf 'only in taxon' some 'Mammalia'
S only_in_taxon T iff: S SubClassOf in_taxon only T.
U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon.
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
Down-propagates. The original name for this in the paper is 'specific_to'. Applicable to genes because some genes are lost in sub-species (strains) of a species.
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Connects a biological entity to its taxon of origin.
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
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
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
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
connects
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
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
relation between an artery and the structure is supplies with blood.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
supplies
Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
drains
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
Terry Meehan
This is the transitive form of the develops from relation
develops from
develops into
Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
directly develops from
directly develops into
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
negatively regulates (process to process)
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
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.
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.
capable of part of
OBSOLETE x has participant y if and only if x realizes some active role that inheres in y
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
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
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.
x adjacent_to y iff: x and y share a boundary
This relation acts as a join point with BSPO
adjacent to
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.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
Relation between occurrents, shares a start boundary with.
starts
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
starts with
x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
develops from part of
x develops_in y if x is located in y whilst x is developing
This relation take from EHDAA2 - precise semantics yet to be defined
develops in
Relation between occurrents, shares an end boundary with.
ends
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
ends with
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
has start location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
has end location
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
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.
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
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T
Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
developmentally induced by
Inverse of developmentally induced by
developmentally induces
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
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.
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.
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.
x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
developmentally replaces
developmentally succeeded by
'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
part of developmental precursor of
p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
results in developmental progression of
every flower development (GO:0009908) results in development of some flower (PO:0009046)
p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
results in development 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)
results in formation of
an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
results in morphogenesis of
an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
results in maturation of
Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview
x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.
A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.
has habitat
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
holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
transports or maintains localization of
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
characteristic of part of
an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
results in acquisition of features of
A relationship that holds via some environmental process
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
evolutionarily related to
A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
ecologically related to
A mereological relationship or a topological relationship
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
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
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.
part of structure that is capable of
c involved_in p if and only if c enables some process p', and p' is part of p
involved in
enabled by
regulated by
negatively regulated by
positively regulated by
A relationship that holds via some process of localization
Do not use this relation directly. It is a grouping relation.
related via localization to
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
has target start location
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
has target end location
Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
results in transport along
'pollen tube growth' results_in growth_of some 'pollen tube'
results in growth of
'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
results in transport to from or in
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
input of
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
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles
has muscle insertion
We need to import uberon muscle into RO to use as a stricter domain constraint
A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
in branching relationship with
Deschutes River tributary_of Columbia River
inferior epigastric vein tributary_of external iliac vein
x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
tributary of
x spatially_coextensive_with y if and inly if x and y have the same location
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S
x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve
branching part of
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
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 potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
has potential to developmentally induce
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
causally downstream of
immediately causally downstream of
This relation groups causal relations between material entities and causal relations between processes
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
immediately causally upstream of
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
inverse of causally upstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
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 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.
p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
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.
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.
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.
An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
An interaction relationship in which the partners are related via a feeding relationship.
A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]
An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members
is subject of predation interaction with
A biotic interaction in which the two organisms live together in more or less intimate association.
We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).
This relation groups a pair of inverse relations, parasite of and parasitized by
interacts with via parasite-host interaction
Pediculus humanus capitis parasite of human
A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.
participates in a abiotic-biotic interaction with
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
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.
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 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 positively regulates activity of
The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y
Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion.
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.
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
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.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
relation between physical entity and a process or stage
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
Relation between continuant and occurrent, such that c comes into existence at the start of p.
x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
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
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)
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.
Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).
This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.
p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.
x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism
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).
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.
x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
participates in a biotic-biotic interaction with
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
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
p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p
p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
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.
causal relation between material entity and a process
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
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.
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
directly positively regulates (process to process)
Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
directly negatively regulates (process to process)
A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system
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
p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
acts upstream of or within, positive effect
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
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
causally upstream of or within, negative effect
causally upstream of or within, positive effect
A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
realized in response to
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.
p acts on population of c iff c' is a collection, has members of type c, and p has participant c
acts on population of
results in fusion of
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.
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'.
s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.
A diagnostic testing device utilizes a specimen.
X utilizes 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
utilizes
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.
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.
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.
p has anatomical participant c iff p has participant c, and c is an anatomical entity
results in changes to anatomical or cellular structure
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
x is a conduit for y iff y passes through the lumen of x.
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity.
Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed
a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s.
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
c site_of p if c is the bearer of a disposition that is realized by a process that has p as part.
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
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
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
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
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
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]
process
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
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
quality
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 shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
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
fiat object
fiat object part
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
site
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
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 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
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 history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
anatomical entity
connected anatomical structure
material anatomical entity
Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
organism or virus
organism
A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms.
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.
Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium.
A carboxylic acid anion resulting from the deprotonation of the carboxy group of a dicarboxylic acid monoester.
A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens.
dicarboxylic acids and O-substituted derivatives
A carbohydrate acid derivative anion obtained by deprotonation of the carboxy groups of hyaluronic acid; major species at pH 7.3.
Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa.
A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water.
Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).
A cyclic tetrapyrrole anion that is the carbanion obtained by removal of the acidic proton from position 21 of any chlorophyll. Major species at pH 7.3
A cyclic tetrapyrrole anion obtained by removal of the acidic proton from position 21 as well as deprotonation of the carboxy group of any chlorophyllide. Major species at pH 7.3
A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it.
A peptide containing ten or more amino acid residues.
A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues.
An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.
A one-carbon compound in which the carbon is attached by single bonds to four hydrogen atoms. It is a colourless, odourless, non-toxic but flammable gas (b.p. -161degreeC).
A sulfur oxoanion obtained by deprotonation of both OH groups of sulfuric acid.
A mucopolysaccharide composed of N-acetylglucosamine and glucuronic acid subunits. It is found in the connective tissues of vertebrates. A principal constituent of the extracellular matrix (ECM), it mediates the growth and metastasis of tumour cells.
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.
A naturally occurring polypeptide synthesized at the ribosome.
Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates.
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001.
An aminoalkylindole consisting of indole having a 2-aminoethyl group at the 3-position.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H).
A compound in which a carbohydrate component is covalently bound to a protein component.
A one-carbon compound in which the carbon is joined only to a single oxygen. It is a colourless, odourless, tasteless, toxic gas.
A nitrogen oxoanion formed by loss of a proton from nitric acid. Principal species present at pH 7.3.
The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group.
A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.
Any polysaccharide containing a substantial proportion of aminomonosaccharide residues.
A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues.
[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl (2(2)R,17S,18S)-7-ethyl-2(1),2(2),17,18-tetrahydro-2(2)-(methoxycarbonyl)-3,8,13,17-tetramethyl-2(1)-oxo-12-ethenylcyclopenta[at]porphyrin-18-propanoato(2-)]magnesium
(SP-4-2)-((2E,7R,11R)-3,7,11,15-tetramethyl-2-hexadecenyl (3S,4S,21R)-9-ethenyl-14-ethyl-21-(methoxycarbonyl)-4,8,13,18-tetramethyl-20-oxo-3-phorbinepropanoato(2-)-kappaN(23),kappaN(24),kappaN(25),kappaN(26))-magnesium
That part of DNA or RNA that may be involved in pairing.
An acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2, and therefore consisting entirely of hydrogen atoms and saturated carbon atoms.
A phosphate ion that is the conjugate base of hydrogenphosphate.
An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids.
Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids.
A monoatomic or polyatomic species having one or more elementary charges of the electron.
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).
The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid.
An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
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.
A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A role played by the molecular entity or part thereof within a biological context.
A defined linked collection of atoms or a single atom within a molecular entity.
A cyclic compound having as ring members atoms of carbon and at least of one other element.
A heterodetic cyclic peptide is a peptide consisting only of amino-acid residues, but in which the linkages forming the ring are not solely peptide bonds; one or more is an isopeptide, disulfide, ester, or other bond.
Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds.
A compound consisting of carbon and hydrogen only.
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
Any compound containing an indole skeleton.
A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
A molecular entity that contains no carbon.
A molecular entity having a net electric charge.
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
Any carboxylic ester resulting from the formal condensation of a carboxy group with methanol.
mitochondrial electron transport chain inhibitors
mitochondrial electron-transport chain inhibitor
mitochondrial respiratory chain inhibitors
mitochondrial respiratory-chain inhibitor
A molecule all atoms of which have the same atomic number.
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
A group of neurotransmitters and neuromodulators that contain one amino group that is connected to an aromatic ring by ethylene group (-CH2-CH2-). Monoamines are derived from the aromatic amino acids phenylalanine, tyrosine, histidine and tryptophan.
An oxoacid containing a single carboxy group.
An endogenous compound that is used to transmit information across the synapse between a neuron and another cell.
Any organic ion with a net negative charge.
Any organic ion with a net positive charge.
An oxide in which the oxygen atom is bonded to a carbon atom.
Compounds of the general formula SO3HOR where R is an organyl group
An alcohol derived from an aliphatic compound.
An oxide is a chemical compound of oxygen with other chemical elements.
Any peptide with hormonal activity in animals, whether endocrine, neuroendocrine, or paracrine.
Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom.
A phosphorus oxoacid that consists of one oxo and three hydroxy groups joined covalently to a central phosphorus atom.
Natural pigments containing a fundamental skeleton of four pyrrole nuclei united through the alpha-positions by four methine groups to form a macrocyclic structure.
An ester of an alcohol and sulfuric acid.
A sulfur oxoacid that consists of two oxo and two hydroxy groups joined covalently to a central sulfur atom.
A natural pigment containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions.
Tryptamine and its substitution derivatives.
A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid.
A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer).
A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised.
A primary amino compound that is the 5-hydroxy derivative of tryptamine.
An onium cation obtained by protonation of ammonia.
A family of magnesium porphyrins, defined by the presence of a fifth ring beyond the four pyrrole-like rings. The rings can have various side chains which usually include a long phytol chain.
The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.
A divalent inorganic anion resulting from the removal of two protons from ammonia.
Particle of zero charge, zero rest mass, spin quantum number 1, energy hnu and momentum hnu/c (h is the Planck constant, nu the frequency of radiation and c the speed of light), carrier of electromagnetic force.
A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.
An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
Intended use of the molecular entity or part thereof by humans.
A particle not known to have substructure.
An assembly consisting of a central atom (usually metallic) to which is attached a surrounding array of other groups of atoms (ligands).
An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system.
Any substituent group which does not contain carbon.
Any substituent group or skeleton containing carbon.
Any organic substituent group, regardless of functional type, having one free valence at a carbon atom.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
Heavy nuclear particle: proton or neutron.
A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
A molecular entity all atoms of which have the same atomic number.
An anion consisting of more than one atom.
A nutrient is a food component that an organism uses to survive and grow.
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
An agrochemical is a substance that is used in agriculture or horticulture.
A fertilizer is any substance that is added to soil or water to assist the growth of plants.
Any material that can be ingested by an organism.
An energy-rich substance that can be transformed with release of usable energy.
An alkaline earth molecular entity is a molecular entity containing one or more atoms of an alkaline earth metal.
Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
A p-block molecular entity containing any pnictogen.
Any p-block element belonging to the group 16 family of the periodic table.
Any p-block molecular entity containing a chalcogen.
An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl.
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
A pnictogen oxoacid which contains phosphorus and oxygen, at least one hydrogen atom bound to oxygen, and forms an ion by the loss of one or more protons.
An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity.
An amino-acid anion obtained by deprotonation of any alpha-amino acid.
Any main group element atom belonging to the p-block of the periodic table.
Any compound containing an o-diphenol component.
4-(2-Aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution.
A catecholamine in which C-1 of the aminoethyl side-chain is hydroxy-substituted.
A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
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.
Any molecule that consists of a series of atoms joined together to form a ring.
A molecule that features two fused rings.
Any acyclic or cyclic, saturated or unsaturated carbon compound, excluding aromatic compounds.
A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character.
A polycyclic compound in which at least one of the rings contains at least one non-carbon atom.
A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.
An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.
A main group molecular entity that contains one or more atoms of a p-block element.
Hydrides are chemical compounds of hydrogen with other chemical elements.
A macromolecule formed by a living organism.
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
A cation consisting of more than one atom.
An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group.
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
A carboxylic acid containing one or more amino groups.
An organic compound having at least one hydroxy group attached to a carbon atom.
Any organic molecule that consists of atoms connected in the form of a ring.
A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2).
Conjugated protein is a protein that contains a non-peptide component, usually in stoichiometric proportion.
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.
Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring.
A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
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.
An ammonium ion that is the conjugate acid of serotonin; major species at pH 7.3.
Saturated acyclic nitrogen hydrides having the general formula NnHn+2.
A substance that diminishes the rate of a chemical reaction.
A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction.
A fuel such as coal, oil and natural gas which has formed over many years through the decomposition of deposited vegetation which was under extreme pressure of an overburden of earth.
The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group.
A derivative of ammonium, NH4(+), in which one (or more) of the hydrogens bonded to the nitrogen have been replaced with univalent organyl groups. The substituting carbon of the organyl group must not itself be directly attached to a heteroatom (thereby excluding protonated amides, hemiaminals, etc).
Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene.
Any heteroorganic entity containing at least one carbon-nitrogen bond.
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
A substance that reduces or suppresses inflammation.
A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume.
A drug used to cause dilation of the blood vessels.
A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter.
A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated.
A phosphorus oxoanion that is the conjugate base of phosphoric acid.
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).
Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).
Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.
Particle of integer spin quantum number following Bose-Einstein statistics. Bosons are named after Satyendra Nath Bose.
A subatomic particle known to have substructure (i.e. consisting of smaller particles).
Hadron is a subatomic particle which experiences the strong force.
A nucleus or any of its constituents in any of their energy states.
Any molecular entity consisting of more than one atom.
An ion consisting of more than one atom.
A coordination entity in which the central atom to which the ligands are attached comes from groups 1, 2, 13, 14, 15, 16, 17, or 18 of the periodic table.
Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.
Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element.
A monoatomic or polyatomic species having one or more elementary charges of the proton.
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
An organochalcogen compound containing at least one carbon-oxygen bond.
Any of the group of polysaccharides composed of alternating units from uronic acids and glycosamines, and commonly partially esterified with sulfuric acid.
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).
A molecular entity consisting of two or more chemical elements.
An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid.
A compound composed of two or more pyrrole units.
Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.
Chlorophylls lacking the terpenoid side chain such as phytyl or farnesyl.
An EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor that interferes with the action of cytochrome c oxidase (EC 1.9.3.1).
EC 1.9.3.1 (cytochrome c oxidase) inhibitors
complex IV (mitochondrial electron transport) inhibitor
complex IV (mitochondrial electron transport) inhibitors
cytochrome c oxidase (EC 1.9.3.1) inhibitor
cytochrome c oxidase (EC 1.9.3.1) inhibitors
ferrocytochrome-c:oxygen oxidoreductase inhibitor
ferrocytochrome-c:oxygen oxidoreductase inhibitors
mitochondrial cytochrome-c oxidase inhibitors
EC 1.9.3.1 (cytochrome c oxidase) inhibitor
Substance which produces loss of feeling or sensation.
An alkaloid containing an indole skeleton.
A molecular entity capable of donating a hydron to an acceptor (Bronsted base).
A molecular entity capable of accepting a hydron from a donor (Bronsted acid).
A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct.
A monovalent inorganic anion that consists of phosphoric acid in which one of the three OH groups has been deprotonated.
A phosphate ion that is the conjugate base of dihydrogenphosphate.
A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
Anything used in a scientific experiment to indicate the presence of a substance or quality, change in a body, etc.
A nitrogen oxoacid of formula HNO3 in which the nitrogen atom is bonded to a hydroxy group and by equivalent bonds to the remaining two oxygen atoms.
A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds.
A polar solvent that is capable of acting as a hydron (proton) donor.
Solvent that is capable of acting as a hydron (proton) acceptor.
Self-ionizing solvent possessing both characteristics of Bronsted acids and bases.
Substance which binds to cell receptors normally responding to naturally occurring substances and which produces a response of its own.
Substance that attaches to and blocks cell receptors that normally bind naturally occurring substances.
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
An enzyme inhibitor that interferes with the activity of cytochrome P450 involved in catalysis of organic substances.
Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families.
A role played by a molecular entity used to study the microscopic environment.
An aliphatic alcohol in which the aliphatic alkane chain is substituted by a hydroxy group at unspecified position.
Any molecular entity that contains carbon.
A role is particular behaviour which a material entity may exhibit.
A poison that interferes with the functions of the nervous system.
A compound formally derived from ammonia by replacing one hydrogen atom by an organyl group.
A role played by the molecular entity or part thereof within a chemical context.
An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case.
Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s).
An organic anion that is the conjugate base of methanol.
A biological role played by the molecular entity or part thereof within a biochemical context.
A role played by the molecular entity or part thereof which causes the development of a pathological process.
A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties.
Any molecule or ion capable of binding to a central metal atom to form coordination complexes.
Any substance introduced into a living organism with therapeutic or diagnostic purpose.
An organic group that consists of a closed ring. It may be a substituent or a skeleton.
A polymer carrying multiple negative charges.
A macromolecule containing ionic groups.
A 29-amino acid peptide hormone consisting of His, Ser, Gln, Gly, Thr, Phe, Thr, Ser, Asp, Tyr, Ser, Lys, Tyr, Leu, Asp, Ser, Arg, Arg, Ala, Gln, Asp, Phe, Val, Gln, Trp, Leu, Met, Asn and Thr residues joined in sequence.
A cyclic compound having as ring members atoms of at least two different elements.
An ammonium ion that is the conjugate acid of tryptamine arising from protonation of the primary amino group; major species at pH 7.3.
A cyclic tetrapyrrole anion that is the conjugate base of chlorophyllide a arising from deprotonation of the carboxy group; major species at pH 7.3.
Conjugate acid of carbon monoxide arising from protonation of the carbon; major species at pH 7.3.
A cyclic tetrapyrrole anion arising from deprotonation at the 21-position of chlorophyll a.
An organic anion arising from deprotonation of a cyclic tetrapyrrole compound.
An organic anion of general formula RS(=O)2O(-) where R is an organyl group.
A substance used as an indicator of a biological state.
Compounds containing one or more phosphoric acid units.
A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons.
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind.
A polymer is a mixture, which is composed of macromolecules of different kinds and which may be differentiated by composition, length, degree of branching etc..
An ionic polymer is a polymer, composed of ionic macromolecules.
An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one.
Zwitterionic form of any peptide where, in general, the amino terminus is positively charged and the carboxy terminus is negatively charged.
Any compound that has a nucleobase as a part.
nucleobase-containing molecular entities
A polymer, composed of polyanion macromolecules.
A molecular messenger in which the molecule is specifically involved in transmitting information between cells. Such molecules are released from the cell sending the signal, cross over the gap between cells by diffusion, and interact with specific receptors in another cell, triggering a response in that cell by activating a series of enzyme controlled reactions which lead to changes inside the cell.
A family of nitrogen molecular entities which are highly reactive and derived from nitric oxide (.NO) and superoxide (O2.(-)) produced via the enzymatic activity of inducible nitric oxide synthase 2 (NOS2) and NADPH oxidase respectively.
A substance that removes electrons from another reactant in a redox reaction.
Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds.
A carbohydrate derivative that is formally obtained from a carbohydrate acid.
An aralylamino compound which contains one amino group connected to an aromatic ring by a two-carbon chain. Monoamines are derived from aromatic amino acids like phenylalanine, tyrosine, tryptophan, and the thyroid hormones by the action of aromatic amino acid decarboxylase enzymes.
A carboxylic acid anion resulting from the deprotonation of the carboxy group of a carbohydrate acid derivative.
Any substance which is added to food to preserve or enhance its flavour and/or appearance.
An organic amino compound in which an aminoalkyl group is linked to an arene.
A fourteen-membered heterodetic cyclic peptide comprising the sequence Ala-Gly-Cys-Lys-Asn-Phe-Phe-Trp-Lys-Thr-Phe-Thr-Ser-Cys cyclised by a disulfide bridge between the two Cys residues at positions 3 and 14.
L-alanylglycyl-L-cysteinyl-L-lysyl-L-asparaginyl-L-phenylalanyl-L-phenylalanyl-L-tryptophyl-L-lysyl-L-threonyl-L-phenylalanyl-L-threonyl-L-seryl-L-cysteine cyclic (3-14) disulfide
Synthetic growth hormone release-inhibiting hormone
An organic molecular entity containing a single carbon atom (C1).
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism.
A carbohydrate derivative that is any derivative of a polysaccharide.
An ammonium ion derivative resulting from the protonation of the nitrogen atom of a primary amino compound. Major species at pH 7.3.
Any compound that has anti-inflammatory effects.
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
A biomacromolecule composed of carbohydrate residues which is secreted by a microorganism into the surrounding environment.
A mancude heterobicyclic organic group consisting of a benzene ring fused to a pyrrole ring.
A bicyclic organic group that contains both carbon and hetero atoms.
Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms.
Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals.
Any animal metabolite produced during a metabolic reaction in mammals.
Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus).
Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae).
Saccharomyces cerevisiae secondary metabolites
Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea.
Any metabolite produced by metabolism of a xenobiotic compound.
A gas in an atmosphere that absorbs and emits radiation within the thermal infrared range, so contributing to the 'greenhouse effect'.
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.
An enzyme inhibitor which interferes with the action of an oxidoreductase (EC 1.*.*.*).
An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on a heme group of donors (EC 1.9.*.*).
EC 1.9.* (oxidoreductase acting on a heme group of donors) inhibitor
EC 1.9.* (oxidoreductase acting on a heme group of donors) inhibitors
EC 1.9.* (oxidoreductase acting on donor heme group) inhibitors
oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitor
oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitors
EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor
An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on hydrogen as donors (EC 1.14.*.*).
EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitors
inhibitor of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*)
inhibitor of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*)
inhibitors of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*)
inhibitors of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*)
oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitor
oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitors
oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitor
oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitors
EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor
Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*).
Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*).
EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor
EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors
EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor
EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors
EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors
EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor
An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*).
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors
non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor
non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor
An EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor that interferes with the action of any such enzyme incorporating one atom of oxygen and using reduced flavin or flavoprotein as donor (EC 1.14.14.*).
EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitors
EC 1.14.14.* (oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor
EC 1.14.14.* (oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitors
oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor (EC 1.14.14.*) inhibitor
oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor (EC 1.14.14.*) inhibitors
EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor
An EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor that interferes with the action of any such enzyme using oxygen as acceptor (EC 1.9.3.*).
EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitors
oxidoreductase acting on donor heme group, oxygen as acceptor (EC 1.9.3.*) inhibitor
oxidoreductase acting on donor heme group, oxygen as acceptor (EC 1.9.3.*) inhibitors
EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor
An EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor that interferes with the action of an unspecified monooxygenase (EC 1.14.14.1).
EC 1.14.14.1 (unspecific monooxygenase) inhibitors
flavoprotein-linked monooxygenase inhibitor
flavoprotein-linked monooxygenase inhibitors
substrate,reduced-flavoprotein:oxygen oxidoreductase (RH-hydroxylating or -epoxidising) inhibitor
substrate,reduced-flavoprotein:oxygen oxidoreductase (RH-hydroxylating or -epoxidising) inhibitors
unspecific monooxygenase (EC 1.14.14.1) inhibitor
unspecific monooxygenase (EC 1.14.14.1) inhibitors
EC 1.14.14.1 (unspecific monooxygenase) inhibitor
Any eukaryotic metabolite produced during a metabolic reaction in plants, the kingdom that include flowering plants, conifers and other gymnosperms.
An enzyme inhibitor that interferes with one or more steps in a metabolic pathway.
Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds.
Any human metabolite produced by metabolism of a xenobiotic compound in humans.
Any prokaryotic metabolite produced during a metabolic reaction in bacteria.
Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.
Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).
An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4).
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.
A propellant that is used to expel foods from an aerosol container.
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.
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.
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.
An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3.
Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation.
carbohydrates and carbohydrate derivatives
Any inorganic anion with a valency of three.
Any inorganic anion with a valency of two.
Any inorganic anion with a valency of one.
A cyclic tetrapyrrole anion arising from deprotonation of the carboxy group and the C-21 posiiton of chlorophyllide a. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.).
Any member of the class of indoles carrying at least one hydroxy group.
Any eukaryotic metabolite produced during a metabolic reaction in algae including unicellular organisms like chlorella and diatoms to multicellular organisms like giant kelps and brown algae.
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.
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).
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).
Any fibroblast that is deriived from the neural crest.
A cell found in the embryo before the formation of all the gem layers is complete.
Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
A smooth muscle cell derived from the neural crest.
A cell that will develop into a neuron often after a migration phase.
A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’.
A stem cell that self-renews as well as give rise to a single mature cell type.
A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119.
Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative.
A progenitor cell committed to the erythroid lineage.
A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.
Originally this term had some plant germ line cell children.
Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors.
A stem cell that can give rise to multiple lineages of cells.
A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages.
colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte
This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059).
A progenitor cell committed to the megakaryocyte and erythroid lineages.
colony forming unit erythroid megakaryocyte
MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2.
A stem cell from which all cells of the body can form.
A precursor cell with a limited number of potential fates.
define using PATO mulit-potent or oligopotent?
A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.
A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.
Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell.
A cell that has a filiform extrusion of the cell surface.
A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
An epithelial cell that is part of a duct.
An endothelial cell that lines the vasculature.
cuboidal endothelial cell of vascular tree
A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.
A flattened epithelial cell of mesenchymal origin that lines the serous cavity.
A cell which moves among different tissues of the body, via blood, lymph, or other medium.
A cell found predominately in the blood.
A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells.
The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710).
Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.
An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement.
Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
A neuron whose cell body is within an autonomic ganglion.
An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm.
From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard].
A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
It is unclear that all glial cells develop from a cell type called a glioblast. Radial glial cells develop from neuroepithelial cells and other types of glial cells develop from other precursors. Unless glioblast is meant to describe any cell that can give rise to a glial cell, this relationship needs further investigation.
A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs.
Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2.
A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.
Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell.
A pigment cell is a cell that contains pigment granules.
A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules.
A cell that specializes in controlled release of one or more substances.
A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.
A cell that secretes glycosaminoglycans.
A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.
An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas.
An endocrine cell that has the specialized function to produce and secrete hormones in response to neuronal signals.
A cell whose primary function is to shorten.
A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
A somatic cell located in skeletal muscle.
A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).
A cell that is capable of detection of a stimulus involved in sensory perception.
A cell specialized to detect and transduce light.
A cell whose function is determined by the generation or the reception of an electric signal.
A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.
A meso-epithelial cell that lies between the cartilaginous fibers in the synovial membrane of a joint and produces hyaluronic acid.
A cell whose primary function is to prevent the transport of stuff across compartments.
A cell that moves by its own activities.
A cell of the outer of the three germ layers of the embryo.
A cell of the middle germ layer of the embryo.
A cell of the inner of the three germ layers of the embryo.
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism.
Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid.
A cell that is specialised to accumulate a particular substance(s).
A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.
A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.
A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.
A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell.
Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo.
A smooth muscle cell associated with the vasculature.
An epithelial cell of the integument (the outer layer of an organism).
Diploid cell produced by the fusion of sperm cell nucleus and egg cell.
A cell whose function is determined by its response to an electric signal.
A cell that initiates an electrical signal and passes that signal to another cell.
A cell type that secretes 5-Hydroxytryptamine (serotonin).
A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme.
A photoreceptor cell that detects visible light.
A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere.
A precursor cell destined to differentiate into cardiac muscle cell.
A precursor cell destined to differentiate into smooth muscle myocytes.
A myoblast that differentiates into skeletal muscle fibers.
A neuron which conveys sensory information centrally from the periphery.
A neuron which sends impulses peripherally to activate muscles or secretory cells.
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.
An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.
A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.
A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.
The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.
The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative).
Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative.
A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm.
Megakaryocytes are reportedly CD181-positive and CD182-positive.
An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.
A mesenchymal stem cell capable of developing into blood vessel endothelium.
These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive.
A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field.
One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision.
The reproductive cell in multicellular organisms.
A steroid hormone secreting cell that secretes androgen.
One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision.
A cell whose primary function is to support other cell types.
An extracellular matrix secreting cell that secretes collagen.
A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells.
A non-terminally differentiated cell that is capable of developing into a muscle cell.
A cell that stores and secretes pancreatic polypeptide hormone.
Epithelial cells derived from neural plate and neural crest.
The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098).
A stem cell that can give rise to cell types of the body other than those of the germ-line.
Muscle cell which has as its direct parts myofilaments organized into sarcomeres.
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve.
Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei.
This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction.
A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
A immature or mature cell in the lineage leading to and including erythrocytes.
Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes.
A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.
A cell of the monocyte, granulocyte, or mast cell lineage.
A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans.
hematopoietic multipotent progenitor cell
A progenitor cell restricted to the myeloid lineage.
Note that this is a class of cell types, not an identified single cell type.
myeloid lineage restricted progenitor cell
A leukocyte with a single non-segmented nucleus in the mature form.
A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers.
hematopoietic oligopotent progenitor cell, lineage-negative
A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative).
A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.
hematopoietic lineage restricted progenitor cell
A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities.
This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060).
hematopoietic oligopotent progenitor cell
An enteroendocrine cell that produces glucagon.
Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter.
A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery.
Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes.
The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides).
An epithelial cell derived from endoderm.
An epithelial cell derived from ectoderm.
Epithelial cell derived from mesoderm or mesenchyme.
A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart.
A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells.
MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense.
A cell in the hilum of the ovary that produces androgens.
An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels.
cubodial endothelial cell of vascular tree
These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive.
An endothelial cell found in capillaries.
Epithelial cells derived from general body ectoderm and ectoderm placodes.
An epithelial cell found in the lining of the stomach.
A mucous cell in the epithelium of the stomach.
A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit.
A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye.
A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth.
A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells).
An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus.
An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver.
A type of enteroendocrine cell found in the stomach that secretes glucagon.
A cell that is part of the nervous system.
A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.
A fat cell derived from a neural crest cell.
An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin.
A hematopoietic stem cell that exists during embryogenesis.
A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic cell located between the lamellae with a large flattened nucleus and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratin sulfate.
An endo-epithelial cell of the respiratory tract.
A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
A transversely striated, synctial muscle cell, formed by the fusion of myoblasts.
A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles.
A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes.
A cell located in the heart, including both muscle and non muscle cells.
From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart.
A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc
A fat cell that is part of subcutaneous adipose tissue.
A mesenchymal stem cell that is part of the bone marrow.
mesenchymal stem cell of the bone marrow
An endothelial cell that is part of the vein.
An endothelial progenitor cell that participates in angiogenesis during development.
embryonic blood vessel endothelial progenitor cell
A mesenchymal stem cell of adipose tissue.
A glial cell that ensheathes axons of neuron in the peripheral nervous system and are necessary for their maintainance and function.
A blood vessel endothelial cell that is part of the retina.
A vascular associated smooth muscle cell of the brain vasculature.
smooth muscle cell of the brain vasculature
A smooth muscle of the pulmonary artery.
smooth muscle cell of the pulmonary artery
Smooth muscle cell of the carotid artery.
epithelial cell of lower respiratory tract
A glandular epithelial cell of the esophagus.
A glandular epithelial cell that is part of the stomach.
A myocardial endocrine cell that is part of the atrium.
A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart.
Discrepancy in develops from origins prevents me from making the assertion that cardioblasts give rise to all instances of cardiocytes as we state cardiac muscle cells develop from cardiac myoblast, which in turn develop from muscle stem cell.
A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells.
A neuroblast derived from a neural crest cell.
A CNS interneuron located in the spinal cord.
Is_a interneuron, part_of UBERON:0002240.
Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized).
Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts)
Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.
Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells.
Any muscle cell in which the fibers are not organised into sarcomeres.
Any hematopoietic cell that is a precursor of some other hematopoietic cell type.
A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
skeletal muscle fiber
A muscle cell that is part of some visceral muscle
visceral muscle cell
A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods.
striated visceral muscle cell
A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods.
transversely striated visceral muscle cell
A skeletal muscle myoblast that is part of a skeletal mucle. These cells are formed following acivation and division of skeletal muscle satellite cells. They form a transient population that is lost when they fuse to form skeletal muscle fibers.
The vast majority of these cells develop from skeletal muscle satellite cells, although there are some reports of other origins.
A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration.
A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves.
Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation.
mural cell
microcirculation associated smooth muscle cell
A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord.
Any cell in the compound eye, a light sensing organ composed of ommatidia.
Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
A stromal cell that is part_of a bone marrow.
A mononuclear cell that is part_of a bone marrow.
zygote
A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement.
A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites.
A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.
A mesothelial cell that is part of the epicardium.
A fibroblast that is part of upper back skin.
A fibroblast that is part of skin of back.
A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses.
Any fibroblast that is part of skeletal muscle tissue.
Any microvascular endothelial cell that is part of the dermis.
A cell that, by division or terminal differentiation, can give rise to other cell types.
Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell.
Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain.
Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions.
Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions.
A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell.
A smooth muscle cell that is part of any blood vessel.
blood vessel smooth muscle cell
A fibroblast that is part of the areolar connective tissue.
A fibroblast that is part of the tunica adventitia of artery.
fibroblast of tunica adventitia of artery
A fibroblast that is part of the dense regular elastic tissue.
fibroblast of dense regular elastic tissue
A fat cell that is part of the epicardial fat.
A fat cell that is part of the epicardial fat of right ventricle.
adipocyte of epicardial fat of right ventricle
A fat cell that is part of the epicardial fat of left ventricle.
adipocyte of epicardial fat of left ventricle
A transitional myocyte that is part of the interatrial septum.
transitional myocyte of interatrial septum
A transitional myocyte that is part of the interventricular septum.
transitional myocyte of interventricular septum
A Purkinje myocyte that is part of the interventricular septum.
Purkinje myocyte of interventricular septum
A muscle cell that is part of the sinoatrial node.
A muscle cell that is part of the atrioventricular node.
An endothelial cell that is part of the arteriole.
A blood vessel endothelial cell that is part of an arterial endothelium.
An endothelial cell that is part of the venule.
A somatic stem cell that is part of the epidermis.
A smooth muscle cell that is part of the ciliary body.
A mesothelial cell that is part of the anterior chamber of eyeball.
mesothelial cell of anterior chamber of eye
A mesothelial cell that is part of the parietal peritoneum.
A mesothelial cell that is part of the visceral peritoneum.
A transitional myocyte that is part of the sinoatrial node.
A Purkinje myocyte that is part of the atrioventricular node.
Purkinje myocyte of atrioventricular node
A myocardial endocrine cell that is part of the interventricular septum.
myocardial endocrine cell of interventricular septum
A mesothelial cell that is part of the peritoneum.
A mesothelial cell that is part of the pleura.
A mesothelial cell that is part of the parietal pleura.
A mesothelial cell that is part of the visceral pleura.
oral cavity mucosa squamous epithelial cell
Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes.
A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood.
Any blood vessel endothelial cell that is part of a microvascular endothelium.
Any blood vessel endothelial cell that is part of a dermis.
Any skin fibroblast that is part of a skin of abdomen.
Any lung endothelial cell that is part of a microvascular endothelium.
Any photoreceptor cell that is part of a compound eye.
Any native cell that is part of a cardiac septum.
Any neuron that is part of a central nervous system.
Any neuron that is part of a peripheral nervous system.
Any fibroblast that is part of a embryo.
Any microvascular endothelial cell that is part of a brain.
Any cardiac muscle cell that is part of a cardiac ventricle.
Any motor neuron that is part of a brainstem.
Any fibroblast that is part of a female gonad.
Any epithelial cell that is part of a female gonad.
Any fibroblast that is part of a cardiac ventricle.
Any fibroblast that is part of a cardiac atrium.
Any fibroblast that is part of a pericardium.
Any fibroblast that is part of a optic choroid.
Any microvascular endothelial cell that is part of a adipose tissue.
Any migratory neural crest cell that is part of a cardiac neural crest.
Any mesenchymal stem cell of adipose tissue that is part of an abdomen.
mesenchymal stem cell of abdominal adipose
mesenchymal stem cell of abdominal adipose tissue
A ciliated epithelial cell of the esophagus.
Any capillary endothelial cell that is part of a lung.
A system in which living entities consume living, dead, or non-living entities or are consumed by other living entities through trophic interactions.
food web
A food web in which the outputs of a trophic interaction are consumed by organisms acting in a lower trophic level relative to the initial interaction.
Definition needs revision, but core intention is captured.
food cycle
A system in which a series of living entities consume living, dead, or non-living entities in successively higher trophic levels.
food chain
A function which inheres in a living entity by virtue of that entity being able to feed on a material.
trophic function
A function which inheres in a living entity by virtue of that entity being able to feed on living or once-living (dead) material.
heterotrophic function
A function which inheres in a living entity by virtue of that entity being able to harvest energy and create biomass from non-living materials.
autotrophic function
A function which inheres in a living entity by virtue of that entity being able to realize autotrophic and heterotrophic functions.
mixotrophic function
A process during which a living entity acquires or generates food and energy from a living, dead, or non-living entity.
All categories of interaction partners should be indentified in subclasses.
trophic process
A trophic process during which a living entity acquires energy and generates biomass from non-living entities.
This should be axiomatised and made a defined class: any trophic interaction which has as input some inorganic material (non-living) that is the only source of carbon or reducing equivalents source is a autotrophic process.
autotrophy
An organism that obtains carbon for growth and development by metabolizing biogenic organic compounds derived from living or dead material.
heterotroph
A trophic process during which a living entity acquires food and energy by consuming another organism or organism part, living or dead.
This should be axiomatised and made a defined class: any trophic interaction which has as input some organic material (living or dead) that is the only source of carbon or reducing equivalents source is a autotrophic process.
heterotrophy
An organism which is capable of heterotrophic and autotrophic trophic processes.
mixotroph
A herbivorous process during which a living entity acquires food and energy by consuming nectar.
nectivory
A trophic process during which a living entity acquires reducing equivalents from inorganic chemicals for use in biosynthesis or energy conservation via aerobic or anaerobic respiration.
lithotrophy
fungivore
A heterotrophic process during which a living entity acquires food and energy by consuming living fungal material.
In this class, we make no commitment to whether the organism belongs to a taxon which has adapted to a fungi-heavy diet: this is a functional defintion, referencing the act of eating, primarily, a fungi-based diet.
fungivory
A trophic process during which a living entity generates food from abiotic sources or through consumption of living or dead material, and captures energy from light.
phototrophy
A history which includes all the processes during which resources are used by an organism to grow, survive, and reproduce over its lifetime.
life history
A heterotroph which consumes plants or macroalgae via ingestion through a type of "mouth". Plant or algal matter is broken down through an internal digestion process.
There is some debate over whether herbivores should be restricted to plants and macroalgae or generalsed to more photoautotrophs. We welcome input on our issue tracker: https://github.com/EcologicalSemantics/ecocore
herbivore
A heterotrophic process during which a living entity acquires food and energy by consuming living plant- or macro-algal material.
In this class, we make no commitment to whether the organism belongs to a taxon which has adapted to a herbivorous diet: this is a functional defintion, referencing the act of eating, primarily, a plant- or macroalga-based diet.
herbivory
A heterotrophic process during which a living entity acquires food and energy from consuming living metazoan (animal) material.
In this class, we make no commitment to whether the organism belongs to a taxon which has adapted to a carnivorous diet: this is a functional defintion, referencing the act of eating, primarily, an animal-based diet.
carnivory
A process during which two living entities engage in a close and long-term biological interaction.
symbiosis
An organism which is capable of incorporating abiogenic (inorganic) carbon into its biomass.
autotroph
Quotient (or ratio) of surface area of an organism divided by the mass of the same organism
A symbiotic process in which one participant gains benefits while the other participant neither benefits nor is harmed.
commensalism
The duration of the development from fertilized, deposited or implanted egg to hatching/birth. Corresponds to egg incubation duration in oviparous animals and to gestation period duration in viviparous animals.
Type of food comprising the majority of the diet of an organism
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring that develop inside a shelled egg, with a large food supply in yolk, after internal fertilization
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring that are born live, or where the development of the offspring is supported by either parent in or on any part of their body
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring that are born live after retaining the eggs inside the body of the female
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring via external fertilization, the oocytes being released and fertilized outside the female's body by the male
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce zygotes that develop in the female's oviducts, but find their nutriments from other tissues, whether skin or glandular tissue
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring that receive nutriments from the female during prenatal development via a specialized structure, such as a placenta
The second post-naupliar life stage of a copepod
The third post-naupliar life stage of a copepod
The fourth post-naupliar life stage of a copepod
The fifth post-naupliar life stage of a copepod
The sixth post-naupliar life stage of a copepod
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for running
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for digging and living underground
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for living in trees
a reproductive quality inhering in the bearer by virtue of the bearer having reproductive organs normally associated with both male and female sexes at the same time
a reproductive quality inhering in the bearer by virtue of the bearer having female reproductive organs at the beginning of its life and then switching to male reproductive organs
The process by which a larvae transforms into an adult wherein the larvae looks like a smaller adult form
heterotroph that acquires nutrition from a symbiont
An organism bearing a symbiont role and capable of living within a plant for at least part of its life cycle without causing apparent disease
A symbiotic process in which one participant gains benefits while the other participant is harmed.
parasitism
anatomical entity that comprises the organism in a distinct juvenile form that is provided with a source of nutrition, usually a yolk sac, to use before metamorphosing into an adult
a community of microscopic, unicellular eukaryotic algae and the prokaryotic Cyanobacteria which live on sediment surfaces
Organism that acquires nutrition by consuming particles of organic matter that have settled to the bottom of a body of water.
A heterotroph that acquires nutrition by consuming particles suspended in water or air.
Organism that acquires nutrition by consuming particles of organic matter that have settled to the bottom of a body of water. The organism lives beneath the surface of the bottom sediment and retrieves food particles without coming into direct contact with the sediment surface.
Organism that acquires nutrition by consuming particles of organic matter that have settled to the bottom of a body of water. The organism lives on or in the bottom sediment and uses a part of its body to retrieve the food particles directly from the surface.
heterotroph that obtains nutrition by breaking down dead or decaying organisms or other organic matter
A decomposer which obtains nutrition by consuming detritus.
A decomposer that obtains nutrition through extracellular digestion of decaying organic matter
A decomposition process during which a living entity acquires food and energy by consuming detritus.
A heterotrophic process during which a living entity acquires food and energy by breaking down organic substances into simpler matter.
A decomposition process during which a living entity acquires food and energy through extracellular digestion of decaying organic matter.
A heterotrophic process during which a living entity acquires food and energy through a symbiotic relationship with another organism.
An organismal quality inhering in a bearer by virtue of the organization of the systems of organs involved with sexual reproduction amongst the bearer's conspecifics.
An organismal quality inhering in a bearer by virtue of the structure of the bearer's conspecifics in relation to sexual behavior.
One male and one female have an exclusive mating relationship
One female has an exclusive mating relationship with two or more males
One male has an exclusive mating relationship with two or more females
Two or more males have an exclusive mating relationship with two or more females
a member of one sex mates with any member of the opposite sex
The ecological state of a species being unique to a defined geographic location, such as an island, nation, or other defined zone or habitat type.
The ecological state of a species or population wherein all individuals are dead.
The ecological state of a species living in a region where its presence is the result of only natural process, with no human intervention
The ecological state of a species living outside its native distributional range, which has arrived there by human activity, either deliberate or accidental.
The ecological state that is not the extinct state
The ecological state of a species being found across all or most of the world in appropriate habitats.
The ecological state of a species being unique to a very small and specific location, such as the side of a mountain or a single lake.
The estimated proportion of members of a population alive in year t that is still alive in year t + 1
A polyphyletic group of diverse photosynthetic organisms that excludes vascular plants and mosses and includes cyanobacteria, seaweed, and some single-celled organisms.
Bacteria that are able to obtain their energy through photosynthesis
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for being active primarily during dawn and dusk
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for being active during the hours of darkness
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for being active during the hours of daylight
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for participating in long-distance movement of conspecifics, usually on a seasonal basis
An herbivore that primarily consumes grasses.
An herbivore that primarily consumes leaves
An herbivore that primarily consumes roots
An herbivore that primarily consumes algae
A heterotroph with a temporary parasitic association with another organism that leads to the death of the host. After which, the parasitoid can continue without the host or can move on to a new host. These organisms are considered partly parasites and partly predators.
A heterotroph that consumes animals in whole or in part via ingestion through a type of "mouth". Animal matter is broken down through an internal digestion process.
A carnivore that actively captures and consumes other animals, causing their immediate or immenent death
A carnivore that feeds on dead and decaying animal matter
A predator that eats primary consumers or herbivores
A predator that eats secondary consumers
a predator residing at the top of a food chain upon which no other creatures prey.
a predator that captures or traps prey by stealth or strategy, rather than by speed or strength.
A herbivorous process during which a living entity acquires food and energy by consuming grasses, leaves, and other soft plant material.
A herbivorous process during which a living entity acquires food and energy by consuming seeds of a plant.
A herbivorous process during which a living entity acquires food and energy by consuming twigs, leaves, and bark of trees and shrubs.
A carnivorous process during which a living entity acquires food and energy by consuming other animals while they are stil alive. Predation leads directly to the imminent death of the prey organism(s).
The definition of predation can be controversial.
A carnivorous process during which a living entity acquires food and energy by consuming dead or decaying animal matter.
A predation process during which a living entity acquires food and energy by consuming all or part of another individual of the same species as food.
A cannibalistic process during which an embryo obtains food and energy by consuming a less-developed sibling while both are still in the uterus.
An intrauterine cannibalistic process during which an embryo obtains food and energy by consuming a less-developed sibling embryo while both are still in the uterus.
An intrauterine cannibalistic process during which an embryo obtains food and energy by consuming less-developed sibling eggs while both are still in the uterus.
A predation process during which a living entity acquires food and energy by consuming insects.
A predation process during which a living entity acquires food and energy by consuming eggs.
A predation process during which a group of predators cooperates to kill creatures larger than those they could overpower singly.
A heterotrophic process during which a living entity acquires food and energy by consuming a very narrow range of food items, sometimes only one.
A heterotrophic process during which a living entity acquires food and energy by consuming a few, very specific food items.
A heterotrophic process during which a living entity acquires food and energy by consuming a wide range of food items.
A heterotrophic process during which a living entity acquires food and energy from consuming bacteria.
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring via external fertilisation, the oocytes being scattered into the environment and fertilised outside the female's body by the male.
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring via external fertilisation, the oocytes being released in an ovigerous sac and fertilised outside the female's body by the male.
a reproductive quality inhering in the bearer by virtue of the bearer having male reproductive organs at the beginning of its life and then switching to female reproductive organs
a reproductive quality inhering in the bearer by virtue of the bearer having female reproductive organs at the beginning of its life and then switching to being a hermaphrodite
a reproductive quality inhering in the bearer by virtue of the bearer having male reproductive organs at the beginning of its life and then switching to being a hermaphrodite
a reproductive quality inhering in the bearer by virtue of the bearer changing sex at some point in its life
A photoautotroph which is capable of using a biogenic organic compound as an electron donor.
A photoautotroph which is capable of using an abiogenic organic compound as an electron donor.
A chemoautotroph which is capable of using a biogenic organic compound as an electron donor.
A chemoautotroph which is capable of using an abiogenic organic compound as an electron donor.
A photoheterotroph which is capable of using a biogenic organic compound as an electron donor.
A photoheterotroph which is capable of using an abiogenic organic compound as an electron donor.
A chemoheterotroph which is capable of using a biogenic organic compound as an electron donor.
A chemoheterotroph which is capable of using an abiogenic organic compound as an electron donor.
An autotroph which is capable of obtaining energy from the bonds in a chemical compound.
An autotroph which is capable of transforming light into chemical energy.
A heterotroph which is capable of transforming light into chemical energy.
A heterotroph which is capable of obtaining energy from the bonds in a chemical compound.
An organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth
An organismal quality inhering in a bearer by virtue of the bearer's ability to live on the surface of the soil and in leaf litter
An herbivore that primarily consumes fruits or fruit-like vegetables
An herbivore that primarily consumes pollen
A heterotrophic process during which a living entity acquires food and energy by eating food off of a surface while slowly moving through the environment.
An herbivore that primarily consumes nectar
An organismal quality inhering in a bearer by virtue of the bearer's ability to live in the top 20 cm of soil and make temporary, horizontal burrows.
An organismal quality inhering in a bearer by virtue of the bearer's ability to burrow more than 20 cm deep into the soil and make permanent, vertical burrows.
An herbivore that primarily consumes seeds
An herbivore that primarily consumes wood
An herbivore that primarily consumes plant exudates - gums, saps, and resins
J.G. Fleagle 1988 Primate Adaptations and Evolution. Academic Press. NY
A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host
A symbiotrophic process during which a living entity acquires food and energy from another living entity via a close association. The entity providing the food and energy is harmed by this process.
An organism that is consumed in whole or in part by a predator
Prey that is successfully captured and consumed at a higher frequency than other types of prey. The predator may be specially adapted for capturing or consuming its preferred prey or have special nutritional requirements that are only met by the preferred prey.
Prey that is consumed only if the preferred prey are unavailable.
A parasite that lives entirely within the body of its host
A parasite that lives on the exterior surface of its host
A parasite that enters the body of the host, but remains partially outside
A predation process during which a living entity acquires food and energy by consuming snakes.
A heterotrophic process during which a living entity acquires food and energy from consuming hard organisms or hard parts of organisms. This can include plants, such as bamboo, animals with hard shells, such as corals, or the hard parts of organisms, such as bone. Durophagy requires special adaptions, such as blunt, strong teeth and a heavy jaw.
A suspension feeder that acquires nutrition by consuming particles using a filtering apparatus.
A suspension feeder that acquires nutrition by consuming planktonic organisms.
A heterotroph that obtains dissolved organic compounds by osmosis for nutrition. An osmotroph is not directly involved in breaking down organic material to create the organic compounds it uses.
A symbiotrophic process in which a bacterium provides chemically-derived energy and nutrients, often via the oxidation of hydrogen sulfide, to a higher organism.
A symbiotrophic process in which a photosynthetic organism provides energy and nutrients to a heterotrophic organism.
A trophic process during which a living entity acquires reducing equivalents from organic chemicals for use in biosynthesis or energy conservation via aerobic or anaerobic respiration.
A trophic process during which a living entity generates food from abiotic sources or through consumption of living or dead material, and captures energy from preformed molecules.
A carnivore that consumes blood, during a brief, temporary interaction.
A carnivorous process during which a living entity acquires food and energy from consuming blood.
A reproductive process wherein a virus uses another cell for reproduction. This process causes the mortality of the host cell via lysis.
a folivore that lives in and eats the leaf tissue of plants
an herbivore that primarily consumes grasses, leaves, and other soft plant material
An herbivore that primarily consumes twigs, leaves, and bark of trees and shrubs.
a carnivore that primarily eats organisms less than 1 cm in their longest dimension
an organism that uses inorganic sulfur compounds as a terminal electron acceptor during cellular respiration
an organism that does not require oxygen for growth
an organism that can survive and grow in an oxygenated environment
an organism capable of producing all amino acids required for its growth
an organism that is unable to synthesize a particular organic compound required for its growth
a decomposer which obtains nutrition by consuming feces
an anaerobe that makes ATP by aerobic respiration if oxygen is present, but is capable of switching to fermentation if oxygen is absent.
an anaerobe that cannot grow in the presence of oxygen
an aerobe that can grow at oxygen levels lower than what is present in the atmosphere
an anaerobe that can tolerate low levels of oxygen
A heterotrophic process during which a living entity acquires food and energy by consuming particles of organic matter that have settled to the bottom of a body of water
deposit feeding
An environmental zone that encompasses the geographical area in which most members of a species as collection of organisms can be found.
I feel that there should be some relationship to "species as collection of organisms" but I don't know which one. Determined by seems a little too strong, but might work.
Not all member of the species are necessarily found within its range, because there may be individuals in zoos or individuals that have strayed beyond the range but which will not be able to form a sustainable population in the new area. The latter individuals are often referred to as vagrants.
species range
A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes.
A biome is an ecosystem to which resident ecological communities have evolved adaptations.
There has been some concern raised (see Issue #143) about the usefulness of the assertion that organisms have evolved within a given biome. They may have evolved adaptations elsewhere and demonstrating one or the other is often not feasible. Consider relabelling to "environmental system determined by an ecological community" or similar.
A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
Everything under this parent must be a mass noun. 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". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.
Anthropogenic material in or on which organisms may live.
A portion of planktonic material is a portion of environmental material primarily composed of plankton.
See Issue #251. Awaiting class creation in PCO to attempt logical definitions.
planktonic material
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
A system which has the disposition to environ one or more material entities.
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.
A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
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.
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.
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.
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.
An organic material primarily composed of a portion of plant root.
Requested in Issue 115 as part of the annotation of metagenomic submissions present in the European Nucleotide Archive.
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.
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.
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.
outer space
An environmental system which can sustain and allow the growth of an ecological population.
A habitat's specificity to an ecological population differentiates it from other environment classes.
habitat
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.
gaseous environmental material
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
An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space.
Astronomical bodies are usually cohesive, thus the use of the term 'object' sensu BFO 'object'.
astronomical body
An object which is composed of one or more gravitationally bound structures that are associated with a position in space.
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
A material part of an astronomical body.
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.
This is a defined class: most of its subclasses will not be asserted, but filled by inference.
liquid environmental material
A biosphere is a part of an astronomical body which includes, as parts, 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.
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 ecosystem which bridges two or more adjoining ecosystems and through which organisms may move or propagate.
Ecological corridors may or may not provide habitats for the organisms which move through them. They serve to mitigate the effects of habitat fragmentation by allowing genetic exchange between populations that would otherwise be separated by, e.g., human activity.
ecological corridor
An envirommental system which bridges two or more biomes and which includes ecological communities which blend these biomes' phylogenetic and phenotypic compositions.
There are many subtypes of ecotone, some with sharp transitions and others with gradual, patchy transitions between communities. From Wikipedia:Ecotone - The word ecotone was coined from a combination of eco(logy) plus -tone, from the Greek tonos or tension – in other words, a place where ecologies are in tension.
ecotone
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.
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
A process during which a natural environmental system is altered by human action.
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 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
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
An environmental system which is determined by a living organism.
environmental system determined by an organism
An environmental system determined by a green plant.
plant-associated environment
An environmental system determined by an animal.
animal-associated environment
An environmental system which has its properties and dynamics determined by a digestive tract.
digestive tract environment
This EMPO class includes examples of microbial environments determined by the "gut intestine, gizzard, crop, lumen, [and] mucosa".
An environmental system determined by a fungal structure.
fungi-associated environment
An environmental system determined by part of a living or dead plant, or a whole small plant.
environment associated with a plant part or small plant
An environmental system determined by part of a living or dead fungus.
environment associated with a fungal tissue
An organic material which is primarily composed of dead particulate matter.
An environmental system which includes both living and non-living components.
This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.
ecosystem
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
This class will be axiomatised with "alga" once an approach to handle this term's ambiguous semantics has been agreed with PCO.
An organic material which is primarily composed of living or dead algae, along with their exudates.
algal material
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 a continuous volume of liquid material, shaped by one or more environmental processes.
liquid astronomical body part
A part of an astronomical body which is primarily composed of a continuous volume of gaseous material, shaped by one or more environmental processes.
gaseous astronomical body part
A part of an astronomical body which is primarily composed of a continuous volume of liquid or gaseous material, shaped by one or more environmental processes.
fluid astronomical body part
An object which is composed primarily of an environmental material
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 object which is composed primarily of a solid environmental material
mass of solid material
An object which is composed primarily of a fluid.
fluid mass
mass of fluid
An object which is composed primarily of a gas.
gaseous mass
mass of gas
An object which is composed primarily of a liquid.
liquid mass
mass of liquid
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.
mass of compounded environmental materials
A part of an astronomical body which is primarily composed of a continuous medium bearing liquid, gaseous, and solid material in varying quantities.
compound astronomical body part
An environmental process either driven by or primarily impacting the parts or emergent properties of an ecosystem.
ecosystem process
An object which is formed as a result of one or more biological processes and is composed primarily of organic material.
organic object
fluid environmental material
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 biogeochemical process during which one or more chemical compounds are sequentially converted into a series of related compounds in a regularly repeating, periodic fashion.
An environmental process which is driven by the action of humans.
A process during which chemicals that are involved in natural ecosystem processes are transported or transformed, and which impact the activity of biological entities
An environment that is determined by a mouth.
An environment which is determined by an anatomical entity.
An environment determined by an area or zone of skin tissue.
An anatomical structure that forms all or part of a fungus.
The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton.
Binding to an acyl group, any group formally derived by removal of the hydroxyl group from the acid function of a carboxylic acid.
The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
mitotic sister-chromatid adhesion release
The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
microtubule cytoskeleton organization and biogenesis
A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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.
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.
The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
A ribosome contained within a subcellular membrane-bounded organelle.
The joining of 2 or more lipid bilayer membranes that surround the nucleus.
The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei.
The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
syncytium formation by plasma membrane fusion
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
A compact and highly condensed form of chromatin that is refractory to transcription.
The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets.
The developmental process in which the size or shape of a cell is generated and organized.
The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
cell morphogenesis involved in differentiation
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 by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form.
This term should be used to describe a response to a specific acid as a chemical. E.g., if an organism were responding to glutamate, then the response would be glutamate-specific; the organism is actually responding to the chemical structure of the anion portion of the dissociated acid. 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. If annotating experiments where an acid is playing a role as a proton donor, please annotate to GO:0010447 'response to acidic pH' instead.
The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
Note that this term does not have a 'developmental process' parent because ossification isn't necessarily developmental, can also occur as part of bone remodeling. Instead use 'ossification involved in bone maturation ; GO:0043931'.
A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.
Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so.
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
blood vessel formation from pre-existing blood vessels
Any process that modulates the frequency, rate, extent or direction of cell growth.
The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.
The process of coordinated growth and sprouting of blood vessels giving rise to the organized vascular system.
branching involved in blood vessel morphogenesis
The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes.
A process that results in a parallel arrangement of microtubules.
The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
A homeostatic process in which an organism modulates its internal body temperature.
Cell migration that is accomplished by extension and retraction of a pseudopodium.
Note that this term refers to a mode of migration rather than to any particular cell type.
Any process that modulates the frequency, rate or extent of chromatin assembly or disassembly.
regulation of chromatin assembly/disassembly
regulation of chromatin assembly or disassembly
Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).
translation initiation ternary complex assembly
formation of translation initiation ternary complex
The regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion.
The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster.
embryonic development via the syncytial blastoderm
The formation of the ectoderm, mesoderm and endoderm during gastrulation.
The formation of ectoderm during gastrulation.
The formation of the endoderm during gastrulation.
The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
The initial developmental process that will lead to the formation of an eye.
The morphogenetic process in which the anatomical structures of the compound eye are generated and organized. The adult compound eye is a precise assembly of 700-800 ommatidia. Each ommatidium is composed of 20 cells, identified by cell type and position. An example of compound eye morphogenesis is found in Drosophila melanogaster.
The process in which a relatively unspecialized cell acquires the specialized features of an eye photoreceptor cell.
compound eye photoreceptor cell differentiation
The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell, as found in the eye, the primary visual organ of most organisms.
The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
The process in which the anatomical structures of branches are generated and organized. A branch is a division or offshoot from a main stem. Examples in animals would include blood vessels, nerves, lymphatics and other endothelial or epithelial tubes.
The process of regulating the proliferation and elimination of cells of the immune system such that the total number of cells of a particular cell type within a whole or part of an organism is stable over time in the absence of an outside stimulus.
Note that this term represents the return of immune system cell levels to stable numbers following an immune response as well as the proliferation and elimination of cells of the immune system required to maintain stable numbers in the absence of an outside stimulus.
The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells.
A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
mesenchymal cell differentiation from epithelial cell
The morphogenesis of an embryonic epithelium into a tube-shaped structure.
The process in which the anatomical structures of the neural plate are generated and organized. The neural plate is a specialized region of columnar epithelial cells in the dorsal ectoderm that will give rise to nervous system tissue.
The process whose specific outcome is the progression of the neural plate over time, from its formation to the mature structure. The neural plate is a flat, thickened layer of ectodermal cells. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system.
The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
The process in which the neural fold is formed. The edges of the neural plate thicken and move up to form a U-shaped structure called the neural groove.
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 from a yeast species.
defined as response to Saccharomycotina (true yeasts). This excludes fission yeast.
The progression of an endothelial cell over time, from its formation to the mature structure.
The change in form (cell shape and size) that occurs during the differentiation of an endothelial cell.
The multiplication or reproduction of endothelial cells, resulting in the expansion of a cell population. Endothelial cells are thin flattened cells which line the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium.
Any process that modulates the frequency, rate, or extent of endothelial cell proliferation.
regulation of endothelial cell proliferation
Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation.
down regulation of endothelial cell proliferation
down-regulation of endothelial cell proliferation
downregulation of endothelial cell proliferation
inhibition of endothelial cell proliferation
negative regulation of endothelial cell proliferation
Any process that activates or increases the rate or extent of endothelial cell proliferation.
up regulation of endothelial cell proliferation
up-regulation of endothelial cell proliferation
upregulation of endothelial cell proliferation
activation of endothelial cell proliferation
stimulation of endothelial cell proliferation
positive regulation of endothelial cell proliferation
The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism.
Direct ossification that occurs within mesenchyme or an accumulation of relatively unspecialized cells.
An instance of intramembranous ossification may also be classified as metaplastic; the former classifies based on tissue type location, and the latter based on mechanism/cell division.
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.
The process in which the anatomical structures of an epithelial sheet are generated and organized. An epithelial sheet is a flat surface consisting of closely packed epithelial cells.
Any process that modulates the frequency or rate of heart contraction.
Any process that activates or increases the rate of neuroblast proliferation.
up regulation of neuroblast proliferation
up-regulation of neuroblast proliferation
upregulation of neuroblast proliferation
positive regulation of neuroblast proliferation
The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells.
up regulation of mesenchymal cell proliferation
up-regulation of mesenchymal cell proliferation
upregulation of mesenchymal cell proliferation
activation of mesenchymal cell proliferation
stimulation of mesenchymal cell proliferation
positive regulation of mesenchymal cell proliferation
Binding to a nucleobase, any of a class of pyrmidines or purines, organic nitrogenous bases.
The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage.
The process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate.
The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface.
The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.
columnar/cuboidal epithelial cell differentiation
The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell over time, from its formation to the mature structure. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.
columnar/cuboidal epithelial cell development
The process in which a relatively unspecialized cell acquires specialized features of a glandular epithelial cell. A glandular epithelial cell is a columnar/cuboidal epithelial cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland.
glandular epithelial cell differentiation
The process whose specific outcome is the progression of a glandular epithelial cell over time, from its formation to the mature structure. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland.
The invagination of the optic vesicle to form two-walled indentations, the optic cups, that will go on to form the retina. This process begins with the optic vesicle becoming a two-walled structure and its subsequent shape changes. It does not include the fate commitment of cells to become the pigmented retina and the neural retina. An example of this process is found in Mus musculus.
optic cup morphogenesis involved in camera-style eye development
optic cup morphogenesis involved in camera-type eye development
Any process that prevents the activation of neuroepithelial cell differentiation. Neuroepithelial cell differentiation is the process in which epiblast cells acquire specialized features of neuroepithelial cells.
negative regulation of neural plate formation
repression of premature neural plate formation
inhibition of neuroepithelial cell differentiation
A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates.
regulation of respiratory gaseous exchange by neurological system process
regulation of respiratory gaseous exchange by nervous system process
The process whose specific outcome is the progression of the lens over time, from its formation to the mature structure. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus.
The process in which the anatomical structures of the lens are generated and organized. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus.
The process whose specific outcome is the progression of the larva over time, from its formation to the mature structure. The larva is the early, immature form of an that at birth or hatching is fundamentally unlike its parent and must metamorphose before assuming the adult characters.
The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
haematopoietic progenitor cell differentiation
haemopoietic progenitor cell differentiation
hemopoietic progenitor cell differentiation
hematopoietic progenitor cell differentiation
Any process of the immune system that executes a component of an immune response. An effector immune process takes place after its activation.
The process of regulating the proliferation and elimination of myeloid cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
The process in which a precursor cell type acquires the specialized features of a myeloid progenitor cell. Myeloid progenitor cells include progenitor cells for any of the myeloid lineages.
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
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).
Any process involved in the carrying out of an immune response by a leukocyte.
Any process involved in the carrying out of an immune response by a myeloid leukocyte.
myeloid leucocyte immune effector process
myeloid leukocyte immune effector process
The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process.
The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage.
Any process that modulates the frequency, rate, or extent of an immune system process.
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
negative regulation of immune system process
Any process that activates or increases the frequency, rate, or extent of an immune system process.
positive regulation of immune system process
Any process that modulates the frequency, rate, or extent of an immune effector process.
Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune effector process.
down regulation of immune effector process
down-regulation of immune effector process
downregulation of immune effector process
negative regulation of immune effector process
Any process that activates or increases the frequency, rate, or extent of an immune effector process.
up regulation of immune effector process
up-regulation of immune effector process
positive regulation of immune effector process
Any process that modulates the frequency, rate, or extent of leukocyte mediated immunity.
regulation of immune cell mediated immunity
regulation of leucocyte mediated immunity
regulation of leukocyte mediated immunity
Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte mediated immunity.
down regulation of leukocyte mediated immunity
down-regulation of leukocyte mediated immunity
downregulation of leukocyte mediated immunity
negative regulation of immune cell mediated immunity
negative regulation of leucocyte mediated immunity
inhibition of leukocyte mediated immunity
negative regulation of leukocyte mediated immunity
Any process that activates or increases the frequency, rate, or extent of leukocyte mediated immunity.
positive regulation of immune cell mediated immunity
positive regulation of leucocyte mediated immunity
up regulation of leukocyte mediated immunity
up-regulation of leukocyte mediated immunity
upregulation of leukocyte mediated immunity
activation of leukocyte mediated immunity
stimulation of leukocyte mediated immunity
positive regulation of leukocyte mediated immunity
Any process that modulates the frequency, rate, or extent of myeloid leukocyte differentiation.
regulation of myeloid leukocyte differentiation
Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte differentiation.
down regulation of myeloid leukocyte differentiation
down-regulation of myeloid leukocyte differentiation
downregulation of myeloid leukocyte differentiation
inhibition of myeloid leukocyte differentiation
negative regulation of myeloid leukocyte differentiation
Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte differentiation.
up regulation of myeloid leukocyte differentiation
up-regulation of myeloid leukocyte differentiation
upregulation of myeloid leukocyte differentiation
activation of myeloid leukocyte differentiation
stimulation of myeloid leukocyte differentiation
positive regulation of myeloid leukocyte differentiation
The controlled release of a peptide from a cell or a tissue.
Any process that modulates the frequency, rate, or extent of peptide secretion.
Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion.
negative regulation of peptide secretion
Any process that activates or increases the frequency, rate, or extent of peptide secretion.
positive regulation of peptide secretion
Any process that modulates the frequency, rate, or extent of a response to biotic stimulus.
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 biotic stimulus
Any process that stops, prevents, or reduces the frequency, rate, or extent of a response to biotic stimulus.
down regulation of response to biotic stimulus
down-regulation of response to biotic stimulus
downregulation of response to biotic stimulus
inhibition of response to biotic stimulus
negative regulation of response to biotic stimulus
Any process that activates or increases the frequency, rate, or extent of a response to biotic stimulus.
up regulation of response to biotic stimulus
up-regulation of response to biotic stimulus
upregulation of response to biotic stimulus
activation of response to biotic stimulus
stimulation of response to biotic stimulus
positive regulation of response to biotic stimulus
Any process that modulates the frequency, rate, or extent of myeloid leukocyte mediated immunity.
regulation of myeloid leukocyte mediated immunity
Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte mediated immunity.
down regulation of myeloid leukocyte mediated immunity
down-regulation of myeloid leukocyte mediated immunity
downregulation of myeloid leukocyte mediated immunity
inhibition of myeloid leukocyte mediated immunity
negative regulation of myeloid leukocyte mediated immunity
Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte mediated immunity.
up regulation of myeloid leukocyte mediated immunity
up-regulation of myeloid leukocyte mediated immunity
upregulation of myeloid leukocyte mediated immunity
activation of myeloid leukocyte mediated immunity
stimulation of myeloid leukocyte mediated immunity
positive regulation of myeloid leukocyte mediated immunity
The process whose specific outcome is the progression of a tendon sheath over time, from its formation to the mature structure. A tendon sheath is a layer of membrane around a tendon. It permits the tendon to move.
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.
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.
developmental process involved in reproduction
The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
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.
A process in which force is generated within skeletal muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the skeletal muscle, the muscle contraction takes advantage of an ordered sarcomeric structure and in most cases it is under voluntary control.
A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers.
A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism.
A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange.
Any process that mediates the transfer of information from endodermal cells to mesodermal cells.
The process in which the anatomical structures of the cardiogenic plate are generated and organized. The cardiogenic plate is the first recognizable structure derived from the heart field.
The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart.
The process that gives rise to the embryonic heart tube. This process pertains to the initial formation of a structure from unspecified parts. The embryonic heart tube is an epithelial tube that will give rise to the mature heart.
The process that gives rise to the embryonic heart tube by the cells of the heart field along a linear axis.
embryonic heart tube formation via epithelial folding
The process in which the anatomical structures of the outflow tract septum are generated and organized. The outflow tract septum is a partition in the outflow tract.
The process in which the muscular septum is generated and organized. The muscular septum is the lower part of the ventricular septum.
The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries.
The morphogenetic process in which an epithelial sheet bends along a linear axis, contributing to embryonic heart tube formation.
morphogenesis of an epithelial fold involved in embryonic heart tube formation
Any process that modulates the rate, frequency or extent of animal organ formation. Organ formation is the process pertaining to the initial formation of an organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment.
The process whose specific outcome is the progression of the endocardium over time, from its formation to the mature structure. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.
The process whose specific outcome is the progression of an endothelium over time, from its formation to the mature structure. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.
The process in which the anatomical structure of an endothelium is generated and organized. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.
The process in which the anatomical structure of the endocardium is generated and organized. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.
The process whose specific outcome is the progression of the cardiac conduction system over time, from its formation to the mature structure. The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat.
cardiac impulse conducting system development
The process whose specific outcome is the progression of the atrioventricular (AV) node over time, from its formation to the mature structure. The AV node is part of the cardiac conduction system that controls the timing of ventricle contraction by receiving electrical signals from the sinoatrial (SA) node and relaying them to the His-Purkinje system.
The process whose specific outcome is the progression of the sinoatrial (SA) node over time, from its formation to the mature structure. The SA node is part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node.
The process whose specific outcome is the progression of the His-Purkinje system over time, from its formation to the mature structure. The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles.
The process whose specific outcome is the progression of a Purkinje myocyte over time, from its formation to the mature structure. The Purkinje myocyte (also known as cardiac Purkinje fiber) is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle.
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a Purkinje myocyte (also known as cardiac Purkinje fiber cell). These cells are specialized cardiomyocytes that receive signals from the bundle of His and innervate the ventricular cardiac muscle.
cardiac Purkinje fiber cell differentiation
The process in which the anatomical structures of veins of the heart are generated and organized.
The progression of a cardiac cushion over time, from its initial formation to the mature structure. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.
The process in which the anatomical structure of the endocardial cushion is generated and organized. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.
The progression of the cardiac skeleton over time, from its formation to the mature structure. The cardiac skeleton is a specialized extracellular matrix that separates the atria from the ventricles and provides physical support for the heart.
The progression of a cardiac chamber over time, from its formation to the mature structure. A cardiac chamber is an enclosed cavity within the heart.
The process in which a cardiac chamber is generated and organized. A cardiac chamber is an enclosed cavity within the heart.
The developmental process pertaining to the initial formation of a cardiac chamber from unspecified parts. A cardiac chamber is an enclosed cavity within the heart.
The process in which the cardiac ventricle is generated and organized. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart.
The process in which the cardiac atrium is generated and organized. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle.
The developmental process pertaining to the initial formation of a cardiac atrium from unspecified parts. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle.
The developmental process pertaining to the initial formation of a cardiac ventricle from unspecified parts. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart.
The process in which the left cardiac atrium is generated and organized.
The process in which the right cardiac atrium is generated and organized.
The process in which the left cardiac ventricle is generated and organized.
The process in which the right cardiac ventricle is generated and organized.
The developmental process pertaining to the initial formation of a left cardiac atrium from unspecified parts.
The developmental process pertaining to the initial formation of a cardiac right atrium from unspecified parts.
The developmental process pertaining to the initial formation of a left cardiac ventricle from unspecified parts.
The developmental process pertaining to the initial formation of a right cardiac ventricle from unspecified parts.
The process in which the anatomical structures of left cardiac ventricle muscle are generated and organized.
left ventricular myocardium morphogenesis
left ventricular cardiac muscle tissue morphogenesis
The process in which the anatomical structures of the right cardiac ventricle muscle are generated and organized.
right ventricle myocardium morphogenesis
right ventricular cardiac muscle tissue morphogenesis
The process whose specific outcome is the progression of cardiac muscle of the atrium over time, from its formation to the mature structure.
atrial cardiac muscle tissue development
The process whose specific outcome is the progression of ventricular cardiac muscle over time, from its formation to the mature structure.
ventricular cardiac muscle tissue development
The process whose specific outcome is the progression of a cardiac atrium over time, from its formation to the mature structure. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle.
The process whose specific outcome is the progression of a cardiac ventricle over time, from its formation to the mature structure. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart.
The progression of the sinus venosus over time, from its formation to the mature structure. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart.
The process in which the sinus venosus is generated and organized. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart.
The developmental process pertaining to the initial formation of the sinus venosus from unspecified parts. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart.
Developmental growth that contributes to the shaping of the heart.
The developmental growth of cardiac muscle tissue that contributes to the shaping of the heart.
cardiac muscle tissue growth involved in heart morphogenesis
The increase in heart capillaries that accompanies physiological hypertrophy of cardiac muscle.
The developmental process pertaining to the initial formation of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.
The orderly movement of a cell from one site to another that will contribute to the formation of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.
cell migration involved in endocardial cushion formation
Any apoptotic process that contributes to the shaping of the outflow tract. The outflow tract is the portion of the heart through which blood flows into the arteries.
apoptosis involved in outflow tract morphogenesis
apoptotic process involved in outflow tract morphogenesis
Any apoptotic process that contributes to the shaping of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.
apoptosis involved in endocardial cushion morphogenesis
apoptotic process involved in endocardial cushion morphogenesis
Any apoptotic process that contributes to the shaping of the heart.
apoptosis involved in heart morphogenesis
apoptotic process involved in heart morphogenesis
The progression of a cardiac septum over time, from its initial formation to the mature structure.
The progression of the ventricular septum over time from its formation to the mature structure.
The progression of the atrial septum over time, from its initial formation to the mature structure.
The process in which an endocardial cushion cell becomes a cell of a cardiac septum.
The enlargement or overgrowth of all or part of a muscle organ or tissue due to an increase in the size of its muscle cells. Physiological hypertrophy is a normal process during development.
The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division.
The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division. This process contributes to the developmental growth of the heart.
physiological cardiac muscle hypertrophy
The progression of the heart rudiment over time, from its initial formation to the mature structure. The heart rudiment is a cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
The process in which the anatomical structures of the heart rudiment are generated and organized.
The developmental process pertaining to the initial formation of the heart rudiment.
The progression of the proepicardium from its formation to the mature structure. The proepicardium is an outpouching of the septum transversum.
The progression of the septum transversum from its initial formation to the mature structure. The septum transversum is a portion of the trunk mesenchyme.
The process in which the anatomical structure of the pericardium is generated and organized.
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cardiac endothelial cell.
cardiac endothelial cell differentiation
The progression of the brainstem from its formation to the mature structure. The brainstem is the part of the brain that connects the brain with the spinal cord.
The change in form that occurs when an epithelial cell progresses from it initial formation to its mature state, contributing to the process of gastrulation.
epithelial cell morphogenesis involved in gastrulation
The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state.
The developmental process pertaining to the initial formation of the optic vesicle from the lateral wall of the forebrain. This process begins with the specific processes that contribute to the appearance of the vesicle and ends when the vesicle has evaginated. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup.
The developmental process pertaining to the formation and shaping of the optic vesicle. This process begins with the specific processes that contribute to the appearance of the vesicle and ends when the vesicle has evaginated. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup.
The progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another and contributes to the physical shaping or formation of the camera-type eye.
cell motility involved in camera-type eye morphogenesis
The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the development of a bone. A chondrocyte is a polymorphic cell that forms cartilage.
chondrocyte differentiation involved in endochondral bone morphogenesis
The process in which the structures of a chondrocyte that will contribute to bone development are generated and organized.
chondrocyte morphogenesis involved in endochondral bone morphogenesis
The increase in size or mass of an endochondral bone that contributes to the shaping of the bone.
The progression of a chondrocyte over time from after its commitment to its mature state where the chondrocyte will contribute to the shaping of an endochondral bone.
chondrocyte development involved in endochondral bone morphogenesis
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
nuclear membrane vesicle binding to chromatin
Binding to an RNA molecule or a portion thereof.
Exportin-5 recognizes 3' overhang of pre-miRNA
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Binding to one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'.
hematopoietin/interferon-class (D200-domain) cytokine receptor binding
hematopoietin/interferon-class (D200-domain) cytokine receptor ligand
Binding to a vascular endothelial growth factor receptor.
vascular endothelial growth factor receptor ligand
vascular endothelial growth factor receptor binding
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
Binding to a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
Binding to collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
Binding to a glycan (polysaccharide) containing a substantial proportion of aminomonosaccharide residues.
Binding to hyaluronic acid, a polymer composed of repeating dimeric units of glucuronic acid and N-acetyl glucosamine.
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.
A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds.
A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
Any triple helical collagen trimer that forms fibrils.
A collagen heterotrimer containing type IV alpha chains; [alpha1(IV)]2alpha2(IV) trimers are commonly observed, although more type IV alpha chains exist and may be present in type IV trimers; type IV collagen triple helices associate to form 3 dimensional nets within basement membranes.
A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer.
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term.
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.
Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing.
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
The volume enclosed within the vacuolar membrane.
A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.
Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.
Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell.
Note that this definition includes vesicles that are transiently associated with the Golgi.
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
A microtubule in the axoneme of a eukaryotic cilium or flagellum; an axoneme contains nine modified doublet microtubules, which may or may not surround a pair of single microtubules.
Any microtubule in the nucleus of a cell.
Any microtubule in the cytoplasm of a cell.
non-spindle-associated astral microtubule
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
A cell junction that forms a connection between two or more cells of an organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects.
A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms.
The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane.
The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
multicellular organismal carbohydrate metabolic process
single-organism carbohydrate metabolic process
The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
multicellular organismal polysaccharide metabolic process
The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
The chemical reactions and pathways involving starch, the most important reserve polysaccharide in plants. It is a glucan consisting of two components, amylose and amylopectin, which are both glucose homopolymers. Starch is synthesized as a temporary storage form of carbon and can be catabolized to produce sucrose.
The chemical reactions and pathways involving aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages.
The chemical reactions and pathways resulting in the formation of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages.
The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars.
The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues, occurring at the level of an individual cell.
The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.
The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
generation of precursor metabolites and energy
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates.
regulation of carbohydrate metabolic process
The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP).
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside and nucleotide metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
nucleobase-containing compound 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.
Any process in which DNA and associated proteins are formed into a compact, orderly structure.
Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
establishment or maintenance of chromatin architecture
The formation or destruction of chromatin structures.
A process in which RNA is transported to, or maintained in, a specific location.
establishment and maintenance of RNA localization
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
Any process that modulates the frequency, rate or extent of translational initiation.
Any process that modulates the frequency, rate, extent or accuracy of translational elongation.
Any process that modulates the frequency, rate or extent of translational termination.
The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
cellular amino acid and derivative metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids.
regulation of cellular amino acid metabolic process
The chemical reactions and pathways occurring at the level of individual cells involving any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters.
cellular biogenic amine metabolic process
The chemical reactions and pathways involving any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
The chemical reactions and pathways involving indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group.
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
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.
cellular aromatic compound metabolic process
The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
phosphate-containing compound metabolic process
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
di-, tri-valent inorganic cation transport
The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems.
The transport of substances that occurs outside cells.
The directed extracellular movement of carbohydrates.
The directed extracellular movement of amino acids.
The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
copper-induced intracellular protein transport
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.
The directed movement of substances from the Golgi to other parts of the cell, including organelles and the plasma membrane, mediated by small transport vesicles.
The directed movement of substances from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane, where they fuse and release their contents by exocytosis.
Golgi to plasma membrane vesicle-mediated transport
The directed movement of substances from the Golgi to the vacuole.
Golgi to vacuole vesicle-mediated transport
The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo.
Fusion of the membrane of a transport vesicle with its target membrane.
A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.
cellular component disassembly involved in apoptotic process
cellular component disassembly involved in apoptosis
cellular component disassembly involved in execution phase of apoptosis
The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
Note that in GO cellular components include whole cells (cell is_a cellular component).
movement of cell or subcellular component
The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
Any process that modulates the frequency, rate or extent of muscle contraction.
A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length.
Any process that modulates the frequency, rate or extent of smooth muscle contraction.
A process in which force is generated within striated muscle tissue, resulting in the shortening of the muscle. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Striated muscle is a type of muscle in which the repeating units (sarcomeres) of the contractile myofibrils are arranged in registry throughout the cell, resulting in transverse or oblique striations observable at the level of the light microscope.
Any process that modulates the frequency, rate or extent of striated muscle contraction.
regulation of striated muscle contraction
The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.
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.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope.
nuclear envelope organization and biogenesis
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane.
plasma membrane organization and biogenesis
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
cytoskeletal organization and biogenesis
cytoskeleton organization and biogenesis
Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
The removal of tubulin heterodimers from one or both ends of a microtubule.
microtubule depolymerization during nuclear congression
The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation).
Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol.
down regulation of microtubule depolymerization
down-regulation of microtubule depolymerization
downregulation of microtubule depolymerization
negative regulation of microtubule disassembly
inhibition of microtubule depolymerization
negative regulation of microtubule catastrophe
negative regulation of microtubule depolymerization
Any process that stops, prevents, or reduces the frequency, rate or extent of the depolymerization of the specialized microtubules of the axoneme.
negative regulation of microtubule depolymerization in axoneme
negative regulation of axonemal microtubule depolymerization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole.
The directed movement of substances into, out of or within a vacuole.
The aggregation, arrangement and bonding together of a set of components to form a junction between cells.
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.
The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells.
The mitotic cell cycle process in which the controlled partial or complete breakdown of the nuclear membranes during occurs during mitosis.
Any process that modulates the frequency, rate or extent of mitosis.
The directed movement of the nucleus to a specific location within a cell.
establishment of cell nucleus localization
establishment of localization of nucleus
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.
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.
Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
signal transduction by cis-phosphorylation
signal transduction by conformational transition
signal transduction by protein phosphorylation
signal transduction by trans-phosphorylation
Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
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).
Note that this term was 'developmental process'.
The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell.
The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
Any process that modulates the rate or extent of progress through the mitotic cell cycle.
modulation of mitotic cell cycle progression
regulation of mitotic cell cycle progression
regulation of progression through mitotic cell cycle
A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
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.
The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation.
The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
The expansion of a neuroblast population by cell division. A neuroblast is any cell that will divide and give rise to a neuron.
Any process that stops, prevents, or reduces the frequency, rate or extent of the proliferation of neuroblasts.
down regulation of neuroblast proliferation
down-regulation of neuroblast proliferation
downregulation of neuroblast proliferation
negative regulation of neuroblast proliferation
The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure.
The process whose specific outcome is the progression of the ectodermal digestive tract over time, from its formation to the mature structure. The ectodermal digestive tract includes those portions that are derived from ectoderm.
The process in which the anatomical structures of the foregut are generated and organized.
The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues.
The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.
The process whose specific outcome is the progression of the gonadal mesoderm over time, from its formation to the mature structure. The gonadal mesoderm is the middle layer of the three primary germ layers of the embryo which will go on to form the gonads of the organism.
The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
The developmental sequence of events leading to the formation of adult skeletal muscle tissue. The main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction.
The establishment of the sex of an organism by physical differentiation.
The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
respiratory gaseous exchange by respiratory system
The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
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.
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.
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.
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.
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 associated with the intake of food.
feeding from vascular tissue of another organism
injection of substance into other organism during feeding on blood of other organism
See also the biological process term 'behavior ; GO:0007610'.
The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body.
Binding to a microtubule, a filament composed of tubulin monomers.
Viral UL47:UL48 Proteins Bind HCMV Tegumented Virion to Host Microtuble and Dynein complexs
The directed movement of organelles or molecules along microtubules in neuron projections.
Binding to a protein component of a cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
Any process in which a protein is transported to, or maintained in, a specific location.
establishment and maintenance of asymmetric protein localization
establishment and maintenance of protein localization
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
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.
metabolic process resulting in cell growth
multicellular organism metabolic process
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
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).
This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term.
The directed movement of sulfate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms.
Any process that activates or increases the rate or extent of cell proliferation.
positive regulation of cell proliferation
positive regulation of cell population proliferation
Any process that stops, prevents or reduces the rate or extent of cell proliferation.
negative regulation of cell proliferation
negative regulation of cell population proliferation
The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones.
The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure.
The process in which the structures of a photoreceptor cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a photoreceptor cell, a sensory cell that reacts to the presence of light. An example of this is found in Drosophila melanogaster.
The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y.
The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
cellular amino acid biosynthetic process
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
multicellular organismal biosynthetic process
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
The chemical reactions and pathways involving glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
The chemical reactions and pathways resulting in the formation of glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine.
The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
The controlled release of proteins from a cell.
protein secretion during cell fate commitment
protein secretion resulting in cell fate commitment
The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
The chemical reactions and pathways resulting in the formation of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
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
Note that 'radiation' refers to electromagnetic radiation of any wavelength.
OBSOLETE. The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
This term was obsoleted because it does not describe a single, normal biological process; rather it is the effect of an interaction between two organisms, under specific conditions.
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.
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.
The directed movement of a motile cell or organism in response to environmental oxygen.
The series of events in which an external stimulus is received by a cell and converted into a molecular signal.
The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal.
The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal.
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.
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.
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 biotic stimulus, a stimulus caused or produced by a living organism.
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 from a bacterium.
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 from a fungus.
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.
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 toxic stimulus.
The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
The chemical reactions and pathways involving a compound containing a pyrocatechol (1,2-benzenediol) nucleus or substituent.
catechol-containing compound metabolic process
The chemical reactions and pathways resulting in the formation of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent.
catechol-containing compound biosynthetic process
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
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 carbohydrate stimulus.
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.
The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell.
embryo development ending in birth or egg hatching
The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases).
The chemical reactions and pathways resulting in the formation of alkaloids, nitrogen-containing natural products which are not otherwise classified as nonprotein amino acids, amines, peptides, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones, or primary metabolite (such as purine or pyrimidine bases).
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.
The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances.
negative regulation of biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
positive regulation of biosynthetic 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.
negative regulation of organismal metabolism
inhibition of organismal metabolic process
negative regulation of multicellular organismal metabolic process
negative 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.
positive regulation of multicellular organismal metabolic process
positive regulation of organismal metabolism
stimulation of organismal metabolic process
up-regulation of organismal metabolic process
positive regulation of metabolic process
The process in which a relatively unspecialized cell acquires specialized features of an epidermal cell, any of the cells making up the epidermis.
The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
anterior/posterior pattern specification
Any process that modulates the frequency, rate or extent of signal transduction.
Any process that activates or increases the frequency, rate or extent of signal transduction.
positive regulation of signaling pathway
positive regulation of signalling pathway
positive regulation of signal transduction
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
negative regulation of signaling pathway
negative regulation of signalling pathway
negative regulation of signal transduction
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.
The process in which a relatively unspecialized cell acquires the specialized features of a glial cell.
The process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
process resulting in tolerance to organic substance
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus.
The regionalization process that specifies animal organ primordium boundaries resulting in a restriction of organogenesis to a limited spatial domain and keeping the organ separate from surrounding tissues.
The process in which the anatomical structures of the soma are generated and organized.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system.
The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.
Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.
regulation of mesenchymal cell proliferation
The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA).
This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation.
Any process that modulates the rate or extent of gastrulation. Gastrulation is the complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals.
Any process resulting in the physical partitioning and separation of an epidermal cell, any of the cells making up the epidermis, into daughter cells.
Any process that modulates the frequency, rate or extent of the physical partitioning and separation of an epidermal cell into daughter cells. An epidermal cell is any of the cells that make up the epidermis.
Any process that modulates the frequency, rate or extent of membrane disassembly.
Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
regulation of macromolecule biosynthetic process
Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
positive regulation of macromolecule biosynthetic process
Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
negative regulation of macromolecule biosynthetic process
Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
regulation of glycoprotein biosynthetic process
Any process that increases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
positive regulation of glycoprotein biosynthetic process
Any process that decreases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
negative regulation of glycoprotein biosynthetic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
positive 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.
negative regulation of phosphorus metabolic 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.
Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
regulation of cellular ketone metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a ketone, carried out by individual cells.
regulation of ketone biosynthetic 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.
positive 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.
negative regulation of macromolecule metabolic process
Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript.
posttranscriptional regulation of gene expression
Any process that modulates the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
regulation of cardiac muscle hypertrophy
Any process that modulates the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors.
Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
positive regulation of cardiac muscle hypertrophy
Any process that decreases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
negative regulation of cardiac muscle hypertrophy
Any process that increases the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors.
positive regulation of cardiac muscle adaptation
Any process that decreases the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors.
negative regulation of cardiac muscle adaptation
The activation of endogenous cellular processes that result in the death of a cell as part of its development.
programmed cell death involved in development
This process is part of the natural developmental program of some cell types, but it does not always happen as part of the development or shaping of a gross anatomical structure.
programmed cell death involved in cell development
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA).
Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA).
This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availability of mRNA or circRNA for translation and thereby reduces the rate of production of the encoded protein via translation.
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
positive regulation of organelle organization and biogenesis
positive 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.
negative regulation of organelle organisation
negative regulation of organelle organization and biogenesis
negative regulation of organelle organization
Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
positive regulation of cell communication
Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
negative regulation of cell communication
Any process that decreases the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death.
negative regulation of muscle cell apoptosis
negative regulation of muscle cell apoptotic process
A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a muscle cell and result in its death. A muscle cell is a mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle.
A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a striated muscle cell and result in its death. Striated muscle cells make up striated muscle fibers which are divided by transverse bands into striations.
A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a cardiac muscle cell and result in its death. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
Any process that modulates the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death.
regulation of muscle cell apoptotic process
Any process that increases the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death.
positive regulation of muscle cell apoptosis
positive regulation of muscle cell apoptotic process
Any process that modulates the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death.
regulation of striated muscle cell apoptosis
regulation of striated muscle cell apoptotic process
Any process that increases the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death.
positive regulation of striated muscle cell apoptosis
positive regulation of striated muscle cell apoptotic process
Any process that decreases the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death.
down regulation of striated muscle cell apoptosis
down-regulation of striated muscle cell apoptosis
downregulation of striated muscle cell apoptosis
inhibition of striated muscle cell apoptosis
negative regulation of striated muscle cell apoptosis
negative regulation of striated muscle cell apoptotic process
Any process that modulates the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death.
regulation of cardiac muscle cell apoptosis
regulation of cardiac muscle cell apoptotic process
Any process that increases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death.
positive regulation of cardiac muscle cell apoptosis
positive regulation of cardiac muscle cell apoptotic process
Any process that decreases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death.
down regulation of cardiac muscle cell apoptosis
down-regulation of cardiac muscle cell apoptosis
downregulation of cardiac muscle cell apoptosis
inhibition of cardiac muscle cell apoptosis
negative regulation of cardiac muscle cell apoptosis
negative regulation of cardiac muscle cell apoptotic process
The process in which relatively unspecialized cells acquire specialized structural and/or functional features of an ectodermal cell. Differentiation includes the processes involved in commitment of a cell to a specific fate.
Any process that decreases the frequency, rate or extent of the regulated release of norepinephrine.
negative regulation of norepinephrine secretion
Any process that increases the frequency, rate or extent of the regulated release of norepinephrine.
positive regulation of norepinephrine secretion
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
regulation of collagen metabolic process
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
negative regulation of collagen metabolic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
positive regulation of collagen metabolism
positive regulation of collagen metabolic process
Any process that modulates the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix.
regulation of extracellular matrix breakdown
regulation of extracellular matrix degradation
regulation of extracellular matrix disassembly
Any process that decreases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix.
down regulation of extracellular matrix disassembly
down-regulation of extracellular matrix disassembly
downregulation of extracellular matrix disassembly
negative regulation of extracellular matrix breakdown
negative regulation of extracellular matrix degradation
inhibition of extracellular matrix disassembly
negative regulation of extracellular matrix disassembly
Any process that modulates the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
regulation of epithelial to mesenchymal transition
Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
positive regulation of epithelial to mesenchymal transition
Any process that decreases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
negative regulation of epithelial to mesenchymal transition
Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
Any process that modulates the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
regulation of cell morphogenesis involved in differentiation
Any process that increases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
positive regulation of cell morphogenesis involved in differentiation
Any process that decreases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
negative regulation of cell morphogenesis involved in differentiation
Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action.
Any process that modulates the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
Any process that activates, maintains or increases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
positive regulation of myotube differentiation
Any process that decreases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
negative regulation of myotube differentiation
The process in which the vertebrate retina is organized into three laminae: the outer nuclear layer (ONL), which contains photoreceptor nuclei; the inner nuclear layer (INL), which contains amacrine, bipolar and horizontal cells; and the retinal ganglion cell (RGC) layer. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells. The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells. Spanning all layers of the retina are the radially oriented Mueller glia.
Any process the modulates the frequency, rate or extent of chromatin assembly. Chromatin assembly is the assembly of DNA, histone proteins, and other associated proteins into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.
Any process that modulates the frequency, rate or extent of chromatin disassembly. Chromatin disassembly is the controlled breakdown of chromatin from a higher order structure into its simpler subcomponents, DNA, histones, and other proteins.
Any process in which a lipid is transported to, or maintained in, a specific location.
Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
positive regulation of steroid biosynthetic process
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
negative regulation of steroid biosynthetic process
The cellular component assembly that is part of the initial shaping of the component during its developmental progression.
cellular component assembly involved in morphogenesis
Any process that modulates the frequency, rate or extent of cytoplasmic microtubule depolymerization.
regulation of cytoplasmic microtubule depolymerization
The removal of tubulin heterodimers from one or both ends of a cytoplasmic microtubule.
cytoplasmic microtubule depolymerization
Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
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.
negative regulation of cell cycle process
Any process that modulates the frequency, rate or extent of phosphate transport. Phosphate transport is the directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell.
The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity.
establishment of localization by movement along microtubule
Any process that modulates the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
regulation of neuron projection development
Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
positive regulation of neurite biosynthesis
positive regulation of neurite development
positive regulation of neurite formation
positive regulation of neuron projection development
Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
negative regulation of neurite biosynthesis
negative regulation of neurite development
negative regulation of neurite formation
negative regulation of neuron projection development
A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children.
A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
The lipid bilayer surrounding any membrane-bounded vesicle in the cell.
The multiplication or reproduction of glial cells by cell division, resulting in the expansion of their population. Glial cells exist throughout the nervous system, and include Schwann cells, astrocytes, and oligodendrocytes among others.
Any process that modulates the frequency, rate or extent of gliogenesis, the formation of mature glia.
Any process that stops, prevents, or reduces the frequency, rate or extent of gliogenesis, the formation of mature glia.
Any process that activates or increases the frequency, rate or extent of gliogenesis, the formation of mature glia.
The process in which a relatively unspecialized cell acquires specialized features of a neuroblast. There are at least four stages through which the pluripotent cells of epiblast or blastula become neuroblasts.
The process aimed at the progression of a neuroblast over time, from initial commitment of the cell to a specific state, to the mature neuroblast. It does not include processes where the neuroblast turns into a glial cell or a neuron.
The formation of the neural tube from an epithelial cell sheet (the neuroepithelium or neural plate). In primary neurulation, the cells surrounding the neural plate direct the neural plate cells to proliferate, invaginate, and pinch off from the surface to form a hollow epithelial tube. Primary neurulation is the typical mechanism of formation of the anterior neural tube.
The formation of a solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts.
The process of rod cavitation, which is the formation of a lumen in the neural rod during primary neurulation, producing the neural tube.
The formation of a thickened region of the neurectoderm that is roughly triangular in cross section. The neural keel develops from the neural plate and develops into the neural rod. Neural keel formation occurs during primary neurulation in teleosts.
The formation of the notochord from the chordamesoderm. The notochord is composed of large cells packed within a firm connective tissue sheath and is found in all chordates at the ventral surface of the neural tube. In vertebrates, the notochord contributes to the vertebral column.
The formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes.
The process aimed at the progression of a mesenchymal cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
The process in which a relatively unspecialized cell acquires specialized features of a neural crest cell.
Any process that modulates the frequency, rate or extent of the regulated release of norepinephrine.
Any process that modulates the frequency, rate or extent of the regulated release of serotonin.
Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of serotonin.
positive regulation of serotonin release
negative regulation of serotonin secretion
Any process that activates or increases the frequency, rate or extent of the regulated release of serotonin.
positive regulation of serotonin secretion
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound 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 amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.
The process whose specific outcome is the progression of a striated muscle over time, from its formation to the mature structure. Striated muscle contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle. Skeletal muscle myoblasts fuse to form myotubes and eventually multinucleated muscle fibers. The fusion of cardiac cells is very rare and can only form binucleate cells.
Any process in which skeletal muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities.
regulation of skeletal muscle plasticity
regulation of skeletal muscle adaptation
The enlargement or overgrowth of all or part of an organ due to an increase in size (not length) of individual muscle fibers without cell division. In the case of skeletal muscle cells this happens due to the additional synthesis of sarcomeric proteins and assembly of myofibrils.
Any process that stops, prevents, or reduces the frequency, rate, or extent of muscle hypertrophy.
negative regulation of muscle hypertrophy
Any process that activates or increases the frequency, rate or extent of muscle hypertrophy.
positive regulation of muscle hypertrophy
Any process that modulates the frequency, rate or extent of muscle hypertrophy.
Any process that activates or increases the frequency, rate or extent of muscle adaptation.
positive regulation of muscle plasticity
positive regulation of muscle adaptation
Any process that stops, prevents, or reduces the frequency, rate, or extent of muscle adaptation.
negative regulation of muscle plasticity
negative regulation of muscle adaptation
Any process in which smooth muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities.
Any process that modulates the frequency, rate or extent of somitogenesis.
Any process that modulates the frequency, rate or extent of skeletal muscle contraction.
regulation of skeletal muscle contraction
The multiplication or reproduction of striated muscle cells, resulting in the expansion of a cell population. Striated muscles contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle.
The multiplication or reproduction of skeletal muscle cells, resulting in the expansion of a cell population.
Any process that modulates the frequency, rate or extent of skeletal muscle cell proliferation.
regulation of skeletal muscle cell proliferation
Any process that activates or increases the frequency, rate or extent of skeletal muscle cell proliferation.
positive regulation of skeletal muscle cell proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle cell proliferation.
negative regulation of skeletal muscle cell proliferation
Any process that modulates the frequency, rate or extent of skeletal muscle contraction by depolarization of muscle membrane and ionic fluxes.
regulation of skeletal muscle contraction via membrane action potential
regulation of skeletal muscle contraction via regulation of action potential
The process whose specific outcome is the progression of the skeletal myofibril over time, from its formation to the mature structure. A skeletal myofibril is a myofibril specific to skeletal muscle cells.
The process resulting in the physical partitioning and separation of a myoblast into daughter cells. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
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. This occurs as part of the regulation of muscle adaptation.
response to stimulus involved in regulation of muscle plasticity
response to stimulus involved in regulation of muscle adaptation
The process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors.
Any process in which striated muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities.
The enlargement or overgrowth of all or part of an organ due to an increase in size of its smooth muscle cells without cell division. Physiological hypertrophy is a normal process during development, and can also occur in mature structures on demand. In the uterus, smooth muscle cells undergo hypertrophy during pregnancy.
The muscle system process that results in enlargement or overgrowth of all or part of a muscle organ due to an increase in the size of its muscle cells. Physiological hypertrophy is a normal process during development (it stops in cardiac muscle after adolescence) and can also be brought on in response to demand. In athletes cardiac and skeletal muscles undergo hypertrophy stimulated by increasing muscle activity on exercise. Smooth muscle cells in the uterus undergo hypertrophy during pregnancy.
The enlargement or overgrowth of all or part of an organ due to an increase in size of muscle cells without cell division. In the case of striated muscle, this happens due to the additional synthesis of sarcomeric proteins and assembly of myofibrils.
The process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotube differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual myotubes can fuse to form bigger myotubes and start to contract. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
The process aimed at the progression of a myotube cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
Binding to monomeric or multimeric forms of tubulin, including microtubules.
The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of organic cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic cations are atoms or small molecules with a positive charge which contain carbon in covalent linkage.
The directed movement of inorganic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage.
The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage.
The directed movement of polysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom.
The directed movement of a nucleobase, any nitrogenous base that is a constituent of a nucleoside, nucleotide, or nucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of norepinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine.
The directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
nucleobase, nucleoside, nucleotide and nucleic acid transport
nucleobase-containing compound transport
The chemical reactions and pathways by which a cell derives energy from inorganic compounds; results in the oxidation of the compounds from which energy is released.
energy derivation by oxidation of reduced inorganic compounds
The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released.
energy derivation by oxidation of organic compounds
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
non-developmental growth of a unicellular organism
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.
The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage.
Hyperpolarization (vertebrates) or depolarization (invertebrates) of the photoreceptor cell membrane via closing/opening of cation specific channels as a result of signals generated by rhodopsin activation by a photon.
changes in polarization state of photoreceptor cell membrane
regulation of membrane potential in photoreceptor cell
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
Any process that modulates the frequency, rate or extent of striated muscle development.
regulation of striated muscle tissue development
OBSOLETE. A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism.
This term was made obsolete because it refers to a phenotype. When death of a cell or tissue is a result of a true biological process, this should be captured using 'programmed cell death' or one of its descendants.
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
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.
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.
The process in which the anatomical structures of embryonic epithelia are generated and organized.
The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
The cytoplasm of a muscle cell; includes the sarcoplasmic reticulum.
Binding to an amino acid, organic acids containing one or more amino substituents.
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.
TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK
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).
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
Binding to a peptide with hormonal activity in animals.
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 insecticide stimulus. Insecticides are chemicals used to kill insects.
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells.
The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
down regulation of protein biosynthetic process
down-regulation of protein biosynthetic process
downregulation of protein biosynthetic process
negative regulation of protein anabolism
negative regulation of protein biosynthesis
negative regulation of protein biosynthetic process
negative regulation of protein formation
negative regulation of protein synthesis
inhibition of protein biosynthetic process
protein biosynthetic process inhibitor activity
Any process that modulates the frequency, rate or extent of exocytosis.
The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
The chemical reactions and pathways involving a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring.
Note that phenol metabolism is not included as a child of 'xenobiotic metabolism' because although it is synthesized industrially, phenol is also found naturally in animal wastes and other organic materials. It is often formed by the activity of microorganisms, which can chemically modify a variety of xenobiotic and naturally occurring phenolic compounds.
phenol-containing compound metabolic process
The specific behavior of an organism that is associated with reproduction.
reproductive behavior in a multicellular organism
multicellular organism reproductive behavior
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids.
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
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
regulation of nucleobase-containing compound metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
regulation of phosphate metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
regulation of multicellular organismal metabolic process
regulation of organismal metabolic process
The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission.
An action potential that occurs in a neuron.
The chemical reactions and pathways resulting in the formation of starch, the most important reserve polysaccharide in plants.
The chemical reactions and pathways by which ammonia or ammonium is converted to molecular nitrogen or another nitrogen compound, with accompanying loss of electrons.
The oxidation of ammonium (NH4) to nitrogen (N2) in the absence of oxygen, using nitrite (NO2) as the electron acceptor. It is suggested that hydroxylamine and ammonium are combined to yield hydrazine, which is subsequently oxidized to N2.
anaerobic respiration, using ammonium as electron donor
The oxidation of nitrite (NO2) to nitrate (NO3), using oxygen (O2) as the electron acceptor. Nitrite oxidation is the final step in nitrification, the oxidation of ammonia to nitrate, and nitrite oxidoreductase (NOR) is the key enzyme complex that catalyzes the conversion of nitrite to nitrate in nitrite oxidizing species.
aerobic respiration, using nitrite as electron donor
The metabolic process in which ammonia (NH3) is oxidized to nitrite (NO2) in the presence of oxygen; enzymatic reactions convert ammonia to hydrazine, and hydrazine to nitrite.
aerobic ammonia oxidation to nitrite via hydrazine
aerobic respiration, using ammonia as electron donor
The metabolic process in which carbon monoxide (CO) is oxidized to carbon dioxide (CO2) to generate energy. Conservation of energy in this process likely uses sodium ion gradients for ATP synthesis and is coupled to quantitative sulfide methylation.
aerobic respiration, using carbon monoxide as electron donor
The oxidation of hydrogen (H2) to water (H2O), using oxygen (O2) as the electron acceptor. A hydrogenase enzyme binds H2 and the hydrogen atoms are passed through an electron transfer chain to O2 to form water.
aerobic respiration, using hydrogen as electron donor
An aerobic respiration process in which a sulfur-containing molecule (hydrogen sulfide, sulfur, sulfite, thiosulfate, and various polythionates) is oxidized.
aerobic respiration, using sulphur or sulphate as electron donor
aerobic respiration, using sulfur or sulfate as electron donor
The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.
aromatic hydrocarbon biosynthetic process
The chemical reactions and pathways involving a protein. Includes protein modification.
protein metabolic process and modification
multicellular organismal protein metabolic process
Any process involved in the maintenance of an internal steady state at the level of the cell.
The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
The directed movement of one-carbon compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.
A reproduction process that creates a new organism by combining the genetic material of two gametes, which may come from two organisms or from a single organism, in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two gametes join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny.
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.
The formation of the prechordal plate. The prechordal plate is a thickening of the endoderm at the cranial end of the primitive streak formed by the involution of Spemann's organizer cells. The prechordal plate and the notochord induce the formation of the neural plate from the overlying ectodermal cells.
The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues.
The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of ventral spinal cord interneurons. Ventral spinal cord interneurons are cells located in the ventral portion of the spinal cord that transmit signals between sensory and motor neurons and are required for reflexive responses. Differentiation includes the processes involved in commitment of a cell to a specific fate.
ventral spinal cord interneuron differentiation
The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the spinal cord. Differentiation includes the processes involved in commitment of a cell to a specific fate.
The process whose specific outcome is the progression of the ventral region of the spinal cord over time, from its formation to the mature structure. The neurons of the ventral region of the mature spinal cord participate in motor output.
The process in which neuroepithelial cells in the ventral neural tube acquire specialized structural and/or functional features of motor neurons. Motor neurons innervate an effector (muscle or glandular) tissue and are responsible for transmission of motor impulses from the brain to the periphery. Differentiation includes the processes involved in commitment of a cell to a specific fate.
spinal cord motor neuron differentiation
The regionalization process that regulates the coordinated growth that establishes the non-random spatial arrangement of the neural tube.
The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mature cells of the hindbrain. Differentiation includes the processes involved in commitment of a cell to a specific fate.
The multiplication or reproduction of cells, resulting in the expansion of a cell population in the hindbrain.
The orderly movement of a cell that will reside in the hindbrain.
The process whose specific outcome is the progression of the cranial nerves over time, from its formation to the mature structure. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions.
The process whose specific outcome is the progression of the rhombomere over time, from its formation to the mature structure. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates.
The regionalization process that gives rise to the midbrain-hindbrain boundary. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate.
midbrain-hindbrain boundary biosynthesis
The process whose specific outcome is the progression of the pons over time, from its formation to the mature structure. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum.
The process whose specific outcome is the progression of the medulla oblongata over time, from its formation to the mature structure. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate.
The process in which the anatomical structure of the central nervous system is generated and organized. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
The process in which the anatomical structure of the midbrain-hindbrain boundary is generated and organized. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate.
midbrain-hindbrain boundary morphogenesis
The process that gives rise to the central nervous system. This process pertains to the initial formation of a structure from unspecified parts. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain, spinal cord and spinal nerves. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
The process whose specific outcome is the progression of the trigeminal nerve over time, from its formation to the mature structure. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae.
The process in which the anatomical structure of the hindbrain is generated and organized. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions.
The process that gives rise to the hindbrain. This process pertains to the initial formation of a structure from unspecified parts. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions.
The process in which the anatomical structure of the medulla oblongata is generated and organized. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate.
The process that gives rise to the medulla oblongata. This process pertains to the initial formation of a structure from unspecified parts. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate.
The process in which the anatomical structure of the pons is generated and organized. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum.
The process that gives rise to the pons. This process pertains to the initial formation of a structure from unspecified parts. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum.
The process in which the anatomical structure of the rhombomere is generated and organized. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates.
The process that gives rise to the rhombomere. This process pertains to the initial formation of a structure from unspecified parts. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates.
The process in which the anatomical structure of the cranial nerves are generated and organized. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions.
The process that gives rise to the cranial nerves. This process pertains to the initial formation of a structure from unspecified parts. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions.
The process in which the anatomical structure of the trigeminal nerve is generated and organized. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae.
The process that gives rise to the trigeminal nerve. This process pertains to the initial formation of a structure from unspecified parts. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae.
The process that gives rise to a rhombomere boundary. This process pertains to the initial formation of a boundary delimiting a rhombomere. Rhombomeres are transverse segments of the developing rhombencephalon that are lineage restricted, express different genes from one another, and adopt different developmental fates. Rhombomeres are numbered in anterior to posterior order.
The process whose specific outcome is the progression of a nerve over time, from its formation to the mature structure.
The process whose specific outcome is the progression of the locus ceruleus over time, from its formation to the mature structure. The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic.
The process in which the anatomical structure of the locus ceruleus is generated and organized. In mice, the locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic.
The process that gives rise to the locus ceruleus. This process pertains to the initial formation of a structure from unspecified parts. In mice, the locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic.
The process whose specific outcome is the progression of the superior olivary nucleus over time, from its formation to the mature structure. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound.
The process in which the anatomical structure of the superior olivary nucleus is generated and organized. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound.
The process that gives rise to the superior olivary nucleus. This process pertains to the initial formation of a structure from unspecified parts. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound.
The process whose specific outcome is the progression of a salivary nucleus over time, from its formation to the mature structure.
The process whose specific outcome is the progression of the superior salivary nucleus over time, from its formation to the mature structure.
The process aimed at the progression of a glial cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
The process in which the neural tube is divided into specific regions along the rostrocaudal axis.
anterior-posterior neural tube patterning
The process whose specific outcome is the formation of the hindbrain-spinal cord boundary.
hindbrain-spinal cord boundary formation
The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium.
The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the central nervous system.
central nervous system neuron differentiation
The process whose specific outcome is the progression of a neuron whose cell body is located in the central nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron.
central nervous system neuron development
The formation of the flat, thickened layer of ectodermal cells known as the neural plate. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system.
The process that regulates the coordinated growth and differentiation that establishes the non-random anterior-posterior spatial arrangement of the neural plate.
neural plate anterior/posterior pattern formation
neural plate anterior/posterior regionalization
Generation of cells within the nervous system.
The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes in the central nervous system. The capillary endothelial cells in the brain are specialized to form the blood-brain barrier.
The movement of a cell within a rhombomere. This process is known to occur as an early step in the generation of anatomical structure from a rhombomere.
The process whose specific outcome is the progression of the metencephalon over time, from its formation to the mature structure.
The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.
The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere.
A cellular process that results in the breakdown of a cellular component.
cellular component disassembly at cellular level
A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism.
reproductive cellular process in multicellular organism
cellular process involved in reproduction in multicellular organism
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.
A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis.
regulation of anatomical structure morphogenesis
Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized.
negative regulation of cell shape and cell size
positive regulation of cell shape and cell size
The aggregation, arrangement and bonding together of a cellular component.
cellular component assembly at cellular level
The process in which the anatomical structures of a gland are generated and organized.
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex.
ribonucleoprotein complex biogenesis and assembly
A process that results in the breakdown of the extracellular matrix.
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.
Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another.
regulation of gene expression as a consequence of signal transmission
signal transduction involved in regulation of gene expression
Any process that modulates the frequency, rate or extent of a signaling process.
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
Any process that activates, maintains or increases the frequency, rate or extent of a signaling process.
positive regulation of signalling process
positive regulation of signaling process
Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.
negative regulation of signaling process
negative regulation of signalling process
The process in which a signal is secreted or discharged into the extracellular medium from a cellular source.
The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism.
The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
cell projection organization and biogenesis
cell surface structure organization and biogenesis
Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
actin cytoskeleton organization and biogenesis
A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella.
The regulated release of a peptide hormone from a cell.
The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.
constitutive secretory pathway transport vesicle
Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'secretory granule ; GO:0030141'.
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
The process in which a relatively unspecialized cell acquires specialized features of a neuron.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
extracellular matrix organization and biogenesis
Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix.
The chemical reactions and pathways involving glycosaminoglycans, any of a group of polysaccharides that contain amino sugars.
The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
The chemical reactions and pathways resulting in the formation of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte.
Formation of myofibrils, the repeating units of striated muscle.
Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
Binding to a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
polysaccharide assembly with MHC class II protein complex
The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis.
The compaction of chromatin during apoptosis.
The breakdown of the nucleus into small membrane-bounded compartments, or blebs, each of which contain compacted DNA.
nuclear fragmentation involved in apoptotic nuclear change
Any process that modulates the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
Any process that stops, prevents, or reduces the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
negative regulation of bone biosynthesis
Any process that activates or increases the frequency, rate, extent or direction of cell growth.
Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space.
The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'.
The process whose specific outcome is the progression of the respiratory tube over time, from its formation to the mature structure. The respiratory tube is assumed to mean any tube in the respiratory tract.
The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
Any process that modulates the frequency, rate or extent of cell migration.
Any process that activates or increases the frequency, rate or extent of cell migration.
Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
The controlled breakdown of any cell membrane in the context of a normal process such as autophagy.
The directed movement of the nucleus along microtubules within the cell, mediated by motor proteins.
microtubule cytoskeleton-dependent nuclear positioning
microtubule cytoskeleton-dependent nucleus positioning
microtubule-dependent nuclear positioning
microtubule-dependent nucleus positioning
transport of nucleus, microtubule-mediated
The contractile fiber of smooth muscle cells.
The lipid bilayer surrounding a transport vesicle.
constitutive secretory pathway transport vesicle membrane
The lipid bilayer surrounding a cytoplasmic vesicle.
The lipid bilayer surrounding a vesicle associated with the Golgi apparatus.
The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell.
cytoskeleton-dependent intracellular transport
The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
Any process that modulates the frequency, rate or extent of epithelial cell differentiation.
regulation of epithelial cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell differentiation.
down regulation of epithelial cell differentiation
down-regulation of epithelial cell differentiation
downregulation of epithelial cell differentiation
inhibition of epithelial cell differentiation
negative regulation of epithelial cell differentiation
Any process that activates or increases the frequency, rate or extent of epithelial cell differentiation.
up regulation of epithelial cell differentiation
up-regulation of epithelial cell differentiation
upregulation of epithelial cell differentiation
activation of epithelial cell differentiation
stimulation of epithelial cell differentiation
positive regulation of epithelial cell differentiation
The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles).
The process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure. The hindbrain is the posterior of the three primary divisions of the developing chordate brain, or the corresponding part of the adult brain (in vertebrates, includes the cerebellum, pons, and medulla oblongata and controls the autonomic functions and equilibrium).
The process whose specific outcome is the progression of the notochord over time, from its formation to the mature structure. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column.
The process whose specific outcome is the progression of the midbrain-hindbrain boundary over time, from its formation to the mature structure. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages.
isthmomesencephalic boundary development
midbrain-hindbrain orgainizer development
A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules.
Note that we deem cilia and microtubule-based flagella to be equivalent.
A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin. The myosin may be organized into filaments.
actomyosin structure organization and biogenesis
Note that this term is a child of 'actin cytoskeleton organization and biogenesis ; GO:0030036' because the actin cytoskeleton is defined as actin filaments and associated proteins.
The process occurring during the embryonic phase whose specific outcome is the progression of the eye over time, from its formation to the mature structure.
A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
Assembly or disassembly of microtubules by the addition or removal of tubulin heterodimers from a microtubule.
microtubule polymerization or depolymerization
Any process that modulates the frequency, rate or extent of microtubule polymerization or depolymerization by the addition or removal of tubulin heterodimers from a microtubule.
regulation of microtubule polymerization or depolymerization
Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization or depolymerization.
down regulation of microtubule polymerization or depolymerization
down-regulation of microtubule polymerization or depolymerization
downregulation of microtubule polymerization or depolymerization
inhibition of microtubule polymerization or depolymerization
negative regulation of microtubule polymerization or depolymerization
Any process that activates or increases the frequency, rate or extent of microtubule polymerization or depolymerization.
up regulation of microtubule polymerization or depolymerization
up-regulation of microtubule polymerization or depolymerization
upregulation of microtubule polymerization or depolymerization
activation of microtubule polymerization or depolymerization
stimulation of microtubule polymerization or depolymerization
positive regulation of microtubule polymerization or depolymerization
Any process that modulates the frequency, rate or extent of microtubule polymerization.
regulation of microtubule polymerization
Any process that modulates the frequency, rate or extent of microtubule depolymerization.
regulation of microtubule depolymerization
Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization.
down regulation of microtubule polymerization
down-regulation of microtubule polymerization
downregulation of microtubule polymerization
inhibition of microtubule polymerization
negative regulation of microtubule polymerization
Any process that activates or increases the frequency, rate or extent of microtubule polymerization.
up regulation of microtubule polymerization
up-regulation of microtubule polymerization
upregulation of microtubule polymerization
activation of microtubule polymerization
stimulation of microtubule polymerization
positive regulation of microtubule polymerization
Any process that activates or increases the frequency, rate or extent of microtubule depolymerization.
positive regulation of microtubule disassembly
up regulation of microtubule depolymerization
up-regulation of microtubule depolymerization
upregulation of microtubule depolymerization
activation of microtubule depolymerization
positive regulation of microtubule catastrophe
stimulation of microtubule depolymerization
positive regulation of microtubule depolymerization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures formed of microtubules and associated proteins in the cytoplasm of a cell.
cytoplasmic microtubule organization and biogenesis
The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
The area of a motile cell closest to the direction of movement.
The portion of the plasma membrane surrounding a plasma membrane bounded cell surface projection.
The portion of the plasma membrane surrounding the leading edge of a motile cell.
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 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.
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
negative 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.
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
positive regulation of cellular metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
regulation of cellular biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
down regulation of cellular biosynthetic process
down-regulation of cellular biosynthetic process
downregulation of cellular biosynthetic process
negative regulation of cellular anabolism
negative regulation of cellular biosynthesis
negative regulation of cellular formation
negative regulation of cellular synthesis
inhibition of cellular biosynthetic process
negative regulation of cellular biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
positive regulation of cellular anabolism
positive regulation of cellular biosynthesis
positive regulation of cellular formation
positive regulation of cellular synthesis
up regulation of cellular biosynthetic process
up-regulation of cellular biosynthetic process
upregulation of cellular biosynthetic process
activation of cellular biosynthetic process
stimulation of cellular biosynthetic process
positive regulation of cellular biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly.
down regulation of protein complex assembly
down-regulation of protein complex assembly
downregulation of protein complex assembly
negative regulation of protein complex assembly
negative regulation of protein-containing complex assembly
Any process that activates or increases the frequency, rate or extent of protein complex assembly.
up regulation of protein complex assembly
up-regulation of protein complex assembly
upregulation of protein complex assembly
positive regulation of protein complex assembly
positive regulation of protein-containing complex assembly
Any process that modulates the frequency, rate or extent of vesicle fusion.
Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion.
Any process that activates or increases the frequency, rate or extent of vesicle fusion.
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.
regulation of cell projection organisation
regulation of cell projection organization and biogenesis
regulation of cell projection 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 projections.
down regulation of cell projection organization
down-regulation of cell projection organization
downregulation of cell projection organization
negative regulation of cell projection organisation
inhibition of cell projection organization
negative regulation of cell projection organization and biogenesis
negative regulation of cell projection organization
Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.
positive regulation of cell projection organisation
up regulation of cell projection organization
up-regulation of cell projection organization
upregulation of cell projection organization
activation of cell projection organization
stimulation of cell projection organization
positive regulation of cell projection organization and biogenesis
positive regulation of cell projection organization
Binding to a carboxylic acid, an organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
A vesicle found in the cytoplasm of a cell.
Any process that modulates the frequency, rate, extent or location of heterochromatin formation.
Any process that stops, prevents, or reduces the frequency, rate or extent of heterochromatin formation.
down regulation of heterochromatin formation
down-regulation of heterochromatin formation
downregulation of heterochromatin formation
negative regulation of heterochromatin formation
negative regulation of heterochromatin assembly
Any process that activates or increases the frequency, rate or extent of heterochromatin formation.
positive regulation of heterochromatin formation
up regulation of heterochromatin formation
up-regulation of heterochromatin formation
upregulation of heterochromatin formation
stimulation of heterochromatin formation
positive regulation of heterochromatin assembly
The assembly of DNA, histone proteins, other associated proteins, and sometimes RNA, into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.
The controlled breakdown of chromatin from a higher order structure into its simpler subcomponents, DNA, histones, other proteins, and sometimes RNA.
A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location.
establishment and maintenance of protein complex localization
cellular protein-containing complex localization
establishment and maintenance of cellular protein complex localization
An epigenetic gene silencing mechanism that involves the assembly of chromatin into heterochromatin, resulting in a chromatin conformation refractory to transcription. This process starts with heterochromatin nucleation, its spreading, and ends with heterochromatin boundary formation.
establishment of heterochromatin architecture
establishment of heterochromatin architecture involved in chromatin silencing at centromere outer repeat region
establishment of heterochromatin architecture involved in chromatin silencing at pericentric region
heterochromatin assembly involved in chromatin silencing at centromere outer repeat region
heterochromatin assembly involved in chromatin silencing at pericentric region
heterochromatin formation involved in chromatin silencing at centromere outer repeat region
heterochromatin formation involved in chromatin silencing at pericentric region
establishment of heterochromatic silencing
heterochromatin assembly involved in chromatin silencing
heterochromatin formation involved in chromatin silencing
The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
In vertebrates, the term 'neuromuscular junction' is limited to synapses targeting skeletal muscle fibers - all of which are cholinergic and excitatory. Both inhibitory and excitatory neuromuscular junctions exist in invertebrates, utilizing a range of neurotransmitters including glutamate, GABA and 5-HT.
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 system process
regulation of neurophysiological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process.
negative regulation of neurological process
negative regulation of neurological system process
negative regulation of neurophysiological process
negative regulation of nervous system process
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
positive regulation of nervous system process
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes.
The outer, i.e. cytoplasm-facing in a cellular organelle, lipid bilayer of an organelle envelope.
The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen.
A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers.
The volume enclosed by the nuclear inner membrane.
Any small, fluid-filled, spherical organelle enclosed by membrane.
A cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Blebs are formed during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses.
The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses.
Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
Any process that activates or increases the frequency, rate or extent of protein binding.
Any process that modulates the frequency, rate or extent of a response to an external stimulus.
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.
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
negative regulation of response to external stimulus
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
positive regulation of response to external stimulus
Any process that modulates the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
regulation of nucleobase-containing compound transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
down regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
downregulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
inhibition of nucleobase, nucleoside, nucleotide and nucleic acid transport
negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
negative regulation of nucleobase-containing compound transport
Any process that activates or increases the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
up regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
upregulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
activation of nucleobase, nucleoside, nucleotide and nucleic acid transport
stimulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
positive regulation of nucleobase-containing compound transport
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
regulation of cellular protein metabolism
regulation of cellular protein metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
down regulation of cellular protein metabolic process
down-regulation of cellular protein metabolic process
downregulation of cellular protein metabolic process
negative regulation of cellular protein metabolism
inhibition of cellular protein metabolic process
negative regulation of cellular protein metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
positive regulation of cellular protein metabolism
up regulation of cellular protein metabolic process
up-regulation of cellular protein metabolic process
upregulation of cellular protein metabolic process
activation of cellular protein metabolic process
stimulation of cellular protein metabolic process
positive regulation of cellular protein metabolic process
Any process that modulates the frequency, rate or extent of the process of creating protein polymers.
Any process that stops, prevents, or reduces the frequency, rate or extent of the process of creating protein polymers.
down regulation of protein polymerization
down-regulation of protein polymerization
downregulation of protein polymerization
negative regulation of protein polymerization
Any process that activates or increases the frequency, rate or extent of the process of creating protein polymers.
positive regulation of protein polymerization
Any process that modulates the frequency, rate or extent of chondrocyte differentiation.
regulation of chondrocyte differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of chondrocyte differentiation.
down regulation of chondrocyte differentiation
down-regulation of chondrocyte differentiation
downregulation of chondrocyte differentiation
inhibition of chondrocyte differentiation
negative regulation of chondrocyte differentiation
Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation.
up regulation of chondrocyte differentiation
up-regulation of chondrocyte differentiation
upregulation of chondrocyte differentiation
activation of chondrocyte differentiation
stimulation of chondrocyte differentiation
positive regulation of chondrocyte differentiation
The directed movement of lipids within cells.
Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells.
regulation of intracellular lipid transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells.
down regulation of intracellular lipid transport
down-regulation of intracellular lipid transport
downregulation of intracellular lipid transport
inhibition of intracellular lipid transport
negative regulation of intracellular lipid transport
Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells.
up regulation of intracellular lipid transport
up-regulation of intracellular lipid transport
upregulation of intracellular lipid transport
activation of intracellular lipid transport
stimulation of intracellular lipid transport
positive regulation of intracellular lipid transport
Any process that modulates the frequency, rate or extent of the directed movement of substances within cells.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells.
down regulation of intracellular transport
down-regulation of intracellular transport
downregulation of intracellular transport
negative regulation of intracellular transport
Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells.
up regulation of intracellular transport
up-regulation of intracellular transport
positive regulation of intracellular transport
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
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.
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.
The portion of the plasma membrane surrounding a neuron projection.
The directed movement of a protein from one location to another within a lipid bilayer.
The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication.
Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study.
The disaggregation of a ribosome into its constituent components; includes the dissociation of ribosomal subunits.
All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection.
plasma membrane bounded cell projection cytoplasm
Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion.
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
regulation of cellular protein localisation
regulation of cellular protein localization
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving polysaccharides.
regulation of polysaccharide metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of polysaccharides.
regulation of polysaccharide biosynthetic process
Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton.
Any process that modulates the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
down regulation of organic acid transport
down-regulation of organic acid transport
downregulation of organic acid transport
negative regulation of organic acid transport
Any process that activates or increases the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
positive regulation of organic acid transport
The controlled release of a substance by a cell.
The expansion of a mononuclear cell population by cell division. A mononuclear cell is a leukocyte with a single non-segmented nucleus in the mature form.
peripheral blood mononuclear cell proliferation
Any process that modulates the frequency, rate or extent of mononuclear cell proliferation.
regulation of peripheral blood mononuclear cell proliferation
regulation of mononuclear cell proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of mononuclear cell proliferation.
negative regulation of PBMC proliferation
negative regulation of peripheral blood mononuclear cell proliferation
negative regulation of mononuclear cell proliferation
Any process that activates or increases the frequency, rate or extent of mononuclear cell proliferation.
up regulation of mononuclear cell proliferation
up-regulation of mononuclear cell proliferation
upregulation of mononuclear cell proliferation
activation of mononuclear cell proliferation
positive regulation of PBMC proliferation
positive regulation of peripheral blood mononuclear cell proliferation
stimulation of mononuclear cell proliferation
positive regulation of mononuclear cell proliferation
Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
regulation of actin cytoskeleton organisation
regulation of actin cytoskeleton organization and biogenesis
regulation of actin cytoskeleton organization
The chemical reactions and pathways involving collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
The chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
regulation of collagen biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
negative regulation of collagen anabolism
negative regulation of collagen biosynthesis
negative regulation of collagen formation
negative regulation of collagen synthesis
negative regulation of collagen biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
positive regulation of collagen anabolism
positive regulation of collagen biosynthesis
positive regulation of collagen formation
positive regulation of collagen synthesis
positive regulation of collagen biosynthetic process
Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the actin cytoskeleton.
regulation of actin filament-based process
The disaggregation of a protein-containing macromolecular complex into its constituent components.
cellular macromolecule complex disassembly
The disaggregation of a protein-RNA complex into its constituent components.
The process in which cellular structures, including whole cells or cell parts, are generated and organized.
The process in which the anatomical structures of a cell part are generated and organized.
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
The expansion of a muscle cell population by cell division.
Any apoptotic process in a myeloid cell, a cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
Any process that modulates the frequency, rate, or extent of myeloid cell apoptotic process.
regulation of myeloid cell apoptotic process
Any process that stops, prevents, or reduces the frequency, rate, or extent of a myeloid cell apoptotic process.
down regulation of myeloid cell apoptosis
down-regulation of myeloid cell apoptosis
downregulation of myeloid cell apoptosis
negative regulation of myeloid cell apoptosis
negative regulation of myeloid cell apoptotic process
Any process that activates or increases the frequency, rate, or extent of myeloid cell apoptotic process.
positive regulation of myeloid cell apoptosis
positive regulation of myeloid cell apoptotic process
Any process in which a macromolecule is transported to, or maintained in, a specific location.
Any process in which a polysaccharide is transported to, or maintained in, a specific location.
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 organization and biogenesis
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome.
regulation of chromosome organization and biogenesis
Any process that modulates the frequency, rate or extent of sister chromatid segregation.
regulation of sister chromatid segregation
Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation.
negative regulation of sister chromatid segregation
Any process that modulates the frequency, rate or extent of sister chromatid segregation during mitosis.
regulation of mitotic sister chromatid segregation
Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation during mitosis.
negative regulation of mitotic sister chromatid segregation
The deposition or aggregation of coloring matter in a cell.
Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells.
regulation of intracellular protein transport
Binding to an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines.
regulation of cellular amine metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines.
negative regulation of cellular amine metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines.
positive regulation of cellular amine metabolic process
The multiplication or reproduction of cells, resulting in the expansion of a cell population in the midbrain.
Any process that modulates the frequency, rate or extent of collagen binding.
Any process that stops, prevents, or reduces the frequency, rate or extent of collagen binding.
Any process that activates or increases the frequency, rate or extent of collagen binding.
A process in which a protein is transported to, or maintained in, a location within an organelle.
Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a catecholamine.
down regulation of catecholamine secretion
down-regulation of catecholamine secretion
downregulation of catecholamine secretion
negative regulation of catecholamine secretion
Any process that activates or increases the frequency, rate or extent of the regulated release of a catecholamine.
up regulation of catecholamine secretion
up-regulation of catecholamine secretion
positive regulation of catecholamine secretion
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.
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.
The chemical reactions and pathways resulting in the formation of polysaccharides, polymers of many (typically more than 10) monosaccharide residues linked glycosidically, occurring at the level of an individual cell.
cellular polysaccharide biosynthetic process
A process that forms a boundary that limits the spreading of heterochromatin along a chromosome.
regulation of extent of heterochromatin formation
maintenance of heterochromatin boundaries
negative regulation of extent of heterochromatin assembly
negative regulation of extent of heterochromatin formation
negative regulation of heterochromatin spreading
regulation of extent of heterochromatin assembly
A process in which a ribosome is transported to, and/or maintained in, a specific location.
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 glucagon 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 lipid stimulus.
A process in which a protein is transported to, or maintained in, a location within the Golgi apparatus.
establishment of protein localisation to Golgi
establishment of protein localization in Golgi
establishment of protein localization to Golgi
establishment of protein localization to Golgi apparatus
Any process of regulating the production and elimination of erythrocytes within an organism.
Any process that decreases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
negative regulation of syncytium formation by plasma membrane fusion
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides.
regulation of cellular amide metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amides.
negative regulation of cellular amide metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amides.
positive regulation of cellular amide metabolic process
A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a cell junction.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix.
Any apoptotic process in a glial cell, a non-neuronal cell of the nervous system.
glial cell programmed cell death by apoptosis
programmed cell death of glia by apoptosis
programmed cell death of glial cells by apoptosis
Any process that modulates the frequency, rate, or extent of glial cell apoptotic process.
regulation of glial cell apoptotic process
Any process that stops, prevents, or reduces the frequency, rate, or extent of glial cell apoptotic process.
negative regulation of glial cell apoptosis
negative regulation of glial cell apoptotic process
Any process that activates or increases the frequency, rate, or extent of glial cell apoptotic process.
positive regulation of glial cell apoptosis
positive regulation of glial cell apoptotic process
Any apoptotic process in a smooth muscle cell. Smooth muscle consists of non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels.
programmed cell death of smooth muscle cells by apoptosis
programmed cell death, smooth muscle cells
smooth muscle cell programmed cell death by apoptosis
Any process that modulates the frequency, rate, or extent of smooth muscle cell apoptotic process.
regulation of smooth muscle cell apoptosis
regulation of smooth muscle cell apoptotic process
Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell apoptotic process.
down regulation of smooth muscle cell apoptosis
down-regulation of smooth muscle cell apoptosis
downregulation of smooth muscle cell apoptosis
inhibition of smooth muscle cell apoptosis
negative regulation of smooth muscle cell apoptosis
negative regulation of smooth muscle cell apoptotic process
Any process that activates or increases the frequency, rate, or extent of smooth muscle cell apoptotic process.
up regulation of smooth muscle cell apoptosis
up-regulation of smooth muscle cell apoptosis
upregulation of smooth muscle cell apoptosis
activation of smooth muscle cell apoptosis
positive regulation of smooth muscle cell apoptosis
stimulation of smooth muscle cell apoptosis
positive regulation of smooth muscle cell apoptotic process
The directed movement of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process in which a protein is transported to, or maintained at, a specific location on a chromosome.
A process in which a protein transports or maintains the localization of another protein to the nucleus.
Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, carried out by individual cells.
cellular carbohydrate biosynthetic process
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
cellular nitrogen compound metabolic process
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells.
cellular biopolymer biosynthetic process
cellular macromolecule biosynthetic process
The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase, nucleoside, nucleotide and nucleic acid anabolism
nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis
nucleobase, nucleoside, nucleotide and nucleic acid formation
nucleobase, nucleoside, nucleotide and nucleic acid synthesis
nucleobase-containing compound biosynthetic process
The controlled breakdown of the basement membrane in the context of a normal process such as imaginal disc eversion.
Note that this term has no relationship to 'membrane disassembly ; GO:0030397' because the basement membrane is not a lipid bilayer.
The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field.
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell that will form part of the cardiac organ of an individual.
The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
Note that cilia and eukaryotic flagella are deemed to be equivalent.
The process in which the anatomical structures of appendages are generated and organized. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch.
The process in which the anatomical structures of genitalia are generated and organized. The genitalia are the organs of reproduction or generation, external and internal.
Creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow.
lumen formation in an anatomical structure
The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex.
Programmed cell death of an errant germ line cell that is outside the normal migratory path or ectopic to the gonad. This is an important mechanism of regulating germ cell survival within the embryo.
programmed cell death of ectopic germ cells
programmed cell death, ectopic germ cells
The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
The process in which the anatomical structures of the internal genitalia are generated and organized. The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals.
The process in which the anatomical structures of the external genitalia are generated and organized. The external genitalia are the outer sex organs, such as the penis or vulva in mammals.
The process in which the anatomical structures of the gonads are generated and organized. A gonad is an animal organ producing gametes, e.g. the testes or the ovary in mammals.
The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function.
Progression of the endocrine system over time, from its formation to a mature structure. The endocrine system is a system of hormones and ductless glands, where the glands release hormones directly into the blood, lymph or other intercellular fluid, and the hormones circulate within the body to affect distant organs. The major glands that make up the human endocrine system are the hypothalamus, pituitary, thyroid, parathryoids, adrenals, pineal body, and the reproductive glands which include the ovaries and testes.
Progression of the exocrine system over time, from its formation to a mature structure. The exocrine system is a system of hormones and glands, where the glands secrete straight to a target site via ducts or tubes. The human exocrine system includes the salivary glands, sweat glands and many glands of the digestive system.
The regionalization process that divides an organism or part of an organism into a series of semi-repetitive parts, or segments, often arranged along a longitudinal axis.
The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts.
A process in which a protein is transported to, or maintained at, a microtubule.
Any process in which a protein is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.
The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form de novo blood vessels and tubes.
cell migration involved in vasculogenesis
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
intracellular signal transduction pathway
signal transmission via intracellular cascade
signal transduction via intracellular signaling cascade
Any process that modulates the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
Any process that stops or reduces the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
negative regulation of chromatin binding
Any process that increases the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
positive regulation of chromatin binding
The directed movement of a protein to a specific location within the extracellular region.
establishment of protein localisation in extracellular region
establishment of protein localization in extracellular region
establishment of protein localization to extracellular region
OBSOLETE. The transfer of information between living organisms.
This term was obsoleted because it was a grouping term but had no subclasses.
The transfer of information occurring at the level of a multicellular organism.
The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly.
intraciliary transport involved in cilium morphogenesis
intraflagellar transport involved in cilium morphogenesis
intraciliary transport involved in cilium assembly
The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to compound eye morphogenesis.
cell proliferation involved in compound eye morphogenesis
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an angioblast cell. Angioblasts are one of the two products formed from hemangioblast cells (the other being pluripotent hemopoietic stem cells).
angioblastic mesenchymal cell differentiation
The process in which an organism effects a change in the structure or processes of another organism.
modification of morphology or physiology of other organism
regulation of morphology of other organism
regulation of physiological process of other organism
regulation of physiology of other organism
regulation of morphology or physiology of other organism
modulation of process of another organism
The chemical reactions and pathways involving an indole alkaloid, an alkaloid containing an indole skeleton.
The chemical reactions and pathways resulting in the formation of an indole alkaloid, an alkaloid containing an indole skeleton.
The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow.
A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm.
Depending on the species, this region may have a distinct geometrically shaped electron-dense structure within the axonemal lumen visible in electron microscopy images; most animals don't display this inner structure. The axoneme extends through the ciliary transition zone, but only consists of the outer doublets. The central pair, axonemal spokes, and dynein complexes are not found in this part of the ciliary shaft. Note that the connecting cilium of the photoreceptor cells is thought to be equivalent to the transition zone.
The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of an enteroendocrine cell. Enteroendocrine cells are hormonally active epithelial cells in the gut that constitute the diffuse neuroendocrine system.
The process in which a relatively unspecialized cell acquires specialized features of a vascular smooth muscle cell.
vascular smooth muscle cell differentiation
vascular associated smooth muscle cell differentiation
The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell surrounding the aorta.
aortic smooth muscle cell differentiation
The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body.
The progression of the descending aorta over time, from its initial formation to the mature structure. The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries. In a two-pass circulatory system blood passes twice through the heart to supply the body once.
The progression of the dorsal aorta over time, from its initial formation to the mature structure. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once.
The process in which the anatomical structures of an aorta are generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body.
The process in which the anatomical structures of the descending aorta are generated and organized. The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries. In a two-pass circulatory system blood passes twice through the heart to supply the body once.
The process in which the anatomical structures of the dorsal aorta are generated and organized. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once.
The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle.
The regulated release of any steroid that acts as a hormone into the circulatory system.
The regulated release of an androgen into the circulatory system. Androgens are steroid hormones that stimulate or control the development and maintenance of masculine characteristics in vertebrates.
The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
The process whose specific outcome is the progression of a tendon over time, from its formation to the mature structure. A tendon is a fibrous, strong, connective tissue that connects muscle to bone or integument and is capable of withstanding tension. Tendons and muscles work together to exert a pulling force.
The process that gives rise to a tendon. This process pertains to the initial formation of a tendon from unspecified parts.
The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance, that does not require the replacement of preexisting tissues.
The multiplication or reproduction of germ cells, reproductive cells in multicellular organisms, resulting in the expansion of a cell population.
Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule.
Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
A prolongation or process extending from a muscle cell. A muscle cell is a mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
The portion of the plasma membrane surrounding a muscle cell projection.
Any biological process involved in the maintenance of the steady-state number of epidermal stem cells within a population of cells.
A form of mutualism between a fungus and the roots of a vascular plant, where hyphae of the fungus penetrate the plant cell wall and invaginate its cell membrane. Once inside, the fungus forms highly branched structures for nutrient exchange with the plant called arbuscules. Aids in the acquisition by the plant of nutrients such as phosphorus from the soil.
The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon.
The joining of two lipid bilayers that surround the Golgi apparatus to form a single Golgi membrane.
membrane fusion involved in Golgi reassembly
The increase in size or mass of an entire organism, a part of an organism or a cell.
See also the biological process term 'cell growth ; GO:0016049'.
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.
Self-propelled movement of a cell or organism from one location to another.
Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.
Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism.
Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
regulation of multicellular organism growth
Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organism to reach its usual body size.
negative regulation of multicellular organism growth
The first few specialized divisions of an activated animal egg.
Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism.
Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size.
positive regulation of multicellular organism growth
Any process that activates or increases the frequency, rate or extent of embryonic development.
positive regulation of embryonic development
A process that modulates the frequency, rate or extent of gene expression by remodelling of chromatin by either modifying the chromatin fiber, the nucleosomal histones, or the DNA. Once established, this regulation may be maintained over many cell divisions. It can also be heritable in the absence of the instigating signal.
regulation of gene expression, epigenetic
Any process that modulates the consistent predetermined time point at which an integrated living unit or organism progresses from an initial condition to a later condition and the rate at which this time point is reached.
regulation of development, heterochronic
The process that results in the generation of glial cells. This includes the production of glial progenitors and their differentiation into mature glia.
Growth of glial cells, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catecholamines.
regulation of catecholamine metabolic process
The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins.
intraflagellar transport involved in cilium organization
intraflagellar transport involved in microtubule-based flagellum organisation
Note that we deem cilium and microtubule-based flagellum to be equivalent.
The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression).
The self-renewing division of a germline stem cell to produce a daughter stem cell and a daughter germ cell, which will divide to form the gametes.
Any process that modulates the frequency, rate or extent of cell proliferation.
regulation of cell population proliferation
The continuous network of membranes encompassing the nuclear outer membrane and the endoplasmic reticulum membrane.
nuclear membrane-endoplasmic reticulum continuum
nuclear envelope-endoplasmic reticulum continuum
nuclear envelope-endoplasmic reticulum network
nuclear outer membrane-endoplasmic reticulum membrane network
The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
The chemical reactions and pathways resulting in the formation of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
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.
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
The aggregation, arrangement and bonding together of the mature ribosome and of its subunits.
Binding to a peptide, an organic compound comprising two or more amino acids linked by peptide bonds.
Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
The directed movement of a motile cell or organism in response to an external stimulus.
directed movement in response to stimulus
Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
The chemical reactions and pathways occurring at the level of individual cells resulting in the formation of any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters.
cellular biogenic amine biosynthetic process
The chemical reactions and pathways involving norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine.
The chemical reactions and pathways resulting in the formation of norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine.
The chemical reactions and pathways resulting in the formation of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
The chemical reactions and pathways resulting in the formation of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
The chemical reactions and pathways involving serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
The chemical reactions and pathways involving compounds that contain an indole (2,3-benzopyrrole) skeleton.
indole-containing compound metabolic process
The chemical reactions and pathways resulting in the formation of compounds that contain an indole (2,3-benzopyrrole) skeleton.
indole-containing compound biosynthetic process
Development of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light.
Development of a photoreceptor, a sensory cell in the eye that reacts to the presence of light. They usually contain a pigment that undergoes a chemical change when light is absorbed, thus stimulating a nerve.
Any process that modulates the frequency, rate or extent of eye photoreceptor development.
regulation of eye photoreceptor development
regulation of eye photoreceptor cell development
Any process that activates or increases the frequency, rate or extent of eye photoreceptor development.
positive regulation of eye photoreceptor development
up regulation of eye photoreceptor cell development
up-regulation of eye photoreceptor cell development
upregulation of eye photoreceptor cell development
activation of eye photoreceptor cell development
stimulation of eye photoreceptor cell development
positive regulation of eye photoreceptor cell development
Any process that stops, prevents, or reduces the frequency, rate or extent of eye photoreceptor development.
down regulation of eye photoreceptor cell development
down-regulation of eye photoreceptor cell development
downregulation of eye photoreceptor cell development
negative regulation of eye photoreceptor development
inhibition of eye photoreceptor cell development
negative regulation of eye photoreceptor cell development
Binding to an hormone, a naturally occurring substance secreted by specialized cells that affect the metabolism or behavior of cells possessing functional receptors for the hormone. Hormones may be produced by the same, or different, cell as express the receptor.
Any biological process involved in the maintenance of an internal steady state.
negative regulation of homeostatic process
positive regulation of homeostatic process
Any complex of actin, myosin, and accessory proteins.
The process in which a relatively unspecialized cell acquires the specialized features of a retinal cone cell.
The process in which a relatively unspecialized cell acquires specialized features of a muscle cell.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur.
The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the occurrence or rate of cell death by apoptotic process.
This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used.
A prolongation or process extending from a cell, e.g. a flagellum or axon.
Any process that modulates the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane.
regulation of Golgi to plasma membrane protein transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane.
down regulation of Golgi to plasma membrane protein transport
down-regulation of Golgi to plasma membrane protein transport
downregulation of Golgi to plasma membrane protein transport
inhibition of Golgi to plasma membrane protein transport
negative regulation of Golgi to plasma membrane protein transport
Any process that activates or increases the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane.
up regulation of Golgi to plasma membrane protein transport
up-regulation of Golgi to plasma membrane protein transport
upregulation of Golgi to plasma membrane protein transport
activation of Golgi to plasma membrane protein transport
stimulation of Golgi to plasma membrane protein transport
positive regulation of Golgi to plasma membrane protein transport
The directed movement of proteins from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane.
Golgi to plasma membrane protein transport
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching.
The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
Binding to a complex of RNA and protein.
The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections.
The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite.
extracellular structure organization and biogenesis
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is positively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used.
positive regulation of apoptotic process
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is negatively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used.
negative regulation of apoptotic process
Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
regulation of non-apoptotic programmed cell death
Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
positive regulation of non-apoptotic programmed cell death
positive regulation of programmed cell death
Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
down regulation of programmed cell death
down-regulation of programmed cell death
negative regulation of non-apoptotic programmed cell death
negative regulation of programmed cell death
The nucleus of a germ cell, a reproductive cell in multicellular organisms.
Any process that activates or increases the activity of an enzyme.
positive regulation of metalloenzyme activity
positive regulation of catalytic activity
Any process that stops or reduces the activity of an enzyme.
down-regulation of metalloenzyme activity
down regulation of metalloenzyme activity
downregulation of metalloenzyme activity
negative regulation of metalloenzyme activity
negative regulation of catalytic activity
Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location.
establishment and maintenance of translational machinery localization
establishment and maintenance of translational protein localization
regulation of translation by machinery localisation
regulation of translation by machinery localization
Binding to an ion, a charged atoms or groups of atoms.
Binding to an anion, a charged atom or group of atoms with a net negative charge.
Binding to a cation, a charged atom or group of atoms with a net positive charge.
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.
multicellular organismal macromolecule metabolic process
Binding to an amine, a weakly basic organic compound that contains an amino or a substituted amino group.
Binding to an organic acid, any acidic compound containing carbon in covalent linkage.
Binding to a vascular endothelial growth factor receptor 2.
vascular endothelial growth factor receptor 2 binding
Binding to sulfate, SO4(2-), a negatively charged small molecule.
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 amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
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 biotic stimulus, an external stimulus caused by, or produced by living things.
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi.
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
intracellular membrane-enclosed organelle
intracellular membrane-bounded organelle
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.
intracellular non-membrane-enclosed organelle
intracellular non-membrane-bounded organelle
The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen.
Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.
down regulation of protein complex disassembly
down-regulation of protein complex disassembly
downregulation of protein complex disassembly
inhibition of protein complex disassembly
negative regulation of protein complex disassembly
negative regulation of protein-containing complex disassembly
Any process that activates or increases the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.
up regulation of protein complex disassembly
up-regulation of protein complex disassembly
upregulation of protein complex disassembly
activation of protein complex disassembly
stimulation of protein complex disassembly
positive regulation of protein complex disassembly
positive regulation of protein-containing complex disassembly
Any process that modulates the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.
regulation of protein complex disassembly
regulation of protein-containing complex disassembly
Any process that modulates the frequency, rate or extent of protein complex assembly.
regulation of protein-containing complex assembly
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of carbohydrates.
regulation of carbohydrate biosynthetic process
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring outside the cell.
extracellular non-membrane-enclosed organelle
extracellular non-membrane-bounded organelle
Any process that modulates the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that activates or increases the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
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 alkaloid stimulus. Alkaloids are a large group of nitrogenous substances found in naturally in plants, many of which have extracts that are pharmacologically active.
Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle.
The process in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus.
enucleate red blood cell differentiation
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte with a nucleus, as found in non-mammalian vertebrates such as birds.
Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
Any process that modulates the frequency, rate or extent of protein binding.
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 peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
response to polypeptide hormone stimulus
The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
A process in which muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities.
Any process in which skeletal muscles change their phenotypic profiles in response to altered functional demands and a variety of signals.
Any process that modulates the frequency, rate or extent of muscle adaptation.
Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons.
regulation of apoptosis of neuronal cells
regulation of neuron programmed cell death
regulation of neuronal cell programmed cell death
regulation of programmed cell death of neuronal cells
regulation of programmed cell death, neurons
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
negative regulation of programmed cell death, neurons
negative regulation of neuron apoptotic process
Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
positive regulation of programmed cell death, neurons
positive regulation of neuron apoptotic process
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.
The oxidation of arsenite to arsenate, using oxygen (O2) as the electron acceptor. Arsenite oxidase provides electrons to an electron carrier which transfers them to oxygen utilizing respiratory systems.
aerobic respiration, using arsenite as electron donor
Any process that modulates the frequency, rate or extent of the process of gaseous exchange between an organism and its environment.
regulation of respiratory gaseous exchange
The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.
The process in which the anatomical structures of the skin are generated and organized. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner, sensitive and vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.
The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells.
The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.
cellular macromolecular complex organization
cellular macromolecular complex subunit organisation
cellular macromolecular complex subunit organization
macromolecular complex subunit organisation
macromolecular complex subunit organization
protein-containing complex subunit organization
OBSOLETE. A biosynthetic process - chemical reactions and pathways resulting in the formation of substances - which involves more than one organism.
This term was obsoleted because there is no evidence that this process exists.
obsolete multi-organism biosynthetic process
The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.
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.
Any process that modulates the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
Any process that modulates the frequency, rate or extent of an endocrine process, a process involving the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system.
Any process that modulates the frequency, rate or extent of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system.
regulation of respiratory system process
Any process that modulates the frequency, rate or extent of the directed movement of anions, atoms or small molecules with a net negative charge into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.
cellular component biogenesis at cellular level
Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component.
regulation of cellular component biogenesis
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole.
Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component.
positive regulation of cellular component biogenesis
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 a vacuole.
positive regulation of vacuole organisation
positive regulation of vacuole biogenesis
positive regulation of vacuole organization
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a membrane.
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.
negative 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.
positive regulation of molecular function
The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group, as carried out by individual cells. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).
translation initiation (ternary) complex
The chemical reactions and pathways by which individual cells transform chemical substances.
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.
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
cellular macromolecule metabolic process
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
main pathways of carbohydrate metabolic process
main pathways of carbohydrate metabolism
The chemical reactions and pathways involving polysaccharides, polymers of more than 10 monosaccharide residues joined by glycosidic linkages, as carried out by individual cells.
cellular polysaccharide metabolic process
The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.
cellular nitrogen compound biosynthetic process
The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.
The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
Any apoptotic process in a fibroblast, a connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules.
A process in which a protein is transported to, or maintained in, a location within the cytoskeleton.
OBSOLETE. Any process in which an organism within a multispecies community gains an advantage in growth or survival over another organism of a different species in that community.
This term was obsoleted because it is outside the scope of GO.
obsolete competition with other organism
A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.
symbiosis, encompassing mutualism through parasitism
symbiotic interaction between host and organism
biological process involved in symbiotic interaction
Any process evolved to enable an interaction with an organism of a different species.
interspecies interaction between organisms
interspecies interaction with other organisms
biological process involved in interspecies interaction between organisms
A biological process that directly contributes to the process of producing new individuals, involving another organism.
Any process that is carried out at the cellular level which involves another organism of the same or different species.
OBSOLETE. The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving more than one organism.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
microtubule-based flagellum organization
A protein complex that plays a role in the process of DNA packaging.
The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell.
The process whose specific outcome is the progression of the primary sexual characteristics over time, from their formation to the mature structures. The primary sexual characteristics are the testes in males and the ovaries in females and they develop in response to sex hormone secretion.
development of primary sexual characteristics
Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
The directed movement of a protein to a specific location.
The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-cell junction. A cell-cell junction is a specialized region of connection between two cells.
cell-cell junction assembly and maintenance
intercellular junction assembly and maintenance
The chemical reactions and pathways resulting in the formation of CD4, a CD marker that occurs on T-helper cells and is involved in MHC class II restricted interactions.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4.
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4.
positive regulation of CD4 biosynthetic process
up regulation of CD4 biosynthetic process
up-regulation of CD4 biosynthetic process
upregulation of CD4 biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4.
down regulation of CD4 biosynthetic process
down-regulation of CD4 biosynthetic process
downregulation of CD4 biosynthetic process
negative regulation of CD4 biosynthetic process
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell.
external encapsulating structure organisation
external encapsulating structure organization and biogenesis
external encapsulating structure organization
Binding to cadherin, a type I membrane protein involved in cell adhesion.
The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration).
The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat.
The process in which a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into striated muscle fibers.
The process in which a mesodermal, bone marrow or neural crest cell acquires specialized features of an endothelial cell, a thin flattened cell. A layer of such cells lines the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium.
Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation.
negative regulation of cell differentiation
Any process that activates or increases the frequency, rate or extent of cell differentiation.
positive regulation of cell differentiation
Any process that modulates the frequency, rate or extent of adipocyte differentiation.
regulation of adipocyte cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation.
down regulation of fat cell differentiation
down-regulation of fat cell differentiation
downregulation of fat cell differentiation
negative regulation of adipocyte cell differentiation
negative regulation of adipocyte differentiation
negative regulation of fat cell differentiation
Any process that activates or increases the frequency, rate or extent of adipocyte differentiation.
positive regulation of adipocyte cell differentiation
positive regulation of adipocyte differentiation
up regulation of fat cell differentiation
up-regulation of fat cell differentiation
upregulation of fat cell differentiation
positive regulation of fat cell differentiation
Any process that modulates the frequency, rate or extent of endothelial cell differentiation.
regulation of endothelial cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of endothelial cell differentiation.
down regulation of endothelial cell differentiation
down-regulation of endothelial cell differentiation
downregulation of endothelial cell differentiation
inhibition of endothelial cell differentiation
negative regulation of endothelial cell differentiation
Any process that activates or increases the frequency, rate or extent of endothelial cell differentiation.
up regulation of endothelial cell differentiation
up-regulation of endothelial cell differentiation
upregulation of endothelial cell differentiation
activation of endothelial cell differentiation
stimulation of endothelial cell differentiation
positive regulation of endothelial cell differentiation
Any process that modulates the frequency, rate or extent of epidermal cell differentiation.
regulation of hypodermal cell differentiation
regulation of epidermal cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal cell differentiation.
down regulation of epidermal cell differentiation
down-regulation of epidermal cell differentiation
downregulation of epidermal cell differentiation
inhibition of epidermal cell differentiation
negative regulation of hypodermal cell differentiation
negative regulation of epidermal cell differentiation
Any process that activates or increases the frequency, rate or extent of epidermal cell differentiation.
up regulation of epidermal cell differentiation
up-regulation of epidermal cell differentiation
upregulation of epidermal cell differentiation
activation of epidermal cell differentiation
stimulation of epidermal cell differentiation
positive regulation of hypodermal cell differentiation
positive regulation of epidermal cell differentiation
Any process that modulates the frequency, rate or extent of myeloid cell differentiation.
regulation of myeloid cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation.
down regulation of myeloid cell differentiation
down-regulation of myeloid cell differentiation
downregulation of myeloid cell differentiation
inhibition of myeloid cell differentiation
negative regulation of myeloid cell differentiation
Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation.
up regulation of myeloid cell differentiation
up-regulation of myeloid cell differentiation
upregulation of myeloid cell differentiation
activation of myeloid cell differentiation
stimulation of myeloid cell differentiation
positive regulation of myeloid cell differentiation
Any process that modulates the frequency, rate or extent of erythrocyte differentiation.
regulation of red blood cell differentiation
regulation of erythrocyte differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation.
down regulation of erythrocyte differentiation
down-regulation of erythrocyte differentiation
downregulation of erythrocyte differentiation
negative regulation of RBC differentiation
negative regulation of red blood cell differentiation
inhibition of erythrocyte differentiation
negative regulation of erythrocyte differentiation
Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
positive regulation of RBC differentiation
positive regulation of red blood cell differentiation
up regulation of erythrocyte differentiation
up-regulation of erythrocyte differentiation
upregulation of erythrocyte differentiation
activation of erythrocyte differentiation
stimulation of erythrocyte differentiation
positive regulation of erythrocyte differentiation
Any process that modulates the frequency, rate or extent of megakaryocyte differentiation.
regulation of megakaryocyte differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation.
down regulation of megakaryocyte differentiation
down-regulation of megakaryocyte differentiation
downregulation of megakaryocyte differentiation
inhibition of megakaryocyte differentiation
negative regulation of megakaryocyte differentiation
Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation.
up regulation of megakaryocyte differentiation
up-regulation of megakaryocyte differentiation
upregulation of megakaryocyte differentiation
activation of megakaryocyte differentiation
stimulation of megakaryocyte differentiation
positive regulation of megakaryocyte differentiation
Any process that modulates the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
Any process that stops, prevents, or reduces the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
down regulation of myoblast differentiation
down-regulation of myoblast differentiation
downregulation of myoblast differentiation
negative regulation of myoblast differentiation
Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
up regulation of myoblast differentiation
up-regulation of myoblast differentiation
upregulation of myoblast differentiation
positive regulation of myoblast differentiation
Any process that modulates the frequency, rate or extent of neuron differentiation.
Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
down regulation of neuron differentiation
down-regulation of neuron differentiation
downregulation of neuron differentiation
negative regulation of neuron differentiation
Any process that activates or increases the frequency, rate or extent of neuron differentiation.
positive regulation of neuron differentiation
Any process that modulates the frequency, rate or extent of epidermis development.
Any process that stops, prevents, or reduces the frequency, rate or extent of epidermis development.
down regulation of epidermis development
down-regulation of epidermis development
negative regulation of epidermal development
negative regulation of hypodermis development
negative regulation of epidermis development
Any process that activates or increases the frequency, rate or extent of epidermis development.
positive regulation of epidermal development
positive regulation of hypodermis development
positive regulation of epidermis development
Any process that modulates the frequency, rate or extent of glia cell differentiation.
regulation of glial cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of glia cell differentiation.
down regulation of glial cell differentiation
down-regulation of glial cell differentiation
downregulation of glial cell differentiation
negative regulation of glia cell differentiation
negative regulation of neuroglia differentiation
inhibition of glial cell differentiation
negative regulation of glial cell differentiation
Any process that activates or increases the frequency, rate or extent of glia cell differentiation.
positive regulation of glia cell differentiation
positive regulation of neuroglia differentiation
up regulation of glial cell differentiation
up-regulation of glial cell differentiation
upregulation of glial cell differentiation
activation of glial cell differentiation
stimulation of glial cell differentiation
positive regulation of glial cell differentiation
Any process that activates or increases the frequency, rate or extent of the formation of a cilium.
positive regulation of flagellum assembly
positive regulation of flagellum biogenesis
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
positive regulation of protein anabolism
positive regulation of protein biosynthesis
positive regulation of protein biosynthetic process
positive regulation of protein formation
positive regulation of protein synthesis
up regulation of protein biosynthetic process
up-regulation of protein biosynthetic process
upregulation of protein biosynthetic process
activation of protein biosynthetic process
stimulation of protein biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid.
down regulation of amino acid metabolic process
down-regulation of amino acid metabolic process
downregulation of amino acid metabolic process
negative regulation of amino acid metabolism
inhibition of amino acid metabolic process
negative regulation of cellular amino acid metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid.
positive regulation of amino acid metabolism
up regulation of amino acid metabolic process
up-regulation of amino acid metabolic process
upregulation of amino acid metabolic process
activation of amino acid metabolic process
stimulation of amino acid metabolic process
positive regulation of cellular amino acid metabolic process
Any process that modulates the frequency, rate or extent of angiogenesis.
Any process that activates or increases angiogenesis.
Any process that activates or increases the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
positive regulation of bone biosynthesis
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
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
Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin assembly or disassembly.
down regulation of chromatin assembly or disassembly
down-regulation of chromatin assembly or disassembly
downregulation of chromatin assembly or disassembly
negative regulation of chromatin assembly/disassembly
inhibition of chromatin assembly or disassembly
negative regulation of chromatin assembly or disassembly
Any process that activates or increases the frequency, rate or extent of chromatin assembly or disassembly.
positive regulation of chromatin assembly/disassembly
up regulation of chromatin assembly or disassembly
up-regulation of chromatin assembly or disassembly
upregulation of chromatin assembly or disassembly
activation of chromatin assembly or disassembly
stimulation of chromatin assembly or disassembly
positive regulation of chromatin assembly or disassembly
An epigenetic process that stops, prevents or reduces the rate of gene expression by remodelling of chromatin by either modifying the chromatin fiber, the nucleosomal histones, or the DNA.
down regulation of gene expression, epigenetic
down-regulation of gene expression, epigenetic
downregulation of gene expression, epigenetic
inhibition of gene expression, epigenetic
negative regulation of gene expression, epigenetic
An epigenetic process that capacitates gene expression by remodelling of chromatin by either modifying the chromatin fiber, the nucleosomal histones, or the DNA.
chromatin-mediated maintenance of transcription
maintenance of chromatin in transcription-competent conformation
positive regulation of gene expression, epigenetic
up regulation of gene expression, epigenetic
up-regulation of gene expression, epigenetic
upregulation of gene expression, epigenetic
activation of gene expression, epigenetic
long-term maintenance of gene activation
stimulation of gene expression, epigenetic
This regulation is exemplified by members of the trithorax group, which maintain the active state of homeotic gene transcription. Do not confuse with GO:0140673 ; co-transcriptional chromatin reassembly, which describes the reforming of chromatin after RNA polymerase II passage.
epigenetic maintenance of chromatin in transcription-competent conformation
Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction.
negative regulation of cardiac contraction
negative regulation of heart contraction
Any process that activates or increases the frequency, rate or extent of heart contraction.
positive regulation of cardiac contraction
positive regulation of heart contraction
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids.
down regulation of lipid metabolic process
down-regulation of lipid metabolic process
downregulation of lipid metabolic process
negative regulation of lipid metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids.
up regulation of lipid metabolic process
up-regulation of lipid metabolic process
positive regulation of lipid metabolic process
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.
negative regulation of mitotic nuclear division
Any process that activates or increases the frequency, rate or extent of mitosis.
positive regulation of mitotic nuclear division
Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle development.
down regulation of striated muscle development
down-regulation of striated muscle development
downregulation of striated muscle development
inhibition of striated muscle development
negative regulation of striated muscle tissue development
Any process that activates or increases the frequency, rate or extent of striated muscle development.
up regulation of striated muscle development
up-regulation of striated muscle development
upregulation of striated muscle development
activation of striated muscle development
stimulation of striated muscle development
positive regulation of striated muscle tissue development
Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation.
down regulation of translational elongation
down-regulation of translational elongation
downregulation of translational elongation
negative regulation of translational elongation
Any process that activates or increases the frequency, rate or extent of translational elongation.
up regulation of translational elongation
up-regulation of translational elongation
upregulation of translational elongation
positive regulation of translational elongation
Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination.
down regulation of translational termination
down-regulation of translational termination
downregulation of translational termination
negative regulation of translational termination
Any process that activates or increases the frequency, rate or extent of translational termination.
up regulation of translational termination
up-regulation of translational termination
upregulation of translational termination
stimulation of translational termination
positive regulation of translational termination
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate.
down regulation of carbohydrate metabolic process
down-regulation of carbohydrate metabolic process
downregulation of carbohydrate metabolic process
negative regulation of carbohydrate metabolism
inhibition of carbohydrate metabolic process
negative regulation of carbohydrate metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate.
positive regulation of carbohydrate metabolism
up regulation of carbohydrate metabolic process
up-regulation of carbohydrate metabolic process
upregulation of carbohydrate metabolic process
activation of carbohydrate metabolic process
stimulation of carbohydrate metabolic process
positive regulation of carbohydrate metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving catecholamine.
down regulation of catecholamine metabolic process
down-regulation of catecholamine metabolic process
downregulation of catecholamine metabolic process
negative regulation of catecholamine metabolism
inhibition of catecholamine metabolic process
negative regulation of catecholamine metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catecholamine.
positive regulation of catecholamine metabolism
up regulation of catecholamine metabolic process
up-regulation of catecholamine metabolic process
upregulation of catecholamine metabolic process
activation of catecholamine metabolic process
stimulation of catecholamine metabolic process
positive regulation of catecholamine metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis.
Any process that activates or increases the frequency, rate or extent of exocytosis.
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.
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.
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
negative regulation of mitotic cell cycle
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
positive regulation of mitotic cell cycle
Any process that stops, prevents, or reduces the frequency, rate or extent of muscle contraction.
negative regulation of muscle contraction
Any process that activates or increases the frequency, rate or extent of muscle contraction.
positive regulation of muscle contraction
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
negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
negative 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.
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
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
positive regulation of nucleobase-containing compound metabolic process
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
negative regulation of phosphate metabolic process
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
positive regulation of phosphate metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving steroids.
down regulation of steroid metabolic process
down-regulation of steroid metabolic process
downregulation of steroid metabolic process
negative regulation of steroid metabolism
negative regulation of steroid metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids.
positive regulation of steroid metabolism
up regulation of steroid metabolic process
up-regulation of steroid metabolic process
upregulation of steroid metabolic process
stimulation of steroid metabolic process
positive regulation of steroid metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation.
down regulation of translational initiation
down-regulation of translational initiation
downregulation of translational initiation
negative regulation of translational initiation
Any process that activates or increases the frequency, rate or extent of translational initiation.
up regulation of translational initiation
up-regulation of translational initiation
upregulation of translational initiation
positive regulation of translational initiation
Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle contraction.
down regulation of smooth muscle contraction
down-regulation of smooth muscle contraction
downregulation of smooth muscle contraction
negative regulation of smooth muscle contraction
Any process that activates or increases the frequency, rate or extent of smooth muscle contraction.
up regulation of smooth muscle contraction
up-regulation of smooth muscle contraction
upregulation of smooth muscle contraction
stimulation of smooth muscle contraction
positive regulation of smooth muscle contraction
Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle contraction.
down regulation of striated muscle contraction
down-regulation of striated muscle contraction
downregulation of striated muscle contraction
inhibition of striated muscle contraction
negative regulation of striated muscle contraction
Any process that activates or increases the frequency, rate or extent of striated muscle contraction.
up regulation of striated muscle contraction
up-regulation of striated muscle contraction
upregulation of striated muscle contraction
activation of striated muscle contraction
stimulation of striated muscle contraction
positive regulation of striated muscle contraction
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
negative regulation of embryonic development
Any process that modulates the frequency, rate or extent of embryonic development.
The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.
The chemical reactions and pathways resulting in the formation of a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring.
phenol-containing compound biosynthetic process
The chemical reactions and pathways resulting in the formation of indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group.
The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups.
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).
The specialization of organization of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light. An example of this process is found in Drosophila melanogaster.
Any process that modulates the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster.
regulation of photoreceptor differentiation
regulation of photoreceptor cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster.
down regulation of photoreceptor cell differentiation
down regulation of photoreceptor differentiation
down-regulation of photoreceptor cell differentiation
down-regulation of photoreceptor differentiation
downregulation of photoreceptor cell differentiation
downregulation of photoreceptor differentiation
negative regulation of photoreceptor differentiation
inhibition of photoreceptor cell differentiation
inhibition of photoreceptor differentiation
negative regulation of photoreceptor cell differentiation
Any process that activates or increases the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster.
positive regulation of photoreceptor differentiation
up regulation of photoreceptor cell differentiation
up regulation of photoreceptor differentiation
up-regulation of photoreceptor cell differentiation
up-regulation of photoreceptor differentiation
upregulation of photoreceptor cell differentiation
upregulation of photoreceptor differentiation
activation of photoreceptor cell differentiation
activation of photoreceptor differentiation
stimulation of photoreceptor cell differentiation
stimulation of photoreceptor differentiation
positive regulation of photoreceptor cell differentiation
The process whose specific outcome is the progression of the primary female sexual characteristics over time, from their formation to the mature structure. The primary female sexual characteristics are the ovaries, and they develop in response to sex hormone secretion.
development of primary female sexual characteristics
Development of a rod cell, one of the sensory cells in the eye that reacts to the presence of light. Rod cells contain the photopigment rhodopsin or porphyropsin and are responsible for vision in dim light.
Development of a cone cell, one of the sensory cells in the eye that reacts to the presence of light. Cone cells contain the photopigment iodopsin or cyanopsin and are responsible for photopic (daylight) vision.
Any process that modulates the frequency, rate or extent of growth of an organ of an organism.
Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organ of an organism.
Any process that activates or increases the frequency, rate or extent of growth of an organ of an organism.
The establishment of the sex of a female organism by physical differentiation.
Programmed cell death that occurs in the developing retina.
Programmed cell death that occurs in the retina to remove excess cells between ommatidia, thus resulting in a hexagonal lattice, precise with respect to cell number and position surrounding each ommatidium.
compound eye retinal cell programmed cell death
Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the retina.
regulation of retinal programmed cell death
regulation of retinal cell programmed cell death
Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the compound eye retina.
regulation of compound eye retinal cell programmed cell death
Any process that activates or increases the frequency, rate or extent of programmed cell death that occurs in the retina.
positive regulation of retinal programmed cell death
up regulation of retinal programmed cell death
up-regulation of retinal programmed cell death
upregulation of retinal programmed cell death
activation of retinal programmed cell death
stimulation of retinal programmed cell death
positive regulation of retinal cell programmed cell death
Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death that occurs in the retina.
down regulation of retinal programmed cell death
down-regulation of retinal programmed cell death
downregulation of retinal programmed cell death
negative regulation of retinal programmed cell death
inhibition of retinal programmed cell death
negative regulation of retinal cell programmed cell death
Any process that activates or increases the frequency, rate or extent of programmed cell death that occurs in the compound eye retina.
activation of retinal cell programmed cell death
stimulation of retinal cell programmed cell death
up regulation of retinal cell programmed cell death
up-regulation of retinal cell programmed cell death
upregulation of retinal cell programmed cell death
positive regulation of compound eye retinal cell programmed cell death
Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death that occurs in the compound eye retina.
down regulation of retinal cell programmed cell death
down-regulation of retinal cell programmed cell death
downregulation of retinal cell programmed cell death
inhibition of retinal cell programmed cell death
negative regulation of retina cell programmed cell death
negative regulation of compound eye retinal cell programmed cell death
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 carbamate stimulus. Carbamates are a group of insecticides and parasiticides that act by inhibiting cholinesterase.
The cellular homeostatic process that preserves a muscle cell in a stable functional or structural state.
The controlled release of acid by a cell or a tissue.
The addition of tubulin heterodimers to one or both ends of a microtubule.
The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells.
Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell.
Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell.
positive regulation of hormone secretion
Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a hormone from a cell.
negative regulation of hormone secretion
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.
positive regulation of lipid biosynthesis
up regulation of lipid biosynthetic process
up-regulation of lipid biosynthetic process
upregulation of lipid biosynthetic process
activation of lipid biosynthetic process
stimulation of lipid biosynthetic process
positive regulation of lipid biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.
regulation of lipid biosynthetic process
The controlled release of a substance by a cell or a tissue.
The directed movement of substances within a cell.
The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-).
The directed movement of a vesicle along a microtubule, mediated by motor proteins. This process begins with the attachment of a vesicle to a microtubule, and ends when the vesicle reaches its final destination.
The process occurring in the embryo by which the anatomical structures of the post-embryonic eye are generated and organized.
The developmental process that results in the deposition of coloring matter in an organism, tissue or cell.
Any process that modulates the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism.
regulation of pigmentation during development
regulation of developmental pigmentation
Any process that decreases the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism.
down regulation of developmental pigmentation
down-regulation of developmental pigmentation
downregulation of developmental pigmentation
negative regulation of developmental pigmentation
Any process that increases the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism.
up regulation of developmental pigmentation
up-regulation of developmental pigmentation
upregulation of developmental pigmentation
activation of developmental pigmentation
stimulation of developmental pigmentation
positive regulation of developmental pigmentation
The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line.
The multiplication or reproduction of fibroblast cells, resulting in the expansion of the fibroblast population.
Any process that modulates the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
up regulation of fibroblast proliferation
up-regulation of fibroblast proliferation
upregulation of fibroblast proliferation
positive regulation of fibroblast proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
down regulation of fibroblast proliferation
down-regulation of fibroblast proliferation
downregulation of fibroblast proliferation
negative regulation of fibroblast proliferation
The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles.
The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation.
vesicle targeting, to, from or within dictyosome
vesicle targeting, to, from or within Golgi
Any process that modulates the frequency, rate, or destination of vesicle-mediated transport to, from or within the Golgi apparatus.
regulation of vesicle targeting, to, from or within Golgi
The regulated release of norepinephrine by a cell. Norepinephrine is a catecholamine and it acts as a hormone and as a neurotransmitter of most of the sympathetic nervous system.
Assembly of the extracellular matrix fibers that enables the matrix to recoil after transient stretching.
The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi.
The creation of a single organelle from two or more organelles.
The creation of two or more organelles by division of one organelle.
The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei.
nuclear membrane fusion during karyogamy
nuclear membrane fusion involved in karyogamy
The partitioning of organelles between daughter cells at cell division.
The partitioning of Golgi apparatus between daughter cells at cell division.
The process whose specific outcome is the progression of the axial mesoderm over time, from its formation to the mature structure. The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
The process in which the anatomical structures of the axial mesoderm are generated and organized.
The process that gives rise to the axial mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
The process in which the anatomical structures of the mesoderm are generated and organized.
The process in which a relatively unspecialized cell acquires the specialized features of a mesoderm cell.
The process whose specific outcome is the progression of the paraxial mesoderm over time, from its formation to the mature structure. The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube.
The process in which the anatomical structures of the paraxial mesoderm are generated and organized.
The process that gives rise to the paraxial mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
The process whose specific outcome is the progression of the lateral mesoderm over time, from its formation to the mature structure.
The process in which the anatomical structures of the lateral mesoderm are generated and organized.
The process that gives rise to the lateral mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
The process whose specific outcome is the progression of the intermediate mesoderm over time, from its formation to the mature structure. The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.
The process in which the anatomical structures of the intermediate mesoderm are generated and organized.
The process that gives rise to the intermediate mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
The process whose specific outcome is the progression of the autonomic nervous system over time, from its formation to the mature structure. The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands.
The process whose specific outcome is the progression of the sympathetic nervous system over time, from its formation to the mature structure. The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter.
The process controlling the activation and/or rate at which relatively unspecialized cells acquire specialized features. Any process that modulates the rate, frequency or extent of the XXX at a consistent predetermined time point during its development.
regulation of timing of cell differentiation
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.
The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood.
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.
positive regulation of physiological process
positive 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.
negative regulation of physiological process
negative regulation of biological 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.
positive regulation of cellular physiological 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.
negative regulation of cellular physiological process
The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation.
haematopoietic or lymphoid organ development
haemopoietic or lymphoid organ development
hemopoietic or lymphoid organ development
hematopoietic or lymphoid organ development
The process whose specific outcome is the progression of the bone marrow over time, from its formation to the mature structure.
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 steroid hormone stimulus.
The process in which the anatomical structures of the digestive tract are generated and organized. The digestive tract is the anatomical structure through which food passes and is processed.
Morphogenesis, during the embryonic phase, of a tissue or 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.
The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.
Development, taking place during the embryonic phase, 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.
The process in which the anatomical structures of the notochord are generated and organized. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column.
Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.
regulation of post-embryonic development
Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.
down regulation of post-embryonic development
down-regulation of post-embryonic development
downregulation of post-embryonic development
inhibition of post-embryonic development
negative regulation of post-embryonic development
Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.
up regulation of post-embryonic development
up-regulation of post-embryonic development
upregulation of post-embryonic development
activation of post-embryonic development
stimulation of post-embryonic development
positive regulation of post-embryonic development
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.
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.
positive 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.
negative regulation of response to stimulus
The growth of a cell, where growth contributes to the progression of the cell over time from one condition to another.
developmental growth of a unicellular organism
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.
The process in which the anatomical structures of the eye are generated and organized.
The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
The process in which the anatomical structures of the eye are generated and organized during embryonic development.
The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants.
embryonic anatomical structure morphogenesis
The reproductive developmental process whose specific outcome is the progression of somatic structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures.
The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.
reproductive process in a multicellular organism
multicellular organismal reproductive process
The process whose specific outcome is the progression of the myoblast over time, from its formation to the mature structure. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
The increase in size or mass of a skeletal muscle. This may be due to a change in the fiber number or size.
Any process that modulates the frequency, rate or extent of skeletal muscle growth.
regulation of skeletal muscle tissue growth
Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle growth.
down regulation of skeletal muscle growth
down-regulation of skeletal muscle growth
downregulation of skeletal muscle growth
negative regulation of skeletal muscle tissue growth
Any process that activates, maintains or increases the rate of skeletal muscle growth.
positive regulation of skeletal muscle tissue growth
Any process that modulates the frequency, rate or extent of muscle development.
Any process that stops, prevents, or reduces the frequency, rate or extent of muscle development.
negative regulation of muscle organ development
Any process that activates, maintains or increases the rate of muscle development.
positive regulation of muscle organ development
Any process that modulates the frequency, rate or extent of developmental growth.
Any process that activates, maintains or increases the rate of developmental growth.
positive regulation of developmental growth
Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth.
negative regulation of developmental growth
Any process that modulates the frequency, rate or extent of skeletal muscle tissue development.
regulation of skeletal muscle tissue development
Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle tissue development.
down regulation of skeletal muscle development
down-regulation of skeletal muscle development
downregulation of skeletal muscle development
inhibition of skeletal muscle development
negative regulation of skeletal muscle tissue development
Any process that activates, maintains or increases the rate of skeletal muscle tissue development.
up regulation of skeletal muscle development
up-regulation of skeletal muscle development
upregulation of skeletal muscle development
activation of skeletal muscle development
stimulation of skeletal muscle development
positive regulation of skeletal muscle tissue development
The process in which the anatomical structures of muscle are generated and organized.
The process pertaining to the initial formation of an animal organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment. Organs are a natural part or structure in an animal or a plant, capable of performing some special action (termed its function), which is essential to the life or well-being of the whole. The heart and lungs are organs of animals, and the petal and leaf are organs of plants. In animals the organs are generally made up of several tissues, one of which usually predominates, and determines the principal function of the organ.
initiation of an animal organ primordium
The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
formation of an anatomical structure involved in morphogenesis
Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense.
anatomical structure formation involved in morphogenesis
The multiplication or reproduction of smooth muscle cells, resulting in the expansion of a cell population.
Any process that modulates the frequency, rate or extent of smooth muscle cell proliferation.
regulation of smooth muscle cell proliferation
Any process that activates or increases the rate or extent of smooth muscle cell proliferation.
positive regulation of SMC proliferation
up regulation of smooth muscle cell proliferation
up-regulation of smooth muscle cell proliferation
upregulation of smooth muscle cell proliferation
activation of smooth muscle cell proliferation
stimulation of smooth muscle cell proliferation
positive regulation of smooth muscle cell proliferation
Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation.
down regulation of smooth muscle cell proliferation
down-regulation of smooth muscle cell proliferation
downregulation of smooth muscle cell proliferation
negative regulation of SMC proliferation
inhibition of smooth muscle cell proliferation
negative regulation of smooth muscle cell proliferation
The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
The process in which the structures of a neuron are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a neuron.
neuron morphogenesis involved in differentiation
cell morphogenesis involved in neuron differentiation
The process in which nerve cells are generated. This includes the production of neuroblasts and their differentiation into neurons.
The process in which the anatomical structures of the skeleton are generated and organized.
The process in which the anatomical structures of a tissue are generated and organized.
The process in which the anatomical structures of the epidermis are generated and organized. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process.
The process whose specific outcome is the progression of a gland over time, from its formation to the mature structure. A gland is an organ specialised for secretion.
The process whose specific outcome is the progression of an appendage over time, from its formation to the mature structure. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch.
The process whose specific outcome is the progression of cardiac muscle over time, from its formation to the mature structure.
The process whose specific outcome is the progression of the skeletal muscle fiber over time, from its formation to the mature structure. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
Any process that modulates the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
regulation of skeletal muscle fibre development
regulation of skeletal myofiber development
regulation of skeletal myofibre development
regulation of skeletal muscle fiber development
Any process that activates, maintains or increases the rate of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
positive regulation of skeletal muscle fibre development
positive regulation of skeletal myofiber development
positive regulation of skeletal myofibre development
up regulation of skeletal muscle fiber development
up-regulation of skeletal muscle fiber development
upregulation of skeletal muscle fiber development
activation of skeletal muscle fiber development
stimulation of skeletal muscle fiber development
positive regulation of skeletal muscle fiber development
Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
down regulation of skeletal muscle fiber development
down-regulation of skeletal muscle fiber development
downregulation of skeletal muscle fiber development
negative regulation of skeletal muscle fibre development
negative regulation of skeletal myofiber development
negative regulation of skeletal myofibre development
inhibition of skeletal muscle fiber development
negative regulation of skeletal muscle fiber development
The process whose specific outcome is the progression of smooth muscle over time, from its formation to the mature structure.
The process whose specific outcome is the progression of the compound eye over time, from its formation to the mature structure. The compound eye is an organ of sight that contains multiple repeating units, often arranged hexagonally. Each unit has its own lens and photoreceptor cell(s) and can generate either a single pixelated image or multiple images, per eye.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pigment granule.
pigment granule organization and biogenesis
The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.
branching morphogenesis of an epithelial tube
The process in which the anatomical structures of branches in a nerve are generated and organized. This term refers to an anatomical structure (nerve) not a cell (neuron).
The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types.
A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes.
The process whose specific outcome is the progression of the genitalia over time, from its formation to the mature structure.
The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure.
The process aimed at the progression of an enucleate erythrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
The process aimed at the progression of a nucleate erythrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs.
The process in which the anatomical structures of venous blood vessels are generated and organized. Veins are blood vessels that transport blood from the body and its organs to the heart.
The process in which the anatomical structures of the brain are generated and organized. The brain is one of the two components of the central nervous system and is the center of thought and emotion. It is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
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.
The biological process whose specific outcome is the progression of a neural nucleus from its initial condition to its mature state. A neural nucleus is an anatomical structure consisting of a discrete aggregate of neuronal soma.
The process in which the anatomical structures of a cell projection are generated and organized.
The process in which the limits of an anatomical structure are generated. 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.
The process resulting in the physical partitioning and separation of a glioblast into daughter cells.
The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
The process whose specific outcome is the progression of the stem cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to its specific fate.
A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
Any process involved in the maintenance of an internal steady state at the level of the multicellular organism.
Any biological process involved in the maintenance of the steady-state number of cells within a population of cells.
The process whose specific outcome is the progression of a sensory system over time from its formation to the mature structure.
The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the peripheral nervous system.
peripheral nervous system neuron differentiation
The process whose specific outcome is the progression of a neuron whose cell body is located in the peripheral nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron.
peripheral nervous system neuron development
Any process in which a chromosome is transported to, or maintained in, a specific location.
establishment and maintenance of chromosome localization
establishment and maintenance of chromosome position
The regulated release of catecholamines by a cell. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
Any process that modulates the frequency, rate or extent of the regulated release of catecholamines.
The directed movement of nucleic acids, single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances.
Any process that modulates the frequency, rate or extent of epithelial cell proliferation.
regulation of epithelial cell proliferation
Any process that activates or increases the rate or extent of epithelial cell proliferation.
up regulation of epithelial cell proliferation
up-regulation of epithelial cell proliferation
upregulation of epithelial cell proliferation
activation of epithelial cell proliferation
stimulation of epithelial cell proliferation
positive regulation of epithelial cell proliferation
Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation.
down regulation of epithelial cell proliferation
down-regulation of epithelial cell proliferation
downregulation of epithelial cell proliferation
inhibition of epithelial cell proliferation
negative regulation of epithelial cell proliferation
Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell.
Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell.
negative regulation of protein secretion
Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
positive regulation of protein secretion
Any process that modulates the frequency, rate or extent of neurogenesis, the generation of cells in the nervous system.
Any process that stops, prevents, or reduces the frequency, rate or extent of neurogenesis, the generation of cells within the nervous system.
Any process that activates or increases the frequency, rate or extent of neurogenesis, the generation of cells within the nervous system.
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.
Any process that modulates the activity of an enzyme.
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).
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.
regulation of cellular physiological process
Any process that modulates the physical form or the activity of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
regulation of synapse structure or activity
Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission.
regulation of chemical synaptic transmission
modulation of chemical synaptic transmission
Any process that stops, prevents, or reduces the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.
down regulation of synaptic transmission
down-regulation of synaptic transmission
negative regulation of synaptic transmission
Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.
positive regulation of synaptic transmission
Any process that modulates the physical form of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
regulation of synapse organization and biogenesis
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
regulation of steroid biosynthetic process
adhesive extracellular matrix constituent
Binding to a component of the extracellular matrix.
extracellular matrix constituent binding
A organ system process carried out by any of the organs or tissues of neurological system.
Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism.
The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system.
The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system.
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.
Any process pertaining to the functions of the nervous and muscular systems of an organism.
The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal.
sensory perception, sensory transduction of stimulus
detection of stimulus involved in sensory perception
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
detection of light stimulus involved in visual perception
The process in which a relatively unspecialized cell acquires the specialized features of a pigmented cell, such as a melanocyte.
Note that the chromatophore mentioned here is distinct from the pigment bearing structure found in certain photosynthetic bacteria and cyanobacteria. It is also different from the plant chromoplast, which is also sometimes called a chromatophore.
Any process that modulates the frequency, rate or extent of pigmented cell differentiation.
regulation of pigment cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of pigment cell differentiation.
down regulation of pigment cell differentiation
down-regulation of pigment cell differentiation
downregulation of pigment cell differentiation
inhibition of pigment cell differentiation
negative regulation of pigment cell differentiation
Any process that activates or increases the frequency, rate or extent of pigment cell differentiation.
up regulation of pigment cell differentiation
up-regulation of pigment cell differentiation
upregulation of pigment cell differentiation
activation of pigment cell differentiation
stimulation of pigment cell differentiation
positive regulation of pigment cell differentiation
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.
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.
sensory perception of mechanical stimulus
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 during sensory perception
sensory perception, sensory detection of light stimulus
sensory perception, sensory transduction of light stimulus
sensory transduction of light stimulus during sensory perception
detection of light stimulus involved in sensory perception
The directed movement of RNA, deoxyribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue.
Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue.
Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue.
Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA.
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
negative regulation of DNA metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA.
positive regulation of DNA metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.
down regulation of lipid biosynthetic process
down-regulation of lipid biosynthetic process
downregulation of lipid biosynthetic process
negative regulation of lipid biosynthesis
inhibition of lipid biosynthetic process
negative regulation of lipid biosynthetic process
The controlled breakdown of the nuclear membranes, for example during cellular division.
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
negative 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).
positive regulation of developmental process
Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that modulates the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
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
regulation of cellular component organization and biogenesis
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.
negative regulation of cell organisation
negative regulation of cellular component organization and biogenesis
negative 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.
positive regulation of cell organisation
positive regulation of cellular component organization and biogenesis
positive regulation of cellular component organization
The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell; smooth muscle lacks transverse striations in its constituent fibers and are almost always involuntary.
The process in which a relatively unspecialized cell acquires specialized features of a striated muscle cell; striated muscle fibers are divided by transverse bands into striations, and cardiac and voluntary muscle are types of striated muscle.
Any process that modulates the frequency, rate or extent of muscle cell differentiation.
regulation of muscle cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of muscle cell differentiation.
down regulation of muscle cell differentiation
down-regulation of muscle cell differentiation
downregulation of muscle cell differentiation
inhibition of muscle cell differentiation
negative regulation of muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of muscle cell differentiation.
up regulation of muscle cell differentiation
up-regulation of muscle cell differentiation
upregulation of muscle cell differentiation
activation of muscle cell differentiation
stimulation of muscle cell differentiation
positive regulation of muscle cell differentiation
Any process that modulates the frequency, rate or extent of smooth muscle cell differentiation.
regulation of smooth muscle cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell differentiation.
down regulation of smooth muscle cell differentiation
down-regulation of smooth muscle cell differentiation
downregulation of smooth muscle cell differentiation
inhibition of smooth muscle cell differentiation
negative regulation of smooth muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of smooth muscle cell differentiation.
up regulation of smooth muscle cell differentiation
up-regulation of smooth muscle cell differentiation
upregulation of smooth muscle cell differentiation
activation of smooth muscle cell differentiation
stimulation of smooth muscle cell differentiation
positive regulation of smooth muscle cell differentiation
Any process that modulates the frequency, rate or extent of striated muscle cell differentiation.
regulation of striated muscle cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle cell differentiation.
down regulation of striated muscle cell differentiation
down-regulation of striated muscle cell differentiation
downregulation of striated muscle cell differentiation
inhibition of striated muscle cell differentiation
negative regulation of striated muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of striated muscle cell differentiation.
up regulation of striated muscle cell differentiation
up-regulation of striated muscle cell differentiation
upregulation of striated muscle cell differentiation
activation of striated muscle cell differentiation
stimulation of striated muscle cell differentiation
positive regulation of striated muscle cell differentiation
The directed movement of substances into, out of, or within the nucleus.
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 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.
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
negative 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.
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
positive regulation of nitrogen compound metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
regulation of phosphorus metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur.
down regulation of sulfur metabolic process
down-regulation of sulfur metabolic process
downregulation of sulfur metabolic process
negative regulation of sulfur metabolism
negative regulation of sulphur metabolic process
negative regulation of sulphur metabolism
negative regulation of sulfur metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur.
positive regulation of sulfur metabolism
positive regulation of sulphur metabolic process
positive regulation of sulphur metabolism
up regulation of sulfur metabolic process
up-regulation of sulfur metabolic process
upregulation of sulfur metabolic process
positive regulation of sulfur metabolic process
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
establishment and maintenance of localization
establishment and maintenance of position
establishment and maintenance of cellular component location
establishment and maintenance of substance location
establishment and maintenance of substrate location
The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
positive regulation of protein transport
Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
negative regulation of protein transport
Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
The directed movement of RNA to a specific location.
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.
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.
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
positive 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.
down regulation of multicellular organismal process
down-regulation of multicellular organismal process
downregulation of multicellular organismal process
inhibition of multicellular organismal process
negative regulation of multicellular organismal process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein.
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein.
positive regulation of protein metabolism
up regulation of protein metabolic process
up-regulation of protein metabolic process
upregulation of protein metabolic process
stimulation of protein metabolic process
positive regulation of protein metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein.
down regulation of protein metabolic process
down-regulation of protein metabolic process
downregulation of protein metabolic process
negative regulation of protein metabolism
negative regulation of protein metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA.
down regulation of RNA metabolic process
down-regulation of RNA metabolic process
negative regulation of RNA metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA.
positive regulation of RNA metabolic process
The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein.
The process in which protein polymers, compounds composed of a large number of component monomers, are broken down. Depolymerization occurs by the successive removal of monomers from an existing poly- or oligomeric protein.
Any process that modulates the frequency, rate or extent of the movement of a cellular component.
regulation of cellular component movement
Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a cellular component.
negative regulation of cellular component motion
negative regulation of cellular component movement
Any process that activates or increases the frequency, rate or extent of the movement of a cellular component.
positive regulation of cellular component motion
positive regulation of cellular component movement
A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
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.
Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.
Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells.
The directed movement of a chromosome to a specific location.
establishment of chromosome localisation
establishment of chromosome localization
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.
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
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.
positive 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.
negative regulation of transferase activity
Binding to serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
Binding to norepinephrine, (3,4-dihydroxyphenyl-2-aminoethanol), a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine.
Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
neuron programmed cell death by apoptosis
neuronal cell programmed cell death by apoptosis
programmed cell death of neuronal cells by apoptosis
programmed cell death of neurons by apoptosis
The multiplication or reproduction of myoblasts, resulting in the expansion of a myoblast cell population. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole.
heterotypic vacuole fusion (non-autophagic)
heterotypic vacuole fusion, non-autophagic
Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
regulation of cytoskeleton organization and biogenesis
Any process that stops, prevents, or reduces the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
down regulation of cytoskeleton organization
down-regulation of cytoskeleton organization
downregulation of cytoskeleton organization
negative regulation of cytoskeleton organisation
negative regulation of cytoskeleton organization and biogenesis
negative regulation of cytoskeleton organization
Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
positive regulation of cytoskeleton organisation
up regulation of cytoskeleton organization
up-regulation of cytoskeleton organization
upregulation of cytoskeleton organization
stimulation of cytoskeleton organization
positive regulation of cytoskeleton organization and biogenesis
positive regulation of cytoskeleton organization
The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
Any process in which an organelle is transported to, and/or maintained in, a specific location.
establishment and maintenance of organelle localization
A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane.
establishment and maintenance of cellular localization
establishment and maintenance of localization in cell or cell membrane
Any process in which the Golgi is transported to, and/or maintained in, a specific location within the cell.
establishment and maintenance of Golgi localization
Any process in which the nucleus is transported to, and/or maintained in, a specific location within the cell.
establishment and maintenance of nucleus localization
Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location.
establishment and maintenance of vesicle localization
Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
establishment of intracellular localization
establishment of localization within cell
The directed movement of a vesicle to a specific location.
The directed movement of an organelle to a specific location.
Any process in which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a membrane.
establishment and maintenance of localization in membrane
establishment and maintenance of position in membrane
Any process in which a cell is transported to, and/or maintained in, a specific location.
establishment and maintenance of cell localization
establishment and maintenance of localization of cell
The directed movement of the Golgi to a specific location.
establishment of Golgi apparatus localization
establishment of Golgi body localization
Any process in which an organism has an effect on an organism of the same species.
intraspecies interaction between organisms
intraspecies interaction with other organisms
biological process involved in intraspecies interaction between organisms
OBSOLETE. A biological process which involves another organism of the same or different species.
physiological interaction between organisms
physiological interaction with other organism
This term was obsoleted because it was not a biologically meaningful grouping class.
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 from another living organism.
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.
Any process that modulates the rate or extent of progression through the cell cycle.
regulation of progression through cell cycle
arrest of mitotic cell cycle progression
negative regulation of cell cycle arrest
positive regulation of cell cycle arrest
Any process that activates or increases the frequency, rate or extent of cell division.
Any process that stops, prevents, or reduces the frequency, rate or extent of cell division.
Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
Any process in which a pigment granule is transported to, and/or maintained in, a specific location within the cell.
Any process that modulates the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating.
regulation of cardioblast differentiation
Any process that activates or increases the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating.
up regulation of cardioblast differentiation
up-regulation of cardioblast differentiation
upregulation of cardioblast differentiation
activation of cardioblast differentiation
stimulation of cardioblast differentiation
positive regulation of cardioblast differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating.
down regulation of cardioblast differentiation
down-regulation of cardioblast differentiation
downregulation of cardioblast differentiation
inhibition of cardioblast differentiation
negative regulation of cardioblast differentiation
The directed movement of pigment granules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of a pigment granule to a specific location.
establishment of pigment granule localisation
establishment of pigment granule localization
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.
The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
Any process that modulates the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
negative regulation of amino acid transmembrane transport
negative regulation of amino acid transport
Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
positive regulation of amino acid transmembrane transport
positive regulation of amino acid transport
Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue.
regulation of nervous system development
Any process that stops, prevents, or reduces the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue.
down regulation of nervous system development
down-regulation of nervous system development
downregulation of nervous system development
inhibition of nervous system development
negative regulation of nervous system development
Any process that activates, maintains or increases the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue.
up regulation of nervous system development
up-regulation of nervous system development
upregulation of nervous system development
activation of nervous system development
stimulation of nervous system development
positive regulation of nervous system development
Any process that modulates the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
Any process that stops, prevents, or reduces the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
negative regulation of synapse biogenesis
Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
positive regulation of synapse biogenesis
Any process that modulates the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation.
regulation of conduction of nerve impulse
regulation of transmission of nerve impulse
Any process that stops, prevents, or reduces the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation.
down regulation of transmission of nerve impulse
down-regulation of transmission of nerve impulse
downregulation of transmission of nerve impulse
negative regulation of conduction of nerve impulse
inhibition of transmission of nerve impulse
negative regulation of transmission of nerve impulse
Any process that activates, maintains or increases the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation.
positive regulation of conduction of nerve impulse
up regulation of transmission of nerve impulse
up-regulation of transmission of nerve impulse
upregulation of transmission of nerve impulse
activation of transmission of nerve impulse
stimulation of transmission of nerve impulse
positive regulation of transmission of nerve impulse
Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets.
Any process that activates or increases the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets.
positive regulation of chromosome segregation
Any process that stops, prevents, or reduces the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets.
down regulation of chromosome segregation
down-regulation of chromosome segregation
downregulation of chromosome segregation
negative regulation of chromosome segregation
OBSOLETE. The chemical reactions and pathways performed by an organism in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
This term was obsoleted because it represents a molecular function.
obsolete metabolism by symbiont of substance in host
OBSOLETE. The chemical reactions and pathways performed by an organism in a second organism, where the two organisms are in a symbiotic interaction.
metabolism of substance in other organism during symbiotic interaction
obsolete metabolism of substance in other organism involved in symbiotic interaction
OBSOLETE. The chemical reactions and pathways performed by an organism in a second organism resulting in the formation of substances, where the two organisms are in a symbiotic interaction.
biosynthesis of substance in other organism during symbiotic interaction
obsolete biosynthesis of substance in other organism involved in symbiotic interaction
The process whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate.
The process whose specific outcome is the progression of a striated muscle cell over time, from its formation to the mature structure. Striated muscle cells contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle.
The process whose specific outcome is the progression of the cardiac myofibril over time, from its formation to the mature structure. A cardiac myofibril is a myofibril specific to cardiac muscle cells.
The process whose specific outcome is the progression of a cardiac cell over time, from its formation to the mature state. A cardiac cell is a cell that will form part of the cardiac organ of an individual.
The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
The process in which the anatomical structures of cardiac muscle tissue are generated and organized.
The process in which the anatomical structure of cardiac atrium muscle is generated and organized.
atrial cardiac muscle tissue morphogenesis
The process in which the anatomical structures of cardiac ventricle muscle is generated and organized.
ventricular cardiac muscle tissue morphogenesis
The process whose specific outcome is the progression of a cardiac muscle cell over time, from its formation to the mature state.
The increase in size or mass of a cardiac muscle, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
Any process that modulates the frequency, rate or extent of cardiac muscle fiber development.
regulation of cardiac muscle fibre development
regulation of heart muscle fiber development
regulation of cardiac muscle fiber development
Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle fiber development.
down regulation of cardiac muscle fiber development
down-regulation of cardiac muscle fiber development
downregulation of cardiac muscle fiber development
negative regulation of cardiac muscle fibre development
inhibition of cardiac muscle fiber development
negative regulation of heart muscle fiber development
negative regulation of cardiac muscle fiber development
Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle fiber development.
positive regulation of cardiac muscle fibre development
positive regulation of heart muscle fiber development
up regulation of cardiac muscle fiber development
up-regulation of cardiac muscle fiber development
upregulation of cardiac muscle fiber development
activation of cardiac muscle fiber development
stimulation of cardiac muscle fiber development
positive regulation of cardiac muscle fiber development
Any process that modulates the frequency, rate or extent of cardiac muscle growth.
regulation of cardiac muscle tissue growth
Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle growth.
down regulation of cardiac muscle growth
down-regulation of cardiac muscle growth
negative regulation of heart muscle growth
negative regulation of cardiac muscle tissue growth
Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle growth.
positive regulation of heart muscle growth
positive regulation of cardiac muscle tissue growth
Any process that modulates the frequency, rate or extent of cardiac muscle tissue development.
regulation of cardiac muscle tissue development
Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle tissue development.
positive regulation of heart muscle development
up regulation of cardiac muscle development
up-regulation of cardiac muscle development
upregulation of cardiac muscle development
activation of cardiac muscle development
stimulation of cardiac muscle development
positive regulation of cardiac muscle tissue development
Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle tissue development.
down regulation of cardiac muscle development
down-regulation of cardiac muscle development
downregulation of cardiac muscle development
negative regulation of heart muscle development
inhibition of cardiac muscle development
negative regulation of cardiac muscle tissue development
The process resulting in the physical partitioning and separation of a neuroblast into daughter cells. A neuroblast is any cell that will divide and give rise to a neuron.
The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
nucleobase, nucleoside and nucleotide metabolism
nucleobase-containing small molecule metabolic process
The directed movement of proteins from the Golgi to a transport vesicle. Continuously secreted proteins are sorted into transport vesicles that fuse with the plasma membrane, releasing their contents by exocytosis.
Any process that modulates the frequency, rate or extent of cardiac muscle contraction.
regulation of cardiac muscle contraction
Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle contraction.
negative regulation of cardiac muscle contraction
The process whose specific outcome is the progression of the digestive system over time, from its formation to the mature structure. The digestive system is the entire structure in which digestion takes place. Digestion is all of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
The process whose specific outcome is the progression of the pharyngeal system over time, from its formation to the mature structure. The pharyngeal system is a transient embryonic complex that is specific to vertebrates. It comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming: the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear.
The expansion of a cardiac muscle cell population by cell division.
The process whose specific outcome is the progression of the pericardium over time, from its formation to the mature structure. The pericardium is a double-walled sac that contains the heart and the roots of the aorta, vena cava and the pulmonary artery.
The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
The process in which the anatomical structure of the retina is generated and organized.
retina morphogenesis in camera-style eye
Any process that modulates the frequency, rate or extent of cardiac muscle cell proliferation.
regulation of heart muscle cell proliferation
regulation of cardiomyocyte proliferation
regulation of cardiac muscle cell proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle cell proliferation.
negative regulation of heart muscle cell proliferation
negative regulation of cardiac muscle cell proliferation
Any process that activates or increases the frequency, rate or extent of cardiac muscle cell proliferation.
positive regulation of heart muscle cell proliferation
positive regulation of cardiac muscle cell proliferation
The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body.
Muscle contraction of cardiac muscle tissue.
embryonic process involved in female pregnancy
Any process that modulates the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
regulation of syncytium formation by plasma membrane fusion
Any process that increases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
positive regulation of syncytium formation by plasma membrane fusion
The portion of the plasma membrane surrounding a cilium.
Formation of the endocardium of the heart. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.
The process in which a relatively unspecialized cell acquires specialized features of a hematopoietic stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
haematopoietic stem cell differentiation
The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell in a camera-type eye.
camera-type eye photoreceptor cell differentiation
The process in which a relatively unspecialized cell acquires the specialized features of a retinal rod cell.
A transition where a mesenchymal cell establishes apical/basolateral polarity, forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell.
epithelial cell differentiation from mesenchymal cell
A homeostatic process involved in the maintenance of an internal steady state within a defined anatomical structure of an organism, including control of cellular proliferation and death and control of metabolic function. 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.
Any process that modulates the frequency, rate or extent of glial cell proliferation.
Any process that activates or increases the rate or extent of glial cell proliferation.
positive regulation of glial cell proliferation
Any process that stops or decreases the rate or extent of glial cell proliferation.
negative regulation of glial cell proliferation
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.
regulation of macromolecule metabolic process
The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
Any process that modulates the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
Any process that increases the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
positive regulation of sarcomere organisation
positive regulation of sarcomere organization
Any process that decreases the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
negative regulation of sarcomere organisation
negative regulation of sarcomere organization
The biological process whose specific outcome is the progression of a head from an initial condition to its mature state. The head is the anterior-most division of the body.
The process in which the anatomical structures of the head are generated and organized. The head is the anterior-most division of the body.
The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head.
The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head.
Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell.
The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
The process in which bones are generated and organized.
The process in which bones are generated and organized as a result of the conversion of initial cartilaginous anlage into bone.
The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones.
cartilage development involved in endochondral bone morphogenesis
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 ammonium stimulus.
The process in which a relatively unspecialized cell acquires specialized features of a cardiac myoblast. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life.
myocardial precursor cell differentiation
cardiac muscle cell myoblast differentiation
The removal of tubulin heterodimers from one or both ends of an axonemal microtubule. An axonemal microtubule is a microtubule in the axoneme of a cilium or flagellum; an axoneme contains nine modified doublet microtubules surrounding a pair of single microtubules.
The process in which the anatomical structure of a cardiac septum is generated and organized. A cardiac septum is a partition that separates parts of the heart.
The developmental process in which a ventricular septum is generated and organized. A ventricular septum is an anatomical structure that separates the lower chambers (ventricles) of the heart from one another.
The developmental process in which atrial septum is generated and organized. The atrial septum separates the upper chambers (the atria) of the heart from one another.
The process in which the structure of the smooth muscle tissue surrounding the aorta is generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body.
aorta smooth muscle tissue morphogenesis
The process in which the anatomical structures of muscle tissue are generated and organized. Muscle tissue consists of a set of cells that are part of an organ and carry out a contractive function.
The increase in size or mass of the heart.
Any process that modulates the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart.
Any process that increases the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart.
The process in which the anatomical structures of the lung are generated and organized.
The biological process whose specific outcome is the progression of a lung vasculature from an initial condition to its mature state. This process begins with the formation of the lung vasculature and ends with the mature structure. The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs.
The biological process whose specific outcome is the progression of lung connective tissue from an initial condition to its mature state. This process begins with the formation of lung connective tissue and ends with the mature structure. The lung connective tissue is a material made up of fibers forming a framework and support structure for the lungs.
The biological process whose specific outcome is the progression of the lung epithelium from an initial condition to its mature state. This process begins with the formation of lung epithelium and ends with the mature structure. The lung epithelium is the specialized epithelium that lines the inside of the lung.
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.
The morphogenetic process in which the foregut region specified to become the lung forms the initial left and right buds.
The increase in size or mass of a lung. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
The process whose specific outcome is the progression of a trachea over time, from its formation to the mature structure. The trachea is the portion of the airway that attaches to the bronchi as it branches.
The process in which a trachea is generated and organized. The trachea is the portion of the airway that attaches to the bronchi as it branches.
The process pertaining to the initial formation of a trachea from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the trachea is recognizable. The trachea is the portion of the airway that attaches to the bronchi as it branches.
The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.
epithelial tube branching involved in lung morphogenesis
Any process that increases the frequency, rate or extent of cardiac muscle contraction.
positive regulation of cardiac muscle contraction
Any process that modulates the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion.
Any process that increases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion.
positive regulation of gastric acid secretion
Any process that decreases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion.
negative regulation of gastric acid secretion
Any process that increases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
positive regulation of digestive system process
Any process that decreases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
negative regulation of digestive system process
The biological process whose specific outcome is the progression of a right lung from an initial condition to its mature state. This process begins with the formation of the right lung and ends with the mature structure. The right lung is the lung which is on the right side of the anterior posterior axis looking from a dorsal to ventral aspect.
The biological process whose specific outcome is the progression of a left lung from an initial condition to its mature state. This process begins with the formation of the left lung and ends with the mature structure. The left lung is the lung which is on the left side of the anterior posterior axis looking from a dorsal to ventral aspect.
The process in which anatomical structures of the left lung are generated and organized.
The process in which anatomical structures of the right lung are generated and organized.
The biological process whose specific outcome is the progression of a pharynx from an initial condition to its mature state. The pharynx is the part of the digestive system immediately posterior to the mouth.
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features of a mature cell found in the lung. Differentiation includes the processes involved in commitment of a cell to a specific fate.
The process whose specific outcome is the progression of a mesenchymal tissue over time, from its formation to the mature structure. A mesenchymal tissue is made up of loosely packed stellate cells.
The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell that contributes to the epithelium of the lung.
pulmonary epithelial cell differentiation
Any process that modulates the rate, frequency, or extent of cell projection assembly.
Any process that mediates the transfer of information from one cell to another and contributes to the progression of the lung, from its initial state to the mature structure.
cell-cell signalling involved in lung development
cell-cell signaling involved in lung development
Any process that increases the rate or frequency of epithelial cell proliferation that results in the lung attaining its shape.
positive regulation of epithelial cell proliferation involved in lung morphogenesis
The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the shaping of the lung.
epithelial cell proliferation involved in lung morphogenesis
The process in which the anatomical structures of cartilage are generated and organized.
The progression of muscle tissue over time, from its initial formation to its mature state. Muscle tissue is a contractile tissue made up of actin and myosin fibers.
The progression of a skeletal muscle organ over time from its initial formation to its mature state. A skeletal muscle organ includes the skeletal muscle tissue and its associated connective tissue.
The progression of the diaphragm over time from its initial formation to the mature structure. The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs.
The process in which the anatomical structures of the diaphragm are generated and organized.
The progression of the respiratory system over time from its formation to its mature structure. The respiratory system carries out respiratory gaseous exchange.
Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape.
developmental growth involved in morphogenesis
Any apoptotic process that contributes to the shaping of an anatomical structure.
apoptotic process involved in morphogenesis
The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
The process in which epiblast cells acquire specialized features of neuroepithelial cells.
The morphogenetic process in which an epithelial sheet bends along a linear axis.
The morphogenetic process in which a bud forms from an epithelial sheet. A bud is a protrusion that forms form the sheet by localized folding.
The process in which the anatomical structure of the pulmonary venous blood vessels are generated and organized. Pulmonary veins are blood vessels that transport blood from the lungs to the heart.
pulmonary venous blood vessel morphogenesis
The process in which a mesenchymal cell, acquires specialized structural and/or functional features of a chondroblast. Differentiation includes the processes involved in commitment of a cell to a chondroblast fate. A chondroblast is a precursor cell to chondrocytes.
chondrocyte progenitor cell differentiation
The formation of a lumen by hollowing out a solid rod or cord.
Any apoptotic process that contributes to the hollowing out of an epithelial rod or cord to form the central hole in a tube.
apoptosis involved in tube lumen cavitation
apoptotic process involved in tube lumen cavitation
The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat.
Any process that modulates the rate, frequency, or extent of chromosome condensation, the progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell.
regulation of vesicle-mediated transport
Any process that modulates the rate, frequency, or extent of microtubule-based movement, the movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins.
regulation of microtubule-based movement
Any process that modulates the rate, frequency, or extent of branching morphogenesis, the process in which the anatomical structures of branches are generated and organized.
regulation of morphogenesis of a branching structure
Behavior by which an organism locates food.
The developmental process in which an ectodermal placode forms. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm.
The process in which a relatively unspecialized cell acquires specialized features of a blood vessel endothelial cell, a thin flattened cell that lines the inside surfaces of blood vessels.
blood vessel endothelial cell differentiation
The progression of the artery over time, from its initial formation to the mature structure. An artery is a blood vessel that carries blood away from the heart to a capillary bed.
The progression of the venous blood vessel over time from its initial formation to the mature structure. Venous blood vessels carry blood back to the heart after the capillary bed.
The process in which a relatively unspecialized endothelial cell acquires specialized features of an arterial endothelial cell, a thin flattened cell that lines the inside surfaces of arteries.
arterial endothelial cell differentiation
The process in which a relatively unspecialized endothelial cell acquires specialized features of a venous endothelial cell, a thin flattened cell that lines the inside surfaces of veins.
The developmental process that results in the creation of defined areas or spaces within the neural plate to which cells respond and eventually are instructed to differentiate.
The pattern specification process that results in the subdivision of an axis or axes of the neural plate 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.
The developmental process pertaining to the initial formation of a camera-type eye from unspecified neurectoderm. This process begins with the differentiation of cells that form the optic field and ends when the optic cup has attained its shape.
The developmental process pertaining to the initial formation of the heart from unspecified parts. This process begins with the specific processes that contribute to the appearance of the heart field and the arrival of cardiac neural crest to the heart region. The process ends when the structural rudiment is recognizable.
The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell of the lung. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types.
mesenchymal cell differentiation involved in lung development
The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population that contributes to the progression of the lung over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.
mesenchymal cell proliferation involved in lung development
The process in which a relatively unspecialized cell acquires specialized features of a pacemaker cell. Pacemaker cells are specialized cardiomyocytes that are responsible for regulating the timing of heart contractions.
The process in which a relatively unspecialized cell acquires specialized features of a sinoatrial (SA) node cell. SA node cells are pacemaker cells that are found in the sinoatrial node.
The process in which a relatively unspecialized cell acquires specialized features of an atrioventricular (AV) node cell. AV node cells are pacemaker cells that are found in the atrioventricular node.
atrioventricular node cell differentiation
The process whose specific outcome is the progression of a pacemaker cell over time, from its formation to the mature state. Pacemaker cells are specialized cardiomyocytes that are responsible for regulating the timing of heart contractions.
The process whose specific outcome is the progression of an atrioventricular (AV) node cell over time, from its formation to the mature state.
The process whose specific outcome is the progression of a sinoatrial (SA) node cell over time, from its formation to the mature state. SA node cells are pacemaker cells that are found in the sinoatrial node.
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell of the His-Purkinje system. These cells form the fibers regulate cardiac muscle contraction in the ventricles.
His-Purkinje system cell differentiation
The process whose specific outcome is the progression of a His-Purkinje cell over time, from its formation to the mature state. These cells form the fibers that regulate cardiac muscle contraction in the ventricles.
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cardiac fibroblast. A cardiac fibroblast is a connective tissue cell in the heart which secretes an extracellular matrix rich in collagen and other macromolecules.
The process whose specific outcome is the progression of a cardiac fibroblast over time, from its formation to the mature state. A cardiac fibroblast is a connective tissue cell of the heart which secretes an extracellular matrix rich in collagen and other macromolecules.
The process in which a relatively unspecialized cell acquires specialized features of a neuron of the heart.
The process in which a relatively unspecialized cell acquires specialized features of a blood vessel endothelial cell of the heart. Blood vessel endothelial cells are thin flattened cells that line the inside surfaces of blood vessels.
cardiac blood vessel endothelial cell differentiation
The process in which a relatively unspecialized cell acquires the specialized features of a glial cell of the heart.
The process aimed at the progression of a cardiac glial cell over time, from its formation to the fully functional mature cell.
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an endocardial cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart. The endocardium is the innermost layer of tissue of the heart, and lines the heart chambers.
The progression of an endocardial cell over time, from its formation to the mature cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart.
The process whose specific outcome is the progression of a cardiac neuron over time, from its formation to the mature state.
The orderly movement of a cell from one site to another that will contribute to the progression of the heart over time, from its initial formation, to the mature organ.
cell migration involved in heart development
The orderly movement of a cell from one site to another that contribute to the formation of the heart. The initial heart structure is made up of mesoderm-derived heart progenitor cells and neural crest-derived cells.
cell migration involved in heart formation
The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure.
The process in which the anatomical structures of blood vessels of the heart are generated and organized. The blood vessel is the vasculature carrying blood.
Blood vessel formation in the heart when new vessels emerge from the proliferation of pre-existing blood vessels.
angiogenesis involved in cardiac vascular morphogenesis
angiogenesis involved in heart vascular morphogenesis
angiogenesis involved in coronary vascular morphogenesis
The differentiation of endothelial cells from progenitor cells that contributes to blood vessel development in the heart, and the de novo formation of blood vessels and tubes.
vasculogenesis involved in coronary blood vessel morphogenesis
vasculogenesis involved in coronary vascular morphogenesis
The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form the blood vessels of the heart.
cell migration involved in coronary vasculogenesis
The orderly movement of a cell from one site to another that will contribute to the formation of new blood vessels in the heart from pre-existing blood vessels.
cell migration involved in coronary angiogenesis
The regulated release of a hormone into the circulatory system.
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.
The membrane organization process that joins two lipid bilayers to form a single membrane.
The progression of the visceral serous pericardium from its formation to the mature structure. The visceral serous pericardium is the inner layer of the pericardium.
Any process that modulates the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
Any process that increases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
positive regulation of cartilage development
Any process that decreases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
negative regulation of cartilage development
The process in which a female gonad is generated and organized.
Any process that modulates the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.
regulation of branching involved in lung morphogenesis
Any process that increases the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.
positive regulation of branching involved in lung morphogenesis
Any process that decreases the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.
negative regulation of branching involved in lung morphogenesis
The growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
cell growth involved in cardiac muscle cell development
Any process that modulates the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
regulation of cell growth involved in cardiac muscle cell development
Any process that increases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
positive regulation of cell growth involved in cardiac muscle cell development
Any process that decreases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
negative regulation of cell growth involved in cardiac muscle cell development
The progression of a somite from its initial formation to the mature structure. Somites are mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
The progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin.
The progression of the myotome over time, from its formation to the mature structure. The myotome is the portion of the somite that will give rise to muscle.
The progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra.
The progression of a muscle structure over time, from its formation to its mature state. Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms.
The process in which the iris is generated and organized. The iris is an anatomical structure in the eye whose opening forms the pupil. The iris is responsible for controlling the diameter and size of the pupil and the amount of light reaching the retina.
The process in which the ciliary body generated and organized. The ciliary body is the circumferential tissue inside the eye composed of the ciliary muscle and ciliary processes.
Any process that modulates the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.
Any process that increases the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.
positive regulation of neural retina development
Any process that decreases the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.
negative regulation of neural retina development
The progression of the right horn of the sinus venosus from its formation to the mature structure.
The process in which a relatively unspecialized cell acquires specialized features of a neuroendocrine cell of the lung epithelium.
lung neuroendocrine cell differentiation
The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a neuroendocrine cell. A neuroendocrine cell is a cell that receives input form a neuron which controls the secretion of an endocrine substance.
The process in which a relatively unspecialized cell acquires specialized features of a neuroendocrine cell of the stomach epithelium.
gastric neuroendocrine cell differentiation
stomach neuroendocrine cell differentiation
Any process that modulates the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach.
regulation of stomach neuroendocrine cell differentiation
Any process that decreases the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach.
negative regulation of stomach neuroendocrine cell differentiation
Any process that decreases the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart.
The process in which the anatomical structures of a branched epithelium are generated and organized.
The process in which a relatively unspecialized cell acquires specialized features of a lung secretory cell. A lung secretory cell is a specialized epithelial cell of the lung that contains large secretory granules in its apical part.
The process in which a relatively unspecialized cell acquires specialized features of a lung ciliated cell. A lung ciliated cell is a specialized lung epithelial cell that contains cilia for moving substances released from lung secretory cells.
The progression of the endocardial endothelium over time, from its initial formation to the mature structure. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.
A process which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix of the endocardium. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.
extracellular matrix organisation involved in endocardium development
extracellular matrix organization involved in endocardium development
The process in which the anatomical structures of a tube are generated and organized from an endothelium. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.
The process in which the anatomical structures of a tube are generated and organized from the pulmonary artery endothelium. An pulmonary artery endothelium is an epithelium that lines the pulmonary artery.
pulmonary artery endothelial tube morphogenesis
The process in which the anatomical structures of the pulmonary artery are generated and organized. The pulmonary artery is the artery that carries blood from the heart to the lungs.
Any process that modulates the rate, frequency, or extent of the process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate.
Any process that decreases the rate, frequency, or extent of the process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate.
negative regulation of chondrocyte development
Any process that modulates the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin.
Any process that increases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin.
positive regulation of dermatome development
Any process that decreases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin.
negative regulation of dermatome development
Any process that increases the rate, frequency, or extent of the progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra.
positive regulation of sclerotome development
Any process that modulates the rate, frequency, or extent of the progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra.
The process whose specific outcome is the progression of the vasculature of the retina over time, from its formation to the mature structure.
retina vasculature development in camera-type eye
The process in which the vasculature of the retina is generated and organized.
retina vasculature morphogenesis in camera-type eye
The progression of the cornea over time, from its formation to the mature structure. The cornea is the transparent structure that covers the anterior of the eye.
The process whose specific outcome is the progression of a blood vessel of the retina over time, from its formation to the mature structure.
The process in which a relatively unspecialized cell acquires specialized features of a cardiac neural crest cell that will migrate to the heart and contribute to its development. Cardiac neural crest cells are specialized cells that migrate toward the heart from the third, fourth and sixth pharyngeal arches.
cardiac neural crest cell differentiation involved in heart development
The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the development of the heart.
cardiac neural crest cell development involved in heart development
The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the shaping of the outflow tract.
cardiac neural crest cell development involved in outflow tract morphogenesis
The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the heart.
cell proliferation involved in heart morphogenesis
The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the outflow tract.
cell proliferation involved in outflow tract morphogenesis
Transfer of an organized electrical impulse across the heart to coordinate the contraction of cardiac muscles. The process begins with generation of an action potential (in the sinoatrial node (SA) in humans) and ends with a change in the rate, frequency, or extent of the contraction of the heart muscles.
The multiplication or reproduction of neural precursor cells, resulting in the expansion of a cell population. A neural precursor cell is either a nervous system stem cell or a nervous system progenitor cell.
The multiplication or reproduction of fibroblasts, resulting in the expansion of a fibroblast population that contributes to the shaping of the heart.
fibroblast proliferation involved in heart morphogenesis
The progression of a connective tissue over time, from its formation to the mature structure.
The progression of the reproductive system over time from its formation to the mature structure. The reproductive system consists of the organs that function in reproduction.
Any biological process involved in the maintenance of the steady-state number of hematopoietic stem cells within a population of cells.
A process in which a protein is transported to, or maintained in, a location within a cilium.
The process whose specific outcome is the progression of a myeloid cell over time, from its formation to the mature structure.
A cellular process that results in the breakdown of a cilium.
The process whose specific outcome is the progression of a ganglion over time, from its formation to the mature structure.
The process whose specific outcome is the progression of a sympathetic ganglion over time, from its formation to the mature structure.
The process whose specific outcome is the progression of a cranial ganglion over time, from its formation to the mature structure.
The process whose specific outcome is the progression of a trigeminal ganglion over time, from its formation to the mature structure.
The process in which the anatomical structures of ganglion are generated and organized.
The process that gives rise to ganglion. This process pertains to the initial formation of a structure from unspecified parts.
The process in which the anatomical structure of a trigeminal ganglion is generated and organized.
The process in which the anatomical structure of a cranial ganglion is generated and organized.
The process that gives rise to a cranial ganglion. This process pertains to the initial formation of a structure from unspecified parts.
The process that gives rise to the trigeminal ganglion. This process pertains to the initial formation of a structure from unspecified parts.
The process in which the anatomical structures of a pharyngeal arch artery is generated and organized. The pharyngeal arch arteries are a series of six paired embryological vascular structures, the development of which give rise to several major arteries, such as the stapedial artery, the middle meningeal artery, the internal carotid artery and the pulmonary artery.
A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
transferase complex, transferring phosphorus-containing groups
A process in which a protein is transported to or maintained in a location within the somatodendritic compartment.
protein localization to somatodendritic compartment
The directed movement of a protein to a specific location in a plasma membrane.
establishment of protein localization to plasma membrane
The process in which bones are generated and organized as a result of the conversion of another structural tissue into bone.
The process in which bone which forms superficially in the organism are generated and organized.
The process in which bone which forms deep in the organism are generated and organized.
Any process that modulates the rate, frequency or extent of a small molecule metabolic process.
regulation of small molecule metabolic process
Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process.
positive regulation of small molecule metabolism
positive regulation of small molecule metabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process.
negative regulation of small molecule metabolism
negative regulation of small molecule metabolic process
An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells.
collagen-containing extracellular matrix
Any process that starts or increases the frequency, rate or extent of sister chromatid segregation during mitosis.
positive regulation of mitotic sister chromatid segregation
The process whose specific outcome is the progression of the stomach over time, from its formation to the mature structure. The stomach is an expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ.
The cellular metabolic process in which organic chemical compounds are synthesized from carbon-containing molecules and nutrients using energy obtained from the oxidation of inorganic compounds or methane.
Any process in which a protein is transported to, and/or maintained at the postsynapse, the part of a synapse that is part of the post-synaptic cell.
The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.
cellular protein-containing complex assembly
Any process that modulates a measurable attribute of any biological process, quality or function.
Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
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.
Organized structure of distinctive morphology and function, bounded by a lipid bilayer membrane and occurring outside the cell.
extracellular membrane-enclosed organelle
extracellular membrane-bounded organelle
An organelle lumen that is part of an intracellular organelle.
The cellular homeostatic process that preserves a neuron in a stable, differentiated functional and structural state.
Binding to fibrinogen, a highly soluble hexameric glycoprotein complex that is found in blood plasma and is converted to fibrin by thrombin in the coagulation cascade.
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans).
Any process that modulates the frequency, rate or extent of the regulated release of glucagon.
Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of glucagon.
negative regulation of glucagon secretion
Any process that activates or increases the frequency, rate or extent of the regulated release of glucagon.
positive regulation of glucagon secretion
A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix.
The directed movement of a protein to a specific location on a chromosome.
establishment of protein localisation to chromosome
establishment of protein localization to chromosome
Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location.
regulation of establishment of protein localisation
regulation of establishment of protein localization
Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location on a chromosome.
regulation of establishment of protein localisation to chromosome
regulation of establishment of protein localization to chromosome
The regulated release of somatostatin from secretory granules in the D cells of the pancreas.
The process whose specific outcome is the progression of a pigment cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a pigment cell fate.
The multiplication or reproduction of fat cells by cell division, resulting in the expansion of their population. A fat cell is an animal connective tissue cell specialized for the synthesis and storage of fat.
Any process that modulates the frequency, rate or extent of fat cell proliferation.
regulation of adipose cell proliferation
Any process that stops or decreases the rate or extent of fat cell proliferation.
down regulation of fat cell proliferation
down-regulation of fat cell proliferation
downregulation of fat cell proliferation
negative regulation of adipocyte proliferation
negative regulation of adipose cell proliferation
negative regulation of fat cell proliferation
Any process that activates or increases the rate or extent of fat cell proliferation.
positive regulation of adipocyte proliferation
positive regulation of adipose cell proliferation
positive regulation of fat cell proliferation
A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis.
exocytic constitutive secretory pathway transport vesicle
Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
regulation of microtubule cytoskeleton organisation
regulation of microtubule cytoskeleton organization
The expansion of a leukocyte population by cell division.
Any process that modulates the frequency, rate or extent of leukocyte proliferation.
Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte proliferation.
down regulation of leukocyte proliferation
down-regulation of leukocyte proliferation
downregulation of leukocyte proliferation
negative regulation of leukocyte proliferation
Any process that activates or increases the frequency, rate or extent of leukocyte proliferation.
up regulation of leukocyte proliferation
up-regulation of leukocyte proliferation
positive regulation of leukocyte proliferation
Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic heterochromatin, a compact and highly condensed form of chromatin.
The aggregation, arrangement and bonding together of a set of components to form a basement membrane, a part of the extracellular region that consists of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue.
Note that this term has no relationship to 'membrane assembly ; GO:0071709' because the basement membrane is not a lipid bilayer.
The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide or use of neuron-specific markers) show that neuron death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the neuron 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'), and the cell type captured as an annotation extension; or the term GO:0051402 'neuron apoptotic process' may be considered, if appropriate.
A cellular process that results in a change in the spatial configuration of a DNA molecule. A conformation change can bend DNA, or alter the, twist, writhe, or linking number of a DNA molecule.
Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into chromatin.
The directed movement of a protein to a part of a chromosome that is organized into chromatin.
establishment of protein localisation to chromatin
establishment of protein localization to chromatin
The expansion of a hematopoietic stem cell population by cell division. A hematopoietic stem cell is a stem cell from which all cells of the lymphoid and myeloid lineages develop.
The process of biting and mashing food with the teeth prior to swallowing.
Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location.
protein localisation in extracellular region
protein localization in extracellular region
protein localization to extracellular region
The progression of an ectodermal placode over time from its initial formation until its mature state. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm.
The process in which the anatomical structures of an ectodermal placode are generated and organized. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm.
The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon.
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
organic molecular entity metabolic process
The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The aggregation, arrangement and bonding together of a set of components to form a membrane.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the basement membrane.
Note that this term has no relationship to 'membrane organization ; GO:0061024' because the basement membrane is not a lipid bilayer.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear inner or outer membrane.
nuclear membrane organization and biogenesis
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear outer membrane.
nuclear outer membrane organization and biogenesis
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex.
RNA-protein complex subunit organization
protein-RNA complex subunit organization
ribonucleoprotein complex subunit organisation
ribonucleoprotein complex subunit organization
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation or biogenesis
cellular component organisation or biogenesis at cellular level
cellular component organization or biogenesis at cellular level
cellular component organization or biogenesis
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 monoamine stimulus. A monoamine is any of a group of molecular messengers that contain one amino group that is connected to an aromatic ring by ethylene group (-CH2-CH2-). Monoamines are derived from the aromatic amino acids phenylalanine, tyrosine, histidine and tryptophan.
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 catecholamine stimulus. A catecholamine is any of a group of biogenic amines that includes 4-(2-aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution.
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 norepinephrine stimulus. Norepinephrine is a catecholamine that has the formula C8H11NO3; it acts as a hormone, and as a neurotransmitter in most of the sympathetic nervous system.
Note that epinephrine and norepinephrine are ligands for the same receptors, and there are multiple adrenergic receptors.
Any apoptotic process in a leukocyte, an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542).
The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
An supramolecular fiber that consists of an insoluble core of polymerized tropoelastin monomers and a surrounding mantle of microfibrils. Elastic fibers provide elasticity and recoiling to tissues and organs, and maintain structural integrity against mechanical strain.
The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm.
extracellular vesicular exosome assembly
The multiplication or reproduction of stem cells, resulting in the expansion of a stem cell population. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
Any process that modulates the frequency, rate or extent of stem cell proliferation. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
The process in which the anatomical structures of a mesenchymal tissue are generated and organized. A mesenchymal tissue is made up of loosely packed stellate cells.
The developmental process pertaining to the initial formation of an epithelial tube.
Any process that decreases the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.
negative regulation of mesenchymal cell proliferation
The directed movement of compounds that contain sulfur, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The process whose specific outcome is the progression of the circulatory system over time, from its formation to the mature structure. The circulatory system is the organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis.
The progression of the vascular cord over time from its initial formation until its mature state. The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis.
The directed movement of an organelle along a microtubule, mediated by motor proteins. This process begins with the attachment of an organelle to a microtubule, and ends when the organelle reaches its final destination.
microtubule-based organelle localization
Any apoptotic process in an endothelial cell. An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal.
endothelial cell programmed cell death by apoptosis
programmed cell death of endothelial cells by apoptosis
programmed cell death, endothelial cells
The chemical reactions and pathways involving diatomic oxygen (O2).
The directed movement of a protein to a specific location on or in an organelle. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle.
establishment of protein localisation to organelle
establishment of protein localization to organelle
A process in which a protein is transported to, or maintained in, a specific location in a membrane.
A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
A process in which a protein is transported to, or maintained at, a location in a vacuole.
The directed movement of a protein to a specific location in a vacuole.
establishment of protein localisation to vacuole
establishment of protein localization to vacuole
A process in which a protein is transported to, or maintained in, the cell cortex.
A cellular protein localization process in which a protein is transported to, or maintained at, a location within the microtubule cytoskeleton.
protein localisation to microtubule cytoskeleton
protein localization to microtubule cytoskeleton
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.
The aggregation, arrangement and bonding together of the extracellular matrix.
A process carried out by symbiont gene products that enables a symbiotic interaction with a host organism, that is beneficial to the host organism.
An action potential that occurs in a cardiac muscle cell.
An action potential that occurs in a sinoatrial node cardiac muscle cell.
SA node cardiac muscle cell action potential
SAN cardiac muscle cell action potential
sinoatrial node cardiac muscle cell action potential
sinus node cardiac muscle cell action potential
An action potential that occurs in an atrioventricular node cardiac muscle cell.
AV node cardiac muscle cell action potential
atrioventricular node cardiac muscle cell action potential
An action potential that occurs in a Purkinje myocyte.
Any process that mediates the transfer of information from an SA node cardiomyocyte to an atrial cardiomyocyte.
SA node cardiac muscle cell to atrial cardiac muscle cell signalling
SA node cardiomyocyte to atrial cardiomyocyte signalling
SAN cardiomyocyte to atrial cardiomyocyte signalling
sinoatrial node cardiomyocyte to atrial cardiomyocyte signalling
sinus node cardiomyocyte to atrial cardiomyocyte signalling
SA node cell to atrial cardiac muscle cell signaling
Any process that mediates the transfer of information from one cell to another and contributes to the heart process that regulates cardiac muscle contraction; beginning with the generation of an action potential in the sinoatrial node and ending with regulation of contraction of the myocardium.
cell-cell signalling involved in cardiac conduction
cell-cell signaling involved in cardiac conduction
Any process that mediates the transfer of information from an AV node cardiac muscle cell to a bundle of His cardiomyocyte.
AV node cell to bundle of His cell signalling
atrioventricular node to bundle of His cell signaling
AV node cell to bundle of His cell signaling
Any process that mediates the transfer of information from a Purkinje myocyte to a ventricular cardiac muscle cell.
Purkinje myocyte to ventricular cardiac muscle cell signalling
Purkinje myocyte to ventricular cardiac muscle cell signaling
Any process that mediates interactions between a cell and its surroundings that contributes to the process of cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
cell communication involved in cardiac conduction
The process that mediates interactions between an AV node cell and its surroundings that contributes to the process of the AV node cell communicating with a bundle of His cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
atrioventricular node cell to bundle of His cell communication
AV node cell to bundle of His cell communication
The process that mediates interactions between a Purkinje myocyte and its surroundings that contributes to the process of the Purkinje myocyte communicating with a ventricular cardiac muscle cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
Purkinje myocyte to ventricular cardiac muscle cell communication
The process that mediates interactions between an SA node cardiomyocyte and its surroundings that contributes to the process of the SA node cardiomyocyte communicating with an atrial cardiomyocyte in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
SA node cardiac muscle cell to atrial cardiac muscle cell communication
SA node cardiomyocyte to atrial cardiomyocyte communication
SAN cardiomyocyte to atrial cardiomyocyte communication
sinoatrial node cardiomyocyte to atrial cardiomyocyte communication
sinus node cardiomyocyte to atrial cardiomyocyte communication
SA node cell to atrial cardiac muscle cell communication
Any process that increases the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell.
positive regulation of microtubule nucleation
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.
positive regulation of cell cycle process
Any process that modulates the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits.
Any process that increases the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits.
positive regulation of ribosome biogenesis
Any process that decreases the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits.
negative regulation of ribosome biogenesis
Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that increases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix.
positive regulation of extracellular matrix disassembly
The directed movement of a protein to a specific location in a membrane.
establishment of protein localisation in membrane
establishment of protein localization in membrane
establishment of protein localization to membrane
A cellular process that results in the breakdown of a Golgi apparatus that contributes to Golgi inheritance.
The reformation of the Golgi following its breakdown and partitioning contributing to Golgi inheritance.
Any process that modulates the rate, frequency or extent of Golgi inheritance. Golgi inheritance is the partitioning of Golgi apparatus between daughter cells at cell division.
The process in which the structures of a chondrocyte are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a chondrocyte.
The joining of two lipid bilayers to form a single organelle membrane.
Any process that modulates the frequency, rate or extent of a muscle system process, a multicellular organismal process carried out by any of the organs or tissues in a muscle system.
Any process that modulates the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas.
Any process that increases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas.
positive regulation of somatostatin secretion
Any process that decreases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas.
negative regulation of somatostatin secretion
Any process that modulates the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules.
Any process that increases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules.
positive regulation of peptide hormone secretion
Any process that decreases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules.
negative regulation of peptide hormone secretion
Any process that modulates the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation proceeds.
Any process that increases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes.
positive regulation of neural crest formation
Any process that decreases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes.
negative regulation of neural crest formation
Any cellular metabolic process involving nucleic acids.
Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells.
positive regulation of intracellular protein transport
Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells.
negative regulation of intracellular protein transport
A process in which a protein is transported to, or maintained at, a location within a nuclear envelope.
protein localization in nuclear envelope
protein localization to nuclear envelope
Morphogenesis of a sensory organ. A sensory organ is defined as a tissue or set of tissues that work together to receive and transmit signals from external or internal stimuli. 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.
A macromolecular localization process in which RNA is transported to and maintained in a location within the nucleus.
Any membrane that is part of a pigment granule.
All of the contents of a cilium, excluding the plasma membrane surrounding the cilium.
Note that we deem cilium and microtubule-based flagellum to be equivalent. Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). For this reason, the term "ciliary plasm" is not linked to "cytoplasm".
Any apoptotic process in a motor neuron, an efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement.
A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.
The process aimed at the progression of a vascular smooth muscle cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels.
vascular associated smooth muscle cell development
Any apoptotic process in a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types.
Binding to an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure.
The chemical reactions and pathways involving the ammonium ion.
A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
induction of apoptosis by extracellular signals
This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways.
A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into heterochromatin.
A prolongation or process extending from a glial cell.
An arrangement of closely apposed microtubules running parallel to each other.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a supramolecular fiber, a polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure.
extracellular fibril organization and biogenesis
Any apoptotic process in a retinal rod cell, one of the two photoreceptor cell types of the vertebrate retina.
Any apoptotic process in a retinal cone cell, one of the two photoreceptor cell types of the vertebrate retina.
A cardiac myofibril is a myofibril specific to cardiac muscle cells.
Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole.
Any vesicle that is part of the intracellular region.
The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane.
anchoring of the basal body to the plasma membrane
Basal bodies in jawed vertebrates appear to first attach to a ciliary vesicle. It is unclear how specific this is to jawed vertebrates or if other organisms also employ this sequence. Some species like Giardia intestinalis do not relocate their basal bodies to the plasma membrane, but have their axonemes extend through the cytosol to then protrude out of the cell to form flagella.
ciliary basal body-plasma membrane docking
The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces.
vesicle targeting, trans-Golgi to periciliary membrane compartment
The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane.
A neuromuscular junction in which the target muscle cell is a myotube.
In vertebrates, the term 'neuromuscular junction' is limited to synapses targeting the myotubes of skeletal muscle (AKA skeletal muscle fibers). Neuromuscular junctions targeting other muscle cell types exist in invertebrates such as the mononucleate somatic muscles of nematodes.
The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle fiber cell. Skeletal muscle fiber differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual skeletal muscle fibers fuse to form bigger myotubes and start to contract.
The lipid bilayer that forms the outer-most layer of an organelle.
Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes.
A membrane that is a (regional) part of the plasma membrane.
Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass.
A supramolecular assembly of fibrillar collagen complexes in the form of a long fiber (fibril) with transverse striations (bands).
A complex of collagen trimers such as a fibril or collagen network.
A supramolecular complex that consists of collagen triple helices associated to form a network.
Any collagen timer that is part of a basement membrane.
The directed movement of some substance from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis.
The process whose specific outcome is the progression of a bone cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
Not to be used for manual annotation. Please choose a more specific cell development term or if not possible, bone or bone tissue development.
The process whose specific outcome is the progression of the skin epidermis over time, from its formation to the mature structure.
The part of a synapse that is part of the presynaptic cell.
The part of a synapse that is part of the post-synaptic cell.
Any protein complex that is part of a membrane.
Any protein complex that is part of the plasma membrane.
The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
The directed movement of a protein along a microtubule, mediated by motor proteins.
The increase in size or mass of an intramembranous bone that contributes to the shaping of the bone.
The increase in size or mass of a bone that contributes to the shaping of that bone.
The actin cytoskeleton that is part of a postsynapse.
The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis.
vesicle-mediated transport to the plasma membrane
A cellular process that results in the controlled breakdown of synapse. After it starts the process is continuous until the synapse has disappeared.
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
The ion channels through which current flows during an action potential should be annotated to the process 'action potential'. Gene products involved in modulating the characteristics of an action potential via changing the expression levels or the activity of these channels (e.g. modulating their kinetics or voltage sensitivity) should be annotated to this regulation term.
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a cardiac muscle cell. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
regulation of cardiac muscle cell action potential
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an atrioventricular node myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
regulation of AV node cardiac muscle cell action potential
regulation of atrioventricular node cardiac muscle cell action potential
regulation of AV node cell action potential
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a Purkinje myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
regulation of Purkinje myocyte action potential
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an SA node cardiac myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
regulation of SA node cardiac muscle cell action potential
regulation of SAN cardiac muscle cell action potential
regulation of sinoatrial node cardiac muscle cell action potential
regulation of sinus node cardiac muscle cell action potential
regulation of SA node cell action potential
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a neuron. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
Cell-cell signaling from pre to post-synapse, across the synaptic cleft.
Cell-cell signaling from post to pre-synapse, across the synaptic cleft.
Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by a lipid ligand.
retrograde trans-synaptic signaling by lipid
Signal transduction in which the initial step occurs in a postsynapse.
Do not directly annotate. This term is intended for automatically grouping annotations to signal transduction classes extended with has_start_location/occurs_in postsynapse or one of its parts.
Signal transduction in which the initial step occurs in a presynapse.
Do not directly annotate. This term intended for grouping. Annotate to either a subclass or to some other subclass of signal transduction extended with has_start_location/occurs_in presynapse or one of its parts. Such extensions will result in automatic annotation to this term.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins in the postsynaptic actin cytoskeleton.
postsynaptic actin cytoskeleton organization
The postsynapse of a neuromuscular junction. In vertebrate muscles this includes the motor end-plate, consisting of postjunctional folds of the sarcolemma.
Any vesicle-mediated transport that occurs in a synapse.
The aggregation, arrangement and bonding together of a set of components to form a presynapse.
The aggregation, arrangement and bonding together of a set of components to form a postsynapse.
A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber.
Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by a neuropeptide.
retrograde trans-synaptic signaling by neuropeptide
Modulation of synaptic transmittion by cell-cell signaling across the synaptic cleft from postsynapse to presynapse, mediated by a neuropeptide.
Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua.
retrograde trans-synaptic signaling by neuropeptide, modulating synaptic transmission
The movement of a cellular component as a result of microtubule polymerization.
microtubule polymerization based movement
A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
The transport of a protein driven by polymerization of a microtubule to which it is attached.
microtubule polymerization based protein transport
A microtubule-based process that results in the transport of proteins.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins in the presynaptic actin cytoskeleton.
presynaptic actin cytoskeleton organization
The actin cytoskeleton that is part of a presynapse.
Cell-cell signaling in which the ligand is carried between cells by an exosome.
Transynaptic signaling in which the ligand is carried across the synapse by an exosome.
exosome mediated transynaptic signalling
Any process, acting in the postsynapse that results in modulation of chemical synaptic transmission.
postsynaptic modulation of chemical synaptic transmission
Any process, acting in the presynapse that results in modulation of chemical synaptic transmission.
presynaptic modulation of chemical synaptic transmission
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a presynapse.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a postsynapse.
Any process that modulates the physical form of a presynapse.
regulation of presynapse organization and biogenesis
Any process that modulates the physical form of a postsynapse.
regulation of postsynapse organization and biogenesis
Any process that modulates the frequency, rate or extent of trans-synaptic signaling.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures and their associated proteins in the presynaptic cytoskeleton.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising cytoskeletal filaments and their associated proteins in the postsynaptic cytoskeleton.
Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space.
The lipid bilayer surrounding an exocytic vesicle.
A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space.
A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure.
A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits.
The directed movement of a vesicle along a cytoskeletal fiber such as a microtubule or and actin filament, mediated by motor proteins.
cytoskeletal fiber-based vesicle localization
The pathway leading to secretion of a neurotransmitter from the presynapse as part of synaptic transmission.
presynaptic process involved in chemical synaptic transmission
Cell-cell signaling to, from or within a synapse.
Cell-cell signaling in either direction across the synaptic cleft.
Cell-cell signaling to or from a synapse, mediated by a peptide.
Cell-cell signaling between presynapse and postsynapse mediated by a peptide ligand crossing the synaptic cleft.
trans-synaptic signaling by neuropeptide
Cell-cell signaling from post to pre-synapse, across the synaptic cleft, mediated by a lipid.
Any process that modulates synaptic transmission by regulating translation occurring at the synapse.
regulation of translation at synapse, modulating synaptic transmission
Cell-cell signaling between presynapse and postsynapse, across the synaptic cleft, that modulates the synaptic transmission properties of the synapse.
trans-synaptic signaling, modulating synaptic transmission
Cell-cell signaling between presynapse and postsynapse, via the vesicular release and reception of neuropeptide molecules, that modulates the synaptic transmission properties of the synapse.
trans-synaptic signaling by neuropeptide, modulating synaptic transmission
Cell-cell signaling between presynapse and postsynapse, via the release and reception of lipid molecules, that modulates the synaptic transmission properties of the synapse.
trans-synaptic signaling by lipid, modulating synaptic transmission
Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.
The portion of the cytoskeleton contained within the presynapse.
The portion of the cytoskeleton contained within the postsynapse.
Any process that modulates synaptic transmission by regulating translation occurring at the presynapse.
regulation of translation at presynapse, modulating synaptic transmission
Any process that modulates synaptic transmission by regulating translation occurring at the postsynapse.
regulation of translation at postsynapse, modulating synaptic transmission
A process in which protein is transported from one region of the plasma membrane to another.
protein transport within plasma membrane
The directed movement of proteins along microtubules in neuron projections.
The complete extent of cell cortex that underlies some some region of the plasma membrane.
Any action potential process that regulates skeletal muscle contraction.
regulation of skeletal muscle contraction by action potential
The multiplication or reproduction of blood vessel endothelial cells, resulting in the expansion of a cell population.
A mitotic cell cycle process which results in the assembly, arrangement, or disassembly of the nuclear inner or outer membrane during mitosis.
nuclear membrane organization involved in mitotic nuclear division
This process only occurs in organisms which undergo 'closed mitosis' without nuclear breakdown.
The process in which a nuclear membrane is synthesized, aggregates, and bonds together.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a neuron, e.g. an axon, or a dendrite.
Any process that modulates the frequency, rate or extent of vesicle fusion with Golgi apparatus.
regulation of vesicle fusion with Golgi apparatus
Any process that stops, prevents or reduces the frequency, rate or extent of vesicle fustion with Golgi apparatus.
negative regulation of vesicle fusion with Golgi apparatus
Any process that activates or increases the frequency, rate or extent of vesicle fusion with Golgi apparatus.
positive regulation of vesicle fusion with Golgi apparatus
Any process that modulates the frequency, rate or extent of the assembly, disassembly or arrangement of constituent parts of the basement membrane.
regulation of basement membrane organization
Any process that modulates the frequency, rate or extent of the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin.
regulation of actomyosin structure organization
The multiplication or reproduction of cardiac muscle myoblasts, resulting in the expansion of a cardiac muscle myoblast cell population. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life.
Any process that modulates the frequency, rate or extent of cardiac muscle myoblast proliferation.
regulation of cardiac muscle myoblast proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle myoblast proliferation.
negative regulation of cardiac muscle myoblast proliferation
Any process that activates or increases the frequency, rate or extent of cardiac muscle myoblast proliferation.
positive regulation of cardiac muscle myoblast proliferation
The process in which the anatomical structures of the pharynx are generated and organized.
Any process that modulates the frequency, rate or extent of pharynx morphogenesis, the process in which the anatomical structure of the pharynx is generated and organized.
Any process that stops, prevents, or reduces the frequency, rate or extent of pharynx morphogenesis.
negative regulation of pharynx morphogenesis
Any process that activates or increases the frequency, rate or extent of pharynx morphogenesis.
positive regulation of pharynx morphogenesis
Any process that modulates the frequency, rate or extent of blood vessel endothelial cell differentiation.
regulation of blood vessel endothelial cell differentiation
Any process that activates or increases the frequency, rate or extent of blood vessel endothelial cell differentiation.
positive regulation of blood vessel endothelial cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel endothelial cell differentiation.
negative regulation of blood vessel endothelial cell differentiation
Any process that activates or increases the frequency, rate or extent of animal organ morphogenesis.
positive regulation of animal organ morphogenesis
Any process that stops, prevents, or reduces the frequency, rate or extent of animal organ morphogenesis.
negative regulation of animal organ morphogenesis
Any process that modulates the frequency, rate or extent of compound eye photoreceptor cell differentiation.
regulation of compound eye photoreceptor cell differentiation
Any process that activates or increases the frequency, rate or extent of compound eye photoreceptor cell differentiation.
positive regulation of compound eye photoreceptor cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of compound eye photoreceptor cell differentiation.
negative regulation of compound eye photoreceptor cell differentiation
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
Binding to somatostatin, a polypeptide hormone involved in regulating pancreatic alpha and pancreatic beta cells and controlling growth hormone secretion as well as many other functions. Somatostatin is produced by several cell types including pancreatic delta cells. There are several different mature forms of somatostatin.
A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon.
Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon.
plasma membrane bounded cell projection assembly
Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly.
regulation of plasma membrane bounded cell projection assembly
Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly.
negative regulation of plasma membrane bounded cell projection assembly
Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly.
positive regulation of plasma membrane bounded cell projection assembly
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of plasma membrane bounded cell projections.
regulation of plasma membrane bounded cell projection organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon.
plasma membrane bounded cell projection organization
The process in which the anatomical structures of a plasma membrane bounded cell projection are generated and organized.
plasma membrane bounded cell projection morphogenesis
All of the contents of a plasma membrane bounded neuron projection, excluding the plasma membrane surrounding the projection.
Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to chromatin.
negative regulation of protein localisation to chromatin
negative regulation of protein localization to chromatin
Any process that activates or increases the frequency, rate or extent of protein localization to chromatin.
positive regulation of protein localisation to chromatin
positive regulation of protein localization to chromatin
Any process that modulates the frequency, rate, extent or location of heterochromatin organization.
regulation of heterochromatin organization
Any process that stops, prevents, or reduces the frequency, rate or extent of heterochromatin organization.
down regulation of heterochromatin organization
down-regulation of heterochromatin organization
downregulation of heterochromatin organization
inhibition of heterochromatin organization
negative regulation of heterochromatin organization
Any process that activates or increases the frequency, rate or extent of heterochromatin organization.
up regulation of heterochromatin organization
up-regulation of heterochromatin organization
upregulation of heterochromatin organization
activation of heterochromatin organization
stimulation of heterochromatin organization
positive regulation of heterochromatin organization
Any process that modulates the frequency, rate or extent of the deposition or modulates the distribution of coloring matter in an organism.
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.
The cellular processes that contribute to exocytosis.
The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other.
organelle localization by membrane tethering
Catalytic activity that acts to modify a protein.
Catalytic activity that acts to modify DNA.
Catalytic activity that acts to modify RNA, driven by ATP hydrolysis.
Catalysis of a biochemical reaction at physiological temperatures in which one of the substrates is a glycoprotein.
catalytic activity, acting on a glycoprotein
The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content.
Translation that occurs at the presynapse.
Translation that occurs at the presynapse, and that modulates chemical synaptic transmission.
translation at presynapse, modulating chemical synaptic transmission
Translation that occurs at the postsynapse.
Any process that regulates translation occurring at the synapse.
Any process that regulates translation occurring at the presynapse.
Any process that regulates translation occurring at the postsynapse.
regulation of translation at postsynapse
A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium.
The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis.
The directed movement of a lipid from a cell, into the extracellular region.
The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis.
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus.
The division of a vacuole within a cell to form two or more separate vacuoles.
Catalytic activity that acts to modify a nucleic acid.
catalytic activity, acting on a nucleic acid
The aggregation, arrangement and bonding together of a set of components to form a non-membrane-bounded organelle.
non-membrane-bounded organelle formation
non-membrane-enclosed organelle assembly
non-membrane-enclosed organelle formation
Any process that modulates the frequency, rate or extent of postsynapse assembly, the aggregation, arrangement and bonding together of a set of components to form a postsynapse.
The process whose specific outcome is the progression of the visual system over time, from its formation to the mature structure, including the eye, parts of the central nervous system (CNS) involved in processing of visual inputs, and connecting nerve pathways.
Cell-cell signaling that mediates the transfer of information from a glial cell to a neuron. This signaling has been shown to be mediated by various molecules, depending on which glial cells release them, and in which tissues the signalling occurs, e.g. microglial cell-derived nerve growth factor (NGF) in the retina, or microglial cell-derived superoxide ions in the cerebellum.
Cell-cell signaling that mediates the transfer of information from a neuron to a glial cell. This signalling has been shown to be mediated by various molecules released by different types of neurons, e.g. glutamate, gamma-amino butyric acid (GABA), noradrenaline, acetylcholine, dopamine and adenosine.
A process in which a protein is transported to, or maintained, in a location within a cell-cell junction.
protein localization to cell-cell junction
Any process that modulates the frequency, rate or extent of protein localization to cell-cell junction.
regulation of protein localization to cell-cell junction
Any process that activates or increases the frequency, rate or extent of protein localization to cell-cell junction.
positive regulation of protein localization to cell-cell junction
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell-cell junction.
negative regulation of protein localisation to cell-cell junction
negative regulation of protein localization to cell-cell junction
The disaggregation of a cell junction into its constituent components.
The disaggregation of a cell-cell junction into its constituent components.
Any regulation of signal transduction that takes place in the extracellular region.
regulation of signaling pathway in extracellular region
regulation of signalling pathway in extracellular region
extracellular regulation of signal transduction
Any negative regulation of signal transduction that takes place in extracellular region.
down regulation of signal transduction in extracellular region
down-regulation of signal transduction in extracellular region
downregulation of signal transduction in extracellular region
negative regulation of signaling pathway in extracellular region
negative regulation of signalling pathway in extracellular region
extracellular inhibition of signaling pathway
inhibition of signal transduction in extracellular region
extracellular negative regulation of signal transduction
Any process that modulates the frequency, rate or extent of execution phase of apoptosis.
regulation of execution phase of apoptosis
Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis.
down regulation of execution phase of apoptosis
down-regulation of execution phase of apoptosis
downregulation of execution phase of apoptosis
inhibition of execution phase of apoptosis
negative regulation of execution phase of apoptosis
Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis.
up regulation of execution phase of apoptosis
up-regulation of execution phase of apoptosis
upregulation of execution phase of apoptosis
activation of execution phase of apoptosis
positive regulation of execution phase of apoptosis
Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor.
Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.
down regulation of receptor-associated protein activity
Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
Any process that modulates the frequency, rate or extent of hyaluronan biosynthetic process.
regulation of hyaluronan biosynthetic process
Any process that stops, prevents or reduces the frequency, rate or extent of hyaluronan biosynthetic process.
down regulation of hyaluronan biosynthesis
down regulation of hyaluronan biosynthetic process
down-regulation of hyaluronan biosynthesis
down-regulation of hyaluronan biosynthetic process
downregulation of hyaluronan biosynthesis
downregulation of hyaluronan biosynthetic process
negative regulation of hyaluronan anabolism
negative regulation of hyaluronan biosynthesis
negative regulation of hyaluronan formation
negative regulation of hyaluronan synthesis
inhibition of hyaluronan biosynthetic process
negative regulation of hyaluronan biosynthetic process
Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process.
positive regulation of hyaluronan anabolism
positive regulation of hyaluronan biosynthesis
positive regulation of hyaluronan formation
positive regulation of hyaluronan synthesis
up regulation of hyaluronan biosynthesis
up regulation of hyaluronan biosynthetic process
up-regulation of hyaluronan biosynthesis
up-regulation of hyaluronan biosynthetic process
upregulation of hyaluronan biosynthetic process
activation of hyaluronan biosynthetic process
positive regulation of hyaluronan biosynthetic process
Any process that modulates the frequency, rate or extent of lipid binding.
Any process that stops, prevents or reduces the frequency, rate or extent of lipid binding.
Any process that activates or increases the frequency, rate or extent of lipid binding.
Any process that modulates the frequency, rate or extent of protein localization to nucleus.
regulation of protein localisation to nucleus
regulation of protein localization in cell nucleus
regulation of protein localization in nucleus
regulation of protein localization to nucleus
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleus.
down regulation of protein localisation to nucleus
down regulation of protein localization in cell nucleus
down regulation of protein localization in nucleus
down regulation of protein localization to nucleus
down-regulation of protein localisation to nucleus
down-regulation of protein localization in cell nucleus
down-regulation of protein localization in nucleus
down-regulation of protein localization to nucleus
downregulation of protein localisation to nucleus
downregulation of protein localization in cell nucleus
downregulation of protein localization in nucleus
downregulation of protein localization to nucleus
negative regulation of protein localisation to nucleus
negative regulation of protein localization in cell nucleus
negative regulation of protein localization in nucleus
inhibition of protein localisation to nucleus
inhibition of protein localization in cell nucleus
inhibition of protein localization in nucleus
inhibition of protein localization to nucleus
negative regulation of protein localization to nucleus
Any process that activates or increases the frequency, rate or extent of protein localization to nucleus.
activation of protein localization in nucleus
positive regulation of protein localisation to nucleus
positive regulation of protein localization in cell nucleus
positive regulation of protein localization in nucleus
up regulation of protein localisation to nucleus
up regulation of protein localization in cell nucleus
up regulation of protein localization in nucleus
up regulation of protein localization to nucleus
up-regulation of protein localisation to nucleus
up-regulation of protein localization in cell nucleus
up-regulation of protein localization in nucleus
up-regulation of protein localization to nucleus
upregulation of protein localisation to nucleus
upregulation of protein localization in cell nucleus
upregulation of protein localization in nucleus
upregulation of protein localization to nucleus
activation of protein localisation to nucleus
activation of protein localization in cell nucleus
activation of protein localization to nucleus
positive regulation of protein localization to nucleus
The chemical reactions and pathways involving carbohydrate derivative.
carbohydrate derivative metabolic process
The chemical reactions and pathways resulting in the formation of carbohydrate derivative.
carbohydrate derivative biosynthetic process
Any gene expression that is involved in extracellular matrix organization. Gene expression includes both transcription to produce an RNA transcript, and the translation of that mRNA into protein. Protein maturation is included in gene expression when required to form an active form of a product from an inactive precursor form.
expression of extracellular matrix proteins
gene expression involved in extracellular matrix organization
The chemical reactions and pathways involving primary amino compound.
primary amino compound metabolic process
The chemical reactions and pathways resulting in the formation of primary amino compound.
primary amino compound biosynthetic process
Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex.
regulation of translation initiation ternary complex assembly
regulation of formation of translation initiation ternary complex
Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation initiation ternary complex.
down regulation of formation of translation initiation ternary complex
down regulation of translation initiation ternary complex assembly
down-regulation of formation of translation initiation ternary complex
down-regulation of translation initiation ternary complex assembly
downregulation of formation of translation initiation ternary complex
downregulation of translation initiation ternary complex assembly
inhibition of translation initiation ternary complex assembly
negative regulation of translation initiation ternary complex assembly
inhibition of formation of translation initiation ternary complex
negative regulation of formation of translation initiation ternary complex
Any process that activates or increases the frequency, rate or extent of formation of translation initiation ternary complex.
activation of translation initiation ternary complex assembly
positive regulation of translation initiation ternary complex assembly
up regulation of formation of translation initiation ternary complex
up regulation of translation initiation ternary complex assembly
up-regulation of formation of translation initiation ternary complex
up-regulation of translation initiation ternary complex assembly
upregulation of formation of translation initiation ternary complex
upregulation of translation initiation ternary complex assembly
activation of formation of translation initiation ternary complex
positive regulation of formation of translation initiation ternary complex
Any process that modulates the frequency, rate or extent of extracellular matrix assembly.
regulation of extracellular matrix assembly
Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix assembly.
down regulation of extracellular matrix assembly
down-regulation of extracellular matrix assembly
downregulation of extracellular matrix assembly
inhibition of extracellular matrix assembly
negative regulation of extracellular matrix assembly
Any process that activates or increases the frequency, rate or extent of extracellular matrix assembly.
up regulation of extracellular matrix assembly
up-regulation of extracellular matrix assembly
upregulation of extracellular matrix assembly
activation of extracellular matrix assembly
positive regulation of extracellular matrix assembly
Any process that modulates the frequency, rate or extent of cardiac chamber formation.
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac chamber formation.
down regulation of cardiac chamber formation
down regulation of heart chamber formation
down-regulation of cardiac chamber formation
down-regulation of heart chamber formation
downregulation of cardiac chamber formation
downregulation of heart chamber formation
negative regulation of heart chamber formation
negative regulation of cardiac chamber formation
Any process that activates or increases the frequency, rate or extent of cardiac chamber formation.
positive regulation of heart chamber formation
up regulation of cardiac chamber formation
up regulation of heart chamber formation
up-regulation of cardiac chamber formation
up-regulation of heart chamber formation
upregulation of cardiac chamber formation
positive regulation of cardiac chamber formation
Any process that modulates the frequency, rate or extent of neuron death.
Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
negative regulation of neuron cell death
negative regulation of neuronal cell death
Any process that activates or increases the frequency, rate or extent of neuron death.
positive regulation of neuron cell death
positive regulation of neuronal cell death
Any process that modulates the frequency, rate or extent of cardiac chamber morphogenesis.
regulation of heart chamber morphogenesis
regulation of cardiac chamber morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac chamber morphogenesis.
down regulation of cardiac chamber morphogenesis
down regulation of heart chamber morphogenesis
down-regulation of cardiac chamber morphogenesis
down-regulation of heart chamber morphogenesis
downregulation of cardiac chamber morphogenesis
downregulation of heart chamber morphogenesis
negative regulation of heart chamber morphogenesis
inhibition of cardiac chamber morphogenesis
inhibition of heart chamber morphogenesis
negative regulation of cardiac chamber morphogenesis
Any process that activates or increases the frequency, rate or extent of cardiac chamber morphogenesis.
positive regulation of heart chamber morphogenesis
up regulation of cardiac chamber morphogenesis
up regulation of heart chamber morphogenesis
up-regulation of cardiac chamber morphogenesis
up-regulation of heart chamber morphogenesis
upregulation of cardiac chamber morphogenesis
upregulation of heart chamber morphogenesis
activation of cardiac chamber morphogenesis
activation of heart chamber morphogenesis
positive regulation of cardiac chamber morphogenesis
Any process that modulates the frequency, rate or extent of lung ciliated cell differentiation.
regulation of lung ciliated cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of lung ciliated cell differentiation.
down regulation of lung ciliated cell differentiation
down-regulation of lung ciliated cell differentiation
downregulation of lung ciliated cell differentiation
inhibition of lung ciliated cell differentiation
negative regulation of lung ciliated cell differentiation
Any process that activates or increases the frequency, rate or extent of lung ciliated cell differentiation.
up regulation of lung ciliated cell differentiation
up-regulation of lung ciliated cell differentiation
upregulation of lung ciliated cell differentiation
activation of lung ciliated cell differentiation
positive regulation of lung ciliated cell differentiation
The directed movement of a carbohydrate derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the frequency, rate or extent of vasculature development.
regulation of vascular system development
Any process that stops, prevents or reduces the frequency, rate or extent of vasculature development.
down regulation of vasculature development
down-regulation of vasculature development
downregulation of vasculature development
down regulation of vascular system development
down-regulation of vascular system development
downregulation of vascular system development
inhibition of vascular system development
negative regulation of vascular system development
negative regulation of vasculature development
The chemical reactions and pathways involving organic cyclic compound.
organic cyclic compound metabolic process
The chemical reactions and pathways resulting in the formation of organic cyclic compound.
organic cyclic compound biosynthetic process
Any process that modulates the frequency, rate or extent of endothelial tube morphogenesis.
regulation of endothelial tube morphogenesis
Any process that modulates the frequency, rate or extent of hematopoietic progenitor cell differentiation.
regulation of haematopoietic progenitor cell differentiation
regulation of haemopoietic progenitor cell differentiation
regulation of hemopoietic progenitor cell differentiation
regulation of hematopoietic progenitor cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic progenitor cell differentiation.
down regulation of haematopoietic progenitor cell differentiation
down regulation of haemopoietic progenitor cell differentiation
down regulation of hemopoietic progenitor cell differentiation
down-regulation of haematopoietic progenitor cell differentiation
down-regulation of haemopoietic progenitor cell differentiation
down-regulation of hemopoietic progenitor cell differentiation
downregulation of haematopoietic progenitor cell differentiation
downregulation of haemopoietic progenitor cell differentiation
downregulation of hemopoietic progenitor cell differentiation
inhibition of haematopoietic progenitor cell differentiation
inhibition of haemopoietic progenitor cell differentiation
negative regulation of haematopoietic progenitor cell differentiation
negative regulation of haemopoietic progenitor cell differentiation
negative regulation of hemopoietic progenitor cell differentiation
inhibition of hemopoietic progenitor cell differentiation
down regulation of hematopoietic progenitor cell differentiation
down-regulation of hematopoietic progenitor cell differentiation
downregulation of hematopoietic progenitor cell differentiation
inhibition of hematopoietic progenitor cell differentiation
negative regulation of hematopoietic progenitor cell differentiation
Any process that activates or increases the frequency, rate or extent of hematopoietic progenitor cell differentiation.
activation of haematopoietic progenitor cell differentiation
activation of haemopoietic progenitor cell differentiation
positive regulation of haematopoietic progenitor cell differentiation
positive regulation of haemopoietic progenitor cell differentiation
positive regulation of hemopoietic progenitor cell differentiation
up regulation of haematopoietic progenitor cell differentiation
up regulation of haemopoietic progenitor cell differentiation
up regulation of hemopoietic progenitor cell differentiation
up-regulation of haematopoietic progenitor cell differentiation
up-regulation of haemopoietic progenitor cell differentiation
up-regulation of hemopoietic progenitor cell differentiation
upregulation of haematopoietic progenitor cell differentiation
upregulation of haemopoietic progenitor cell differentiation
upregulation of hemopoietic progenitor cell differentiation
activation of hemopoietic progenitor cell differentiation
activation of hematopoietic progenitor cell differentiation
up regulation of hematopoietic progenitor cell differentiation
up-regulation of hematopoietic progenitor cell differentiation
upregulation of hematopoietic progenitor cell differentiation
positive regulation of hematopoietic progenitor cell differentiation
Any process that modulates the frequency, rate or extent of endothelial cell development.
regulation of endothelial cell development
Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell development.
down regulation of endothelial cell development
down-regulation of endothelial cell development
downregulation of endothelial cell development
inhibition of endothelial cell development
negative regulation of endothelial cell development
Any process that activates or increases the frequency, rate or extent of endothelial cell development.
up regulation of endothelial cell development
up-regulation of endothelial cell development
upregulation of endothelial cell development
activation of endothelial cell development
positive regulation of endothelial cell development
The chemical reactions and pathways involving organonitrogen compound.
organonitrogen compound metabolic process
The chemical reactions and pathways resulting in the formation of organonitrogen compound.
organonitrogen compound biosynthetic process
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
organic molecular entity biosynthetic process
The chemical reactions and pathways involving an alpha-amino acid.
The chemical reactions and pathways resulting in the formation of an alpha-amino acid.
Any process that modulates the frequency, rate or extent of vesicle transport along microtubule.
regulation of microtubule-based vesicle localization
regulation of vesicle transport along microtubule
Any process that stops, prevents or reduces the frequency, rate or extent of vesicle transport along microtubule.
down regulation of microtubule-based vesicle localization
down regulation of vesicle transport along microtubule
down-regulation of microtubule-based vesicle localization
down-regulation of vesicle transport along microtubule
downregulation of microtubule-based vesicle localization
downregulation of vesicle transport along microtubule
inhibition of microtubule-based vesicle localization
negative regulation of microtubule-based vesicle localization
inhibition of vesicle transport along microtubule
negative regulation of vesicle transport along microtubule
Any process that activates or increases the frequency, rate or extent of vesicle transport along microtubule.
activation of microtubule-based vesicle localization
positive regulation of microtubule-based vesicle localization
up regulation of microtubule-based vesicle localization
up regulation of vesicle transport along microtubule
up-regulation of microtubule-based vesicle localization
up-regulation of vesicle transport along microtubule
upregulation of microtubule-based vesicle localization
upregulation of vesicle transport along microtubule
activation of vesicle transport along microtubule
positive regulation of vesicle transport along microtubule
The chemical reactions and pathways involving organic hydroxy compound.
organic hydroxy compound metabolic process
The chemical reactions and pathways resulting in the formation of organic hydroxy compound.
organic hydroxy compound biosynthetic process
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 peptide stimulus.
A response that results in a state of tolerance to ketone.
process resulting in tolerance to ketone
Any process that modulates the frequency, rate or extent of compound eye retinal cell apoptotic process.
regulation of compound eye retinal cell apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of compound eye retinal cell apoptotic process.
down regulation of compound eye retinal cell apoptotic process
down-regulation of compound eye retinal cell apoptotic process
downregulation of compound eye retinal cell apoptotic process
inhibition of compound eye retinal cell apoptotic process
negative regulation of compound eye retinal cell apoptotic process
Any process that activates or increases the frequency, rate or extent of compound eye retinal cell apoptotic process.
up regulation of compound eye retinal cell apoptotic process
up-regulation of compound eye retinal cell apoptotic process
upregulation of compound eye retinal cell apoptotic process
activation of compound eye retinal cell apoptotic process
induction of compound eye retinal cell programmed cell death
positive regulation of compound eye retinal cell apoptotic process
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 nitrogen compound 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 oxygen-containing compound stimulus.
The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of bone as it progresses from its formation to the mature state.
mesenchymal cell differentiation involved in bone development
Any process that modulates the frequency, rate or extent of muscle tissue development.
Any process that stops, prevents or reduces the frequency, rate or extent of muscle tissue development.
down regulation of muscle tissue development
down-regulation of muscle tissue development
downregulation of muscle tissue development
negative regulation of muscle tissue development
Any process that activates or increases the frequency, rate or extent of muscle tissue development.
up regulation of muscle tissue development
up-regulation of muscle tissue development
upregulation of muscle tissue development
positive regulation of muscle tissue development
Any process that modulates the frequency, rate or extent of protein depolymerization.
regulation of protein polymer catabolic process
regulation of protein polymer catabolism
regulation of protein polymer degradation
Any process that stops, prevents or reduces the frequency, rate or extent of protein depolymerization.
down regulation of protein depolymerization
down regulation of protein polymer breakdown
down regulation of protein polymer catabolic process
down regulation of protein polymer catabolism
down regulation of protein polymer degradation
down-regulation of protein depolymerization
down-regulation of protein polymer breakdown
down-regulation of protein polymer catabolic process
down-regulation of protein polymer catabolism
down-regulation of protein polymer degradation
downregulation of protein depolymerization
downregulation of protein polymer breakdown
downregulation of protein polymer catabolic process
downregulation of protein polymer catabolism
downregulation of protein polymer degradation
inhibition of protein polymer catabolic process
inhibition of protein polymer catabolism
inhibition of protein polymer degradation
negative regulation of protein polymer breakdown
negative regulation of protein polymer catabolic process
negative regulation of protein polymer catabolism
negative regulation of protein polymer degradation
negative regulation of protein depolymerization
Any process that activates or increases the frequency, rate or extent of protein depolymerization.
activation of protein polymer catabolic process
activation of protein polymer catabolism
activation of protein polymer degradation
positive regulation of protein polymer breakdown
positive regulation of protein polymer catabolic process
positive regulation of protein polymer catabolism
positive regulation of protein polymer degradation
up regulation of protein depolymerization
up regulation of protein polymer breakdown
up regulation of protein polymer catabolic process
up regulation of protein polymer catabolism
up regulation of protein polymer degradation
up-regulation of protein depolymerization
up-regulation of protein polymer breakdown
up-regulation of protein polymer catabolic process
up-regulation of protein polymer catabolism
up-regulation of protein polymer degradation
upregulation of protein depolymerization
upregulation of protein polymer breakdown
upregulation of protein polymer catabolic process
upregulation of protein polymer catabolism
upregulation of protein polymer degradation
positive regulation of protein depolymerization
Any process that modulates the frequency, rate or extent of cell junction assembly.
Any process that stops, prevents or reduces the frequency, rate or extent of cell junction assembly.
down regulation of cell junction assembly
down-regulation of cell junction assembly
downregulation of cell junction assembly
negative regulation of cell junction assembly
Any process that activates or increases the frequency, rate or extent of cell junction assembly.
positive regulation of cell junction assembly
Any process that modulates the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis.
regulation of cell proliferation involved in outflow tract morphogenesis
Any process that activates or increases the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis.
up regulation of cell proliferation involved in outflow tract morphogenesis
up-regulation of cell proliferation involved in outflow tract morphogenesis
upregulation of cell proliferation involved in outflow tract morphogenesis
activation of cell proliferation involved in outflow tract morphogenesis
positive regulation of cell proliferation involved in outflow tract morphogenesis
Any process that modulates the frequency, rate or extent of cilium assembly.
Any process that stops, prevents or reduces the frequency, rate or extent of cilium assembly.
negative regulation of cilium biogenesis
Any process that modulates the frequency, rate or extent of hematopoietic stem cell proliferation.
regulation of hemopoietic stem cell proliferation
regulation of hematopoietic stem cell proliferation
Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell proliferation.
down regulation of hematopoietic stem cell proliferation
down regulation of hemopoietic stem cell proliferation
down-regulation of hematopoietic stem cell proliferation
down-regulation of hemopoietic stem cell proliferation
downregulation of hematopoietic stem cell proliferation
downregulation of hemopoietic stem cell proliferation
negative regulation of hemopoietic stem cell proliferation
inhibition of hematopoietic stem cell proliferation
inhibition of hemopoietic stem cell proliferation
negative regulation of hematopoietic stem cell proliferation
Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell proliferation.
positive regulation of hemopoietic stem cell proliferation
up regulation of hematopoietic stem cell proliferation
up regulation of hemopoietic stem cell proliferation
up-regulation of hematopoietic stem cell proliferation
up-regulation of hemopoietic stem cell proliferation
upregulation of hematopoietic stem cell proliferation
upregulation of hemopoietic stem cell proliferation
activation of hematopoietic stem cell proliferation
activation of hemopoietic stem cell proliferation
positive regulation of hematopoietic stem cell proliferation
Any process that modulates the frequency, rate or extent of hematopoietic stem cell differentiation.
regulation of haematopoietic stem cell differentiation
regulation of haemopoietic stem cell differentiation
regulation of hemopoietic stem cell differentiation
regulation of hematopoietic stem cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell differentiation.
down regulation of haematopoietic stem cell differentiation
down regulation of haemopoietic stem cell differentiation
down regulation of hematopoietic stem cell differentiation
down regulation of hemopoietic stem cell differentiation
down-regulation of haematopoietic stem cell differentiation
down-regulation of haemopoietic stem cell differentiation
down-regulation of hematopoietic stem cell differentiation
down-regulation of hemopoietic stem cell differentiation
downregulation of haematopoietic stem cell differentiation
downregulation of haemopoietic stem cell differentiation
downregulation of hematopoietic stem cell differentiation
downregulation of hemopoietic stem cell differentiation
negative regulation of haematopoietic stem cell differentiation
negative regulation of haemopoietic stem cell differentiation
negative regulation of hemopoietic stem cell differentiation
inhibition of haematopoietic stem cell differentiation
inhibition of haemopoietic stem cell differentiation
inhibition of hematopoietic stem cell differentiation
inhibition of hemopoietic stem cell differentiation
negative regulation of hematopoietic stem cell differentiation
Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell differentiation.
positive regulation of haematopoietic stem cell differentiation
positive regulation of haemopoietic stem cell differentiation
positive regulation of hemopoietic stem cell differentiation
up regulation of haematopoietic stem cell differentiation
up regulation of haemopoietic stem cell differentiation
up regulation of hematopoietic stem cell differentiation
up regulation of hemopoietic stem cell differentiation
up-regulation of haematopoietic stem cell differentiation
up-regulation of haemopoietic stem cell differentiation
up-regulation of hematopoietic stem cell differentiation
up-regulation of hemopoietic stem cell differentiation
upregulation of haematopoietic stem cell differentiation
upregulation of haemopoietic stem cell differentiation
upregulation of hematopoietic stem cell differentiation
upregulation of hemopoietic stem cell differentiation
activation of haematopoietic stem cell differentiation
activation of haemopoietic stem cell differentiation
activation of hematopoietic stem cell differentiation
activation of hemopoietic stem cell differentiation
positive regulation of hematopoietic stem cell differentiation
Any process that modulates the frequency, rate or extent of leukocyte differentiation.
regulation of immune cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte differentiation.
down regulation of immune cell differentiation
down regulation of leucocyte differentiation
down regulation of leukocyte differentiation
down-regulation of immune cell differentiation
down-regulation of leucocyte differentiation
down-regulation of leukocyte differentiation
downregulation of immune cell differentiation
downregulation of leucocyte differentiation
downregulation of leukocyte differentiation
negative regulation of immune cell differentiation
negative regulation of leucocyte differentiation
inhibition of immune cell differentiation
negative regulation of leukocyte differentiation
Any process that activates or increases the frequency, rate or extent of leukocyte differentiation.
positive regulation of immune cell differentiation
positive regulation of leucocyte differentiation
up regulation of immune cell differentiation
up regulation of leucocyte differentiation
up regulation of leukocyte differentiation
up-regulation of immune cell differentiation
up-regulation of leucocyte differentiation
up-regulation of leukocyte differentiation
upregulation of immune cell differentiation
upregulation of leucocyte differentiation
upregulation of leukocyte differentiation
activation of immune cell differentiation
positive regulation of leukocyte differentiation
Any process that modulates the frequency, rate or extent of organelle assembly.
Any process that stops, prevents or reduces the frequency, rate or extent of organelle assembly.
negative regulation of organelle assembly
Any process that activates or increases the frequency, rate or extent of organelle assembly.
positive regulation of organelle assembly
Any apoptotic process in an erythrocyte.
Any process that modulates the frequency, rate or extent of erythrocyte apoptotic process.
regulation of red blood cell apoptotic process
regulation of erythrocyte apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of erythrocyte apoptotic process.
down regulation of RBC apoptotic process
down regulation of erythrocyte apoptotic process
down regulation of red blood cell apoptotic process
down-regulation of RBC apoptotic process
down-regulation of erythrocyte apoptotic process
down-regulation of red blood cell apoptotic process
downregulation of erythrocyte apoptotic process
downregulation of red blood cell apoptotic process
negative regulation of RBC apoptotic process
negative regulation of red blood cell apoptotic process
down regulation of erythrocyte apoptosis
down regulation of red blood cell apoptosis
down-regulation of erythrocyte apoptosis
down-regulation of red blood cell apoptosis
downregulation of red blood cell apoptosis
inhibition of erythrocyte apoptotic process
inhibition of red blood cell apoptotic process
negative regulation of erythrocyte apoptosis
negative regulation of red blood cell apoptosis
negative regulation of erythrocyte apoptotic process
Any process that activates or increases the frequency, rate or extent of erythrocyte apoptotic process.
positive regulation of RBC apoptotic process
positive regulation of red blood cell apoptotic process
up regulation of erythrocyte apoptotic process
up regulation of red blood cell apoptotic process
up-regulation of erythrocyte apoptotic process
up-regulation of red blood cell apoptotic process
upregulation of erythrocyte apoptotic process
upregulation of red blood cell apoptotic process
activation of erythrocyte apoptotic process
activation of red blood cell apoptotic process
positive regulation of erythrocyte apoptosis
positive regulation of red blood cell apoptosis
up regulation of red blood cell apoptosis
up-regulation of red blood cell apoptosis
upregulation of red blood cell apoptosis
positive regulation of erythrocyte apoptotic process
Any process that modulates the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis.
regulation of apoptosis involved in outflow tract morphogenesis
regulation of apoptotic process involved in outflow tract morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis.
down regulation of apoptotic process involved in outflow tract morphogenesis
down-regulation of apoptotic process involved in outflow tract morphogenesis
downregulation of apoptotic process involved in outflow tract morphogenesis
down regulation of apoptosis involved in outflow tract morphogenesis
down-regulation of apoptosis involved in outflow tract morphogenesis
downregulation of apoptosis involved in outflow tract morphogenesis
inhibition of apoptosis involved in outflow tract morphogenesis
inhibition of apoptotic process involved in outflow tract morphogenesis
negative regulation of apoptosis involved in outflow tract morphogenesis
negative regulation of apoptotic process involved in outflow tract morphogenesis
Any process that activates or increases the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis.
up regulation of apoptotic process involved in outflow tract morphogenesis
up-regulation of apoptotic process involved in outflow tract morphogenesis
upregulation of apoptotic process involved in outflow tract morphogenesis
activation of apoptosis involved in outflow tract morphogenesis
activation of apoptotic process involved in outflow tract morphogenesis
positive regulation of apoptosis involved in outflow tract morphogenesis
up regulation of apoptosis involved in outflow tract morphogenesis
up-regulation of apoptosis involved in outflow tract morphogenesis
upregulation of apoptosis involved in outflow tract morphogenesis
positive regulation of apoptotic process involved in outflow tract morphogenesis
Any apoptotic process that is involved in blood vessel morphogenesis.
apoptotic cell death involved in patterning of blood vessels
apoptotic programmed cell death involved in patterning of blood vessels
programmed cell death by apoptosis involved in patterning of blood vessels
apoptosis involved in patterning of blood vessels
apoptotic program involved in patterning of blood vessels
type I programmed cell death involved in patterning of blood vessels
signaling (initiator) caspase activity involved in patterning of blood vessels
apoptotic process involved in blood vessel morphogenesis
Any process that modulates the frequency, rate or extent of chromatin organization.
regulation of establishment or maintenance of chromatin architecture
Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis.
regulation of apoptosis involved in morphogenesis
regulation of apoptosis involved in development
regulation of apoptotic process involved in morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis.
down regulation of apoptotic process involved in morphogenesis
down-regulation of apoptotic process involved in morphogenesis
downregulation of apoptotic process involved in morphogenesis
down regulation of apoptosis involved in morphogenesis
down-regulation of apoptosis involved in morphogenesis
downregulation of apoptosis involved in morphogenesis
inhibition of apoptosis involved in morphogenesis
inhibition of apoptotic process involved in morphogenesis
negative regulation of apoptosis involved in morphogenesis
down regulation of apoptosis involved in development
down regulation of morphogenetic apoptosis
down-regulation of apoptosis involved in development
down-regulation of morphogenetic apoptosis
downregulation of apoptosis involved in development
downregulation of morphogenetic apoptosis
inhibition of apoptosis involved in development
negative regulation of apoptosis involved in development
negative regulation of morphogenetic apoptosis
negative regulation of apoptotic process involved in morphogenesis
Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis.
up regulation of apoptotic process involved in morphogenesis
up-regulation of apoptotic process involved in morphogenesis
upregulation of apoptotic process involved in morphogenesis
activation of apoptosis involved in morphogenesis
activation of apoptotic process involved in morphogenesis
positive regulation of apoptosis involved in morphogenesis
up regulation of apoptosis involved in morphogenesis
up-regulation of apoptosis involved in morphogenesis
upregulation of apoptosis involved in morphogenesis
activation of apoptosis involved in development
positive regulation of apoptosis involved in development
positive regulation of morphogenetic apoptosis
up regulation of apoptosis involved in development
up regulation of morphogenetic apoptosis
up-regulation of apoptosis involved in development
up-regulation of morphogenetic apoptosis
upregulation of apoptosis involved in development
positive regulation of apoptotic process involved in morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of chromosome condensation.
down regulation of chromosome condensation
down regulation of eukaryotic chromosome condensation
down regulation of nuclear chromosome condensation
down-regulation of chromosome condensation
down-regulation of eukaryotic chromosome condensation
down-regulation of nuclear chromosome condensation
downregulation of chromosome condensation
downregulation of eukaryotic chromosome condensation
downregulation of nuclear chromosome condensation
negative regulation of eukaryotic chromosome condensation
negative regulation of nuclear chromosome condensation
inhibition of eukaryotic chromosome condensation
inhibition of nuclear chromosome condensation
negative regulation of chromosome condensation
A process in which a protein is transported to, or maintained in, a location within a cell junction.
A process in which a protein is transported to, or maintained in, a location within a cell leading edge.
protein localisation in cell leading edge
protein localisation to cell leading edge
protein localization in cell leading edge
protein localization to cell leading edge
Any process that modulates the frequency, rate or extent of protein localization to synapse.
regulation of protein localisation to synapse
regulation of protein localization to synapse
Any process that activates or increases the frequency, rate or extent of protein localization to synapse.
positive regulation of protein localisation to synapse
up regulation of protein localisation to synapse
up regulation of protein localization to synapse
up-regulation of protein localisation to synapse
up-regulation of protein localization to synapse
upregulation of protein localisation to synapse
upregulation of protein localization to synapse
activation of protein localisation to synapse
activation of protein localization to synapse
positive regulation of protein localization to synapse
A protein complex which is capable of catalytic activity.
Any process that modulates the frequency, rate or extent of organelle transport along microtubule.
regulation of microtubule-based organelle localization
regulation of organelle transport along microtubule
Any process that modulates the frequency, rate or extent of intracellular signal transduction.
regulation of intracellular signaling cascade
regulation of intracellular signaling chain
regulation of intracellular protein kinase cascade
regulation of intracellular signal transduction pathway
regulation of signal transmission via intracellular cascade
regulation of intracellular signaling pathway
regulation of signal transduction via intracellular signaling cascade
regulation of intracellular signal transduction
Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction.
down regulation of intracellular signal transduction
down regulation of intracellular signaling chain
down-regulation of intracellular signal transduction
down-regulation of intracellular signaling chain
downregulation of intracellular signal transduction
downregulation of intracellular signaling chain
negative regulation of intracellular protein kinase cascade
negative regulation of intracellular signaling cascade
negative regulation of intracellular signaling chain
down regulation of intracellular signal transduction pathway
down regulation of intracellular signaling cascade
down regulation of signal transmission via intracellular cascade
down-regulation of intracellular signal transduction pathway
downregulation of intracellular signal transduction pathway
downregulation of intracellular signaling cascade
downregulation of signal transmission via intracellular cascade
inhibition of intracellular signal transduction
inhibition of intracellular signal transduction pathway
inhibition of intracellular signaling cascade
inhibition of intracellular signaling chain
inhibition of signal transmission via intracellular cascade
negative regulation of intracellular signal transduction pathway
negative regulation of signal transmission via intracellular cascade
down regulation of intracellular signaling pathway
down regulation of signal transduction via intracellular signaling cascade
down-regulation of intracellular signaling cascade
down-regulation of intracellular signaling pathway
down-regulation of signal transduction via intracellular signaling cascade
down-regulation of signal transmission via intracellular cascade
downregulation of intracellular signaling pathway
downregulation of signal transduction via intracellular signaling cascade
inhibition of intracellular signaling pathway
inhibition of signal transduction via intracellular signaling cascade
negative regulation of intracellular signaling pathway
negative regulation of signal transduction via intracellular signaling cascade
negative regulation of intracellular signal transduction
Any process that activates or increases the frequency, rate or extent of intracellular signal transduction.
positive regulation of intracellular signaling chain
up regulation of intracellular signal transduction
up regulation of intracellular signaling chain
up-regulation of intracellular signal transduction
up-regulation of intracellular signaling chain
upregulation of intracellular signal transduction
upregulation of intracellular signaling chain
activation of intracellular signal transduction
activation of intracellular signal transduction pathway
activation of intracellular signaling cascade
activation of intracellular signaling chain
activation of signal transmission via intracellular cascade
positive regulation of intracellular protein kinase cascade
positive regulation of intracellular signal transduction pathway
positive regulation of signal transmission via intracellular cascade
up regulation of intracellular signal transduction pathway
up regulation of signal transmission via intracellular cascade
up-regulation of intracellular signal transduction pathway
up-regulation of signal transmission via intracellular cascade
upregulation of intracellular signal transduction pathway
upregulation of signal transmission via intracellular cascade
activation of intracellular signaling pathway
activation of signal transduction via intracellular signaling cascade
positive regulation of intracellular signaling cascade
positive regulation of intracellular signaling pathway
positive regulation of signal transduction via intracellular signaling cascade
up regulation of intracellular signaling cascade
up regulation of intracellular signaling pathway
up regulation of signal transduction via intracellular signaling cascade
up-regulation of intracellular signaling cascade
up-regulation of intracellular signaling pathway
up-regulation of signal transduction via intracellular signaling cascade
upregulation of intracellular signaling cascade
upregulation of intracellular signaling pathway
upregulation of signal transduction via intracellular signaling cascade
positive regulation of intracellular signal transduction
A process in which a protein is transported to, or maintained in, a location within a nucleolus.
Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process.
down regulation of RNA biosynthetic process
down-regulation of RNA biosynthetic process
downregulation of RNA biosynthetic process
negative regulation of RNA biosynthetic process
Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process.
up regulation of RNA biosynthetic process
up-regulation of RNA biosynthetic process
upregulation of RNA biosynthetic process
positive regulation of RNA biosynthetic process
Any process that modulates the frequency, rate or extent of neuroblast proliferation.
Any process that modulates the rate, frequency, or extent of the process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the development of a bone. A chondrocyte is a polymorphic cell that forms cartilage.
regulation of chondrocyte differentiation involved in endochondral bone morphogenesis
Any apoptotic process that is involved in anatomical structure development.
apoptotic cell death involved in anatomical structure development
apoptotic cell death involved in development of an anatomical structure
apoptotic process involved in anatomical structure development
apoptotic process involved in development of an anatomical structure
apoptotic programmed cell death involved in anatomical structure development
apoptotic programmed cell death involved in development of an anatomical structure
programmed cell death by apoptosis involved in anatomical structure development
programmed cell death by apoptosis involved in development of an anatomical structure
activation of apoptosis involved in anatomical structure development
activation of apoptosis involved in development of an anatomical structure
apoptosis involved in anatomical structure development
apoptosis involved in development of an anatomical structure
apoptosis signaling involved in anatomical structure development
apoptosis signaling involved in development of an anatomical structure
apoptotic program involved in anatomical structure development
apoptotic program involved in development of an anatomical structure
type I programmed cell death involved in anatomical structure development
type I programmed cell death involved in development of an anatomical structure
apoptosis activator activity involved in anatomical structure development
apoptosis activator activity involved in development of an anatomical structure
commitment to apoptosis involved in anatomical structure development
commitment to apoptosis involved in development of an anatomical structure
induction of apoptosis by p53 involved in anatomical structure development
induction of apoptosis by p53 involved in development of an anatomical structure
induction of apoptosis involved in anatomical structure development
induction of apoptosis involved in development of an anatomical structure
signaling (initiator) caspase activity involved in anatomical structure development
signaling (initiator) caspase activity involved in development of an anatomical structure
apoptotic process involved in development
Any process that activates or increases the frequency, rate or extent of chondrocyte development.
up regulation of chondrocyte development
up-regulation of chondrocyte development
positive regulation of chondrocyte development
Any process that modulates the frequency, rate or extent of skeletal muscle fiber differentiation.
regulation of skeletal muscle fiber differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle fiber differentiation.
down regulation of skeletal muscle fiber differentiation
down-regulation of skeletal muscle fiber differentiation
downregulation of skeletal muscle fiber differentiation
inhibition of skeletal muscle fiber differentiation
negative regulation of skeletal muscle fiber differentiation
Any process that activates or increases the frequency, rate or extent of skeletal muscle fiber differentiation.
up regulation of skeletal muscle fiber differentiation
up-regulation of skeletal muscle fiber differentiation
upregulation of skeletal muscle fiber differentiation
activation of skeletal muscle fiber differentiation
positive regulation of skeletal muscle fiber differentiation
Any process that modulates the frequency, rate or extent of protein localization to microtubule.
regulation of protein localisation to microtubule
regulation of protein localization to microtubule
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to microtubule.
down regulation of protein localisation to microtubule
down regulation of protein localization to microtubule
down-regulation of protein localisation to microtubule
down-regulation of protein localization to microtubule
downregulation of protein localisation to microtubule
downregulation of protein localization to microtubule
negative regulation of protein localisation to microtubule
inhibition of protein localisation to microtubule
inhibition of protein localization to microtubule
negative regulation of protein localization to microtubule
Any process that modulates the frequency, rate or extent of nuclear migration along microtubule.
regulation of nuclear movement, microtubule-mediated
regulation of microtubule cytoskeleton-dependent nuclear positioning
regulation of microtubule cytoskeleton-dependent nucleus positioning
regulation of microtubule-dependent nuclear positioning
regulation of microtubule-dependent nucleus positioning
regulation of microtubule-mediated nuclear migration
regulation of nuclear migration, microtubule-mediated
regulation of transport of nucleus by microtubules
regulation of transport of nucleus, microtubule-mediated
regulation of nuclear migration along microtubule
Any process that stops, prevents or reduces the frequency, rate or extent of nuclear migration along microtubule.
down regulation of microtubule cytoskeleton-dependent nuclear positioning
down regulation of microtubule cytoskeleton-dependent nucleus positioning
down regulation of microtubule-dependent nuclear positioning
down regulation of microtubule-dependent nucleus positioning
down regulation of microtubule-mediated nuclear migration
down regulation of nuclear migration along microtubule
down regulation of nuclear migration, microtubule-mediated
down regulation of transport of nucleus by microtubules
down regulation of transport of nucleus, microtubule-mediated
down-regulation of microtubule cytoskeleton-dependent nuclear positioning
down-regulation of microtubule cytoskeleton-dependent nucleus positioning
down-regulation of microtubule-dependent nuclear positioning
down-regulation of microtubule-dependent nucleus positioning
down-regulation of microtubule-mediated nuclear migration
down-regulation of nuclear migration along microtubule
down-regulation of nuclear migration, microtubule-mediated
down-regulation of transport of nucleus by microtubules
down-regulation of transport of nucleus, microtubule-mediated
downregulation of microtubule cytoskeleton-dependent nuclear positioning
downregulation of microtubule cytoskeleton-dependent nucleus positioning
downregulation of microtubule-dependent nuclear positioning
downregulation of microtubule-dependent nucleus positioning
downregulation of microtubule-mediated nuclear migration
downregulation of nuclear migration along microtubule
downregulation of nuclear migration, microtubule-mediated
downregulation of transport of nucleus by microtubules
downregulation of transport of nucleus, microtubule-mediated
negative regulation of microtubule cytoskeleton-dependent nuclear positioning
negative regulation of microtubule cytoskeleton-dependent nucleus positioning
negative regulation of microtubule-dependent nuclear positioning
negative regulation of microtubule-dependent nucleus positioning
negative regulation of microtubule-mediated nuclear migration
negative regulation of nuclear migration, microtubule-mediated
negative regulation of transport of nucleus by microtubules
negative regulation of transport of nucleus, microtubule-mediated
inhibition of microtubule cytoskeleton-dependent nuclear positioning
inhibition of microtubule cytoskeleton-dependent nucleus positioning
inhibition of microtubule-dependent nuclear positioning
inhibition of microtubule-dependent nucleus positioning
inhibition of microtubule-mediated nuclear migration
inhibition of nuclear migration along microtubule
inhibition of nuclear migration, microtubule-mediated
inhibition of transport of nucleus by microtubules
inhibition of transport of nucleus, microtubule-mediated
negative regulation of nuclear migration along microtubule
Any process that activates or increases the frequency, rate or extent of nuclear migration along microtubule.
positive regulation of microtubule cytoskeleton-dependent nuclear positioning
positive regulation of microtubule cytoskeleton-dependent nucleus positioning
positive regulation of microtubule-dependent nuclear positioning
positive regulation of microtubule-dependent nucleus positioning
positive regulation of microtubule-mediated nuclear migration
positive regulation of nuclear migration, microtubule-mediated
positive regulation of transport of nucleus by microtubules
positive regulation of transport of nucleus, microtubule-mediated
up regulation of microtubule cytoskeleton-dependent nuclear positioning
up regulation of microtubule cytoskeleton-dependent nucleus positioning
up regulation of microtubule-dependent nuclear positioning
up regulation of microtubule-dependent nucleus positioning
up regulation of microtubule-mediated nuclear migration
up regulation of nuclear migration along microtubule
up regulation of nuclear migration, microtubule-mediated
up regulation of transport of nucleus by microtubules
up regulation of transport of nucleus, microtubule-mediated
up-regulation of microtubule cytoskeleton-dependent nuclear positioning
up-regulation of microtubule cytoskeleton-dependent nucleus positioning
up-regulation of microtubule-dependent nuclear positioning
up-regulation of microtubule-dependent nucleus positioning
up-regulation of microtubule-mediated nuclear migration
up-regulation of nuclear migration along microtubule
up-regulation of nuclear migration, microtubule-mediated
up-regulation of transport of nucleus by microtubules
up-regulation of transport of nucleus, microtubule-mediated
upregulation of microtubule cytoskeleton-dependent nuclear positioning
upregulation of microtubule cytoskeleton-dependent nucleus positioning
upregulation of microtubule-dependent nuclear positioning
upregulation of microtubule-dependent nucleus positioning
upregulation of microtubule-mediated nuclear migration
upregulation of nuclear migration along microtubule
upregulation of nuclear migration, microtubule-mediated
upregulation of transport of nucleus by microtubules
upregulation of transport of nucleus, microtubule-mediated
activation of microtubule cytoskeleton-dependent nuclear positioning
activation of microtubule cytoskeleton-dependent nucleus positioning
activation of microtubule-dependent nuclear positioning
activation of microtubule-dependent nucleus positioning
activation of microtubule-mediated nuclear migration
activation of nuclear migration along microtubule
activation of nuclear migration, microtubule-mediated
activation of transport of nucleus by microtubules
activation of transport of nucleus, microtubule-mediated
positive regulation of nuclear migration along microtubule
Any microtubule cytoskeleton organization that is involved in mitosis.
microtubule cytoskeleton organisation involved in mitosis
microtubule dynamics involved in mitosis
microtubule cytoskeleton organization and biogenesis involved in mitosis
microtubule cytoskeleton organization involved in mitosis
Any process that modulates the frequency, rate or extent of embryonic camera-type eye development.
regulation of embryonic camera-type eye development
Any process that stops, prevents or reduces the frequency, rate or extent of embryonic camera-type eye development.
down regulation of embryonic camera-type eye development
down regulation of embryonic eye development
down-regulation of embryonic camera-type eye development
down-regulation of embryonic eye development
downregulation of embryonic camera-type eye development
downregulation of embryonic eye development
negative regulation of embryonic eye development
inhibition of embryonic camera-type eye development
negative regulation of embryonic camera-type eye development
Any process that activates or increases the frequency, rate or extent of embryonic camera-type eye development.
positive regulation of embryonic eye development
up regulation of embryonic camera-type eye development
up regulation of embryonic eye development
up-regulation of embryonic camera-type eye development
up-regulation of embryonic eye development
upregulation of embryonic camera-type eye development
upregulation of embryonic eye development
activation of embryonic camera-type eye development
positive regulation of embryonic camera-type eye development
Any process that modulates the frequency, rate or extent of retina development in camera-type eye.
regulation of retina development in camera-style eye
regulation of retina development in camera-type eye
Any process that stops, prevents or reduces the frequency, rate or extent of retina development in camera-type eye.
down regulation of retina development in camera-style eye
down regulation of retina development in camera-type eye
down-regulation of retina development in camera-style eye
down-regulation of retina development in camera-type eye
downregulation of retina development in camera-style eye
downregulation of retina development in camera-type eye
negative regulation of retina development in camera-style eye
inhibition of retina development in camera-style eye
inhibition of retina development in camera-type eye
negative regulation of retinal development
negative regulation of retina development in camera-type eye
Any process that activates or increases the frequency, rate or extent of retina development in camera-type eye.
positive regulation of retina development in camera-style eye
up regulation of retina development in camera-style eye
up regulation of retina development in camera-type eye
up-regulation of retina development in camera-style eye
up-regulation of retina development in camera-type eye
upregulation of retina development in camera-style eye
upregulation of retina development in camera-type eye
activation of retina development in camera-style eye
activation of retina development in camera-type eye
positive regulation of retinal development
positive regulation of retina development in camera-type eye
Any process that modulates the frequency, rate or extent of supramolecular fiber organization.
HSPA8, human, P11142 in PMID:23921388 inferred from direct assay to negatively regulate fibrillation of alpha-Syn in vitro
regulation of supramolecular fiber organization
Any process that stops, prevents or reduces the frequency, rate or extent of fibril organization.
negative regulation of fibril organisation
negative regulation of supramolecular fiber organization
Any process that activates or increases the frequency, rate or extent of supramolecular fiber organization.
positive regulation of fibril organisation
positive regulation of supramolecular fiber organization
Any process that activates or increases the frequency, rate or extent of neuroepithelial cell differentiation.
up regulation of neuroepithelial cell differentiation
up-regulation of neuroepithelial cell differentiation
upregulation of neuroepithelial cell differentiation
activation of neuroepithelial cell differentiation
positive regulation of neuroepithelial cell differentiation
The disaggregation of an organelle into its constituent components.
Any process that modulates the frequency, rate or extent of bone development.
Any process that stops, prevents or reduces the frequency, rate or extent of bone development.
Any process that activates or increases the frequency, rate or extent of bone development.
Any process that modulates the frequency, rate or extent of glycoprotein metabolic process.
human serum amyloid P component (SAP) P02743 inhibits viral neuraminidase, NA (exo-alpha-sialidase activity) and thus the metabolism of glycoproteins, demonstrated in Figure 4A PMID:23544079, (IDA), the negative regulation term would be applied to this protein
regulation of glycoprotein metabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of glycoprotein metabolic process.
down regulation of glycoprotein metabolic process
down regulation of glycoprotein metabolism
down-regulation of glycoprotein metabolic process
down-regulation of glycoprotein metabolism
downregulation of glycoprotein metabolic process
downregulation of glycoprotein metabolism
negative regulation of glycoprotein metabolism
inhibition of glycoprotein metabolic process
negative regulation of glycoprotein metabolic process
Any process that activates or increases the frequency, rate or extent of glycoprotein metabolic process.
positive regulation of glycoprotein metabolism
up regulation of glycoprotein metabolic process
up regulation of glycoprotein metabolism
up-regulation of glycoprotein metabolic process
up-regulation of glycoprotein metabolism
upregulation of glycoprotein metabolic process
activation of glycoprotein metabolic process
positive regulation of glycoprotein metabolic process
A process that is part of the mitotic cell cycle.
Any process that modulates the frequency, rate or extent of extracellular matrix organization.
regulation of extracellular matrix organisation
regulation of extracellular matrix organization and biogenesis
regulation of extracellular matrix organization
Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix organization.
down regulation of extracellular matrix organisation
down regulation of extracellular matrix organization
down-regulation of extracellular matrix organisation
down-regulation of extracellular matrix organization
downregulation of extracellular matrix organisation
downregulation of extracellular matrix organization
negative regulation of extracellular matrix organisation
inhibition of extracellular matrix organisation
inhibition of extracellular matrix organization
down regulation of extracellular matrix organization and biogenesis
down-regulation of extracellular matrix organization and biogenesis
downregulation of extracellular matrix organization and biogenesis
inhibition of extracellular matrix organization and biogenesis
negative regulation of extracellular matrix organization and biogenesis
negative regulation of extracellular matrix organization
Any process that activates or increases the frequency, rate or extent of extracellular matrix organization.
positive regulation of extracellular matrix organisation
up regulation of extracellular matrix organisation
up regulation of extracellular matrix organization
up-regulation of extracellular matrix organisation
up-regulation of extracellular matrix organization
upregulation of extracellular matrix organisation
upregulation of extracellular matrix organization
activation of extracellular matrix organisation
activation of extracellular matrix organization
activation of extracellular matrix organization and biogenesis
positive regulation of extracellular matrix organization and biogenesis
up regulation of extracellular matrix organization and biogenesis
up-regulation of extracellular matrix organization and biogenesis
upregulation of extracellular matrix organization and biogenesis
positive regulation of extracellular matrix organization
Any process that modulates the frequency, rate or extent of protein localization to plasma membrane.
regulation of protein localization in plasma membrane
regulation of establishment of protein localisation in plasma membrane
regulation of establishment of protein localization in plasma membrane
regulation of establishment of protein localization to plasma membrane
regulation of protein localisation in plasma membrane
regulation of protein targeting to plasma membrane
regulation of protein-plasma membrane targeting
regulation of protein localization to plasma membrane
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to plasma membrane.
down regulation of protein localisation in plasma membrane
down regulation of protein localization in plasma membrane
down regulation of protein localization to plasma membrane
down-regulation of protein localisation in plasma membrane
down-regulation of protein localization in plasma membrane
down-regulation of protein localization to plasma membrane
downregulation of protein localisation in plasma membrane
downregulation of protein localization in plasma membrane
downregulation of protein localization to plasma membrane
negative regulation of protein localization in plasma membrane
inhibition of protein localisation in plasma membrane
inhibition of protein localization in plasma membrane
inhibition of protein localization to plasma membrane
inhibition of protein targeting to plasma membrane
inhibition of protein-plasma membrane targeting
down regulation of protein targeting to plasma membrane
down regulation of protein-plasma membrane targeting
down-regulation of protein targeting to plasma membrane
down-regulation of protein-plasma membrane targeting
downregulation of protein targeting to plasma membrane
downregulation of protein-plasma membrane targeting
negative regulation of establishment of protein localisation in plasma membrane
negative regulation of establishment of protein localization in plasma membrane
negative regulation of establishment of protein localization to plasma membrane
negative regulation of protein localisation in plasma membrane
negative regulation of protein targeting to plasma membrane
negative regulation of protein-plasma membrane targeting
negative regulation of protein localization to plasma membrane
Any process that activates or increases the frequency, rate or extent of protein localization to plasma membrane.
positive regulation of protein localisation in plasma membrane
positive regulation of protein localization in plasma membrane
up regulation of protein localisation in plasma membrane
up regulation of protein localization in plasma membrane
up regulation of protein localization to plasma membrane
up-regulation of protein localisation in plasma membrane
up-regulation of protein localization in plasma membrane
up-regulation of protein localization to plasma membrane
upregulation of protein localisation in plasma membrane
upregulation of protein localization in plasma membrane
upregulation of protein localization to plasma membrane
activation of protein localisation in plasma membrane
activation of protein localization in plasma membrane
activation of protein localization to plasma membrane
activation of protein targeting to plasma membrane
activation of protein-plasma membrane targeting
positive regulation of establishment of protein localisation in plasma membrane
positive regulation of establishment of protein localization to plasma membrane
positive regulation of protein targeting to plasma membrane
positive regulation of protein-plasma membrane targeting
up regulation of protein targeting to plasma membrane
up regulation of protein-plasma membrane targeting
up-regulation of protein targeting to plasma membrane
up-regulation of protein-plasma membrane targeting
upregulation of protein targeting to plasma membrane
upregulation of protein-plasma membrane targeting
positive regulation of protein localization to plasma membrane
A process in which a protein is transported to, or maintained in, the location of an actin cytoskeleton.
protein localisation in actin cytoskeleton
protein localisation to actin cytoskeleton
protein localization in actin cytoskeleton
protein localization to actin cytoskeleton
The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell.
Any process that modulates the frequency, rate or extent of tube lumen cavitation.
Any process that stops, prevents or reduces the frequency, rate or extent of tube lumen cavitation.
negative regulation of tube lumen cavitation
Any process that modulates the frequency, rate or extent of endodermal cell differentiation.
regulation of endoderm cell differentiation
regulation of endodermal cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of endodermal cell differentiation.
down regulation of endoderm cell differentiation
down regulation of endodermal cell differentiation
down-regulation of endoderm cell differentiation
down-regulation of endodermal cell differentiation
downregulation of endoderm cell differentiation
downregulation of endodermal cell differentiation
negative regulation of endoderm cell differentiation
inhibition of endoderm cell differentiation
inhibition of endodermal cell differentiation
negative regulation of endodermal cell differentiation
Any process that activates or increases the frequency, rate or extent of endodermal cell differentiation.
positive regulation of endoderm cell differentiation
up regulation of endoderm cell differentiation
up regulation of endodermal cell differentiation
up-regulation of endoderm cell differentiation
up-regulation of endodermal cell differentiation
upregulation of endoderm cell differentiation
upregulation of endodermal cell differentiation
activation of endoderm cell differentiation
activation of endodermal cell differentiation
positive regulation of endodermal cell differentiation
A process in which a protein is transported to, or maintained in, a location within a Golgi membrane.
Any process that modulates the frequency, rate or extent of vacuolar transport.
Any process that stops, prevents or reduces the frequency, rate or extent of vacuolar transport.
negative regulation of vacuolar transport
Any process that activates or increases the frequency, rate or extent of vacuolar transport.
positive regulation of vacuolar transport
Any process that modulates the frequency, rate or extent of nucleus organization.
regulation of nuclear organization and biogenesis
regulation of nucleus organization and biogenesis
Any process that modulates the frequency, rate or extent of Golgi organization.
regulation of Golgi organization and biogenesis
Any process that modulates the frequency, rate or extent of mitotic chromosome condensation.
regulation of mitotic chromosome condensation
Any process that activates or increases the frequency, rate or extent of mitotic chromosome condensation.
up regulation of mitotic chromosome condensation
up-regulation of mitotic chromosome condensation
upregulation of mitotic chromosome condensation
activation of mitotic chromosome condensation
positive regulation of mitotic chromosome condensation
A process in which a protein is transported to, or maintained in, a location within a ciliary membrane.
protein localisation in ciliary membrane
protein localisation to ciliary membrane
protein localization in ciliary membrane
protein localization to ciliary membrane
The chemical reactions and pathways involving mucopolysaccharide.
Any process that modulates the frequency, rate or extent of blood circulation.
Any process that stops, prevents or reduces the frequency, rate or extent of blood circulation.
down regulation of hemolymph circulation
down-regulation of hemolymph circulation
negative regulation of hemolymph circulation
negative regulation of blood circulation
Any process that activates or increases the frequency, rate or extent of blood circulation.
positive regulation of hemolymph circulation
positive regulation of blood circulation
Any process that modulates the frequency, rate or extent of secretion by cell.
Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell.
negative regulation of cellular secretion
negative regulation of secretion by cell
Any process that activates or increases the frequency, rate or extent of secretion by cell.
positive regulation of cellular secretion
positive regulation of secretion by cell
Any process that modulates the frequency, rate or extent of exosomal secretion.
regulation of exosomal secretory pathway
regulation of extracellular vesicular exosome secretion
regulation of exosomal protein secretion
Any process that stops, prevents or reduces the frequency, rate or extent of exosomal secretion.
down regulation of exosomal secretory pathway
down regulation of extracellular vesicular exosome secretion
down-regulation of exosomal secretory pathway
down-regulation of extracellular vesicular exosome secretion
downregulation of exosomal secretory pathway
downregulation of extracellular vesicular exosome secretion
negative regulation of exosomal secretory pathway
negative regulation of extracellular vesicular exosome secretion
negative regulation of secretion of exosome
down regulation of exosomal protein secretion
down-regulation of exosomal protein secretion
downregulation of exosomal protein secretion
inhibition of exosomal protein secretion
inhibition of exosomal secretory pathway
inhibition of extracellular vesicular exosome secretion
negative regulation of exosomal protein secretion
negative regulation of exosomal secretion
Any process that activates or increases the frequency, rate or extent of exosomal secretion.
positive regulation of exosomal secretory pathway
positive regulation of extracellular vesicular exosome secretion
positive regulation of secretion of exosome
up regulation of exosomal secretory pathway
up regulation of extracellular vesicular exosome secretion
up-regulation of exosomal secretory pathway
up-regulation of extracellular vesicular exosome secretion
upregulation of exosomal secretory pathway
upregulation of extracellular vesicular exosome secretion
activation of exosomal protein secretion
activation of exosomal secretory pathway
activation of extracellular vesicular exosome secretion
positive regulation of exosomal protein secretion
up regulation of exosomal protein secretion
up-regulation of exosomal protein secretion
upregulation of exosomal protein secretion
positive regulation of exosomal secretion
Any process that modulates the frequency, rate or extent of extracellular vesicular exosome assembly.
regulation of extracellular vesicular exosome assembly
regulation of extracellular exosome assembly
Any process that stops, prevents or reduces the frequency, rate or extent of extracellular vesicular exosome assembly.
down regulation of extracellular vesicular exosome assembly
down-regulation of extracellular vesicular exosome assembly
downregulation of extracellular vesicular exosome assembly
negative regulation of extracellular vesicular exosome assembly
inhibition of extracellular vesicular exosome assembly
negative regulation of extracellular exosome assembly
Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly.
up regulation of extracellular vesicular exosome assembly
up-regulation of extracellular vesicular exosome assembly
upregulation of extracellular vesicular exosome assembly
activation of extracellular vesicular exosome assembly
positive regulation of extracellular vesicular exosome assembly
positive regulation of extracellular exosome assembly
Any vesicle that is part of the extracellular region.
Any process that modulates the frequency, rate or extent of protein localization to cilium.
regulation of protein localization to cilium
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cilium.
down regulation of protein localization to cilium
down-regulation of protein localization to cilium
downregulation of protein localization to cilium
inhibition of protein localization to cilium
negative regulation of protein localization to cilium
Any process that activates or increases the frequency, rate or extent of protein localization to cilium.
up regulation of protein localization to cilium
up-regulation of protein localization to cilium
upregulation of protein localization to cilium
activation of protein localization to cilium
positive regulation of protein localization to cilium
Any process that modulates the frequency, rate or extent of protein localization to ciliary membrane.
regulation of protein localisation in ciliary membrane
regulation of protein localisation to ciliary membrane
regulation of protein localization in ciliary membrane
regulation of protein localization to ciliary membrane
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to ciliary membrane.
down regulation of protein localisation in ciliary membrane
down regulation of protein localisation to ciliary membrane
down regulation of protein localization in ciliary membrane
down regulation of protein localization to ciliary membrane
down-regulation of protein localisation in ciliary membrane
down-regulation of protein localisation to ciliary membrane
down-regulation of protein localization in ciliary membrane
down-regulation of protein localization to ciliary membrane
downregulation of protein localisation in ciliary membrane
downregulation of protein localisation to ciliary membrane
downregulation of protein localization in ciliary membrane
downregulation of protein localization to ciliary membrane
negative regulation of protein localisation in ciliary membrane
negative regulation of protein localisation to ciliary membrane
negative regulation of protein localization in ciliary membrane
inhibition of protein localisation in ciliary membrane
inhibition of protein localisation to ciliary membrane
inhibition of protein localization in ciliary membrane
inhibition of protein localization to ciliary membrane
negative regulation of protein localization to ciliary membrane
Any process that activates or increases the frequency, rate or extent of protein localization to ciliary membrane.
positive regulation of protein localisation in ciliary membrane
positive regulation of protein localisation to ciliary membrane
positive regulation of protein localization in ciliary membrane
up regulation of protein localisation in ciliary membrane
up regulation of protein localisation to ciliary membrane
up regulation of protein localization in ciliary membrane
up regulation of protein localization to ciliary membrane
up-regulation of protein localisation in ciliary membrane
up-regulation of protein localisation to ciliary membrane
up-regulation of protein localization in ciliary membrane
up-regulation of protein localization to ciliary membrane
upregulation of protein localisation in ciliary membrane
upregulation of protein localisation to ciliary membrane
upregulation of protein localization in ciliary membrane
upregulation of protein localization to ciliary membrane
activation of protein localisation in ciliary membrane
activation of protein localisation to ciliary membrane
activation of protein localization in ciliary membrane
activation of protein localization to ciliary membrane
positive regulation of protein localization to ciliary membrane
The process whose specific outcome is the progression of a substantia propria of cornea over time, from its formation to the mature structure.
substantia propria of cornea development
The process whose specific outcome is the progression of an esophagus over time, from its formation to the mature structure.
Any process that modulates the frequency, rate or extent of hemopoiesis.
An example of this is Atg7 in mouse (UniProt symbol, Q9D906) in PMID:20080761, inferred from mutant phenotype.
Any process that stops, prevents or reduces the frequency, rate or extent of hemopoiesis.
down regulation of blood cell biosynthesis
down-regulation of blood cell biosynthesis
downregulation of blood cell biosynthesis
negative regulation of blood cell biosynthesis
negative regulation of blood cell formation
Any process that activates or increases the frequency, rate or extent of hemopoiesis.
positive regulation of blood cell biosynthesis
positive regulation of blood cell formation
up regulation of blood cell biosynthesis
up-regulation of blood cell biosynthesis
Any process that modulates the frequency, rate or extent of plasma membrane organization.
regulation of plasma membrane organisation
regulation of plasma membrane organization and biogenesis
regulation of plasma membrane organization
A process in which a protein is transported to, or maintained in, a location within a vacuolar membrane.
protein localisation in vacuolar membrane
protein localisation to vacuolar membrane
protein localization in vacuolar membrane
protein localization to vacuolar membrane
Any process that modulates the frequency, rate or extent of cardiac conduction.
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac conduction.
negative regulation of cardiac conduction
Any process that activates or increases the frequency, rate or extent of cardiac conduction.
positive regulation of cardiac conduction
Any process that stops, prevents or reduces the frequency, rate or extent of anion transport.
Any process that activates or increases the frequency, rate or extent of anion transport.
Any process that stops, prevents or reduces the frequency, rate or extent of a protein localization.
down regulation of cellular protein localisation
down regulation of cellular protein localization
down-regulation of cellular protein localisation
down-regulation of cellular protein localization
downregulation of cellular protein localisation
downregulation of cellular protein localization
negative regulation of cellular protein localisation
negative regulation of cellular protein localization
inhibition of cellular protein localisation
inhibition of cellular protein localization
negative regulation of protein localization
Any process that activates or increases the frequency, rate or extent of a protein localization.
positive regulation of cellular protein localisation
positive regulation of cellular protein localization
up regulation of cellular protein localisation
up regulation of cellular protein localization
up-regulation of cellular protein localisation
up-regulation of cellular protein localization
upregulation of cellular protein localisation
upregulation of cellular protein localization
positive regulation of protein localization
Any process that modulates the frequency, rate or extent of aorta morphogenesis.
Any process that stops, prevents or reduces the frequency, rate or extent of aorta morphogenesis.
negative regulation of aorta morphogenesis
Any process that activates or increases the frequency, rate or extent of aorta morphogenesis.
positive regulation of aorta morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of respiratory gaseous exchange.
down regulation of respiratory gaseous exchange
down-regulation of respiratory gaseous exchange
downregulation of respiratory gaseous exchange
inhibition of respiratory gaseous exchange
negative regulation of respiratory gaseous exchange
Any process that activates or increases the frequency, rate or extent of respiratory gaseous exchange.
up regulation of respiratory gaseous exchange
up-regulation of respiratory gaseous exchange
upregulation of respiratory gaseous exchange
activation of respiratory gaseous exchange
positive regulation of respiratory gaseous exchange
Any process that stops, prevents or reduces the frequency, rate or extent of AV node cell action potential.
down regulation of AV node cardiac muscle cell action potential
down regulation of AV node cell action potential
down regulation of atrioventricular node cardiac muscle cell action potential
down-regulation of AV node cardiac muscle cell action potential
down-regulation of AV node cell action potential
down-regulation of atrioventricular node cardiac muscle cell action potential
downregulation of AV node cardiac muscle cell action potential
downregulation of AV node cell action potential
downregulation of atrioventricular node cardiac muscle cell action potential
negative regulation of AV node cardiac muscle cell action potential
negative regulation of atrioventricular node cardiac muscle cell action potential
inhibition of AV node cardiac muscle cell action potential
inhibition of AV node cell action potential
inhibition of atrioventricular node cardiac muscle cell action potential
negative regulation of AV node cell action potential
Any process that activates or increases the frequency, rate or extent of AV node cell action potential.
positive regulation of AV node cardiac muscle cell action potential
positive regulation of atrioventricular node cardiac muscle cell action potential
up regulation of AV node cardiac muscle cell action potential
up regulation of AV node cell action potential
up regulation of atrioventricular node cardiac muscle cell action potential
up-regulation of AV node cardiac muscle cell action potential
up-regulation of AV node cell action potential
up-regulation of atrioventricular node cardiac muscle cell action potential
upregulation of AV node cardiac muscle cell action potential
upregulation of AV node cell action potential
upregulation of atrioventricular node cardiac muscle cell action potential
activation of AV node cardiac muscle cell action potential
activation of AV node cell action potential
activation of atrioventricular node cardiac muscle cell action potential
positive regulation of AV node cell action potential
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 serotonin stimulus.
Any process that activates or increases the frequency, rate or extent of vasculature development.
up regulation of vasculature development
up-regulation of vasculature development
activation of vascular system development
positive regulation of vascular system development
up regulation of vascular system development
up-regulation of vascular system development
upregulation of vascular system development
positive regulation of vasculature development
Any apoptotic process in an epithelial cell.
Any process that modulates the frequency, rate or extent of collagen fibril organization.
regulation of collagen fibril organisation
regulation of fibrillar collagen organization
regulation of collagen fibril organization
Any process that stops, prevents or reduces the frequency, rate or extent of collagen fibril organization.
down regulation of collagen fibril organisation
down regulation of collagen fibril organization
down regulation of fibrillar collagen organization
down-regulation of collagen fibril organisation
down-regulation of collagen fibril organization
down-regulation of fibrillar collagen organization
downregulation of collagen fibril organisation
downregulation of collagen fibril organization
downregulation of fibrillar collagen organization
negative regulation of collagen fibril organisation
negative regulation of fibrillar collagen organization
inhibition of collagen fibril organisation
inhibition of collagen fibril organization
inhibition of fibrillar collagen organization
negative regulation of collagen fibril organization
Any process that activates or increases the frequency, rate or extent of collagen fibril organization.
positive regulation of collagen fibril organisation
positive regulation of fibrillar collagen organization
up regulation of collagen fibril organisation
up regulation of collagen fibril organization
up regulation of fibrillar collagen organization
up-regulation of collagen fibril organisation
up-regulation of collagen fibril organization
up-regulation of fibrillar collagen organization
upregulation of collagen fibril organisation
upregulation of collagen fibril organization
upregulation of fibrillar collagen organization
activation of collagen fibril organisation
activation of collagen fibril organization
activation of fibrillar collagen organization
positive regulation of collagen fibril organization
Any process that modulates the frequency, rate or extent of epithelial cell apoptotic process.
regulation of epitheliocyte apoptotic process
regulation of epithelial cell apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell apoptotic process.
down regulation of epithelial cell apoptotic process
down regulation of epitheliocyte apoptotic process
down-regulation of epithelial cell apoptotic process
down-regulation of epitheliocyte apoptotic process
downregulation of epithelial cell apoptotic process
downregulation of epitheliocyte apoptotic process
negative regulation of epitheliocyte apoptotic process
down regulation of epithelial cell apoptosis
down regulation of epitheliocyte apoptosis
down-regulation of epithelial cell apoptosis
down-regulation of epitheliocyte apoptosis
downregulation of epithelial cell apoptosis
downregulation of epitheliocyte apoptosis
inhibition of epithelial cell apoptotic process
inhibition of epitheliocyte apoptotic process
negative regulation of epithelial cell apoptosis
negative regulation of epitheliocyte apoptosis
negative regulation of epithelial cell apoptotic process
Any process that activates or increases the frequency, rate or extent of epithelial cell apoptotic process.
positive regulation of epitheliocyte apoptotic process
up regulation of epithelial cell apoptotic process
up regulation of epitheliocyte apoptotic process
up-regulation of epithelial cell apoptotic process
up-regulation of epitheliocyte apoptotic process
upregulation of epithelial cell apoptotic process
upregulation of epitheliocyte apoptotic process
activation of epithelial cell apoptotic process
activation of epitheliocyte apoptotic process
positive regulation of epithelial cell apoptosis
positive regulation of epitheliocyte apoptosis
up regulation of epithelial cell apoptosis
up regulation of epitheliocyte apoptosis
up-regulation of epithelial cell apoptosis
up-regulation of epitheliocyte apoptosis
upregulation of epithelial cell apoptosis
positive regulation of epithelial cell apoptotic process
Any process that modulates the frequency, rate or extent of bleb assembly.
Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly.
Any process that activates or increases the frequency, rate or extent of bleb assembly.
Any process that modulates the frequency, rate or extent of adipose tissue development.
regulation of adipose tissue development
Any process that stops, prevents or reduces the frequency, rate or extent of adipose tissue development.
down regulation of adipose tissue development
down-regulation of adipose tissue development
downregulation of adipose tissue development
inhibition of adipose tissue development
negative regulation of adipose tissue development
Any process that activates or increases the frequency, rate or extent of adipose tissue development.
up regulation of adipose tissue development
up-regulation of adipose tissue development
upregulation of adipose tissue development
activation of adipose tissue development
positive regulation of adipose tissue development
Any process that modulates the frequency, rate or extent of skeletal muscle hypertrophy.
regulation of skeletal muscle hypertrophy
Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle hypertrophy.
down regulation of skeletal muscle hypertrophy
down-regulation of skeletal muscle hypertrophy
downregulation of skeletal muscle hypertrophy
inhibition of skeletal muscle hypertrophy
negative regulation of skeletal muscle hypertrophy
Any process that activates or increases the frequency, rate or extent of skeletal muscle hypertrophy.
up regulation of skeletal muscle hypertrophy
up-regulation of skeletal muscle hypertrophy
upregulation of skeletal muscle hypertrophy
activation of skeletal muscle hypertrophy
positive regulation of skeletal muscle hypertrophy
The cell cortex of the leading edge of a cell.
peripheral cytoplasm of cell leading edge
peripheral cytoplasm of leading edge of cell
Any process that modulates the frequency, rate or extent of gastric mucosal blood circulation.
regulation of stomach mucosal blood circulation
regulation of gastric mucosal blood circulation
Any process that stops, prevents or reduces the frequency, rate or extent of gastric mucosal blood circulation.
down regulation of gastric mucosal blood circulation
down regulation of stomach mucosal blood circulation
down-regulation of gastric mucosal blood circulation
down-regulation of stomach mucosal blood circulation
downregulation of gastric mucosal blood circulation
downregulation of stomach mucosal blood circulation
negative regulation of stomach mucosal blood circulation
inhibition of gastric mucosal blood circulation
inhibition of stomach mucosal blood circulation
negative regulation of gastric mucosal blood circulation
Any process that activates or increases the frequency, rate or extent of gastric mucosal blood circulation.
positive regulation of stomach mucosal blood circulation
up regulation of gastric mucosal blood circulation
up regulation of stomach mucosal blood circulation
up-regulation of gastric mucosal blood circulation
up-regulation of stomach mucosal blood circulation
upregulation of gastric mucosal blood circulation
upregulation of stomach mucosal blood circulation
activation of gastric mucosal blood circulation
activation of stomach mucosal blood circulation
positive regulation of gastric mucosal blood circulation
Any process that modulates the frequency, rate or extent of protein localization to cell periphery.
regulation of protein localization to cell periphery
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell periphery.
down regulation of protein localization to cell periphery
down-regulation of protein localization to cell periphery
downregulation of protein localization to cell periphery
inhibition of protein localization to cell periphery
negative regulation of protein localization to cell periphery
Any process that activates or increases the frequency, rate or extent of protein localization to cell periphery.
up regulation of protein localization to cell periphery
up-regulation of protein localization to cell periphery
upregulation of protein localization to cell periphery
activation of protein localization to cell periphery
positive regulation of protein localization to cell periphery
Any process that modulates the frequency, rate or extent of neuromuscular junction development.
regulation of neuromuscular junction organization
regulation of neuromuscular junction stability
regulation of neuromuscular junction development
Any process that stops, prevents or reduces the frequency, rate or extent of neuromuscular junction development.
down regulation of neuromuscular junction development
down regulation of neuromuscular junction organization
down-regulation of neuromuscular junction development
down-regulation of neuromuscular junction organization
downregulation of neuromuscular junction development
downregulation of neuromuscular junction organization
negative regulation of neuromuscular junction organization
inhibition of neuromuscular junction development
inhibition of neuromuscular junction organization
down regulation of neuromuscular junction stability
down-regulation of neuromuscular junction stability
downregulation of neuromuscular junction stability
inhibition of neuromuscular junction stability
negative regulation of neuromuscular junction stability
negative regulation of neuromuscular junction development
Any process that activates or increases the frequency, rate or extent of neuromuscular junction development.
positive regulation of neuromuscular junction organization
up regulation of neuromuscular junction development
up regulation of neuromuscular junction organization
up-regulation of neuromuscular junction development
up-regulation of neuromuscular junction organization
upregulation of neuromuscular junction development
upregulation of neuromuscular junction organization
activation of neuromuscular junction development
activation of neuromuscular junction organization
activation of neuromuscular junction stability
positive regulation of neuromuscular junction stability
up regulation of neuromuscular junction stability
up-regulation of neuromuscular junction stability
upregulation of neuromuscular junction stability
positive regulation of neuromuscular junction development
Any process that modulates the frequency, rate or extent of cardiac ventricle development.
regulation of cardiac ventricle development
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac ventricle development.
down regulation of cardiac ventricle development
down-regulation of cardiac ventricle development
downregulation of cardiac ventricle development
inhibition of cardiac ventricle development
negative regulation of cardiac ventricle development
Any process that activates or increases the frequency, rate or extent of cardiac ventricle development.
up regulation of cardiac ventricle development
up-regulation of cardiac ventricle development
upregulation of cardiac ventricle development
activation of cardiac ventricle development
positive regulation of cardiac ventricle development
Any process that stops, prevents or reduces the frequency, rate or extent of neuronal action potential.
down regulation of neuronal action potential
down-regulation of neuronal action potential
downregulation of neuronal action potential
down regulation of generation of action potential
down-regulation of generation of action potential
downregulation of generation of action potential
inhibition of generation of action potential
negative regulation of generation of action potential
negative regulation of neuronal action potential
Any process that activates or increases the frequency, rate or extent of neuronal action potential.
up regulation of neuronal action potential
up-regulation of neuronal action potential
upregulation of neuronal action potential
activation of generation of action potential
positive regulation of generation of action potential
up regulation of generation of action potential
up-regulation of generation of action potential
upregulation of generation of action potential
positive regulation of neuronal action potential
A process in which a protein is transported to, or maintained in, a location within a ciliary transition zone.
protein localisation in ciliary transition zone
protein localisation to ciliary transition zone
protein localization in ciliary transition zone
protein localization to ciliary transition zone
Any process that modulates the frequency, rate or extent of microtubule binding.
regulation of microtubule severing activity
regulation of microtubule/chromatin interaction
Any process that stops, prevents or reduces the frequency, rate or extent of microtubule binding.
down regulation of microtubule severing activity
down regulation of microtubule/chromatin interaction
down-regulation of microtubule severing activity
down-regulation of microtubule/chromatin interaction
downregulation of microtubule severing activity
downregulation of microtubule/chromatin interaction
inhibition of microtubule severing activity
inhibition of microtubule/chromatin interaction
negative regulation of microtubule severing activity
negative regulation of microtubule/chromatin interaction
negative regulation of microtubule binding
Any process that activates or increases the frequency, rate or extent of microtubule binding.
activation of microtubule severing activity
activation of microtubule/chromatin interaction
positive regulation of microtubule severing activity
positive regulation of microtubule/chromatin interaction
up regulation of microtubule severing activity
up regulation of microtubule/chromatin interaction
up-regulation of microtubule severing activity
up-regulation of microtubule/chromatin interaction
upregulation of microtubule severing activity
upregulation of microtubule/chromatin interaction
positive regulation of microtubule binding
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 glycoprotein stimulus.
Any process that modulates the frequency, rate or extent of fat cell apoptotic process.
regulation of adipocyte apoptotic process
regulation of adipose cell apoptotic process
regulation of fat cell apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of fat cell apoptotic process.
down regulation of adipocyte apoptotic process
down regulation of adipose cell apoptotic process
down regulation of fat cell apoptotic process
down-regulation of adipocyte apoptotic process
down-regulation of adipose cell apoptotic process
down-regulation of fat cell apoptotic process
downregulation of adipocyte apoptotic process
downregulation of adipose cell apoptotic process
downregulation of fat cell apoptotic process
negative regulation of adipocyte apoptotic process
negative regulation of adipose cell apoptotic process
down regulation of adipose cell apoptosis
down-regulation of adipose cell apoptosis
downregulation of adipose cell apoptosis
inhibition of adipocyte apoptotic process
inhibition of adipose cell apoptotic process
inhibition of fat cell apoptotic process
negative regulation of adipocyte apoptosis
negative regulation of adipose cell apoptosis
negative regulation of fat cell apoptosis
negative regulation of fat cell apoptotic process
Any process that activates or increases the frequency, rate or extent of fat cell apoptotic process.
positive regulation of adipocyte apoptotic process
positive regulation of adipose cell apoptotic process
up regulation of adipocyte apoptotic process
up regulation of adipose cell apoptotic process
up regulation of fat cell apoptotic process
up-regulation of adipocyte apoptotic process
up-regulation of adipose cell apoptotic process
up-regulation of fat cell apoptotic process
upregulation of adipocyte apoptotic process
upregulation of adipose cell apoptotic process
upregulation of fat cell apoptotic process
activation of adipocyte apoptotic process
activation of adipose cell apoptotic process
activation of fat cell apoptotic process
positive regulation of adipocyte apoptosis
positive regulation of adipose cell apoptosis
positive regulation of fat cell apoptosis
positive regulation of fat cell apoptotic process
Any process that modulates the frequency, rate or extent of somatic stem cell division.
regulation of somatic stem cell division
Any process that stops, prevents or reduces the frequency, rate or extent of somatic stem cell division.
down regulation of somatic stem cell division
down regulation of somatic stem cell renewal
down-regulation of somatic stem cell division
down-regulation of somatic stem cell renewal
downregulation of somatic stem cell division
downregulation of somatic stem cell renewal
negative regulation of somatic stem cell renewal
inhibition of somatic stem cell division
negative regulation of somatic stem cell division
Any process that activates or increases the frequency, rate or extent of somatic stem cell division.
positive regulation of somatic stem cell renewal
up regulation of somatic stem cell division
up regulation of somatic stem cell renewal
up-regulation of somatic stem cell division
up-regulation of somatic stem cell renewal
upregulation of somatic stem cell division
upregulation of somatic stem cell renewal
activation of somatic stem cell division
positive regulation of somatic stem cell division
The developmental process by which a midbrain is generated and organized.
Any process that modulates the frequency, rate or extent of vascular smooth muscle cell proliferation.
regulation of vascular smooth muscle cell proliferation
regulation of vascular associated smooth muscle cell proliferation
Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell proliferation.
down regulation of vascular smooth muscle cell proliferation
down-regulation of vascular smooth muscle cell proliferation
downregulation of vascular smooth muscle cell proliferation
negative regulation of VSMC proliferation
negative regulation of vascular smooth muscle cell proliferation
inhibition of vascular smooth muscle cell proliferation
negative regulation of vascular associated smooth muscle cell proliferation
Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell proliferation.
positive regulation of VSMC proliferation
positive regulation of vascular smooth muscle cell proliferation
up regulation of vascular smooth muscle cell proliferation
up-regulation of vascular smooth muscle cell proliferation
upregulation of vascular smooth muscle cell proliferation
activation of vascular smooth muscle cell proliferation
positive regulation of vascular associated smooth muscle cell proliferation
A posttranscriptional regulation of gene expression that results in regulation of synapse organization.
regulation of synapse development by posttranscriptional regulation of gene expression
regulation of synapse organisation by posttranscriptional regulation of gene expression
regulation of synapse morphogenesis by posttranscriptional regulation of gene expression
regulation of synapse organization and biogenesis by posttranscriptional regulation of gene expression
regulation of synapse organization by posttranscriptional regulation of gene expression
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development.
down regulation of apoptotic cell death involved in anatomical structure development
down regulation of apoptotic cell death involved in development of an anatomical structure
down regulation of apoptotic process involved in anatomical structure development
down regulation of apoptotic process involved in development
down regulation of apoptotic process involved in development of an anatomical structure
down regulation of apoptotic programmed cell death involved in anatomical structure development
down regulation of apoptotic programmed cell death involved in development of an anatomical structure
down regulation of programmed cell death by apoptosis involved in anatomical structure development
down regulation of programmed cell death by apoptosis involved in development of an anatomical structure
down-regulation of apoptotic cell death involved in anatomical structure development
down-regulation of apoptotic cell death involved in development of an anatomical structure
down-regulation of apoptotic process involved in anatomical structure development
down-regulation of apoptotic process involved in development
down-regulation of apoptotic process involved in development of an anatomical structure
down-regulation of apoptotic programmed cell death involved in anatomical structure development
down-regulation of apoptotic programmed cell death involved in development of an anatomical structure
down-regulation of programmed cell death by apoptosis involved in anatomical structure development
down-regulation of programmed cell death by apoptosis involved in development of an anatomical structure
downregulation of apoptotic cell death involved in anatomical structure development
downregulation of apoptotic cell death involved in development of an anatomical structure
downregulation of apoptotic process involved in anatomical structure development
downregulation of apoptotic process involved in development
downregulation of apoptotic process involved in development of an anatomical structure
downregulation of apoptotic programmed cell death involved in anatomical structure development
downregulation of apoptotic programmed cell death involved in development of an anatomical structure
downregulation of programmed cell death by apoptosis involved in anatomical structure development
downregulation of programmed cell death by apoptosis involved in development of an anatomical structure
negative regulation of apoptotic cell death involved in anatomical structure development
negative regulation of apoptotic cell death involved in development of an anatomical structure
negative regulation of apoptotic process involved in anatomical structure development
negative regulation of apoptotic process involved in development of an anatomical structure
negative regulation of apoptotic programmed cell death involved in anatomical structure development
negative regulation of apoptotic programmed cell death involved in development of an anatomical structure
negative regulation of programmed cell death by apoptosis involved in anatomical structure development
negative regulation of programmed cell death by apoptosis involved in development of an anatomical structure
down regulation of activation of apoptosis involved in anatomical structure development
down regulation of activation of apoptosis involved in development of an anatomical structure
down regulation of apoptosis involved in anatomical structure development
down regulation of apoptosis involved in development of an anatomical structure
down regulation of apoptosis signaling involved in anatomical structure development
down regulation of apoptosis signaling involved in development of an anatomical structure
down regulation of apoptotic program involved in anatomical structure development
down regulation of apoptotic program involved in development of an anatomical structure
down regulation of type I programmed cell death involved in anatomical structure development
down regulation of type I programmed cell death involved in development of an anatomical structure
down-regulation of activation of apoptosis involved in anatomical structure development
down-regulation of activation of apoptosis involved in development of an anatomical structure
down-regulation of apoptosis involved in anatomical structure development
down-regulation of apoptosis involved in development of an anatomical structure
down-regulation of apoptosis signaling involved in anatomical structure development
down-regulation of apoptosis signaling involved in development of an anatomical structure
down-regulation of apoptotic program involved in anatomical structure development
down-regulation of apoptotic program involved in development of an anatomical structure
down-regulation of type I programmed cell death involved in anatomical structure development
down-regulation of type I programmed cell death involved in development of an anatomical structure
downregulation of activation of apoptosis involved in anatomical structure development
downregulation of activation of apoptosis involved in development of an anatomical structure
downregulation of apoptosis involved in anatomical structure development
downregulation of apoptosis involved in development of an anatomical structure
downregulation of apoptosis signaling involved in anatomical structure development
downregulation of apoptosis signaling involved in development of an anatomical structure
downregulation of apoptotic program involved in anatomical structure development
downregulation of apoptotic program involved in development of an anatomical structure
downregulation of type I programmed cell death involved in anatomical structure development
downregulation of type I programmed cell death involved in development of an anatomical structure
inhibition of activation of apoptosis involved in anatomical structure development
inhibition of activation of apoptosis involved in development of an anatomical structure
inhibition of apoptosis involved in anatomical structure development
inhibition of apoptosis involved in development of an anatomical structure
inhibition of apoptosis signaling involved in anatomical structure development
inhibition of apoptosis signaling involved in development of an anatomical structure
inhibition of apoptotic cell death involved in anatomical structure development
inhibition of apoptotic cell death involved in development of an anatomical structure
inhibition of apoptotic process involved in anatomical structure development
inhibition of apoptotic process involved in development
inhibition of apoptotic process involved in development of an anatomical structure
inhibition of apoptotic program involved in anatomical structure development
inhibition of apoptotic program involved in development of an anatomical structure
inhibition of apoptotic programmed cell death involved in anatomical structure development
inhibition of apoptotic programmed cell death involved in development of an anatomical structure
inhibition of programmed cell death by apoptosis involved in anatomical structure development
inhibition of programmed cell death by apoptosis involved in development of an anatomical structure
inhibition of type I programmed cell death involved in anatomical structure development
inhibition of type I programmed cell death involved in development of an anatomical structure
negative regulation of activation of apoptosis involved in anatomical structure development
negative regulation of activation of apoptosis involved in development of an anatomical structure
negative regulation of apoptosis involved in anatomical structure development
negative regulation of apoptosis involved in development of an anatomical structure
negative regulation of apoptosis signaling involved in anatomical structure development
negative regulation of apoptosis signaling involved in development of an anatomical structure
negative regulation of apoptotic program involved in anatomical structure development
negative regulation of apoptotic program involved in development of an anatomical structure
negative regulation of type I programmed cell death involved in anatomical structure development
negative regulation of type I programmed cell death involved in development of an anatomical structure
down regulation of apoptosis activator activity involved in anatomical structure development
down regulation of apoptosis activator activity involved in development of an anatomical structure
down regulation of commitment to apoptosis involved in anatomical structure development
down regulation of commitment to apoptosis involved in development of an anatomical structure
down regulation of induction of apoptosis by p53 involved in anatomical structure development
down regulation of induction of apoptosis by p53 involved in development of an anatomical structure
down regulation of induction of apoptosis involved in anatomical structure development
down regulation of induction of apoptosis involved in development of an anatomical structure
down regulation of signaling (initiator) caspase activity involved in anatomical structure development
down regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
down-regulation of apoptosis activator activity involved in anatomical structure development
down-regulation of apoptosis activator activity involved in development of an anatomical structure
down-regulation of commitment to apoptosis involved in anatomical structure development
down-regulation of commitment to apoptosis involved in development of an anatomical structure
down-regulation of induction of apoptosis by p53 involved in anatomical structure development
down-regulation of induction of apoptosis by p53 involved in development of an anatomical structure
down-regulation of induction of apoptosis involved in anatomical structure development
down-regulation of induction of apoptosis involved in development of an anatomical structure
down-regulation of signaling (initiator) caspase activity involved in anatomical structure development
down-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
downregulation of apoptosis activator activity involved in anatomical structure development
downregulation of apoptosis activator activity involved in development of an anatomical structure
downregulation of commitment to apoptosis involved in anatomical structure development
downregulation of commitment to apoptosis involved in development of an anatomical structure
downregulation of induction of apoptosis by p53 involved in anatomical structure development
downregulation of induction of apoptosis by p53 involved in development of an anatomical structure
downregulation of induction of apoptosis involved in anatomical structure development
downregulation of induction of apoptosis involved in development of an anatomical structure
downregulation of signaling (initiator) caspase activity involved in anatomical structure development
downregulation of signaling (initiator) caspase activity involved in development of an anatomical structure
inhibition of apoptosis activator activity involved in anatomical structure development
inhibition of apoptosis activator activity involved in development of an anatomical structure
inhibition of commitment to apoptosis involved in anatomical structure development
inhibition of commitment to apoptosis involved in development of an anatomical structure
inhibition of induction of apoptosis by p53 involved in anatomical structure development
inhibition of induction of apoptosis by p53 involved in development of an anatomical structure
inhibition of induction of apoptosis involved in anatomical structure development
inhibition of induction of apoptosis involved in development of an anatomical structure
inhibition of signaling (initiator) caspase activity involved in anatomical structure development
inhibition of signaling (initiator) caspase activity involved in development of an anatomical structure
negative regulation of apoptosis activator activity involved in anatomical structure development
negative regulation of apoptosis activator activity involved in development of an anatomical structure
negative regulation of commitment to apoptosis involved in anatomical structure development
negative regulation of commitment to apoptosis involved in development of an anatomical structure
negative regulation of induction of apoptosis by p53 involved in anatomical structure development
negative regulation of induction of apoptosis by p53 involved in development of an anatomical structure
negative regulation of induction of apoptosis involved in anatomical structure development
negative regulation of induction of apoptosis involved in development of an anatomical structure
negative regulation of signaling (initiator) caspase activity involved in anatomical structure development
negative regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
U4PR86 in PMID:22801495 inferred from mutant phenotype
negative regulation of apoptotic process involved in development
Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development.
positive regulation of apoptotic cell death involved in anatomical structure development
positive regulation of apoptotic cell death involved in development of an anatomical structure
positive regulation of apoptotic process involved in anatomical structure development
positive regulation of apoptotic process involved in development of an anatomical structure
positive regulation of apoptotic programmed cell death involved in anatomical structure development
positive regulation of apoptotic programmed cell death involved in development of an anatomical structure
positive regulation of programmed cell death by apoptosis involved in anatomical structure development
positive regulation of programmed cell death by apoptosis involved in development of an anatomical structure
up regulation of apoptotic cell death involved in anatomical structure development
up regulation of apoptotic cell death involved in development of an anatomical structure
up regulation of apoptotic process involved in anatomical structure development
up regulation of apoptotic process involved in development
up regulation of apoptotic process involved in development of an anatomical structure
up regulation of apoptotic programmed cell death involved in anatomical structure development
up regulation of apoptotic programmed cell death involved in development of an anatomical structure
up regulation of programmed cell death by apoptosis involved in anatomical structure development
up regulation of programmed cell death by apoptosis involved in development of an anatomical structure
up-regulation of apoptotic cell death involved in anatomical structure development
up-regulation of apoptotic cell death involved in development of an anatomical structure
up-regulation of apoptotic process involved in anatomical structure development
up-regulation of apoptotic process involved in development
up-regulation of apoptotic process involved in development of an anatomical structure
up-regulation of apoptotic programmed cell death involved in anatomical structure development
up-regulation of apoptotic programmed cell death involved in development of an anatomical structure
up-regulation of programmed cell death by apoptosis involved in anatomical structure development
up-regulation of programmed cell death by apoptosis involved in development of an anatomical structure
upregulation of apoptotic cell death involved in anatomical structure development
upregulation of apoptotic cell death involved in development of an anatomical structure
upregulation of apoptotic process involved in anatomical structure development
upregulation of apoptotic process involved in development
upregulation of apoptotic process involved in development of an anatomical structure
upregulation of apoptotic programmed cell death involved in anatomical structure development
upregulation of apoptotic programmed cell death involved in development of an anatomical structure
upregulation of programmed cell death by apoptosis involved in anatomical structure development
upregulation of programmed cell death by apoptosis involved in development of an anatomical structure
activation of activation of apoptosis involved in anatomical structure development
activation of activation of apoptosis involved in development of an anatomical structure
activation of apoptosis signaling involved in anatomical structure development
activation of apoptosis signaling involved in development of an anatomical structure
activation of apoptotic cell death involved in anatomical structure development
activation of apoptotic cell death involved in development of an anatomical structure
activation of apoptotic process involved in anatomical structure development
activation of apoptotic process involved in development
activation of apoptotic process involved in development of an anatomical structure
activation of apoptotic program involved in anatomical structure development
activation of apoptotic program involved in development of an anatomical structure
activation of apoptotic programmed cell death involved in anatomical structure development
activation of apoptotic programmed cell death involved in development of an anatomical structure
activation of programmed cell death by apoptosis involved in anatomical structure development
activation of programmed cell death by apoptosis involved in development of an anatomical structure
activation of type I programmed cell death involved in anatomical structure development
activation of type I programmed cell death involved in development of an anatomical structure
positive regulation of activation of apoptosis involved in anatomical structure development
positive regulation of activation of apoptosis involved in development of an anatomical structure
positive regulation of apoptosis involved in anatomical structure development
positive regulation of apoptosis involved in development of an anatomical structure
positive regulation of apoptosis signaling involved in anatomical structure development
positive regulation of apoptosis signaling involved in development of an anatomical structure
positive regulation of apoptotic program involved in anatomical structure development
positive regulation of apoptotic program involved in development of an anatomical structure
positive regulation of type I programmed cell death involved in anatomical structure development
positive regulation of type I programmed cell death involved in development of an anatomical structure
up regulation of activation of apoptosis involved in anatomical structure development
up regulation of activation of apoptosis involved in development of an anatomical structure
up regulation of apoptosis involved in anatomical structure development
up regulation of apoptosis involved in development of an anatomical structure
up regulation of apoptosis signaling involved in anatomical structure development
up regulation of apoptosis signaling involved in development of an anatomical structure
up regulation of apoptotic program involved in anatomical structure development
up regulation of apoptotic program involved in development of an anatomical structure
up regulation of type I programmed cell death involved in anatomical structure development
up regulation of type I programmed cell death involved in development of an anatomical structure
up-regulation of activation of apoptosis involved in anatomical structure development
up-regulation of activation of apoptosis involved in development of an anatomical structure
up-regulation of apoptosis involved in anatomical structure development
up-regulation of apoptosis involved in development of an anatomical structure
up-regulation of apoptosis signaling involved in anatomical structure development
up-regulation of apoptosis signaling involved in development of an anatomical structure
up-regulation of apoptotic program involved in anatomical structure development
up-regulation of apoptotic program involved in development of an anatomical structure
up-regulation of type I programmed cell death involved in anatomical structure development
up-regulation of type I programmed cell death involved in development of an anatomical structure
upregulation of activation of apoptosis involved in anatomical structure development
upregulation of activation of apoptosis involved in development of an anatomical structure
upregulation of apoptosis involved in anatomical structure development
upregulation of apoptosis involved in development of an anatomical structure
upregulation of apoptosis signaling involved in anatomical structure development
upregulation of apoptosis signaling involved in development of an anatomical structure
upregulation of apoptotic program involved in anatomical structure development
upregulation of apoptotic program involved in development of an anatomical structure
upregulation of type I programmed cell death involved in anatomical structure development
upregulation of type I programmed cell death involved in development of an anatomical structure
activation of apoptosis activator activity involved in anatomical structure development
activation of apoptosis activator activity involved in development of an anatomical structure
activation of commitment to apoptosis involved in anatomical structure development
activation of commitment to apoptosis involved in development of an anatomical structure
activation of induction of apoptosis by p53 involved in anatomical structure development
activation of induction of apoptosis by p53 involved in development of an anatomical structure
activation of induction of apoptosis involved in anatomical structure development
activation of induction of apoptosis involved in development of an anatomical structure
activation of signaling (initiator) caspase activity involved in anatomical structure development
activation of signaling (initiator) caspase activity involved in development of an anatomical structure
positive regulation of apoptosis activator activity involved in anatomical structure development
positive regulation of apoptosis activator activity involved in development of an anatomical structure
positive regulation of commitment to apoptosis involved in anatomical structure development
positive regulation of commitment to apoptosis involved in development of an anatomical structure
positive regulation of induction of apoptosis by p53 involved in anatomical structure development
positive regulation of induction of apoptosis by p53 involved in development of an anatomical structure
positive regulation of induction of apoptosis involved in anatomical structure development
positive regulation of induction of apoptosis involved in development of an anatomical structure
positive regulation of signaling (initiator) caspase activity involved in anatomical structure development
positive regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
up regulation of apoptosis activator activity involved in anatomical structure development
up regulation of apoptosis activator activity involved in development of an anatomical structure
up regulation of commitment to apoptosis involved in anatomical structure development
up regulation of commitment to apoptosis involved in development of an anatomical structure
up regulation of induction of apoptosis by p53 involved in anatomical structure development
up regulation of induction of apoptosis by p53 involved in development of an anatomical structure
up regulation of induction of apoptosis involved in anatomical structure development
up regulation of induction of apoptosis involved in development of an anatomical structure
up regulation of signaling (initiator) caspase activity involved in anatomical structure development
up regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
up-regulation of apoptosis activator activity involved in anatomical structure development
up-regulation of apoptosis activator activity involved in development of an anatomical structure
up-regulation of commitment to apoptosis involved in anatomical structure development
up-regulation of commitment to apoptosis involved in development of an anatomical structure
up-regulation of induction of apoptosis by p53 involved in anatomical structure development
up-regulation of induction of apoptosis by p53 involved in development of an anatomical structure
up-regulation of induction of apoptosis involved in anatomical structure development
up-regulation of induction of apoptosis involved in development of an anatomical structure
up-regulation of signaling (initiator) caspase activity involved in anatomical structure development
up-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
upregulation of apoptosis activator activity involved in anatomical structure development
upregulation of apoptosis activator activity involved in development of an anatomical structure
upregulation of commitment to apoptosis involved in anatomical structure development
upregulation of commitment to apoptosis involved in development of an anatomical structure
upregulation of induction of apoptosis by p53 involved in anatomical structure development
upregulation of induction of apoptosis by p53 involved in development of an anatomical structure
upregulation of induction of apoptosis involved in anatomical structure development
upregulation of induction of apoptosis involved in development of an anatomical structure
upregulation of signaling (initiator) caspase activity involved in anatomical structure development
upregulation of signaling (initiator) caspase activity involved in development of an anatomical structure
positive regulation of apoptotic process involved in development
Any process that modulates the frequency, rate or extent of apoptotic process involved in development.
regulation of apoptotic cell death involved in anatomical structure development
regulation of apoptotic cell death involved in development of an anatomical structure
regulation of apoptotic process involved in anatomical structure development
regulation of apoptotic process involved in development of an anatomical structure
regulation of apoptotic programmed cell death involved in anatomical structure development
regulation of apoptotic programmed cell death involved in development of an anatomical structure
regulation of programmed cell death by apoptosis involved in anatomical structure development
regulation of programmed cell death by apoptosis involved in development of an anatomical structure
regulation of activation of apoptosis involved in anatomical structure development
regulation of activation of apoptosis involved in development of an anatomical structure
regulation of apoptosis involved in anatomical structure development
regulation of apoptosis involved in development of an anatomical structure
regulation of apoptosis signaling involved in anatomical structure development
regulation of apoptosis signaling involved in development of an anatomical structure
regulation of apoptotic program involved in anatomical structure development
regulation of apoptotic program involved in development of an anatomical structure
regulation of type I programmed cell death involved in anatomical structure development
regulation of type I programmed cell death involved in development of an anatomical structure
regulation of apoptosis activator activity involved in anatomical structure development
regulation of apoptosis activator activity involved in development of an anatomical structure
regulation of commitment to apoptosis involved in anatomical structure development
regulation of commitment to apoptosis involved in development of an anatomical structure
regulation of induction of apoptosis by p53 involved in anatomical structure development
regulation of induction of apoptosis by p53 involved in development of an anatomical structure
regulation of induction of apoptosis involved in anatomical structure development
regulation of induction of apoptosis involved in development of an anatomical structure
regulation of signaling (initiator) caspase activity involved in anatomical structure development
regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
Q10943 in PMID:22801495, inferred from mutant phenotype
regulation of apoptotic process involved in development
Any process that modulates the frequency, rate or extent of protein localization to nucleolus.
regulation of protein localisation in nucleolus
regulation of protein localisation to nucleolus
regulation of protein localization in nucleolus
regulation of protein localization to nucleolus
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleolus.
down regulation of protein localisation in nucleolus
down regulation of protein localisation to nucleolus
down regulation of protein localization in nucleolus
down regulation of protein localization to nucleolus
down-regulation of protein localisation in nucleolus
down-regulation of protein localisation to nucleolus
down-regulation of protein localization in nucleolus
down-regulation of protein localization to nucleolus
downregulation of protein localisation in nucleolus
downregulation of protein localisation to nucleolus
downregulation of protein localization in nucleolus
downregulation of protein localization to nucleolus
negative regulation of protein localisation in nucleolus
negative regulation of protein localisation to nucleolus
negative regulation of protein localization in nucleolus
inhibition of protein localisation in nucleolus
inhibition of protein localisation to nucleolus
inhibition of protein localization in nucleolus
inhibition of protein localization to nucleolus
negative regulation of protein localization to nucleolus
Any process that activates or increases the frequency, rate or extent of protein localization to nucleolus.
positive regulation of protein localisation in nucleolus
positive regulation of protein localisation to nucleolus
positive regulation of protein localization in nucleolus
up regulation of protein localisation in nucleolus
up regulation of protein localisation to nucleolus
up regulation of protein localization in nucleolus
up regulation of protein localization to nucleolus
up-regulation of protein localisation in nucleolus
up-regulation of protein localisation to nucleolus
up-regulation of protein localization in nucleolus
up-regulation of protein localization to nucleolus
upregulation of protein localisation in nucleolus
upregulation of protein localisation to nucleolus
upregulation of protein localization in nucleolus
upregulation of protein localization to nucleolus
activation of protein localisation in nucleolus
activation of protein localisation to nucleolus
activation of protein localization in nucleolus
activation of protein localization to nucleolus
positive regulation of protein localization to nucleolus
The developmental process by which an intramembranous bone is generated and organized.
Any process that modulates the frequency, rate or extent of protein localization to cell cortex.
regulation of protein localisation to cell cortex
An example is cye-1 in C. elegans, UniProt ID O01501 in PMID:17115027.
regulation of protein localization to cell cortex
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell cortex.
down regulation of protein localisation to cell cortex
down regulation of protein localization to cell cortex
down-regulation of protein localisation to cell cortex
down-regulation of protein localization to cell cortex
downregulation of protein localisation to cell cortex
downregulation of protein localization to cell cortex
negative regulation of protein localisation to cell cortex
inhibition of protein localisation to cell cortex
inhibition of protein localization to cell cortex
negative regulation of protein localization to cell cortex
Any process that activates or increases the frequency, rate or extent of protein localization to cell cortex.
positive regulation of protein localisation to cell cortex
up regulation of protein localisation to cell cortex
up regulation of protein localization to cell cortex
up-regulation of protein localisation to cell cortex
up-regulation of protein localization to cell cortex
upregulation of protein localisation to cell cortex
upregulation of protein localization to cell cortex
activation of protein localisation to cell cortex
activation of protein localization to cell cortex
positive regulation of protein localization to cell cortex
The process whose specific outcome is the progression of a serous membrane over time, from its formation to the mature structure.
The process whose specific outcome is the progression of a visceral peritoneum over time, from its formation to the mature structure.
The process whose specific outcome is the progression of a parietal peritoneum over time, from its formation to the mature structure.
The process whose specific outcome is the progression of a peritoneum over time, from its formation to the mature structure.
Any process that modulates the frequency, rate or extent of aortic smooth muscle cell differentiation.
regulation of aortic smooth muscle cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of aortic smooth muscle cell differentiation.
down regulation of aortic smooth muscle cell differentiation
down-regulation of aortic smooth muscle cell differentiation
downregulation of aortic smooth muscle cell differentiation
inhibition of aortic smooth muscle cell differentiation
negative regulation of aortic smooth muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of aortic smooth muscle cell differentiation.
up regulation of aortic smooth muscle cell differentiation
up-regulation of aortic smooth muscle cell differentiation
upregulation of aortic smooth muscle cell differentiation
activation of aortic smooth muscle cell differentiation
positive regulation of aortic smooth muscle cell differentiation
The process whose specific outcome is the progression of a cranial skeletal system over time, from its formation to the mature structure. The cranial skeletal system is the skeletal subdivision of the head, and includes the skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
Any process that modulates the frequency, rate or extent of cell proliferation in midbrain.
regulation of cell proliferation in mesencephalon
regulation of mesencepahalic cell proliferation
regulation of cell proliferation in midbrain
Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation in midbrain.
down regulation of cell proliferation in mesencephalon
down regulation of cell proliferation in midbrain
down-regulation of cell proliferation in mesencephalon
down-regulation of cell proliferation in midbrain
downregulation of cell proliferation in mesencephalon
downregulation of cell proliferation in midbrain
negative regulation of cell proliferation in mesencephalon
inhibition of cell proliferation in mesencephalon
inhibition of cell proliferation in midbrain
down regulation of mesencepahalic cell proliferation
down-regulation of mesencepahalic cell proliferation
downregulation of mesencepahalic cell proliferation
inhibition of mesencepahalic cell proliferation
negative regulation of mesencepahalic cell proliferation
negative regulation of cell proliferation in midbrain
Any process that activates or increases the frequency, rate or extent of cell proliferation in midbrain.
positive regulation of cell proliferation in mesencephalon
up regulation of cell proliferation in mesencephalon
up regulation of cell proliferation in midbrain
up-regulation of cell proliferation in mesencephalon
up-regulation of cell proliferation in midbrain
upregulation of cell proliferation in mesencephalon
upregulation of cell proliferation in midbrain
activation of cell proliferation in mesencephalon
activation of cell proliferation in midbrain
activation of mesencepahalic cell proliferation
positive regulation of mesencepahalic cell proliferation
up regulation of mesencepahalic cell proliferation
up-regulation of mesencepahalic cell proliferation
upregulation of mesencepahalic cell proliferation
positive regulation of cell proliferation in midbrain
Any process that modulates the frequency, rate or extent of cardiac ventricle formation.
regulation of cardiac ventricle formation
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac ventricle formation.
down regulation of cardiac ventricle formation
down-regulation of cardiac ventricle formation
downregulation of cardiac ventricle formation
inhibition of cardiac ventricle formation
negative regulation of cardiac ventricle formation
Any process that activates or increases the frequency, rate or extent of cardiac ventricle formation.
up regulation of cardiac ventricle formation
up-regulation of cardiac ventricle formation
upregulation of cardiac ventricle formation
activation of cardiac ventricle formation
positive regulation of cardiac ventricle formation
Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization.
down regulation of establishment of protein localisation
down regulation of establishment of protein localization
down-regulation of establishment of protein localisation
down-regulation of establishment of protein localization
downregulation of establishment of protein localisation
downregulation of establishment of protein localization
negative regulation of establishment of protein localisation
negative regulation of protein positioning
negative regulation of protein recruitment
inhibition of establishment of protein localisation
inhibition of establishment of protein localization
negative regulation of establishment of protein localization
Any process that activates or increases the frequency, rate or extent of establishment of protein localization.
positive regulation of establishment of protein localisation
positive regulation of protein positioning
positive regulation of protein recruitment
up regulation of establishment of protein localisation
up regulation of establishment of protein localization
up-regulation of establishment of protein localisation
up-regulation of establishment of protein localization
upregulation of establishment of protein localisation
upregulation of establishment of protein localization
activation of establishment of protein localisation
activation of establishment of protein localization
positive regulation of establishment of protein localization
Any process that modulates the frequency, rate or extent of vascular smooth muscle cell differentiation.
regulation of vascular smooth muscle cell differentiation
regulation of vascular associated smooth muscle cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell differentiation.
down regulation of vascular associated smooth muscle cell differentiation
down regulation of vascular smooth muscle cell differentiation
down-regulation of vascular associated smooth muscle cell differentiation
down-regulation of vascular smooth muscle cell differentiation
downregulation of vascular associated smooth muscle cell differentiation
downregulation of vascular smooth muscle cell differentiation
negative regulation of VSMC differentiation
negative regulation of vascular smooth muscle cell differentiation
inhibition of vascular associated smooth muscle cell differentiation
inhibition of vascular smooth muscle cell differentiation
negative regulation of vascular associated smooth muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell differentiation.
positive regulation of VSMC differentiation
positive regulation of vascular smooth muscle cell differentiation
up regulation of vascular associated smooth muscle cell differentiation
up regulation of vascular smooth muscle cell differentiation
up-regulation of vascular associated smooth muscle cell differentiation
up-regulation of vascular smooth muscle cell differentiation
upregulation of vascular associated smooth muscle cell differentiation
upregulation of vascular smooth muscle cell differentiation
activation of vascular associated smooth muscle cell differentiation
activation of vascular smooth muscle cell differentiation
positive regulation of vascular associated smooth muscle cell differentiation
Any process that modulates the frequency, rate or extent of axo-dendritic protein transport.
regulation of axo-dendritic protein transport
Any process that stops, prevents or reduces the frequency, rate or extent of axo-dendritic protein transport.
down regulation of axo-dendritic protein transport
down-regulation of axo-dendritic protein transport
downregulation of axo-dendritic protein transport
down regulation of axonal protein transport
down-regulation of axonal protein transport
downregulation of axonal protein transport
inhibition of axo-dendritic protein transport
negative regulation of axonal protein transport
negative regulation of axo-dendritic protein transport
Any process that activates or increases the frequency, rate or extent of axo-dendritic protein transport.
up regulation of axo-dendritic protein transport
up-regulation of axo-dendritic protein transport
upregulation of axo-dendritic protein transport
activation of axo-dendritic protein transport
positive regulation of axonal protein transport
up regulation of axonal protein transport
up-regulation of axonal protein transport
upregulation of axonal protein transport
positive regulation of axo-dendritic protein transport
Any process that modulates the frequency, rate or extent of smooth muscle hypertrophy.
Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle hypertrophy.
down regulation of smooth muscle hypertrophy
down-regulation of smooth muscle hypertrophy
downregulation of smooth muscle hypertrophy
negative regulation of smooth muscle hypertrophy
Any process that activates or increases the frequency, rate or extent of smooth muscle hypertrophy.
up regulation of smooth muscle hypertrophy
up-regulation of smooth muscle hypertrophy
upregulation of smooth muscle hypertrophy
positive regulation of smooth muscle hypertrophy
Any process that modulates the frequency, rate or extent of cardiocyte differentiation.
regulation of cardiac cell differentiation
regulation of heart cell differentiation
regulation of cardiocyte differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of cardiocyte differentiation.
down regulation of cardiac cell differentiation
down regulation of cardiocyte differentiation
down regulation of heart cell differentiation
down-regulation of cardiac cell differentiation
down-regulation of cardiocyte differentiation
down-regulation of heart cell differentiation
downregulation of cardiac cell differentiation
downregulation of cardiocyte differentiation
downregulation of heart cell differentiation
negative regulation of cardiac cell differentiation
negative regulation of heart cell differentiation
inhibition of cardiac cell differentiation
inhibition of cardiocyte differentiation
inhibition of heart cell differentiation
negative regulation of cardiocyte differentiation
Any process that activates or increases the frequency, rate or extent of cardiocyte differentiation.
positive regulation of cardiac cell differentiation
positive regulation of heart cell differentiation
up regulation of cardiac cell differentiation
up regulation of cardiocyte differentiation
up regulation of heart cell differentiation
up-regulation of cardiac cell differentiation
up-regulation of cardiocyte differentiation
up-regulation of heart cell differentiation
upregulation of cardiac cell differentiation
upregulation of cardiocyte differentiation
upregulation of heart cell differentiation
activation of cardiac cell differentiation
activation of cardiocyte differentiation
activation of heart cell differentiation
positive regulation of cardiocyte differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of mitotic chromosome condensation.
negative regulation of mitotic chromosome condensation
Any process that modulates the frequency, rate or extent of RNA binding.
Any process that stops, prevents or reduces the frequency, rate or extent of RNA binding.
Any process that activates or increases the frequency, rate or extent of RNA binding.
The developmental process by which an epicardium is generated and organized.
visceral serous pericardium of heart morphogenesis
visceral serous pericardium proper morphogenesis
pericardium visceral mesothelium morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of chromatin organization.
down regulation of chromatin organisation
down regulation of chromatin organization
down regulation of establishment or maintenance of chromatin architecture
down-regulation of chromatin organisation
down-regulation of chromatin organization
down-regulation of establishment or maintenance of chromatin architecture
downregulation of chromatin organisation
downregulation of chromatin organization
downregulation of establishment or maintenance of chromatin architecture
negative regulation of chromatin organisation
negative regulation of establishment or maintenance of chromatin architecture
inhibition of establishment or maintenance of chromatin architecture
negative regulation of chromatin modification
negative regulation of chromatin organization
Any process that activates or increases the frequency, rate or extent of chromatin organization.
positive regulation of chromatin organisation
positive regulation of establishment or maintenance of chromatin architecture
up regulation of establishment or maintenance of chromatin architecture
up-regulation of establishment or maintenance of chromatin architecture
upregulation of establishment or maintenance of chromatin architecture
activation of establishment or maintenance of chromatin architecture
positive regulation of chromatin modification
positive regulation of chromatin organization
Any process that modulates the frequency, rate or extent of epithelial tube formation.
An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay).
Any process that stops, prevents or reduces the frequency, rate or extent of epithelial tube formation.
down regulation of epithelial tube formation
down-regulation of epithelial tube formation
downregulation of epithelial tube formation
negative regulation of epithelial tube formation
Any process that activates or increases the frequency, rate or extent of epithelial tube formation.
up regulation of epithelial tube formation
up-regulation of epithelial tube formation
upregulation of epithelial tube formation
positive regulation of epithelial tube formation
Any apoptotic process in a vascular associated smooth muscle cell.
vascular smooth muscle cell apoptotic process
vascular associated smooth muscle cell apoptosis
vascular associated smooth muscle cell apoptotic process
Any process that modulates the frequency, rate or extent of neural crest cell differentiation.
regulation of neural crest cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of neural crest cell differentiation.
down regulation of neural crest cell differentiation
down-regulation of neural crest cell differentiation
downregulation of neural crest cell differentiation
inhibition of neural crest cell differentiation
negative regulation of neural crest cell differentiation
Any process that activates or increases the frequency, rate or extent of neural crest cell differentiation.
up regulation of neural crest cell differentiation
up-regulation of neural crest cell differentiation
upregulation of neural crest cell differentiation
activation of neural crest cell differentiation
positive regulation of neural crest cell differentiation
Any process that modulates the frequency, rate or extent of cardiac myofibril assembly.
regulation of cardiac myofibril development
regulation of cardiac myofibril morphogenesis
regulation of cardiac myofibril assembly
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac myofibril assembly.
down regulation of cardiac myofibril assembly
down regulation of cardiac myofibril development
down regulation of cardiac myofibril morphogenesis
down-regulation of cardiac myofibril assembly
down-regulation of cardiac myofibril development
down-regulation of cardiac myofibril morphogenesis
downregulation of cardiac myofibril assembly
downregulation of cardiac myofibril development
downregulation of cardiac myofibril morphogenesis
negative regulation of cardiac myofibril development
negative regulation of cardiac myofibril morphogenesis
inhibition of cardiac myofibril assembly
inhibition of cardiac myofibril development
inhibition of cardiac myofibril morphogenesis
down regulation of heart myofibril assembly
down-regulation of heart myofibril assembly
downregulation of heart myofibril assembly
negative regulation of heart myofibril assembly
negative regulation of cardiac myofibril assembly
Any process that activates or increases the frequency, rate or extent of cardiac myofibril assembly.
positive regulation of cardiac myofibril development
positive regulation of cardiac myofibril morphogenesis
up regulation of cardiac myofibril assembly
up regulation of cardiac myofibril development
up regulation of cardiac myofibril morphogenesis
up-regulation of cardiac myofibril assembly
up-regulation of cardiac myofibril development
up-regulation of cardiac myofibril morphogenesis
upregulation of cardiac myofibril assembly
upregulation of cardiac myofibril development
upregulation of cardiac myofibril morphogenesis
activation of cardiac myofibril assembly
activation of cardiac myofibril development
activation of cardiac myofibril morphogenesis
positive regulation of heart myofibril assembly
up regulation of heart myofibril assembly
up-regulation of heart myofibril assembly
upregulation of heart myofibril assembly
positive regulation of cardiac myofibril assembly
Any cell proliferation that is involved in endocardial cushion morphogenesis.
cell proliferation involved in endocardial cushion morphogenesis
Any process that modulates the frequency, rate or extent of morphogenesis of an epithelium.
regulation of morphogenesis of an epithelium
Any process that stops, prevents or reduces the frequency, rate or extent of morphogenesis of an epithelium.
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 morphogenesis of an epithelium
negative regulation of morphogenesis of an epithelium
Any process that activates or increases the frequency, rate or extent of morphogenesis of an epithelium.
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 morphogenesis of an epithelium
positive regulation of morphogenesis of an epithelium
The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone.
A process in which a protein is transported to, or maintained in, a location within a presynapse.
Any process that modulates the frequency, rate or extent of protein localization to presynapse.
regulation of protein localisation in presynapse
regulation of protein localisation to presynapse
regulation of protein localization in presynapse
regulation of recruitment of presynaptic proteins
regulation of protein localization to presynapse
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to presynapse.
down regulation of protein localisation in presynapse
down regulation of protein localisation to presynapse
down regulation of protein localization in presynapse
down regulation of protein localization to presynapse
down regulation of recruitment of presynaptic proteins
down-regulation of protein localisation in presynapse
down-regulation of protein localisation to presynapse
down-regulation of protein localization in presynapse
down-regulation of protein localization to presynapse
down-regulation of recruitment of presynaptic proteins
downregulation of protein localisation in presynapse
downregulation of protein localisation to presynapse
downregulation of protein localization in presynapse
downregulation of protein localization to presynapse
downregulation of recruitment of presynaptic proteins
negative regulation of protein localisation in presynapse
negative regulation of protein localisation to presynapse
negative regulation of protein localization in presynapse
negative regulation of recruitment of presynaptic proteins
inhibition of protein localisation in presynapse
inhibition of protein localisation to presynapse
inhibition of protein localization in presynapse
inhibition of protein localization to presynapse
inhibition of recruitment of presynaptic proteins
negative regulation of protein localization to presynapse
Any process that activates or increases the frequency, rate or extent of protein localization to presynapse.
positive regulation of protein localisation in presynapse
positive regulation of protein localisation to presynapse
positive regulation of protein localization in presynapse
positive regulation of recruitment of presynaptic proteins
up regulation of protein localisation in presynapse
up regulation of protein localisation to presynapse
up regulation of protein localization in presynapse
up regulation of protein localization to presynapse
up regulation of recruitment of presynaptic proteins
up-regulation of protein localisation in presynapse
up-regulation of protein localisation to presynapse
up-regulation of protein localization in presynapse
up-regulation of protein localization to presynapse
up-regulation of recruitment of presynaptic proteins
upregulation of protein localisation in presynapse
upregulation of protein localisation to presynapse
upregulation of protein localization in presynapse
upregulation of protein localization to presynapse
upregulation of recruitment of presynaptic proteins
activation of protein localisation in presynapse
activation of protein localisation to presynapse
activation of protein localization in presynapse
activation of protein localization to presynapse
activation of recruitment of presynaptic proteins
positive regulation of protein localization to presynapse
Any intracellular signal transduction that is involved in positive regulation of cell growth.
intracellular signal transduction involved in up regulation of cell growth
intracellular signal transduction involved in up-regulation of cell growth
intracellular signal transduction involved in upregulation of cell growth
intracellular signaling chain involved in positive regulation of cell growth
intracellular signaling chain involved in up regulation of cell growth
intracellular signaling chain involved in up-regulation of cell growth
intracellular signaling chain involved in upregulation of cell growth
intracellular protein kinase cascade involved in activation of cell growth
intracellular protein kinase cascade involved in positive regulation of cell growth
intracellular protein kinase cascade involved in stimulation of cell growth
intracellular protein kinase cascade involved in up regulation of cell growth
intracellular protein kinase cascade involved in up-regulation of cell growth
intracellular protein kinase cascade involved in upregulation of cell growth
intracellular signal transduction involved in activation of cell growth
intracellular signal transduction involved in stimulation of cell growth
intracellular signal transduction pathway involved in activation of cell growth
intracellular signal transduction pathway involved in positive regulation of cell growth
intracellular signal transduction pathway involved in stimulation of cell growth
intracellular signal transduction pathway involved in up regulation of cell growth
intracellular signal transduction pathway involved in up-regulation of cell growth
intracellular signal transduction pathway involved in upregulation of cell growth
intracellular signaling chain involved in activation of cell growth
intracellular signaling chain involved in stimulation of cell growth
protein kinase cascade involved in activation of cell growth
protein kinase cascade involved in positive regulation of cell growth
protein kinase cascade involved in stimulation of cell growth
protein kinase cascade involved in up regulation of cell growth
protein kinase cascade involved in up-regulation of cell growth
protein kinase cascade involved in upregulation of cell growth
signal transmission via intracellular cascade involved in activation of cell growth
signal transmission via intracellular cascade involved in positive regulation of cell growth
signal transmission via intracellular cascade involved in stimulation of cell growth
signal transmission via intracellular cascade involved in up regulation of cell growth
signal transmission via intracellular cascade involved in up-regulation of cell growth
signal transmission via intracellular cascade involved in upregulation of cell growth
intracellular signaling cascade involved in activation of cell growth
intracellular signaling cascade involved in positive regulation of cell growth
intracellular signaling cascade involved in stimulation of cell growth
intracellular signaling cascade involved in up regulation of cell growth
intracellular signaling cascade involved in up-regulation of cell growth
intracellular signaling cascade involved in upregulation of cell growth
intracellular signaling pathway involved in activation of cell growth
intracellular signaling pathway involved in positive regulation of cell growth
intracellular signaling pathway involved in stimulation of cell growth
intracellular signaling pathway involved in up regulation of cell growth
intracellular signaling pathway involved in up-regulation of cell growth
intracellular signaling pathway involved in upregulation of cell growth
signal transduction via intracellular signaling cascade involved in activation of cell growth
signal transduction via intracellular signaling cascade involved in positive regulation of cell growth
signal transduction via intracellular signaling cascade involved in stimulation of cell growth
signal transduction via intracellular signaling cascade involved in up regulation of cell growth
signal transduction via intracellular signaling cascade involved in up-regulation of cell growth
signal transduction via intracellular signaling cascade involved in upregulation of cell growth
intracellular signal transduction involved in positive regulation of cell growth
Any process that modulates the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide.
regulation of neuropeptide-mediated retrograde trans-synaptic signaling
regulation of retrograde trans-synaptic signaling by neuropeptide
Any process that stops, prevents or reduces the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide.
down regulation of retrograde trans-synaptic signaling by neuropeptide
down-regulation of retrograde trans-synaptic signaling by neuropeptide
downregulation of retrograde trans-synaptic signaling by neuropeptide
inhibition of retrograde trans-synaptic signaling by neuropeptide
inhibition of neuropeptide-mediated retrograde trans-synaptic signaling
negative regulation of neuropeptide-mediated retrograde trans-synaptic signaling
negative regulation of retrograde trans-synaptic signaling by neuropeptide
Any process that activates or increases the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide.
up regulation of retrograde trans-synaptic signaling by neuropeptide
up-regulation of retrograde trans-synaptic signaling by neuropeptide
upregulation of retrograde trans-synaptic signaling by neuropeptide
activation of retrograde trans-synaptic signaling by neuropeptide
positive regulation of neuropeptide-mediated retrograde trans-synaptic signaling
positive regulation of retrograde trans-synaptic signaling by neuropeptide
Any process that modulates the frequency, rate or extent of myeloid progenitor cell differentiation.
regulation of myeloid progenitor cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of myeloid progenitor cell differentiation.
down regulation of myeloid progenitor cell differentiation
down-regulation of myeloid progenitor cell differentiation
downregulation of myeloid progenitor cell differentiation
inhibition of myeloid progenitor cell differentiation
negative regulation of myeloid progenitor cell differentiation
Any process that activates or increases the frequency, rate or extent of myeloid progenitor cell differentiation.
up regulation of myeloid progenitor cell differentiation
up-regulation of myeloid progenitor cell differentiation
upregulation of myeloid progenitor cell differentiation
activation of myeloid progenitor cell differentiation
positive regulation of myeloid progenitor cell differentiation
Any process that modulates the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process.
regulation of vascular smooth muscle cell apoptotic process
regulation of vascular associated smooth muscle cell apoptosis
regulation of vascular smooth muscle cell apoptosis
regulation of vascular associated smooth muscle cell apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process.
down regulation of VSMC apoptotic process
down regulation of vascular associated smooth muscle cell apoptotic process
down regulation of vascular smooth muscle cell apoptotic process
down-regulation of VSMC apoptotic process
down-regulation of vascular associated smooth muscle cell apoptotic process
down-regulation of vascular smooth muscle cell apoptotic process
downregulation of VSMC apoptotic process
downregulation of vascular associated smooth muscle cell apoptotic process
downregulation of vascular smooth muscle cell apoptotic process
negative regulation of VSMC apoptotic process
negative regulation of vascular smooth muscle cell apoptotic process
down regulation of vascular associated smooth muscle cell apoptosis
down regulation of vascular smooth muscle cell apoptosis
down-regulation of vascular associated smooth muscle cell apoptosis
down-regulation of vascular smooth muscle cell apoptosis
downregulation of vascular associated smooth muscle cell apoptosis
downregulation of vascular smooth muscle cell apoptosis
inhibition of vascular associated smooth muscle cell apoptosis
inhibition of vascular associated smooth muscle cell apoptotic process
inhibition of vascular smooth muscle cell apoptosis
inhibition of vascular smooth muscle cell apoptotic process
negative regulation of vascular associated smooth muscle cell apoptosis
negative regulation of vascular smooth muscle cell apoptosis
negative regulation of vascular associated smooth muscle cell apoptotic process
Any process that activates or increases the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process.
positive regulation of VSMC apoptotic process
positive regulation of vascular smooth muscle cell apoptotic process
up regulation of vascular associated smooth muscle cell apoptotic process
up regulation of vascular smooth muscle cell apoptotic process
up-regulation of vascular associated smooth muscle cell apoptotic process
up-regulation of vascular smooth muscle cell apoptotic process
upregulation of vascular associated smooth muscle cell apoptotic process
upregulation of vascular smooth muscle cell apoptotic process
activation of vascular associated smooth muscle cell apoptosis
activation of vascular associated smooth muscle cell apoptotic process
activation of vascular smooth muscle cell apoptosis
activation of vascular smooth muscle cell apoptotic process
positive regulation of vascular associated smooth muscle cell apoptosis
positive regulation of vascular smooth muscle cell apoptosis
up regulation of vascular associated smooth muscle cell apoptosis
up regulation of vascular smooth muscle cell apoptosis
up-regulation of vascular associated smooth muscle cell apoptosis
up-regulation of vascular smooth muscle cell apoptosis
upregulation of vascular associated smooth muscle cell apoptosis
upregulation of vascular smooth muscle cell apoptosis
positive regulation of vascular associated smooth muscle cell apoptotic process
Any process that modulates the frequency, rate or extent of protein localization to membrane.
regulation of protein localisation in membrane
regulation of protein localization in membrane
regulation of protein localization to membrane
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to membrane.
down regulation of protein localisation in membrane
down regulation of protein localization in membrane
down regulation of protein localization to membrane
down-regulation of protein localisation in membrane
down-regulation of protein localization in membrane
down-regulation of protein localization to membrane
downregulation of protein localisation in membrane
downregulation of protein localization in membrane
downregulation of protein localization to membrane
negative regulation of protein localisation in membrane
negative regulation of protein localization in membrane
inhibition of protein localisation in membrane
inhibition of protein localization in membrane
inhibition of protein localization to membrane
negative regulation of protein localization to membrane
Any process that activates or increases the frequency, rate or extent of protein localization to membrane.
positive regulation of protein localisation in membrane
positive regulation of protein localization in membrane
up regulation of protein localisation in membrane
up regulation of protein localization in membrane
up regulation of protein localization to membrane
up-regulation of protein localisation in membrane
up-regulation of protein localization in membrane
up-regulation of protein localization to membrane
upregulation of protein localisation in membrane
upregulation of protein localization in membrane
upregulation of protein localization to membrane
activation of protein localisation in membrane
activation of protein localization in membrane
activation of protein localization to membrane
positive regulation of protein localization to membrane
Any process that activates or increases the frequency, rate or extent of branching morphogenesis of a nerve.
up regulation of branching morphogenesis of a nerve
up-regulation of branching morphogenesis of a nerve
upregulation of branching morphogenesis of a nerve
activation of branching morphogenesis of a nerve
positive regulation of branching morphogenesis of a nerve
Any process that modulates the frequency, rate or extent of blood vessel branching.
regulation of branching involved in blood vessel morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of blood vessel branching.
down regulation of branching involved in blood vessel morphogenesis
down regulation of patterning of blood vessels
down-regulation of branching involved in blood vessel morphogenesis
down-regulation of patterning of blood vessels
downregulation of branching involved in blood vessel morphogenesis
downregulation of patterning of blood vessels
negative regulation of branching involved in blood vessel morphogenesis
inhibition of branching involved in blood vessel morphogenesis
inhibition of patterning of blood vessels
Any process that activates or increases the frequency, rate or extent of blood vessel branching.
positive regulation of branching involved in blood vessel morphogenesis
up regulation of branching involved in blood vessel morphogenesis
up regulation of patterning of blood vessels
up-regulation of branching involved in blood vessel morphogenesis
up-regulation of patterning of blood vessels
upregulation of branching involved in blood vessel morphogenesis
upregulation of patterning of blood vessels
activation of branching involved in blood vessel morphogenesis
activation of patterning of blood vessels
positive regulation of blood vessel branching
Any process that modulates the frequency, rate or extent of mitotic nuclear envelope disassembly.
regulation of mitotic nuclear envelope breakdown
regulation of mitotic nuclear envelope catabolism
regulation of mitotic nuclear envelope degradation
regulation of mitotic nuclear envelope disassembly
Any process that stops, prevents or reduces the frequency, rate or extent of mitotic nuclear envelope disassembly.
down regulation of mitotic nuclear envelope breakdown
down regulation of mitotic nuclear envelope catabolism
down regulation of mitotic nuclear envelope degradation
down regulation of mitotic nuclear envelope disassembly
down-regulation of mitotic nuclear envelope breakdown
down-regulation of mitotic nuclear envelope catabolism
down-regulation of mitotic nuclear envelope degradation
down-regulation of mitotic nuclear envelope disassembly
downregulation of mitotic nuclear envelope breakdown
downregulation of mitotic nuclear envelope catabolism
downregulation of mitotic nuclear envelope degradation
downregulation of mitotic nuclear envelope disassembly
negative regulation of mitotic nuclear envelope breakdown
negative regulation of mitotic nuclear envelope catabolism
negative regulation of mitotic nuclear envelope degradation
inhibition of mitotic nuclear envelope breakdown
inhibition of mitotic nuclear envelope catabolism
inhibition of mitotic nuclear envelope degradation
inhibition of mitotic nuclear envelope disassembly
negative regulation of mitotic nuclear envelope disassembly
Any process that activates or increases the frequency, rate or extent of mitotic nuclear envelope disassembly.
positive regulation of mitotic nuclear envelope breakdown
positive regulation of mitotic nuclear envelope catabolism
positive regulation of mitotic nuclear envelope degradation
up regulation of mitotic nuclear envelope breakdown
up regulation of mitotic nuclear envelope catabolism
up regulation of mitotic nuclear envelope degradation
up regulation of mitotic nuclear envelope disassembly
up-regulation of mitotic nuclear envelope breakdown
up-regulation of mitotic nuclear envelope catabolism
up-regulation of mitotic nuclear envelope degradation
up-regulation of mitotic nuclear envelope disassembly
upregulation of mitotic nuclear envelope breakdown
upregulation of mitotic nuclear envelope catabolism
upregulation of mitotic nuclear envelope degradation
upregulation of mitotic nuclear envelope disassembly
activation of mitotic nuclear envelope breakdown
activation of mitotic nuclear envelope catabolism
activation of mitotic nuclear envelope degradation
activation of mitotic nuclear envelope disassembly
positive regulation of mitotic nuclear envelope disassembly
Any process that modulates the frequency, rate or extent of vascular endothelial cell proliferation.
regulation of vascular endothelial cell proliferation
Any process that stops, prevents or reduces the frequency, rate or extent of vascular endothelial cell proliferation.
down regulation of vascular endothelial cell proliferation
down-regulation of vascular endothelial cell proliferation
downregulation of vascular endothelial cell proliferation
inhibition of vascular endothelial cell proliferation
negative regulation of vascular endothelial cell proliferation
Any process that activates or increases the frequency, rate or extent of vascular endothelial cell proliferation.
up regulation of vascular endothelial cell proliferation
up-regulation of vascular endothelial cell proliferation
upregulation of vascular endothelial cell proliferation
activation of vascular endothelial cell proliferation
positive regulation of vascular endothelial cell proliferation
Any process that modulates the frequency, rate or extent of presynapse assembly.
regulation of presynaptic terminal assembly
Any process that stops, prevents or reduces the frequency, rate or extent of presynapse assembly.
down regulation of presynapse biogenesis
down regulation of presynaptic terminal assembly
down-regulation of presynapse biogenesis
down-regulation of presynaptic terminal assembly
downregulation of presynaptic terminal assembly
negative regulation of presynapse biogenesis
negative regulation of presynaptic terminal assembly
inhibition of presynaptic terminal assembly
negative regulation of presynapse assembly
Any process that activates or increases the frequency, rate or extent of presynapse assembly.
positive regulation of presynapse biogenesis
positive regulation of presynaptic terminal assembly
up regulation of presynaptic terminal assembly
up-regulation of presynaptic terminal assembly
upregulation of presynaptic terminal assembly
activation of presynaptic terminal assembly
positive regulation of presynapse assembly
Any process that modulates the frequency, rate or extent of serotonin biosynthetic process.
regulation of serotonin biosynthetic process
Any process that stops, prevents or reduces the frequency, rate or extent of serotonin biosynthetic process.
down regulation of serotonin biosynthesis
down regulation of serotonin biosynthetic process
down-regulation of serotonin biosynthesis
down-regulation of serotonin biosynthetic process
downregulation of serotonin biosynthesis
downregulation of serotonin biosynthetic process
negative regulation of serotonin anabolism
negative regulation of serotonin biosynthesis
negative regulation of serotonin formation
negative regulation of serotonin synthesis
inhibition of serotonin biosynthetic process
negative regulation of serotonin biosynthetic process
Any process that activates or increases the frequency, rate or extent of serotonin biosynthetic process.
positive regulation of serotonin anabolism
positive regulation of serotonin biosynthesis
positive regulation of serotonin formation
positive regulation of serotonin synthesis
up regulation of serotonin biosynthetic process
up-regulation of serotonin biosynthetic process
upregulation of serotonin biosynthetic process
activation of serotonin biosynthetic process
positive regulation of serotonin biosynthetic process
Any process that modulates the frequency, rate or extent of protein localization to chromatin.
regulation of protein localisation to chromatin
regulation of protein localization to chromatin
Any process that modulates the frequency, rate or extent of artery morphogenesis.
Any process that stops, prevents or reduces the frequency, rate or extent of artery morphogenesis.
down regulation of arterial morphogenesis
down-regulation of arterial morphogenesis
downregulation of arterial morphogenesis
negative regulation of arterial morphogenesis
negative regulation of artery morphogenesis
Any process that activates or increases the frequency, rate or extent of artery morphogenesis.
positive regulation of arterial morphogenesis
positive regulation of artery morphogenesis
The disaggregation of a nucleus into its constituent components.
Any microtubule bundle that is part of a cytoplasm.
A process in which a protein is transported to, or maintained in, a location within a cytoplasmic microtubule.
protein localisation to cytoplasmic microtubule
protein localization to cytoplasmic microtubule
Any process that modulates the frequency, rate or extent of mesodermal cell differentiation.
regulation of mesoderm cell differentiation
regulation of mesodermal cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of mesodermal cell differentiation.
down regulation of mesoderm cell differentiation
down regulation of mesodermal cell differentiation
down-regulation of mesoderm cell differentiation
down-regulation of mesodermal cell differentiation
downregulation of mesoderm cell differentiation
downregulation of mesodermal cell differentiation
negative regulation of mesoderm cell differentiation
inhibition of mesoderm cell differentiation
inhibition of mesodermal cell differentiation
negative regulation of mesodermal cell differentiation
Any process that activates or increases the frequency, rate or extent of mesodermal cell differentiation.
positive regulation of mesoderm cell differentiation
up regulation of mesoderm cell differentiation
up regulation of mesodermal cell differentiation
up-regulation of mesoderm cell differentiation
up-regulation of mesodermal cell differentiation
upregulation of mesoderm cell differentiation
upregulation of mesodermal cell differentiation
activation of mesoderm cell differentiation
activation of mesodermal cell differentiation
positive regulation of mesodermal cell differentiation
Any process that modulates the frequency, rate or extent of synapse pruning.
Any process that stops, prevents or reduces the frequency, rate or extent of synapse pruning.
Any process that activates or increases the frequency, rate or extent of synapse pruning.
Any process that stops, prevents or reduces the frequency, rate or extent of synapse organization.
negative regulation of synapse development
negative regulation of synapse organisation
down regulation of synapse morphogenesis
down regulation of synapse organization and biogenesis
down-regulation of synapse morphogenesis
down-regulation of synapse organization and biogenesis
downregulation of synapse organization and biogenesis
inhibition of synapse organization and biogenesis
negative regulation of synapse morphogenesis
negative regulation of synapse organization and biogenesis
negative regulation of synapse organization
Any process that activates or increases the frequency, rate or extent of chromosome condensation.
positive regulation of eukaryotic chromosome condensation
positive regulation of nuclear chromosome condensation
up regulation of chromosome condensation
up regulation of eukaryotic chromosome condensation
up regulation of nuclear chromosome condensation
up-regulation of chromosome condensation
up-regulation of eukaryotic chromosome condensation
up-regulation of nuclear chromosome condensation
upregulation of eukaryotic chromosome condensation
upregulation of nuclear chromosome condensation
activation of eukaryotic chromosome condensation
activation of nuclear chromosome condensation
positive regulation of chromosome condensation
Any process that stops, prevents or reduces the frequency, rate or extent of microtubule nucleation.
down regulation of microtubule nucleation
down-regulation of microtubule nucleation
downregulation of microtubule nucleation
negative regulation of microtubule nucleation
Any process that modulates the frequency, rate or extent of protein localization to cell leading edge.
regulation of protein localisation in cell leading edge
regulation of protein localisation to cell leading edge
regulation of protein localization in cell leading edge
regulation of protein localization to cell leading edge
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell leading edge.
down regulation of protein localisation in cell leading edge
down regulation of protein localisation to cell leading edge
down regulation of protein localization in cell leading edge
down regulation of protein localization to cell leading edge
down-regulation of protein localisation in cell leading edge
down-regulation of protein localisation to cell leading edge
down-regulation of protein localization in cell leading edge
down-regulation of protein localization to cell leading edge
downregulation of protein localisation in cell leading edge
downregulation of protein localisation to cell leading edge
downregulation of protein localization in cell leading edge
downregulation of protein localization to cell leading edge
negative regulation of protein localisation in cell leading edge
negative regulation of protein localisation to cell leading edge
negative regulation of protein localization in cell leading edge
inhibition of protein localisation in cell leading edge
inhibition of protein localisation to cell leading edge
inhibition of protein localization in cell leading edge
inhibition of protein localization to cell leading edge
negative regulation of protein localization to cell leading edge
Any process that activates or increases the frequency, rate or extent of protein localization to cell leading edge.
positive regulation of protein localisation in cell leading edge
positive regulation of protein localisation to cell leading edge
positive regulation of protein localization in cell leading edge
up regulation of protein localisation in cell leading edge
up regulation of protein localisation to cell leading edge
up regulation of protein localization in cell leading edge
up regulation of protein localization to cell leading edge
up-regulation of protein localisation in cell leading edge
up-regulation of protein localisation to cell leading edge
up-regulation of protein localization in cell leading edge
up-regulation of protein localization to cell leading edge
upregulation of protein localisation in cell leading edge
upregulation of protein localisation to cell leading edge
upregulation of protein localization in cell leading edge
upregulation of protein localization to cell leading edge
activation of protein localisation in cell leading edge
activation of protein localisation to cell leading edge
activation of protein localization in cell leading edge
activation of protein localization to cell leading edge
positive regulation of protein localization to cell leading edge
Any process that modulates the frequency, rate or extent of smooth muscle tissue development.
regulation of smooth muscle tissue development
Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle tissue development.
down regulation of smooth muscle tissue development
down-regulation of smooth muscle tissue development
downregulation of smooth muscle tissue development
inhibition of smooth muscle tissue development
negative regulation of smooth muscle tissue development
Any process that activates or increases the frequency, rate or extent of smooth muscle tissue development.
up regulation of smooth muscle tissue development
up-regulation of smooth muscle tissue development
upregulation of smooth muscle tissue development
activation of smooth muscle tissue development
positive regulation of smooth muscle tissue development
Any process that modulates the frequency, rate or extent of mesoderm formation.
Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm formation.
negative regulation of mesoderm formation
Any process that activates or increases the frequency, rate or extent of mesoderm formation.
positive regulation of mesoderm formation
The developmental process by which a pharyngeal gland is generated and organized.
Any process that modulates the frequency, rate or extent of germ cell proliferation.
Any process that stops, prevents or reduces the frequency, rate or extent of germ cell proliferation.
down regulation of germ cell proliferation
down-regulation of germ cell proliferation
downregulation of germ cell proliferation
negative regulation of germ cell proliferation
Any process that activates or increases the frequency, rate or extent of germ cell proliferation.
up regulation of germ cell proliferation
up-regulation of germ cell proliferation
positive regulation of germ cell proliferation
Any process that modulates the frequency, rate or extent of gonad development.
Any process that stops, prevents or reduces the frequency, rate or extent of gonad development.
negative regulation of gonad development
Any process that activates or increases the frequency, rate or extent of gonad development.
positive regulation of gonad development
Any process that modulates the frequency, rate or extent of lipid localization.
Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization.
negative regulation of lipid localisation
negative regulation of lipid localization
Any process that activates or increases the frequency, rate or extent of lipid localization.
positive regulation of lipid localisation
positive regulation of lipid localization
Any process that stops, prevents or reduces the frequency, rate or extent of endothelial tube morphogenesis.
down regulation of endothelial tube morphogenesis
down-regulation of endothelial tube morphogenesis
downregulation of endothelial tube morphogenesis
inhibition of endothelial tube morphogenesis
negative regulation of endothelial tube morphogenesis
Any process that activates or increases the frequency, rate or extent of endothelial tube morphogenesis.
up regulation of endothelial tube morphogenesis
up-regulation of endothelial tube morphogenesis
upregulation of endothelial tube morphogenesis
activation of endothelial tube morphogenesis
positive regulation of endothelial tube morphogenesis
Any apoptotic process in a retinal cell.
induction of retinal programmed cell death
Any apoptotic process in a compound eye retinal cell.
compound eye retinal cell apoptotic process
A protein-DNA complex that contains DNA in combination with a protein which binds to and bends DNA. Often plays a role in DNA compaction.
The process whereby a membrane-bounded vesicle is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane.
extracellular vesicular exosome secretion
multi-vesicular body fusion with plasma membrane
A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor).
A process in which RNA is transported to and maintained in a part of a chromosome that is organized into chromatin.
The flow of blood through the gastric mucosa of an animal, enabling the transport of nutrients and the removal of waste products.
A process in which a protein is transported to, or maintained in, the cell periphery.
Any process in which the vacuole is transported to, and/or maintained in, a specific location within the cell.
The multiplication or reproduction of vascular smooth muscle cells, resulting in the expansion of a cell population. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels.
vascular smooth muscle cell proliferation
vascular associated smooth muscle cell proliferation
A macromolecular complex that contains both RNA and protein molecules.
Any process that modulates the frequency, rate or extent of multicellular organismal development.
regulation of multicellular organismal development
Any process that modulates the frequency, rate or extent of animal organ morphogenesis.
regulation of histogenesis and organogenesis
regulation of animal organ morphogenesis
Any process that modulates the frequency, rate or extent of stem cell division.
Any process that modulates the frequency, rate or extent of leukocyte apoptotic process.
regulation of leukocyte apoptotic process
Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte apoptotic process.
negative regulation of leukocyte apoptosis
negative regulation of leukocyte apoptotic process
Any process that activates or increases the frequency, rate or extent of leukocyte apoptotic process.
positive regulation of leukocyte apoptosis
positive regulation of leukocyte apoptotic process
Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process.
regulation of cellular biopolymer biosynthetic process
regulation of cellular macromolecule anabolism
regulation of cellular macromolecule biosynthesis
regulation of cellular macromolecule formation
regulation of cellular macromolecule synthesis
regulation of cellular macromolecule biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process.
negative regulation of cellular biopolymer biosynthetic process
negative regulation of cellular macromolecule anabolism
negative regulation of cellular macromolecule biosynthesis
negative regulation of cellular macromolecule formation
negative regulation of cellular macromolecule synthesis
negative regulation of cellular macromolecule biosynthetic process
Any process that modulates the frequency, rate or extent of cell proliferation involved in heart morphogenesis.
regulation of cell proliferation involved in heart morphogenesis
Any process that stops, prevents, or reduces the frequency, rate or extent of cell proliferation involved in heart morphogenesis.
negative regulation of cell proliferation involved in heart morphogenesis
Any process that activates or increases the frequency, rate or extent of cell proliferation involved in heart morphogenesis.
positive regulation of cell proliferation involved in heart morphogenesis
Any process that modulates the frequency, rate or extent of cell motility.
Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility.
negative regulation of movement of a cell
Any process that activates or increases the frequency, rate or extent of cell motility.
positive regulation of movement of a cell
Any process that modulates the frequency, rate or extent of branching morphogenesis of a nerve.
regulation of branching morphogenesis of a nerve
Any process that stops, prevents, or reduces the frequency, rate or extent of branching morphogenesis of a nerve.
negative regulation of branching morphogenesis of a nerve
Any process that modulates the frequency, rate or extent of neural precursor cell proliferation.
regulation of neural precursor cell proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of neural precursor cell proliferation.
negative regulation of neural precursor cell proliferation
Any process that activates or increases the frequency, rate or extent of neural precursor cell proliferation.
positive regulation of neural precursor cell proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel morphogenesis.
negative regulation of blood vessel morphogenesis
Any process that modulates the frequency, rate or extent of female gonad development.
Any process that stops, prevents, or reduces the frequency, rate or extent of female gonad development.
negative regulation of ovarian development
negative regulation of ovary development
negative regulation of female gonad development
Any process that activates or increases the frequency, rate or extent of female gonad development.
positive regulation of ovarian development
positive regulation of ovary development
positive regulation of female gonad development
Any process that modulates the frequency, rate or extent of reproductive process.
Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process.
negative regulation of reproductive process
Any process that activates or increases the frequency, rate or extent of reproductive process.
positive regulation of reproductive process
Any process that modulates the frequency, rate or extent of fibroblast apoptotic process.
regulation of fibroblast apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of fibroblast apoptotic process.
negative regulation of fibroblast apoptosis
negative regulation of fibroblast apoptotic process
Any process that activates or increases the frequency, rate or extent of fibroblast apoptotic process.
positive regulation of fibroblast apoptosis
positive regulation of fibroblast apoptotic process
Any process that modulates the frequency, rate or extent of DNA biosynthetic process.
Any process that stops, prevents or reduces the frequency, rate or extent of DNA biosynthetic process.
negative regulation of DNA biosynthetic process
Any process that modulates the frequency, rate or extent of cellular amino acid biosynthetic process.
regulation of amino acid biosynthetic process
regulation of cellular amino acid anabolism
regulation of cellular amino acid biosynthesis
regulation of cellular amino acid formation
regulation of cellular amino acid synthesis
regulation of cellular amino acid biosynthetic process
Any process that stops, prevents or reduces the frequency, rate or extent of cellular amino acid biosynthetic process.
negative regulation of amino acid biosynthetic process
negative regulation of cellular amino acid anabolism
negative regulation of cellular amino acid biosynthesis
negative regulation of cellular amino acid formation
negative regulation of cellular amino acid synthesis
negative regulation of cellular amino acid biosynthetic process
Any process that activates or increases the frequency, rate or extent of cellular amino acid biosynthetic process.
positive regulation of amino acid biosynthetic process
positive regulation of cellular amino acid anabolism
positive regulation of cellular amino acid biosynthesis
positive regulation of cellular amino acid formation
positive regulation of cellular amino acid synthesis
positive regulation of cellular amino acid biosynthetic process
Any process that activates or increases the frequency, rate or extent of myotome development.
positive regulation of myotome development
Any process that activates or increases the frequency, rate or extent of myoblast proliferation.
positive regulation of myoblast proliferation
Any process that modulates the frequency, rate or extent of myotome development.
Any process that modulates the frequency, rate or extent of myoblast proliferation.
Any process that modulates the frequency, rate or extent of endothelial cell apoptotic process.
regulation of apoptosis of endothelial cells
regulation of endothelial cell programmed cell death by apoptosis
regulation of killing of endothelial cells
regulation of programmed cell death of endothelial cells by apoptosis
regulation of programmed cell death, endothelial cells
regulation of endothelial cell apoptosis
regulation of endothelial cell apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process.
negative regulation of apoptosis of endothelial cells
negative regulation of endothelial cell programmed cell death by apoptosis
negative regulation of killing of endothelial cells
negative regulation of programmed cell death of endothelial cells by apoptosis
negative regulation of programmed cell death, endothelial cells
negative regulation of endothelial cell apoptosis
negative regulation of endothelial cell apoptotic process
Any process that activates or increases the frequency, rate or extent of endothelial cell apoptotic process.
positive regulation of apoptosis of endothelial cells
positive regulation of endothelial cell programmed cell death by apoptosis
positive regulation of killing of endothelial cells
positive regulation of programmed cell death of endothelial cells by apoptosis
positive regulation of programmed cell death, endothelial cells
positive regulation of endothelial cell apoptosis
positive regulation of endothelial cell apoptotic process
Any process that modulates the frequency, rate or extent of oxygen metabolic process.
regulation of diatomic oxygen metabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of oxygen metabolic process.
negative regulation of diatomic oxygen metabolic process
negative regulation of oxygen metabolism
negative regulation of oxygen metabolic process
Any process that activates or increases the frequency, rate or extent of oxygen metabolic process.
positive regulation of diatomic oxygen metabolic process
positive regulation of oxygen metabolism
positive regulation of oxygen metabolic process
Any process that modulates the frequency, rate or extent of mesoderm development.
Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm development.
negative regulation of mesoderm development
Any process that activates or increases the frequency, rate or extent of mesoderm development.
positive regulation of mesoderm development
Any process that modulates the frequency, rate or extent of ectoderm development.
Any process that stops, prevents or reduces the frequency, rate or extent of ectoderm development.
negative regulation of ectoderm development
Any process that activates or increases the frequency, rate or extent of ectoderm development.
positive regulation of ectoderm development
Any process that modulates the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis.
regulation of cell proliferation involved in compound eye morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis.
negative regulation of cell proliferation involved in compound eye morphogenesis
Any process that activates or increases the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis.
positive regulation of cell proliferation involved in compound eye morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of gastrulation.
Any process that activates or increases the frequency, rate or extent of gastrulation.
Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process.
positive regulation of DNA biosynthetic process
Any process that stops, prevents or reduces the frequency, rate or extent of stem cell proliferation.
negative regulation of stem cell proliferation
Any process that activates or increases the frequency, rate or extent of stem cell proliferation.
positive regulation of stem cell proliferation
Any process that modulates the frequency, rate or extent of motor neuron apoptotic process.
regulation of motor neuron apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of motor neuron apoptotic process.
negative regulation of motoneuron apoptosis
negative regulation of motor neuron apoptosis
negative regulation of motor neuron apoptotic process
Any process that activates or increases the frequency, rate or extent of motor neuron apoptotic process.
positive regulation of motoneuron apoptosis
positive regulation of motor neuron apoptosis
positive regulation of motor neuron apoptotic process
Any process that modulates the frequency, rate or extent of cardiac muscle cell myoblast differentiation.
regulation of myocardial precursor cell differentiation
regulation of cardiac myoblast differentiation
regulation of cardiac muscle cell myoblast differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle cell myoblast differentiation.
negative regulation of myocardial precursor cell differentiation
negative regulation of cardiac myoblast differentiation
negative regulation of cardiac muscle cell myoblast differentiation
Any process that activates or increases the frequency, rate or extent of cardiac muscle cell myoblast differentiation.
positive regulation of myocardial precursor cell differentiation
positive regulation of cardiac myoblast differentiation
positive regulation of cardiac muscle cell myoblast differentiation
Any process that modulates the frequency, rate or extent of cardiac muscle cell differentiation.
regulation of cardiomyocyte differentiation
regulation of heart muscle cell differentiation
regulation of cardiac muscle cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle cell differentiation.
negative regulation of cardiomyocyte differentiation
negative regulation of heart muscle cell differentiation
negative regulation of cardiac muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of cardiac muscle cell differentiation.
positive regulation of cardiomyocyte differentiation
positive regulation of heart muscle cell differentiation
positive regulation of cardiac muscle cell differentiation
Any process that modulates the frequency, rate or extent of stem cell differentiation.
Any process that stops, prevents or reduces the frequency, rate or extent of stem cell differentiation.
negative regulation of stem cell differentiation
Any process that activates or increases the frequency, rate or extent of stem cell differentiation.
positive regulation of stem cell differentiation
Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation involved in lung development.
regulation of mesenchymal cell proliferation involved in lung development
Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell proliferation involved in lung development.
negative regulation of mesenchymal cell proliferation involved in lung development
Any process that activates or increases the frequency, rate or extent of mesenchymal cell proliferation involved in lung development.
positive regulation of mesenchymal cell proliferation involved in lung development
Any process that modulates the frequency, rate or extent of epithelial cell proliferation involved in lung morphogenesis.
regulation of epithelial cell proliferation involved in lung morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell proliferation involved in lung morphogenesis.
negative regulation of epithelial cell proliferation involved in lung morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of myoblast proliferation.
negative regulation of myoblast proliferation
Any process that modulates the frequency, rate or extent of heart morphogenesis.
Any process that modulates the frequency, rate or extent of steroid hormone secretion.
Any process that stops, prevents or reduces the frequency, rate or extent of steroid hormone secretion.
negative regulation of steroid hormone secretion
Any process that activates or increases the frequency, rate or extent of steroid hormone secretion.
positive regulation of steroid hormone secretion
Any process that modulates the frequency, rate or extent of androgen secretion.
Any process that stops, prevents or reduces the frequency, rate or extent of androgen secretion.
negative regulation of androgen secretion
Any process that activates or increases the frequency, rate or extent of androgen secretion.
positive regulation of androgen secretion
Any process that modulates the frequency, rate or extent of skeletal muscle cell differentiation.
regulation of skeletal muscle cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle cell differentiation.
negative regulation of skeletal muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of skeletal muscle cell differentiation.
positive regulation of skeletal muscle cell differentiation
Any process that modulates the frequency, rate or extent of mesenchymal cell apoptotic process.
regulation of mesenchymal cell apoptosis
regulation of mesenchymal cell apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell apoptotic process.
negative regulation of mesenchymal cell apoptosis
negative regulation of mesenchymal cell apoptotic process
Any process that activates or increases the frequency, rate or extent of mesenchymal cell apoptotic process.
positive regulation of mesenchymal cell apoptosis
positive regulation of mesenchymal cell apoptotic process
Any process that modulates the frequency, rate or extent of RNA biosynthetic process.
Any process that modulates the frequency, rate or extent of vasculogenesis.
Any process that stops, prevents or reduces the frequency, rate or extent of vasculogenesis.
negative regulation of vascular morphogenesis
Any process that activates or increases the frequency, rate or extent of vasculogenesis.
positive regulation of vascular morphogenesis
Any process that modulates the frequency, rate or extent of apoptotic signaling pathway.
regulation of apoptotic signalling pathway
regulation of apoptotic signaling pathway
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway.
negative regulation of apoptotic signalling pathway
negative regulation of apoptotic signaling pathway
Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway.
positive regulation of apoptotic signalling pathway
positive regulation of apoptotic signaling pathway
Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization.
negative regulation of chromosome organisation
negative regulation of chromosome organization and biogenesis
negative regulation of maintenance of genome integrity
negative regulation of nuclear genome maintenance
negative regulation of chromosome organization
Any process that activates or increases the frequency, rate or extent of chromosome organization.
positive regulation of chromosome organisation
positive regulation of chromosome organization and biogenesis
positive regulation of maintenance of genome integrity
positive regulation of nuclear genome maintenance
positive regulation of chromosome organization
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Melanie Courtot
denotator type
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
"Behavior related to the complex psychophysiological experience of an individual's state of mind as interacting with biochemical (internal) and environmental (external) influences." [wikipedia:Emotions]
Behavior directly related to the production of offspring [NBO:AC]
reproduction
"A behavior that occurs predominantly or only, in individuals that are part of a group." [Wikipedia:Social_behavior]
"Behavior related to the interactions between organisms for the purpose of mating." [NBO:GVG]
"A behavioral interaction between organisms in which one organism has the intention of inflicting damage on another individual using physical or verbal means." [wikipedia:Aggression]
"Behaviour related to the activity which primary purpose is the sexual reproduction." [NBO:GVG]
Male's insertion of sperm-transfer organ into the body of the female [NBO:SMAC]
copulate
"A feeding behavior associated with the intake or the frequency of intake or preference or manner of intake of food." [NBO:GVG]
"A feeding behavior associated with the intake or the frequency of intake or preference or manner of intake of liquids." [NBO:GVG]
"The behavioral interactions between organisms for the purpose of attracting sexual partners." [GOC:dph]
courtship
"Behavior related to the specific actions or reactions of an organism following mating." [GOC:bf]
post-copulatory behavior
The act of bringing an object or substance into the body by swallowing, surrounding or absorbing it [NBO:SMAC]
"Behavior related to defence against predation or predators." [NBO:GVG]
antipredator behavior
"Behavior related to the preparation of the body to \"fight\" or \"flee\" from perceived attack, harm or threat." [NBO:GVG]
"A physical aggression behavior involving attack on prey by a predator." [NBO:GVG]
"Exhibiting a domineering, assault posture and/or hostile physical action towards animals." [NBO:GVG]
"An aggressive behavior that aims to inflicting damage on another entity using physical means." [NBO:GVG]
agonism
Any behavior that tends to prevent further or future attack, often by signalling a willingness to yield or surrender [NBO:AC]
Behavior by which an animal removes itself spatially from an agonistic encounter in which it is not the winner [NBO:AC]
retreat
"Behavior characterized by a quick excitability to annoyance, impatience, or anger." [NBO:GVG]
"A behavior associated with the intake of liquid." [NBO:GVG]
"A feeding behavior associated with the intake of food." [NBO:GVG]
"Behavior related to the tendency of an organism to maintain internal equilibrium." [NBO:GVG]
"Behavior related to the deprivation of food." [NBO:GVG]
"A helping behavior (without expectation of extrinsic rewards and sometimes involving personal risk or sacrifice) that benefits individuals or society." [NBO:GVG]
"Prosocial behavior is caring about the welfare and rights of others, feeling concern and empathy for them, and acting in ways that benefit others." [wikipedia:Prosocial_behavior]
"Helping behavior refers to voluntary actions intended to help the others, with reward regarded or disregarded." [wikipedia:Helping_behavior]
"Reciprocal altruism is the idea that the incentive for an individual to help in the present is based on the expectation of the potential receipt in the future." [wikipedia:Helping_behavior]
Behavior that facilitates the restoration of normal interactions between parties that recently engaged in a conflict.[NBO:AC]
reconciliation
reconciliation behavior
"The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610]
"Behavior related to how the body reacts to a stressor ( a stimulus that causes stress), real or imagined." [wikipedia:Stress_(biological)]
It refers to the consequence of the failure of an organism to respond adequately to mental, emotional or physical demands, whether actual or imagined.
"Behavior related to the identification or realization of a threat or a stressor." [wikipedia:Stress_(biological)]
"Behaviour related to the male activity which primary purpose is the sexual reproduction." [NBO:GVG]
"Behaviour related to the female activity which primary purpose is the sexual reproduction." [NBO:GVG]
"A social behavior related to the activity of conveying information." [wikipedia:Communication]
"Communication behavior related to the process of conveying meaning in the form of non-word messages through for example gesture, body language or posture; facial expression and eye contact etc." [wikipedia:.wikipedia.org/wiki/Nonverbal_communication]
"Aggressive behavior related to the defence of a fixed area against intruders, typically conspecifics." [GOC:hjd]
"Behavior related to the activity seen in animals exposed to adverse stimuli, in which the tendency to act defensively is stronger than the tendency to attack." [web:http\://www.britannica.com/EBchecked/topic/45916/avoidance-behavior]
"Behavior related to the activity seen in animals exposed to potential danger in which they exhibit the tendency to act defensively." [NBO:SD]
"The actions or reactions of a male, for the purpose of attracting a sexual partner." [GOC:bf]
"The actions or reactions of a female, for the purpose of attracting a sexual partner." [GOC:bf]
"An aggressive behavior towards other members of the society." [NBO:RH]
"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]
regulation of behavior
"Behavior related to the intake of substances." [NBOC:GVG]
consumption behavior
"Any process that modulates the frequency, rate or extent of consumption behavior, the specific actions or reactions of an organism in response to external or internal stimuli." [NBOC:GVG]
regulation of consumption behavior
"Any process that modulates the frequency, rate or extent of consumption of food or liquid" [NBOC:GVG]
regulation of feeding behavior
"Any process that modulates the frequency, rate or extent of sexual activity, the specific actions or reactions of an organism in response to external or internal stimuli." [NBOC:GVG]
regulation of sexual activity
A predator behavior involving actively stalking prey over a distance.
hunting behavior
A predator behavior involving a surprise attack on unsuspecting prey. The predator remains in one place and waits for prey to come near. The predator conceals itself and then subdues its prey with its own body or body parts.
ambush behavior
A predator behavior involving subduing prey using a structure or modification of the environment created by the predator for that purpose.
trapping behavior
Feeding behavior during which a living entity acquires food and energy by actively searching for food resources.
active foraging behavior
Behavior in which one animal causes the death of another.
killing
kill
Agonistic behavior involving direct physical contact including (but not limited to) biting, kicking, grabbing.
contact aggression
Deposition of eggs either into the medium, or onto a substrate.
facilitating oviposition
Forcible alteration of behavior of one animal by another.
coercion
Facilitating release or transfer of gametes.
gamete release function
Active search for possible mates.
mate finding behavior
A behavior on the part of one individual associated with evaluating the fighting ability or correlates of fighting ability of a potential opponent.
assessment behavior
Behavior by one animals soliciting food provision by a potential mate.
courtship begging
Consumption of one member of a mating pair, usually the male, usually after the mating.
sexual cannibalism
Behavior that signifies hostility and predicts an increased probability of attack.
threat
Behavior in which one animal causes bodily damage to another.
injuring
injure
Carrying or manipulation of infants or equivalent items to reduce chances of aggression on carrier by other animals.
agonistic buffering
Chasing of one animal by another during an agonistic conflict.
agonistic chase
Alarm behavior triggered by agonistic actions or postures
agonistic alarm
Increasing intensity of directed agonistic behavior.
escalation
Behavior that serves to exlude an animal from a group.
exclusion
Display behavior by the winner of a prior agonistic contest.
triumph
Behavior that serves to demonstrate non-aggressive intent by one member of a courting or potentially mating pair to the other.
mating appeasement
Any of several behaviors directed towards one animal unwilling to mate by another eager to do so.
sexual harassment
An acitvity that seems irrelevant to its behavioral context to a human observer and often occurs when its performer is in a conflict situation.
displacement behavior
Provision of food to a potential mate
courtship feeding
Actions resulting in establishment or use of one locale for reproductive activity.
breeding site selection
Behaviors that appear to signifiy lack of hostility and to reduce chances of attack.
appeasement
Usually interference by members of one sex in the completion of courtship or mating activities by one or more members of the same sex.
sexual interference
Behavior associated with refusing courtship or solicitation behaviors by avoidance, retreat, or other active repulsion of suitor.
mate rejection
A process that realizes a plan which is the concretization of a plan specification.
planned process
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.
For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood).
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
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).
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.
TODO: define this or obsolete it and move children somewhere else.
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
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.
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.
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.
A reproductive quality inhering in a bearer by virtue of the bearer's initiating, sustaining, or supporting reproduction.
A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
A quality inhering in a bearer by virtue of the bearer's having a horizontal surface without a slope, tilt, or curvature.
A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center.
A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
A size quality which is relatively high.
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.
A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section.
A fertility quality inhering in a bearer by virtue of the bearer's being capable of initiating, sustaining, or supporting reproduction.
A fertility quality inhering in a bearer by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction.
An optical quality which obtains by virtue of the ability of the bearer to absorb visible light.
A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy.
A optical quality inhering in a bearer by virtue of the bearer's lacking opacity.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A physical quality inhering in a bearer by virtue of the bearer's disposition to recover its size and shape after deformation in any way.
An elasticity quality inhering in a bearer by virtue of the bearer's ability to recover its size and shape after deformation in any way.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
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.
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism.
A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes.
A monadic quality of continuant that exists at the cellular level of organisation.
A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types.
A cellular potency that is the capacity to produce only one differentiated cell type.
Unipotent cells have the quality of self-renewal which distinguishes them from non-stem cells.
A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity.
Less potent than multipotent, often thought of as precursor or progenitor cell status.
A cellular potency that is the capacity to form multiple differentiated cell types.
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
A cellular quality inhering in a bearer by virtue of the bearer's having thin, tail-like projections extending outwards from the cell body.
A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel.
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
A quality inhering in a bearer by virtue of the bearer's decomposition into component parts.
An organismal quality inhering in a bearer by virtue of the bearer's ability to produce new life or offspring.
A reproductive quality inhering in the young of an animal by virtue of the bearer's disposition to survive and develop normally.
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.
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.
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.
A physical quality that is the ability to contract or shrink.
A contractility which is relatively high.
A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending.
A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted.
This refers to the disposition of the bearer.
A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of solids.
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
A shape quality in which a portion of the outermost boundary of an entity folds in space such that a portion that was originally convex is now concave.
A composition quality inhering in a bearer by virtue of the bearer's containing granules.
A viability quality inhering in a population by virtue of some of it's members' ability to survive.
A shape quality in a bearer by virtue of the bearer's curving inward.
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
An organismal quality inhering in a bearer by virtue of the bearer's consisting cells.
A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell.
A quality that inheres in an entire organism or part of an organism.
A quality that inheres in an entire population or part of a population.
Surface shape that refers to the inward or outward curvature of the surface.
A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave.
Use this term or an is_a child of this term when the entire shape of the object is known.
A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity.
A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas.
A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces.
A branched quality inhering in a bearer by virtue of the bearer's having smaller branches arising from larger branches. Resembling a tree in branching structure.
A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within.
An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific pH conditions.
A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
A quality inhering in a bearer by virtue of its constitution.
A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical.
A quality inhering in a bearer by virtue of the bearer's surface becoming more extended in a plane.
Becoming flat but not necessarily completely flat.
Texture quality inhering in a bearer by virtue of the bearer's being marked with one or more channels.
A shape that inheres in a 3 dimensional entity.
A quality that has a value that is increased compared to normal or average.
A quality that has a value that is decreased compared to normal or average.
A quality of an object that has a value that is decreased compared to normal or average.
A quality of an object that has a value that is increased compared to normal or average.
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter.
Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope).
A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt
An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for acidic dyes under specific pH conditions.
Pertaining to the individual parts making up an aggregate fruit like a many-lobed "berry," such as a raspberry.
A composition quality inhering in an bearer by virtue of the bearer's consisting of collagen.
A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer.
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
A quality inhering in a structure by virtue of it consisting of many of repeated, similar or identical subunits, arranged in some orderly array.
A complete coverage of this domain would subclasses homopolymeric, copolymeric, crystalline.
A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components.
A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes.
An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions.
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.
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.
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
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 quality that inheres in a population of organisms.
See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2.
This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community.
Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term.
quality of a population
A quality that inheres in a community.
These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2.
Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual.
quality of an ecological community
A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction.
The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes.
population process
The number of different species represented in an ecological community.
This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019).
adapted from http://en.wikipedia.org/wiki/Species_richness
community species richness
A process that leads to a change in the number of individuals (positive or negative) in a population.
A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat.
A population growth process that leads to an exponential increase in the number of individuals in a population.
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
The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness.
If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity.
adapted from http://en.wikipedia.org/wiki/Species_diversity
The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified.
community species diversity
A population process that ultimately leads to the death of all individuals in a population.
population extinction
A process that ultimately leads to the death of all individuals in a population.
species extinction
If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even.
A quality of an ecological community that reflects how close in abundance all species in a community are.
adapted from http://en.wikipedia.org/wiki/Species_evenness
community species evenness
A collection of organisms of the same species that has as members only humans.
human community
human population
collection of humans
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
A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other.
pair of interacting organisms
A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other.
pair of interacting organisms of the same species
A plant structure (PO:0005679) which is a whole organism.
Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280).
A floral structure primordium (PO:0025477) that is committed to the development of an ovule (PO:0020003).
portion of ovule primordium tissue (exact)
The transition from ovule primordium to ovule occurs when an integument (PO:0020021) begins to develop from the protoderm (PO:0006210).
A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062).
portion of gynoecium primordium tissue (exact)
Use carpel primordium (PO:0004703) for the primordium (PO:0025127) of an individual carpel (PO:0009030).
A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127).
&#225pice del epiblasto (epiblastema) (Spanish, exact)
A portion of meristem tissue (PO:0009013) which is the organogenic region of the meristem, characterized by higher rates of cell division.
A portion of reproductive shoot apical meristem tissue (PO:0008028) that gives rise to the floral organs (PO:0025395).
In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311).
A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall.
c&#233lula meristem&#225tica (Spanish, exact)
A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005).
portion of root primordium tissue (exact)
A root primordium may arise from cells of a pericycle (PO:0006203) in a root in most seed plant (pericyclic lateral root primordium; PO:0025492), from cells of an endodermis (PO:0000252) in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493), or from cells of a shoot axis (PO:0025029), in the case of a basal root primordium (PO:0025479) or shoot-borne root primordium (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).
A lateral plant organ (PO:0009008) produced by a shoot apical meristem (PO:0020148).
A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006).
meristema del epiblasto (epiblastema) (Spanish, exact)
A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679).
A protoderm may or may not arise from independent initial cells (PO:0004011). Some researchers also refer to it as an epidermis in a meristematic state.
A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003).
Solanaceae whole plant growth stages (SGN:0000001) (related)
cereal plant growth stage ontology (GRO:0007199) (related)
maize growth stage (GRO:0007002) (related)
plant growth stages in Arabidopsis (TAIR:0000021) (related)
rice growth stage (GRO:0007040) (related)
sorghum growth stage (GRO:0007124) (related)
wheat, barley and oat growth stage (GRO:0007156) (related)
A shoot apical meristem (PO:0020148) that gives rise to the apical growth of reproductive tissues and organs.
meristema apical reproductivo del epiblasto (epiblastema) (Spanish, exact)
A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010).
A fruit (PO:0009001) may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds (PO:0009010). When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms.
A cell which is a plant structure (PO:0009011).
Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall.
A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately.
Roots function in the absorption of water and inorganic nutrients, anchoring the plant body to the substrate and supporting it, storage of food and nutrients, and vegetative reproduction. The roots of most vascular plant species enter into symbiosis with soil-borne microorganisms. Roots are usually positively geotropic and found underground, although there are many exceptions such as the aerial roots of orchids. Roots often form secondary thickening from the root lateral meristem (PO:0006308). Commonly thought of as one of the three basic parts of the plant body, along with the shoot axis (PO:0025029) and leaves (PO:0025034).
A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them.
sistema de epiblasto (epiblastema) (Spanish, exact)
The shoot system is generally used to refer to the above-ground plant parts, although some plants have parts of their shoot system underground. For example, a rhizome (PO:0004542), bulb (PO:0025356), a corm (PO:0025355) or a subterranean tuber (PO:0004547), as in Solanum tuberosum (potato) or yam, are all part of the shoot system.
A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types.
porci&#243n de un tejido vegetal (Spanish, exact)
A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts.
A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.
Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003).
A whole plant (PO:0000003) that participates in the plant embryo stage (PO:0007631).
A plant embryo is generally formed after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa; the beginning of a seed germination stage (PO:0007057) in seed plants, formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).
A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088).
A seed generally develops from an ovule (PO:0020003) after fertilization, but may develop without fertilization in the case of apogamy (e.g., adventitious embryos or somatic embryos). A seed is a reproductive unit of seed plants (gymnosperms, angiosperms, and fossil pteridosperms).
A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant.
'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome.
A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes.
etapa de desarrollo de estructura vegetal (Spanish, exact)
plant growth and development stage (exact)
Refers to GO:0032502 'developmental process', which includes growth, differentiation, and senescence, and BFO:0000003 'ocurrent'.
A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth.
A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part.
The characteristic reproductive structure of angiosperms. May have as part one or more petals, sepals or tepals. May contain one or more pistillode (PO:0009078), staminode (PO:0009077) or other aborted organs that don't show up in mature form.
A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046).
gynoecium of lower floret of pedicellate spikelet of ear (narrow)
gynoecium of lower floret of pedicellate spikelet of tassel (narrow)
gynoecium of lower floret of sessile spikelet of ear (narrow)
gynoecium of lower floret of sessile spikelet of tassel (narrow)
gynoecium of upper floret of pedicellate spikelet of ear (narrow)
gynoecium of upper floret of pedicellate spikelet of tassel (narrow)
gynoecium of upper floret of sessile spikelet of ear (narrow)
gynoecium of upper floret of sessile spikelet of tassel (narrow)
If annotating gene expression to a gynoecium with a single carpel (PO:0009030), the annotation should go on carpel. A gynoecium with two or more carpels may be either syncarpous (carpels fused) or apopcarpous (carpels free) or the carpels may be partially fused. The word pistil is used synonymously with gynoecium for a synocarpous gynoecium, and synonymously with carpel for an apocarpous gynoecium, whether it has one or more carpels. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) in which a female gametophyte (PO:0025279) is located, one or two integuments (PO:0020021), and a funicle (PO:0020006).
A seed (PO:0009010) develops from a plant ovule. In angiosperms, a plant ovule is part of a plant ovary (PO:0009072). In conifers, a plant ovule is part of an ovuliferous scale (add term). If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352).
A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025).
A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232).
meristema apical del epiblasto (epiblastema) (Spanish, exact)
A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).
estructura vegetal colectiva de &#243rgano (Spanish, exact)
Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure.
A collective plant organ structure (PO:0025007) that consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005).
estructura colectiva del filoma (Spanish, exact)
A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof.
Generally the below ground portion of a vascular plant.
A native plant cell (PO:0025606) that is part of a plant embryo (PO:0009009).
c&#233lula embri&#243nica vegetal (Spanish, exact)
A plant axis (PO:0025004) that is part of a shoot system (PO:0009006).
eje del epiblasto (epiblastema) (Spanish, exact)
Often bears leaves and branches. In vascular plants, has at least one node and one internode.
A phyllome (PO:0006001) that is not associated with a reproductive structure.
A shoot system (PO:0009006) in the sporophytic phase that has as part at least one sporangium (PO:0025094).
sistema de brote reproductivo (Spanish, exact)
A plant structure (PO:0009011) that is part of an plant embryo (PO:0009009).
estructura vegetal embri&#243nica (Spanish, exact)
Includes plant structures that only occur in embryos (such as suspensor) as well as plant structures that are part of an embryo when a plant is in the embryonic phase (such as embryonic radicle).
A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011).
A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition.
A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) and is part of a shoot apex (PO:0000037) and is committed to the development of a phyllome (PO:0006001).
portion of phyllome primordium tissue (exact)
The transition from phyllome primordium to phyllome occurs when the first non-meristematic tissue develops begins to develop.
An anatomical entity that is or was part of a plant.
entidad anat&#243mica vegetal (Spanish, exact)
Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'.
A shoot apex that has as part a reproductive shoot apical meristem.
&#225pice reproductivo del epiblasto (epiblastema) (Spanish, exact)
A portion of plant tissue (PO:0009007) that is part of a plant embryo (PO:0009009).
portion of embryonic plant tissue (exact)
tejido embri&#243nico vegetal (Spanish, exact)
This class is for tissues that only occur as part of an embryo.
A maximal whole plant development stage.
vida de la planta entera (Spanish, exact)
There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage.
A plant structure development stage (PO:0009012) that has as primary participant a collective plant structure (PO:0025497).
etapa de desarrollo de una estructura colectiva de la planta (Spanish, exact)
Includes flower development stage (PO:0007615), corolla development stage (PO:0007604), and inflorescence development stage (PO:0001083).
collective plant organ structure development stage
A plant organ (PO:0009008) that is part of a flower (PO:0009046).
Includes phyllomes such as anthers and petals, as well as shoot axes such as androphores and gynophores.
A portion of meristem tissue (PO:0009013) that is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and will give rise to a phyllome primordium (PO:0025128).
The phyllome anlagen is only detectable by gene expression, not morphology.
A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029).
Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as for lateral roots in most seed plants, an endodermis (PO:0000252), as for lateral roots in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042).
A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) and is part of a reproductive shoot apex (PO:0025222).
floral structure primordia (exact, plural)
portion of floral structure primordium tissue (exact)
primordio de organo floral (Spanish, exact)
If annotating to a primordium of a floral structure, it is better to use the more specific term, such as petal primordium (PO:0000021) or anther primordium (PO:0006089).
A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types.
estructura vegetal con m&#250ltiples tejidos (Spanish, exact)
Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types.
A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007).
estructura vegetal colectiva (Spanish, exact)
This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006).
A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death.
The shoot system (PO:0009006) develops fron the shoot apical meristem (PO:0020148) in the plant embryo (PO:0009009) in vascular plants. In lower plants the gametophore (PO:0030018) arises from a gametophore meristematic apical cell (PO:0030019) in the protonema (PO:0030003).
A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082).
reproductive shoot system development stage
A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment).
A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004).
A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death.
A whole plant (PO:0000003) in the sporophyte development stage usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy. Examples of apogamy include both naturally occurring instances (such as sporophytes arising form haploid cells as in bryophytes or ferns) as well as in vitro instances (such as haploid embryo culture or in vitro fusion of non-gamete cells or protoplasts). During the sporophyte development stage, a plant may produce meiospores by meiosis.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].
A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction.
A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved.
hematopoietic progenitor cell antigen CD34
A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence.
An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage.
An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1.
cell surface glycoprotein MAC-1 subunit alpha
A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.
A CD3 subunit with immunoglobulin domain that is a translation product of the human CD3E gene or a 1:1 ortholog thereof.
T-cell surface antigen T3/Leu-4 epsilon chain
A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain.
A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration.
A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain.
T-lymphocyte differentiation antigen T8/Leu-2
T-cell surface glycoprotein CD8 alpha chain
A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof.
membrane-spanning 4-domains subfamily A member 1
A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues.
A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof.
myeloid cell-specific leucine-rich glycoprotein
A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof.
A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain.
vascular endothelial growth factor receptor
A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof.
vascular endothelial growth factor receptor 2
A protein that is the translation product of any of the LY6 genes (LY6A-LY6I).
An Ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof.
A protein that is a translation product of the Ly76 gene in mouse.
Category=organism-gene. Requested by=CL.
A protein that is a translation product of the human FGF8 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human SHH gene or a 1:1 ortholog thereof.
Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains
A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof.
class A basic helix-loop-helix protein 17
T-cell acute lymphocytic leukemia protein 1
An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif.
Category=family. Integrins are heterodimeric complexes of an alpha and a beta subunit. They are a structurally elaborate family of adhesion molecules that transmit signals bidirectionally across the plasma membrane by undergoing large-scale structural rearrangements. By regulating cell-cell and cell-matrix contacts, integrins participate in a wide-range of biological interactions including development, tissue repair, angiogenesis, inflammation and hemostasis. [PMID:10402956, PMID:11988479, PMID:9676575].
A protein that is encoded in the genome of Mus musculus.
A protein that is encoded in the genome of some Eukaryota.
A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of mouse.
T-cell surface glycoprotein Lyt-2 (mouse)
T-cell surface glycoprotein CD8 alpha chain (mouse)
An integrin alpha-M that is encoded in the genome of mouse.
CD11 antigen-like family member B (mouse)
cell surface glycoprotein MAC-1 subunit alpha (mouse)
A CD4 molecule that is encoded in the genome of mouse.
T-cell differentiation antigen L3T4 (mouse)
A CD2 molecule that is encoded in the genome of mouse.
T-cell surface antigen T11/Leu-5 (mouse)
A CD14 molecule that is encoded in the genome of mouse.
myeloid cell-specific leucine-rich glycoprotein (mouse)
monocyte differentiation antigen CD14 (mouse)
A T-cell surface glycoprotein CD5 that is encoded in the genome of mouse.
A neural cell adhesion molecule 1 that is encoded in the genome of mouse.
An interleukin-7 receptor subunit alpha that is encoded in the genome of mouse.
interleukin-7 receptor subunit alpha (mouse)
A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of mouse.
B-cell differentiation antigen Ly-44 (mouse)
membrane-spanning 4-domains subfamily A member 1 (mouse)
A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of mouse.
T-cell acute lymphocytic leukemia protein 1 homolog (mouse)
A CD3 epsilon that is encoded in the genome of mouse.
T-cell surface antigen T3/Leu-4 epsilon chain (mouse)
T-cell surface glycoprotein CD3 epsilon chain (mouse)
A CD19 molecule that is encoded in the genome of mouse.
A lymphocyte antigen 6G that is encoded in the genome of mouse.
A vascular endothelial growth factor receptor 2 that is encoded in the genome of mouse.
protein-tyrosine kinase receptor flk-1 (mouse)
vascular endothelial growth factor receptor 2 (mouse)
A cadherin-5 that is encoded in the genome of mouse.
A sonic hedgehog protein that is encoded in the genome of mouse.
Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains (mouse)
A transferrin receptor protein 1 that is encoded in the genome of mouse.
A CD34 molecule that is encoded in the genome of mouse.
hematopoietic progenitor cell antigen CD34 (mouse)
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
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted].
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)
Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors.
somatic nervous system, somatic division
somatic part of peripheral nervous system
The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO].
Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO]
The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG]
has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest)
pars sympathica divisionis autonomici systematis nervosi
sympathetic part of autonomic division of nervous system
ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms.
A light sensing organ composed of ommatidia.
The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures
An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
A cavitated compound organ that transduces light waves into neural signals.[TAO]
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this
camera-type eye plus associated structures
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
An organ that is capable of transducing sensory stimulus to the nervous system.
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)
Major subdivision of an organism that protrudes from the body[DOS, CARO].
An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018].
Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736].
this is currently a subtype of organism subdivision - which would exclude feathers
A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions.
A lamina propria that is part of a respiratory airway.
The head is the anterior-most division of the body [GO].
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82
Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
Dense regular connective tissue that connects muscle to bone[VSAO].
Dense regular connective tissue that connects muscle to bone.[VSAO]
Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]
in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis
DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)
A biological tissue mass, most commonly a mass of nerve cell bodies.
TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.
A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures
Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]
Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302].
Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG]
DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005)
An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.
A tubular structure that contains, conveys body fluid, such as blood or lymph.
A tubular structure that transports secreted or excreted substances.
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction
Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball.
Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal.
A multicellular structure that is a part of an organ.
currently defined in a very broad sense, may be replaced by more specific classes in the future
Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts.
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
Uberon includes clade-specific subclasses, e.g. nematod larva
It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form
MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole
proximo-distal subdivision of respiratory tract
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)
(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
An anatomical structure that develops from the endoderm and the mesoderm.
Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
mixed endoderm/mesoderm-derived structure
An anatomical structure that develops from the ectoderm, mesoderm and endoderm.
mixed ectoderm/mesoderm/endoderm-derived structure
Stage succeeding embryo, including mature structure.
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]
Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia].
A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751].
The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO].
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
consider adding a preceding stage 'morula stage' as part of cleavage
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
The stage of being a sexually immature adult animal[XAO:1000010].
In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)
The stage of being a sexually mature adult animal.
The connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin.
it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces
A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]
A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)
Structure derived from foregut that becomes a lung[GO].
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO).
Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021].
Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate.
we limit this structure by definition to chordate and vertebrate nervous systems
Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves.
Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].
in FMA, this is an anatomical conduit *space*, rather than anatomical conduit
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts
DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)
The orifice that connects the mouth to the exterior of the body.
(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]
DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)
Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present)
Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]
The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]
Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32
The pair of anatomical structures comprised of a left lung and right lung.
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath.
TODO - add layer relations. 'tendon sheath' GAT in FMA.
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula
The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin.
The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
We model the digestive tract as consisting of two parts: the wall and the lumen.
Bone marrow in which the fat cells predominate in the meshes of the reticular network.
A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]
FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately
Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues.
Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin
the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated
A mucosa that is part of a pharynx [Automatically generated definition].
The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream.
The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses.
Medial ramus (sensory) of the trigeminal nerve.[AAO]
relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO]
maxillary division of fifth cranial nerve
maxillary division of trigeminal nerve (Vb; V2)
A mucosa that is part of a respiratory airway.
The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77
Anatomical system that consists of the muscles of the body.[VSAO]
we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
The core of the crystalline lens, surrounded by the cortex.
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
An anatomical wall that is part of an artery [Automatically generated definition].
A portion of organism substance that is produced by exocrine glands.
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
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.
this relationship may be too strong and may be weakened in future
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
The organs and associated structures associated with bearing offspring in a female animal.
By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]
ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43
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.
Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
Anatomical group that has its parts adjacent to one another.
Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]
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.
see also conceptus extraembryonic component in EHDAA2.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
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.
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]
Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it?
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59
Unilaminar epithelium that consists of a single layer of cuboidal cells.
needs to be synchronized with CL - there is no distinct cuboidal cell in CL
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA].
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]
Epithelium that consists of more than one layer of epithelial cells.[CARO]
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
Epithelium that consists of epithelial cells not arranged in one ore more layers.
Compound organ that contains one or more macroscopic anatomical spaces.
this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable
Epithelium that consists of a single layer of epithelial cells.[CARO]
Subdivision of trunk that lies between the head and the abdomen.
note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest
The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
The middle germ layer of the embryo, between the endoderm and ectoderm.
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates
Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.
consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence
Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx
This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity.
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)
The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation.
This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae.
The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO]
When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]
All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481
Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]
DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
requires review for applicability to invertebrate structures, e.g. synganglion
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted].
Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP]
this term should be ceded to the arthropod anatomy ontology
The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure.
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water
Transparent part of camera-type eye that helps to refract light to be focused on the retina.
This class excludes compound eye corneal lenses.
The lens is avascular and nourished by diffusion from the aqueous and vitreous
The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]
Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods
This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)
Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,
The smallest morphological and functional unit of the compound eye that consists of a usually limited and often constant number of rhabdomeric photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells.
An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck.
The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).
The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]
In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum.
The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved
The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG]
During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474
Anatomical system that has as its parts the organs concerned with reproduction.
consider splitting genitalia from reproductive system
Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]
PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]
DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
The gonad of a female organism which contains germ cells.
Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]
Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
female organism reproductive system gonad
female organism reproductive system gonada
gonad of female organism reproductive system
gonad of reproductive system of female organism
gonada of female organism reproductive system
gonada of reproductive system of female organism
reproductive system of female organism gonad
reproductive system of female organism gonada
DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
The outer epithelial layer of the skin that is superficial to the dermis.
A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]
The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes).
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72
Functional system which consists of structures involved in respiration.
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23
An airway through which respiratory air passes in organisms.
This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
the cardiovascular system and the lymphatic system are parts of the circulatory system
Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
WBbt coelomocyte currently classified as circulating cell
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
Connective tissue in which fat is stored.[TAO]
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
in FMA this is dense irregular connective tissue
DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)
A subdivision of the muscular system corresponding to a subdisivision of an organism.
In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here.
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
Part of the nervous system which includes the brain and spinal cord.[AAO]
The brain and spinal cord. Kimmel et al, 1995.[TAO]
The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)
An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.
A portion of tissue which is a fasiculated group of axons.[TAO]
A nerve that transmits from sensory receptors on the surface of the body to the central nervous system.
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)
Anterior subdivision of a digestive tract.
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure
The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder.
The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].
The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme
Consider generalizing to deuterostome pharynx
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503
Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]
The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]
esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)
DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996)
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
A zone of skin that is part of a back [Automatically generated definition].
TODO - distinguish between entire skin of region and arbitrary zone of skin on region
A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP].
not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO
It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery.
superficial branch of transverse cervical artery
The transverse cervical artery splits into two branches, a superficial one and a deep one[WP]
A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart.
Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA].
Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455
A potential space between the visceral and parietal layers of the pericardium.
Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal)
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206
Endocardium that is part of the cardiac ventricle.
An epicardial layer that lines a cardiac ventricle
The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO]
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer.
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]
A zone of skin that is part of a head [Automatically generated definition].
A zone of skin that is part of a trunk [Automatically generated definition].
Transudate contained in the pleural cavity.
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
It provides nutrients and lubrication for articular cartilage
The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma
An anatomical wall that is part of a esophagus [Automatically generated definition].
A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control.
The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO].
The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG]
The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3]
The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution)
barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus
originate from the cervical somites, likely C3-C5[PMID:23586979]
ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278
Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified].
check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit
Muscle tissue that consists primarily of skeletal muscle fibers.
TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]
PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)
Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO].
A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]
GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.
textus muscularis levis; textus muscularis nonstriatus
DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body
A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries.
gonad of female reproductive system vein
gonada of female reproductive system vein
vein of female reproductive system gonad
vein of female reproductive system gonada
vein of gonad of female reproductive system
vein of gonada of female reproductive system
The layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between.
The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space.
Anatomical cavity bounded by visceral and parietal peritoneum.
The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP].
The mucosal layer that lines the stomach.
The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa].
The fibrous connective tissue layer beneath the stomach mucosa.
The outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum.
anatomical wall of stomach serous membrane
anatomical wall of ventriculus serous membrane
serosa of anatomical wall of ventriculus
serous membrane of anatomical wall of stomach
serous membrane of anatomical wall of ventriculus
serous membrane of stomach anatomical wall
serous membrane of ventriculus anatomical wall
ventriculus anatomical wall serous membrane
Transudate contained in the peritoneal cavity.
The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions.
this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented
Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]
in FMA this is classified as simple columnar, MA divides this into squamous and glandular
Muscle (organ) which is a part of the pelvis. Examples: levator ani,.
The outer layer of peritoneum that is attached to the abdominal and pelvic walls.
Peritoneum attached to the abdominal wall.[AAO]
A zone of skin that is part of a pelvis [Automatically generated definition].
A zone of skin that is part of an abdomen [Automatically generated definition].
A zone of skin that is part of a neck [Automatically generated definition].
A zone of skin that is part of a thorax [Automatically generated definition].
An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions.
this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831).
An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO]
Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
System that provides physical support to the organism.[AAO]
By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]
GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates
DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)
A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).
Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face.
The area that extends from the median ocellus to the oral foramen[HAO].
The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)
A zone of skin that is part of a lip [Automatically generated definition].
Skeletal element that is composed of bone tissue.
Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
Skeletal element that is composed of bone tissue.[VSAO]
The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart's axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia].
Any muscle organ that is part of a pelvic girdle [Automatically generated definition].
Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle.
The convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery.
The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG]
The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG]
birds have right aortic arch, mammals left.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 and p.461 Figure 12.20
The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted].
results from fusion of left and right dorsal aortae
The part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest.
Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted].
Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates
The short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery.
A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm].
we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery'
This class represents the adult and developing structures'
in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae
One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta.
Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO)
Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO]
In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP]
The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO]
The subclavian artery that supplies the right pectoral appendage.
in humans, arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery
proximal part arises from right 4th aortic arch in humans
A tube extending from the mouth to the anus.
The alimentary or digestive tract, and associated organs.[TAO]
FMA also has a term 'gastrointestinal tract', but this includes the liver.
we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509
we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified].
The subclavian artery that supplies the left pectoral appendage.
in humans, branches off the arch of aorta
arises from left intersegmental 6th artery in the region of the 6th -7th cervical segment in humans
A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart.
The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003). In the mouse, The right pulmonary vein passes dorsal to the right superior vena cava, the left pulmonary dorsal to the left superior vena cava (Biology of the Laboratory Mouse, Green).
One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted].
Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]
The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted].
The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP]
in aves, stromal mesenchymal cells may migrate to the iris and become skeletal
A branch of the external carotid artery that supplies structures of the face. [WP,unvetted].
An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted].
...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
Portion of tissue composed of contractile fibers.[TAO]
It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme.
Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system.
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
TODO - check with MA - vein vs venous blood vessel
Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]
Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw).
Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]
the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625
The pulmonary artery that supplies the right lung.
TODO - add class 'pulmonary artery tree organ'
The pulmonary artery that supplies the left lung.
The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted].
Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]
MA and NCITA also has 'anterior facial vein'
The cranial ganglion that is associated with and extends fibers into the trigeminal nerve.
consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks)
A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO]
In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.
The bone at the lower, posterior part of the skull.
formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII
fusion of basi-, exo- and supra-occipitals (and maybe tabular)
basi paired exo and supra occipital bones
Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof.
Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO]
It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP].
It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ...
Subdivision of skeleton which includes upper and lower jaw skeletons.
TODO - move ZFA:0001227 (it is the entire jaw skeleton).
Skeletal and cartilage elements of the first pharyngeal arch.[TAO]
There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983).
in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates
Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
See notes for jaw w.r.t skeletal element vs subdivision of head
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)
The groups of nerve cell bodies associated with the twelve cranial nerves.
Ganglion which is located in the head.[TAO]
cranial ganglion part of peripheral nervous system
A anatomical space that is enclosed by a pharynx.
An anatomical space that is enclosed by a pharynx.
See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship
The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens.
The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]
space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball
The pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited].
TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus
The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye.
The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019]
The smooth stratified squamous epithelium that covers the outer surface of the cornea.
Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]
In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei
In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals
Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].
The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera].
The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]
in fish, reptiles and monotremes the connective tissue of the sclera is skeletal
continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe.
Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson].
Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709].
Disease notes: implicated in rheumatoid arthritis.
A skeletal muscle organ that is part of the trunk region.
Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'.
Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here.
The thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes.
Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP].
check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA
MP treats posterior uvea and optic choroid as distinct
The lamellated connective tissue of the cornea between the Bowman and Descemet membranes.
Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO]
relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO]
relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO]
A double layer covering the ciliary body that produces aqueous humor.
The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae.
The any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified].
Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG]
Any of the layers that make up the retina[MP].
MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers
Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord.
classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN.
Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG]
See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
A thick watery refractive medium that fills the space between the lens and the cornea[WP].
The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa.
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24
The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells.
Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive).
Any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive).
A layer of epithelial cells that is part of the eye.
this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former
The elastic, clear, membrane-like structure, that is outer most layer of the lens.
The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens
FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular
Ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion.
A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia.
ganglion of sympathetic part of autonomic division of nervous system
sympathetic part of autonomic division of nervous system ganglion
One of the two fleshy folds which surround the opening of the mouth.
Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]
Lip that covers the lower portion of the mouth.[TAO].
A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium.
A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG]
The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].
developmental relationships need revised
Middle part of the brain composed of the optic tectum and penducular region.[AAO]
The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]
Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]
part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships
DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)
A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP].
A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]
Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]
In human embryonic development, the rhombomeres are present by day 29
DHBA divides this into A(1-3),B(4),C(5-7) and D(8)
DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002)
Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified].
Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965].
The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG]
The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]
the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA].
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]
The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]
DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)
An endothelium that is part of a capillary [Automatically generated definition].
An endothelium that is part of an arteriole [Automatically generated definition].
An endothelium that is part of an artery [Automatically generated definition].
The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207
An endothelium that is part of a venule [Automatically generated definition].
An endothelium that is part of a vein [Automatically generated definition].
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].
Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]
'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum
DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)
A multi-tissue structure that is part of a spinal cord.
The liquid component of blood, in which erythrocytes are suspended.
A submucosa that is part of a esophagus [Automatically generated definition].
A lamina propria that is part of a esophagus [Automatically generated definition].
A serous membrane that is part of a esophagus [Automatically generated definition].
The epithelial layer that lines the luminal space of the esophagus.
TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar
Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO]
One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins
Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]
The smallest division of the artery located between the muscular arteries and the capillaries[GO].
Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]
Small, terminal branch of an artery which generally connects to capillaries.[AAO]
A vessel through which blood circulates in the body.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
Any of the vessels through which blood circulates in the body.[AAO]
annelids have blood vessels, but this class is not applicable to annelids.
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
Any of the smallest blood vessels connecting arterioles with venules.
not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]
capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs
A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP].
A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]
The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)
An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood..
Major artery which supplies blood to the lungs.[AAO]
One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG]
On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]
In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP]
Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO].
Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO]
One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG]
the veins that return oxygenated blood from the lungs to the left atrium of the heart
A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons.
Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]
The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]
The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]
relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]
in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps
Muscle tissue that contains fibers that are divided by transverse bands into striations.
Voluntary muscle tissue arranged in bundles of fibers.[AAO]
A systemic artery that supplies the lung with with oxygenated blood.
rami bronchiales partis thoracicae aortae
Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung.
The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted].
Respiration organ that develops as an outpocketing of the esophagus.
Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)
An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
see also: vascular system. Consider merging?
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
In humans this includes the superior and inferior phrenic arteries
The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles.
The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA].
Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO]
relationship loss: develops_from endocardial ring (TAO:0005072)[TAO]
(Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG]
GO graph seems to suggest this is an endothelium. WP: The endocardial cushions are thought to arise from a subset of endothelial cells that undergo epithelial to mesenchymal transformation, a process whereby these cells break cell-to-cell contacts and migrate into the cardiac jelly (towards to interior of the heart tube). Latest (2010-06-01) new def suggested for GO, added above. Note that EHDAA2 has a more detailed model which we may later adopt. JB: Patterning makes the cushions lay down connective tissue in three domains that force out the local endothelial lining and so the leaflets form
DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3
The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart.
Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO]
Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]
In fish, receives venous blood from the systemic circulation through paired hepatic veins, anterior jugular veins and Cuvierian ducts[PMID:20735616]
In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu
In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract
ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
Consider adding a layer-of-skin grouping class for all skin layers
A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]
When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544].
BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument.
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
A cardiac atrium that is in the left side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve.
Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA]
The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]
A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve.
Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA]
The chamber of the heart that receives blood from the lungs[XAO:EJS].
A cardiac ventricle that is in the right side of the heart.
The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG]
In mammals continuous with the pulmonary arteries
Cardiac chamber in which blood enters the heart.
One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]
Cardiac chamber through which blood leaves the heart.
A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG]
A cardiac ventricle that is in the left side of the heart.
Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG]
DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)
A cardiac septum that divides the left and right atria of the heart.
The partition separating the right and left atria of the heart. [TFD][VHOG]
The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]
The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]
The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]
previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)
Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].
Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]
Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]
The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]
ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved.
Cardiac septum which separates the right ventricle from the left ventricle.[FMA].
The partition separating the right and left ventricles of the heart. [TFD][VHOG]
The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG]
involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999)
ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430
The organ covering the body that consists of the dermis and epidermis.
consider 'integumentary system' for invertebrates
MA uses the term skin to refer to what is called here: zone of skin
The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.
'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'
in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this
Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
The sensory system subserving the sense of vision.
Sensory system responsible for the perception of spatial orientation and auditory stimuli.
The sensory system used for balance and hearing.[AAO]
A portion of smooth muscle tissue that is part of an artery [Automatically generated definition].
A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition].
An ovary that is part of a right side of organism [Automatically generated definition].
An ovary that is part of a left side of organism [Automatically generated definition].
In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
A collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system.
In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718]
The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates.
superior olivary nucleus (Barr & Kiernan)
The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID].
TODO - check ZFA/pons. also GO says part of dorsorostral pons
Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703).
The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO].
Layer that lines the lumen of the heart.[TAO]
Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]
Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber.
fixed in GO to reflect FMA. See email to David/Varsha June 18 2010
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA].
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210
Lung which consists of the left upper lobe and left lower lobe.[FMA].
A portion of adipose tissue that is part of the hypodermis, beneath the dermis.
the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition.
Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]
Surface structure that is the outer protective covering of the body.[VSAO]
The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]
Vasculature that is part of a head [Automatically generated definition].
A vasculature that is part of a trunk [Automatically generated definition].
Vasculature that is part of the eye region.
not part of the eye in ZFA. Note this changed to a blood vessel in ZFA
Anatomical system that consists of the muscular and skeletal systems.
Anatomical system that provides locomotion and physical support to the organism.[AAO]
There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)
Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA].
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.
In many species, the diaphragm separates thoracic and abdominal cavities
Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)
TODO - add superclass to unify with VNC?
Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD].
we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal)
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO]
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO]
covers the brain dorsally in chondrichthyans
The ventral grey column of the spinal cord[MP]. The neurons of the ventral region of the mature spinal cord participate in motor output[GO].
The anterior horn of the spinal cord (or anterior cornu, or anterior column, or ventral horn) is the ventral (front) grey matter section of the spinal cord. The anterior horn contains motor neurons that affect the axial muscles while the posterior horn receives information regarding touch and sensation. The anterior horn is where the cell bodies of alpha motorneurons are located[Wikipedia:Anterior_horn_of_spinal_cord].
columna grisea anterior medullae spinalis
A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ).
this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation.
It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain.
FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure
Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707].
the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]
'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
The atrial part of middle layer of the heart, comprised of involuntary muscle.
A neural nucleus that is part of the brain.
The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue.
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.
check the FMA placement here; ncit placement of body cavity here probably not correct
Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO].
In mammals it forms the peritoneal, pleural, and pericardial cavities
Any muscle organ that is part of a back [Automatically generated definition].
A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube.
Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]
Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]
Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]
In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord.
The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]
relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]
relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]
relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]
(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]
When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
An arterial trunk which is continuous with the heart and branches into the pulmonary arteries.
An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG]
As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG]
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]
We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]
Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells
pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest
DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)
distinction between abdomen muscle and abdomen musculature
The part of the aorta that extends from the arch of the aorta to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest.
Embryonic ectoderm that gives rise to nervous tissue.
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here
epithelium tubi neuralis; neuroectoderma
A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart.
TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer.
The inner layer of the pericardium that is in contact with the surface of the heart.[AAO]
The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium]
The middle layer of the heart, comprised mainly of striated cardiac muscle fibers.
TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium
Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The middle layer of the heart, consisting of cardiac muscle.[AAO]
The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO]
EHDAA2 divides the system from the tissue
The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG]
DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)
The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA].
WP:Heart states: "The SA node is found in all amniotes but not in more primitive vertebrates. In these animals, the muscles of the heart are relatively continuous and the sinus venosus coordinates the beat which passes in a wave through the remaining chambers. Indeed, since the sinus venosus is incorporated into the right atrium in amniotes, it is likely homologous with the SA node. In teleosts, with their vestigial sinus venosus, the main centre of coordination is, instead, in the atrium.". Note however that ZFA has SA node.
An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles.
Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG]
The cardiac Purkinje fiber is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle.
The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs.
MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs
Serous membrane which is divided into parietal and visceral serous pericardium.
A serous membrane that lines the peritoneal cavity[VHOG,modified].
An epithelium that lines the peritoneal cavity.[TAO]
Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO]
Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA]
most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium]
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
The soft tissue that fills the cavities of bones.
TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs
consider placement of NCIT:C53466 medullary bone
The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]
In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]
Any skeletal muscle that is part of the head region.
defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984)
Any muscle that is part of the cervical (neck) region.
Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis.
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
Anatomical system that is involved in the production of hematopoietic cells.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)
The outer serous membrane of the pulmonary pleural.
the part of the pleura external to the visceral pleura. It lines the inner surface of the chest wall, covers the diaphragm, and is reflected over the structures occupying the middle of the thorax
The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs.
Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura].
The fluid-filled cavity that lies between the visceral and parietal pleurae.
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
The contraction of the diaphragm creates a negative pressure within the pleural cavity which forces the lungs to expand resulting in passive exhalation and active inhalation. This breathing process can be made forceful through the contraction of the external intercostal muscles which forces the rib cage to expand and add to the negative pressure in the pleural cavity causing the lungs to fill with air. The fluid in the cavity provides lubrication and cushioning
the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86
Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]
PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)
A double-walled sac containing the heart and the roots of the great vessels.
The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium.
Peritoneum that surrounds the heart.[AAO]
In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity
this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO)
we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium
Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac.
Transudate contained in the pericardial cavity.[FMA]
The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO].
Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO]
From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]
FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib
autonomic division of peripheral nervous system
autonomic part of peripheral nervous system
divisio autonomica systematis nervosi peripherici
pars autonomica systematis nervosi peripherici
DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.
A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]
Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]
Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]
Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W]
DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012)
A gland that is part of a skin of body [Automatically generated definition].
check FMA, use plural for now as general class not there
An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues
consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)
The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24].
the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme
Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA].
A blood vessel that is part of a choroid [Automatically generated definition].
cannot find singular in FMA, using Set class
The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries.
Arteries that connect the dorsal aorta and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these vessels don't have venous or arteriproperty_value external_definitionmarkers. They form from the primary sprouts from the dorsal aorta[ZFA:0001061].
Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.612
A mucosa that is part of a esophagus [Automatically generated definition].
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
see https://github.com/obophenotype/uberon/issues/27
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]
An epithelium that is part of a iris [Automatically generated definition].
Replacement bone that forms within cartilage.
Replacement bone that forms within cartilage.[VSAO]
some structures, e.g. in ZFA are both intramembrane and endochondral
Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO]
[In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO]
Connective tissue composed of elastic fibers.
The middle layer of an artery or vein. [WP,unvetted].
May be composed of smooth muscle and elastic tissue
The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong].
the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure
the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts
The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]
An organ that functions as a secretory or excretory organ.
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)
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 organised unit with a largely bona-fide boundary.[FBbt].
One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches.
One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]
Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering
DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.
Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons
The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass
A distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
TODO discriminate between stages and organisms
Whole organism that is premetamorphic or a very immature individual.[TAO]
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia.
A spinal cord segment that adjacent_to a cervical region.
segmenta cervicalia medullae spinalis [1-8
A nucleus of brain that is part of a trigeminal nuclear complex.
massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA.
nucleus tractus mesencephali nervi trigeminalis
Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133).
involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum]
A wall, dividing a cavity or structure into smaller ones[WP].
The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted].
segmenta thoracica medullae spinalis [1-12]
The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.
consider adding class for organizer. Consider adding separate class for isthmus as a structure
Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]
DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)
A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.
The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]
In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis
Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)
The portion of neural plate anterior to the mid-hindbrain junction.
The portion of neural plate posterior to the mid-hindbrain junction.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]
DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]
Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]
EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)
A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue
TODO - check; developmental relationship to anterior hypoblast in ZFA?
Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]
Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]
There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]
DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008)
The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.
Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]
(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]
all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm').
Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43
Lateral neurogenic placodes positioned dorsal of the epibranchial placodes.
In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]
The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode
The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion.
The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO]
The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO]
The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]
Consider naming this 'trigeminal placode complex'. Also, Fig9-5 of ISBN:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...'
Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles.
TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium.
Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].
Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]
Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)
A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]
The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]
Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]
note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)
DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)
Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia.
Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG]
These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]
Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively
in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A, The development and evolution of the pharyngeal arches. J Anat (2001)
TODO - add grouping class for the anterior end of the neural tube at all stages
Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]
A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.
The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere.
Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]
In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]
DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)
Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia].
Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
should probably be merged with heart rudiment.
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]
The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]
relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]
Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.
Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]
Neural crest that is part of the head.[TAO]
Gonochoristic organism that can produce female gametes.
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]
Anatomical structure that has as its parts two or more multi-tissue structures 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 anatomical structures of different types.
this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.
the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]
Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified].
wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007
Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO]
Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO]
Contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus.
The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]
in XAO, called branchial arch 2 and df VP4
The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles.
The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]
DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
The vessels formed within the first pair of branchial arches in embryogenesis.
Disappears early in development in tetrapods
ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas
The vessels formed within the fourth pair of branchial arches in embryogenesis.
Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO]
The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO]
The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4].
Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta
The vessels formed within the sixth pair of branchial arches in embryogenesis.
The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]
The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO]
The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6].
the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries
Upper portion of the skull that excludes the mandible (when present in the organism).
the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium
The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible.
in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton
A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates
GO uses genitalia for the singular organ
A female organ involved in reproduction.
female organism reproductive system organ
reproductive structure of female organism
reproductive system organ of female organism
Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO].
An epithelium that is part of a lower jaw [Automatically generated definition].
epithelial tissue of ventral mandibular arch
ventral mandibular arch epithelial tissue
An endoderm that is part of a foregut [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition].
A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage.
The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]
The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]
Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101
A gland that is part of a foregut [Automatically generated definition].
Racemose mucous glands beneath the mucous membrane of the pharynx.
A gland that is part of a integumental system [Automatically generated definition].
A blood island that is part of a mesoderm.
in EHDAA2, gives rise to blood and dorsal aorta
Mesenchyme that is part of a developing camera-type eye.
TODO - change mesenchyme relationships to precursor_of
Mesenchyme that is part of a developing ovary [Automatically generated definition].
female reproductive system gonad mesenchyme
female reproductive system gonada mesenchyme
gonad of female reproductive system mesenchyme
gonada of female reproductive system mesenchyme
mesenchyme of female reproductive system gonad
mesenchyme of female reproductive system gonada
mesenchyme of gonad of female reproductive system
mesenchyme of gonada of female reproductive system
Mesenchyme that is part of a developing lower jaw [Automatically generated definition].
A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO).
we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS
A ganglion that is part of a central nervous system [Automatically generated definition].
this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia
A mucosa that is part of a oral opening [Automatically generated definition].
A layer of epithelial cells on the surface of the mucosa.
An epithelium that is part of a pharynx [Automatically generated definition].
Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]
An epithelium that is part of a right lung [Automatically generated definition].
An epithelium that is part of a left lung [Automatically generated definition].
An unilaminar epithelium that surrounds a pelvic appendage bud.
An unilaminar epithelium that surrounds a pectoral appendage bud.
A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition].
cardiac muscle tissue of heart right atrium
cardiac muscle tissue of right atrium of heart
textus muscularis of myocardium of right atrium
textus muscularis of myocardium of right atrium of heart
textus muscularis of myocardium of right cardiac atrium
A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition].
cardiac left atrium cardiac muscle tissue
textus muscularis of myocardium of cardiac left atrium
textus muscularis of myocardium of heart left atrium
textus muscularis of myocardium of left atrium
textus muscularis of myocardium of left atrium of heart
textus muscularis of myocardium of left cardiac atrium
A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition].
cardiac muscle tissue of right ventricle
A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition].
A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition].
cardiac muscle of interventricular septum
cardiac muscle tissue of interventricular septum
A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition].
Any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi.
Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle
A mesothelium that is part of a pericardium [Automatically generated definition].
cavity of pericardial sac meso-epithelium
meso-epithelium of cavity of pericardial sac
mesothelium of cavity of pericardial sac
A mesothelium that is part of a diaphragm [Automatically generated definition].
A mesothelium that is part of a pleural cavity [Automatically generated definition].
A cartilage element that is part of a respiratory system [Automatically generated definition].
A gland that is part of a digestive tract [Automatically generated definition].
Mesenchyme that is part of a pelvic appendage bud.
Mesenchyme that is part of a pectoral appendage bud.
Mesoderm that is part of the pectoral fin bud.[TAO]
An adipose tissue that is part of a dermis [Automatically generated definition].
A nerve that is part of an abdomen [Automatically generated definition].
A nerve that is part of a neck [Automatically generated definition].
added for consistency with mouse ontologies. The term 'ciliary nerve' is usually used to denote either of the two nerves (with different origins) that innervate the iris, as well as ciliary muscles and cornea
A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk).
A nerve that is located in a thoracic cavity [Automatically generated definition].
consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve
A nerve that is part of a pelvis [Automatically generated definition].
A bone that is part of a head [Automatically generated definition].
Different sources vary regarding which bones are craniofacial; e.g. hyoid bone
A bone that is part of a neck [Automatically generated definition].
A bone that is part of a facial skeleton [Automatically generated definition].
test whether 'facial bone' is an exact synonym
A bone that is part of a trunk [Automatically generated definition].
An artery that is part of a respiratory system [Automatically generated definition].
The inferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery.
ramus labialis inferior (arteria facialis)
ramus labialis inferior arteriae facialis
An artery that is part of a thoracic cavity[cjm].
in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity
A vein that is part of a respiratory system [Automatically generated definition].
The inferior labial vein is the vein receiving blood from the lower lip.
A vein that is part of a thoracic cavity [Automatically generated definition].
An endothelium of capillary that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius blood capillary endothelium
apparatus respiratorius capillary endothelium
apparatus respiratorius capillary vessel endothelium
apparatus respiratorius endothelium of blood capillary
apparatus respiratorius endothelium of capillary
apparatus respiratorius endothelium of capillary vessel
blood capillary endothelium of apparatus respiratorius
blood capillary endothelium of respiratory system
capillary endothelium of apparatus respiratorius
capillary endothelium of respiratory system
capillary vessel endothelium of apparatus respiratorius
capillary vessel endothelium of respiratory system
endothelium of blood capillary of apparatus respiratorius
endothelium of blood capillary of respiratory system
endothelium of capillary of apparatus respiratorius
endothelium of capillary of respiratory system
endothelium of capillary vessel of apparatus respiratorius
endothelium of capillary vessel of respiratory system
respiratory system blood capillary endothelium
respiratory system capillary vessel endothelium
respiratory system endothelium of blood capillary
respiratory system endothelium of capillary
respiratory system endothelium of capillary vessel
respiratory system capillary endothelium
A venule that is part of a respiratory system [Automatically generated definition].
An arteriole that is part of a respiratory system [Automatically generated definition].
A blood vessel that is part of a head [Automatically generated definition].
A blood vessel that is part of an abdomen [Automatically generated definition].
A blood vessel that is part of a heart [Automatically generated definition].
A blood vessel that is part of a brain [Automatically generated definition].
A blood vessel that is part of a cornea [Automatically generated definition].
A blood vessel that is part of a retina [Automatically generated definition].
blood vessel of tunica interna of eyeball
A blood vessel that is part of a neck [Automatically generated definition].
A blood vessel that is part of a respiratory system [Automatically generated definition].
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
only in MA - supertype of artery, arteriole, aorta.
A blood vessel that is part of a iris [Automatically generated definition].
A blood vessel that is part of a lung [Automatically generated definition].
A blood vessel that is part of a trunk [Automatically generated definition].
A blood vessel that is part of a thoracic cavity [Automatically generated definition].
A blood vessel that is part of a pelvis [Automatically generated definition].
A capillary that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius capillary vessel
blood capillary of apparatus respiratorius
capillary vessel of apparatus respiratorius
A gray matter that is part of a brain [Automatically generated definition].
A portion of connective tissue that is part of a head [Automatically generated definition].
portion of connective tissue of adult head
A portion of connective tissue that is part of an abdomen [Automatically generated definition].
A portion of connective tissue that is part of a neck [Automatically generated definition].
neck (volume) portion of connective tissue
portion of connective tissue of neck (volume)
A portion of connective tissue that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius connective tissue
apparatus respiratorius portion of connective tissue
apparatus respiratorius textus connectivus
connective tissue of apparatus respiratorius
portion of connective tissue of apparatus respiratorius
portion of connective tissue of respiratory system
respiratory system portion of connective tissue
textus connectivus of apparatus respiratorius
textus connectivus of respiratory system
A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition].
connective tissue of lower respiratory tract
lower respiratory tract portion of connective tissue
lower respiratory tract textus connectivus
portion of connective tissue of lower respiratory tract
textus connectivus of lower respiratory tract
lower respiratory tract connective tissue
A portion of connective tissue that is part of a dermis [Automatically generated definition].
A portion of connective tissue that is part of a trunk [Automatically generated definition].
A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition].
cavity of chest portion of connective tissue
cavity of thorax portion of connective tissue
chest cavity portion of connective tissue
pectoral cavity portion of connective tissue
portion of connective tissue of cavity of chest
portion of connective tissue of cavity of thorax
portion of connective tissue of chest cavity
portion of connective tissue of pectoral cavity
portion of connective tissue of thoracic cavity
thoracic cavity portion of connective tissue
A portion of connective tissue that is part of a pelvis [Automatically generated definition].
A cartilage that is part of a neck [Automatically generated definition].
A cartilage that is part of a lower respiratory tract [Automatically generated definition].
A skin gland that is part of a camera-type eye [Automatically generated definition].
The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall.
adult aorta textus connectivus elasticus
dorsal aorta textus connectivus elasticus
elastic connective tissue of adult aorta
elastic connective tissue of dorsal aorta
elastic connective tissue of trunk of aortic tree
textus connectivus elasticus of adult aorta
textus connectivus elasticus of dorsal aorta
textus connectivus elasticus of trunk of aortic tree
trunk of aortic tree elastic connective tissue
trunk of aortic tree textus connectivus elasticus
The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers.
An elastic tissue that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius elastic connective tissue
apparatus respiratorius textus connectivus elasticus
elastic connective tissue of apparatus respiratorius
elastic connective tissue of respiratory system
elastic tissue of apparatus respiratorius
respiratory system elastic connective tissue
respiratory system textus connectivus elasticus
textus connectivus elasticus of apparatus respiratorius
textus connectivus elasticus of respiratory system
An elastic tissue that is part of a circulatory system [Automatically generated definition].
cardiovascular system elastic connective tissue
cardiovascular system textus connectivus elasticus
circulatory system elastic connective tissue
circulatory system textus connectivus elasticus
elastic connective tissue of cardiovascular system
elastic connective tissue of circulatory system
textus connectivus elasticus of cardiovascular system
textus connectivus elasticus of circulatory system
Elastic tissue layer that lines a blood vessel layer.
blood vessel textus connectivus elasticus
elastic connective tissue of blood vessel
textus connectivus elasticus of blood vessel
Elastic tissue that is part of a lung [Automatically generated definition].
The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers.
The innermost layer of the aorta, containing the endothelium and an inner elastic membrane.
An arterial blood vessel that is part of a respiratory system [Automatically generated definition].
respiratory system arterial blood vessel
The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity).
in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity
In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted].
Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO]
Design pattern notes: check whether this fits the foramen design pattern
The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles.
The left and right brachiocephalic veins in the upper chest are formed by the union of each corresponding internal jugular vein and subclavian vein. This is at the level of the sternoclavicular joint. These great vessels merge to form the superior vena cava. The brachiocephalic veins are the major veins returning blood to the superior vena cava.
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia.
All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers
The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls.
The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted].
this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)
the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa].
A nerve that is part of a thorax [Automatically generated definition].
A nerve that is part of an abdominal segment of trunk [Automatically generated definition].
A bone that is part of a thorax [Automatically generated definition].
A bone that is part of an abdominal segment of trunk [Automatically generated definition].
bone organ of abdominal segment of trunk
Any muscle organ that is part of a thorax [Automatically generated definition].
Any muscle organ that is part of a respiratory system [Automatically generated definition].
Any muscle organ that is part of a esophagus [Automatically generated definition].
A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition].
muscle organ of abdominal segment of trunk
A blood vessel that is part of a thorax [Automatically generated definition].
A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition].
blood vessel of abdominal segment of trunk
A skin of body that is part of an abdominal segment of trunk [Automatically generated definition].
A portion of connective tissue that is part of a thorax [Automatically generated definition].
A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition].
abdominal segment of trunk connective tissue
abdominal segment of trunk portion of connective tissue
abdominal segment of trunk textus connectivus
connective tissue of abdominal segment of trunk
portion of connective tissue of abdominal segment of trunk
textus connectivus of abdominal segment of trunk
An anatomical space that surrounded_by a neural tube.
In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted].
A neural crest that has_potential_to_developmentally_contribute_to a midbrain.
A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.
Cranial neural crest that is part of the hindbrain.[TAO]
A neural crest that has_potential_to_developmentally_contribute_to a spinal cord.
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]
A neural plate that develops_from a future spinal cord.
Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]
Mesenchyme that is part of a developing gonad [Automatically generated definition].
A presumptive structure that has the potential to develop into a ganglion.
An anatomical cavity that has the potential to develop into a coelemic cavity lumen.
The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom
consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults
(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166
Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma.
One of the skeletal muscles of the head and neck, spine, and ribs.
A portion of skeletal muscle tissue in the trunk.
The part of the retina that contains neurons and photoreceptor cells[GO].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]
Small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP].
Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO]
some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined).
endothelium of irregular blood filled space
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers
Any endothelium that has the quality of being cylindrical [Automatically generated definition].
A blood vessel that carries blood from the capillaries toward the heart
A duct that is part of a digestive system [Automatically generated definition].
An epithelium that lines the lumen of the digestive tract.
Epithelium lining the lumen of the gut.[TAO]
A cartilage element of chondrocranium. Example: neurocranial trabecula.
A cartilage element that is part of the cranial skeleton.
Cartilage which is part of the cranium.[TAO]
Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
The sensory system for the sense of touch and pain.
The neural tissue involved in the transmission of sensory signals
MP defines this in a may more appropriate to somatosensory cortex
The anterior segment of the lamellated connective tissue layer of the cornea.
The posterior segment of the lamellated connective tissue layer of the cornea.
The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity
The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina.
internal genitalia of female reproductive system
TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547
The connection between the embryo proper and extraembryonic tissues
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
Not to be confused with 'dermatome segment of skin'.
The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells
As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]
The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium
consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure
The layer of undifferentiated, proliferating cells that line the neural tube lumen
The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.
The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter
The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons.
Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart.
The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present
note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
A vasculature that is part of a iris [Automatically generated definition].
An anatomical structure that develops (entirely or partially) from the endoderm.
An anatomical structure that develops (entirely or partially) from the mesoderm.
An anatomical structure that develops (entirely or partially) from the ectoderm.
The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]
Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288]
The first recognizable structure derived from the heart field
TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO
(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]
PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)
A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]
An epithelial tube that will give rise to the mature heart.
the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube.
The outflow tract septum is a partition in the outflow tract.
The outflow tract is the portion of the heart through which blood flows into the arteries.
Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616]
The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles.
the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles.
Vein of heart that drains the myocardium
A cardiac chamber surrounds an enclosed cavity within the heart
generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus
An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium
Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA]
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG].
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.
in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum
The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals.
TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
The external genitalia are the outer sex organs, such as the penis or vulva in mammals.
Organ that is part of the hematopoietic system.
consider splitting out lymph organ, compare with lymph node
the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs].
the FMA class 'lymphoid organ' is a general anatomical term
The nonstriated, involuntary muscle tissue located in the wall of the aorta.
A portions of the gut that is derived from endoderm.
A nerve that is part of a back [Automatically generated definition].
A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition].
A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition].
A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition].
smooth muscle tissue of gastrointestinal system
A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition].
involuntary muscle of lower respiratory tract
lower respiratory tract involuntary muscle
lower respiratory tract non-striated muscle
lower respiratory tract smooth muscle tissue
non-striated muscle of lower respiratory tract
smooth muscle of lower respiratory tract
smooth muscle tissue of lower respiratory tract
A portion of smooth muscle tissue that is part of a iris [Automatically generated definition].
A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition].
Smooth muscle found within, and composing the majority of the wall of blood vessels.
Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension.
A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition].
A bone that is part of the dorsal region of an animal.
this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93
Any muscle organ that is part of a skin of body [Automatically generated definition].
review as part of general integumentary system review - part of skin, or more generally, integumental system
in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only
A blood vessel that is part of a back [Automatically generated definition].
A myocardium that is part of a outflow tract [Automatically generated definition].
(...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG]
PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997)
A portion of connective tissue that is part of a back [Automatically generated definition].
A pericardium that is part of a outflow tract [Automatically generated definition].
A muscle that is part of the eye region.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
The bilaminar epithelium formed from the myotome and dermatome.
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768].
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]
Portion of somites that gives rise to dermis and muscles.[AAO]
all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.
Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]
DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)
A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]
Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart.
It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support[WP]
A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition].
smooth muscle tissue of blood vessel of respiratory system
respiratory system blood vessel smooth muscle
The embryonic structure that gives rise to the corneal ectoderm
Multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP].
note that media, dorsal fins etc have AERs.
Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO]
Proliferative region that is part of the developing fin fold or fin.[TAO]
relationship loss: subclass proliferative region (TAO:0000098)[TAO]
The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold
maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop
An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG]
Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056]
DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)
The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries
The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery
One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP].
Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]
Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods
The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches
A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP].
Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN]
The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed)
A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane.
Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals
A bone that is part of an appendage [Automatically generated definition].
bone of free segment of appendicular skeleton
Sum of all sensory systems in an organism.
Any collection of skeletal muscles that is part of a head [Automatically generated definition].
This class is restricted to skeletal muscles that attach to the cranial skeleton. This seems to be consistent with FMA and EMAPA usage. Note that by definition this excludes invertebrate head musculature. It corresponds to the individual muscle organ term UBERON:0002376
Any collection of muscles that is part of a thorax [Automatically generated definition].
BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm
Any collection of muscles that is part of a neck [Automatically generated definition].
Any collection of muscles that is part of a back [Automatically generated definition].
Any collection of muscles that is part of a pelvic girdle [Automatically generated definition].
A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles.
Any collection of muscles that is part of a face.
originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose
Any collection of muscles that is part of a trunk [Automatically generated definition].
currently defined by location rather than attachment
A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition].
in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging.
A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition].
interatrial septum cardiac muscle tissue
cardiac muscle tissue of interatrial septum
A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition].
A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition].
Note placement of MA class based on parthood relationship
A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition].
A vasculature that is part of a muscle organ [Automatically generated definition].
A vasculature that is part of a musculoskeletal system [Automatically generated definition].
Anatomical system that has as its parts the heart and blood vessels.
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451
A vascular network consisting of blood vessels.
An eye that is part of a left side of organism [Automatically generated definition].
An eye that is part of a right side of organism [Automatically generated definition].
The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart.
The part of the cardiovascular system consisting of all arteries.
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)
An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart.
The part of the venous system that drains the general body tissues[Kardong]
In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]
Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]
The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.
An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart
An anatomical wall that is part of an aorta, enclosing the luminal space.
The outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers.
The muscular portion of the wall between the two lower chambers of the heart.
The muscular septum is the lower part of the ventricular septum[GO]
muscular part of interventricular septum
pars muscularis (septi interventricularis)
pars muscularis septi interventricularis
The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane.
we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is 'set of raphe nuclei'
The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted].
A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition].
A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition].
An endothelium that is part of a vena cava [Automatically generated definition].
An endothelium that is part of a outflow tract [Automatically generated definition].
It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG]
DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001)
An endothelium that is part of an arterial system [Automatically generated definition].
An endothelium that is part of a venous system [Automatically generated definition].
A blood vessel endothelium that is part of a respiratory system [Automatically generated definition].
respiratory system blood vessel endothelium
A transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches.
TODO - check relationship to bulbus arteriosus
A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO]
An appendage that is part of an appendage girdle complex.
this class is the union of the classes limb, pectoral fin and pelvic fin.
Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues.
Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues.
While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG]
DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004)
The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava.
The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus
A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres).
We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted
A metameric segment of the central nervous system.[ZFA]
Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres.
revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)
An organ subunit that is part of a hindbrain [Automatically generated definition].
We explicitly merge the NCITA terms here
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO].
Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from
taken from version of VSAO used in TAO and used directly in Uberon
Dermis-derived entity that is made of skeletal tissue.
The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP].
in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)
cartiligionous skeletal structure of skull
Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular.
Do not manually classify under here - bones are automatically classified
Anatomical system that consists of all the joints of the body.
A submucosa that is part of a respiratory system [Automatically generated definition].
A lamina propria that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius lamina propria mucosa
lamina propria mucosa of apparatus respiratorius
lamina propria mucosa of respiratory system
lamina propria of apparatus respiratorius
respiratory system lamina propria mucosa
A lamina propria that is part of a gastrointestinal system.
A serous membrane that is part of a digestive system [Automatically generated definition].
serous membrane of gastrointestinal system
An anatomical wall that is part of a cardiac ventricle [Automatically generated definition].
anatomical wall of lower chamber of heart
The mucous membrane lining the respiratory tract.
TODO - split respiratory tract mucosa from respiratory system mucosa
mucosa of organ of apparatus respiratorius
mucous membrane of apparatus respiratorius
A mucosa that is part of a gastrointestinal system.
The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468
A secretion that is part of a esophagus [Automatically generated definition].
Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia.
The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi.
An epithelium that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius epithelial tissue
epithelial tissue of apparatus respiratorius
An epithelium that is part of a digestive system [Automatically generated definition].
epithelial tissue of gastrointestinal system
gastrointestinal system epithelial tissue
An epithelium that is part of a lower respiratory tract [Automatically generated definition].
epithelial tissue of lower respiratory tract
lower respiratory tract epithelial tissue
A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition].
respiratory system skeletal muscle tissue
skeletal muscle of apparatus respiratorius
skeletal muscle tissue of apparatus respiratorius
skeletal muscle tissue of respiratory system
A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition].
Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal
A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition].
this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: Wikipedia:Lip#Muscles_acting_on_the_lips
An endothelium of artery that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius arterial endothelium
apparatus respiratorius artery endothelium
apparatus respiratorius endothelium of artery
arterial endothelium of apparatus respiratorius
arterial endothelium of respiratory system
artery endothelium of apparatus respiratorius
artery endothelium of respiratory system
endothelium of artery of apparatus respiratorius
endothelium of artery of respiratory system
respiratory system endothelium of artery
An endothelium of vein that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius endothelium of vein
apparatus respiratorius vein endothelium
apparatus respiratorius venous endothelium
endothelium of vein of apparatus respiratorius
endothelium of vein of respiratory system
vein endothelium of apparatus respiratorius
venous endothelium of apparatus respiratorius
venous endothelium of respiratory system
The thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall.
endothelium of trunk of systemic arterial tree
trunk of systemic arterial tree endothelium
An endothelium that is part of the cardiovascular system.
A connective tissue that surrounds a skeletal muscle tissue.
connective tissue of skeletal muscle tissue
portion of connective tissue of skeletal muscle
portion of connective tissue of skeletal muscle tissue
skeletal muscle portion of connective tissue
skeletal muscle tissue connective tissue
skeletal muscle tissue portion of connective tissue
skeletal muscle tissue textus connectivus
textus connectivus of skeletal muscle tissue
A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid.
Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands
A vasculature that is part of a retina [Automatically generated definition].
Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].
We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors
splanchnic layer of lateral plate mesoderm
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP].
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP].
Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/
sources differ as to whether this is part-of or develops-from the LPM
The central region of trunk mesoderm. This tissue forms the notochord
Notochord rudiment[ZFIN:ZDB-PUB-961014-576].
WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
The mass of tissue made up of mesenchymal cells in the lung.
A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila.
for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II)
neuron projection bundle connecting eye with brain
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
A portion of the gut that is derived from ectoderm.
The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum.
WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus
after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
A part of a wall of an organ that forms a layer.
The tissue underlying the tunica mucosa of the pharynx.
A mucosa that is part of a lower lip [Automatically generated definition].
An external genitalia that is part of a female reproductive system [Automatically generated definition].
in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126]
external genitalia of female reproductive system
An organ that is part of a immune system [Automatically generated definition].
A gland that is part of a hemolymphoid system [Automatically generated definition].
The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove].
One of the two elevated edges of the neural groove[GO,MP].
In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold].
A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].
An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]
An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord.
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]
consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness
With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates.
in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila
Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG]
DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003
A bud is a protrusion that forms from an epithelial sheet by localized folding.
Any anatomical structure that is part of the reproductive system.
An epithelial sheet bent on a linear axis.
The functional tissue of the central nervous system consisting of neurons and glial cells.
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis.
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
A vein that is part of a thorax [Automatically generated definition].
An external ectoderm that is part of a optic eminence [Automatically generated definition].
An ectoderm that is part of a optic eminence [Automatically generated definition].
The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG]
An endocardium that is part of a interventricular septum [Automatically generated definition].
interventricular septum endocardial tissue
A myocardium that is part of a bulbus cordis [Automatically generated definition].
Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.
Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Mesenchyme that is part of a developing trunk.
The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].
The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]
the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes
A portion of tissue that is part of an embryo.
Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
The endothelial lining of the endocardium.
An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO].
A lamina propria that is part of a mucosa of oral region.
A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP].
An outflow tract that is part of a aorta.
An array of photoreceptors and any supporting cells found in an eye.
A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array.
directing or focusing light onto light receptors
One of: the common carotid artery, or its branches, the external and internal carotid arteries.
This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries
Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO]
A sex gland that is part of a female reproductive system.
The part of the digestive system that excludes the hepatobiliary system.
the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system
The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System].
All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]
that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla.
alimentary part of gastrointestinal system
ISBN:978-0721676685 Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3
A limb bud that develops into a forelimb or pectoral fin.
Fin bud that develops into the pectoral fin.[TAO]
at this time we have no need to name a more specific 'pectoral fin bud' class, but we may in future
A limb bud that develops into a hindlimb or pelvic fin.
Fin bud that develops into the pelvic fin.[TAO]
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future
ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268
An apical ectodermal ridge that is part of a pectoral appendage bud.
An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG]
Apical ectodermal ridge that is part of the pectoral fin bud.[TAO]
Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG]
apical ectodermal ridge pectoral fin bud
pectoral appendage apical ectodermal ridge
An apical ectodermal ridge that is part of a pelvic appendage bud.
An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG]
Apical ectodermal ridge that is part of the pelvic fin bud.[TAO]
pelvic appendage apical ectodermal ridge
Portion of tissue that is the inner layer of the optic cup and will become the neural retina.
Portion of tissue that gives rise to the lens.
A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]
the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals
Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea.
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA].
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO]
In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5)
The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates.
the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac].
A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD].
neural tube lateral wall sulcus limitans
Portion of tissue on the side of the lumen of the neural tube.
todo - epidermis? todo - track down EHDAA2 class in new release
In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG]
After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm.
Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998).
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
A neural tube lateral wall that is part of a rhombomere.
Cranial neural crest which gives rise to the trigeminal ganglion.
todo - compare ZFA and EHDAA2 representation
Portion of tissue that gives rise to the immature gonad.
Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]
Somite located in the head region, caudal to the otic vesicle.
They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983)
EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter
A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum.
A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]
Contributes to the arch of aorta in humans
ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572
A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex.
Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm
An epithelium that is part of a anterior chamber of eyeball.
An epithelium that is part of a lens vesicle.
An ectoderm that is part of a pharyngeal arch 4.
In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]
An endoderm that is part of a pharyngeal arch 4.
A mesothelium that is part of a peritoneal cavity.
we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood
An endothelium that is part of a right lung.
An endothelium that is part of a left lung.
An anatomical cavity that is part of a lens vesicle.
Mesenchyme that is part of a pharyngeal arch 4.
Mesenchyme that is part of a optic eminence.
A venous system that is part of a hindbrain.
A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme.
Embryonic region that develops into the pectoral fin bud.[TAO]
pectoral appendage field of lateral plate mesoderm
A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme.
Embryonic region that develops into the pelvic fin bud.[TAO]
pelvic appendage field of lateral plate mesoderm
A ring of cells capable of forming a limb or paired fin[Gilbert,modified].
we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this.
limb/fin field of lateral plate mesoderm
The outermost layer of a blood vessel, composed mainly of fibrous tissue.
TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings
The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)].
A tunica intima that is part of a artery.
An outermost connective tissue covering of an organ, vessel, or other structure[WP].
Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves.
in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper).
A acellular anatomical structure that is the bounding layer of a anatomical structure.
An acellular anatomical structure that is the bounding layer of a anatomical structure.
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell.
Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle.
The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once.
Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP].
Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO]
The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch
relationship loss: part_of axial vasculature (TAO:0001073)[TAO]
This is currently used loosely to refer to cervical, lumbar, etc as well as the metamerically repeated segments, which may correspond more closely with the ZFA neuromere term
A delimited region of dense mesenchyme within looser mesenchyme.
Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.
isa cell condensation in VSAO; has_part chondroblast in AEO
A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.
A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage.
The paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip.
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles.
An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO]
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO]
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
An outflow tract that is part of a cardiac atrium.
Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk.
Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta.
Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA].
An outflow tract of atrium that is part of a left atrium.
The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium.
Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation
The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve.
Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis.
the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]
The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions.
The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx.
The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)
A tendon that has the potential to develop into a central tendon.
The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm.
cranial derivative of septum transversum
An anatomical junctions that overlaps the mouth and foregut.
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.
TODO - check ordering; awaiting confirmation from JB
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot
The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus.
Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity.
Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG]
Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle.
presumptive cardiac ventricle heart tube
The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP]
See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model
A segment of the eyeball that is filled with refractive media
Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
A nucleus of brain that is part of a brainstem.
An artery that connects two larger arteries.
A portion of organism substance that secreted_by a zone of skin.
A portion of organism substance that is secreted by a female reproductive gland.
female reproductive system fluid/secretion
A portion of organism substance that secreted_by a respiratory system.
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA].
A myocardium that is part of a left ventricle of a heart.
Myocardium of ventricle which is continuous with the tunica media of aorta.
A myocardium that is part of a right ventricle of a heart.
Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk.
Presumptive structure of the blastula that will develop into endoderm.
Portion of embryonic tissue determined by fate mapping to become a structure.
Presumptive structure of the blastula that will develop into ectoderm.
Presumptive structure of the blastula that will develop into mesoderm.
The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers.
In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG]
An anatomical boundary that adjacent_to a epithelium.
The edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm.
This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343
An epithelium that is composed primarily of secretory cells.
consider splitting epithelium from epithelial tissue
Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand.
Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO]
A subdivision of a the reproductive tract in a female organism that is the site of embryo development.
A head mesenchyme that develops_from a mesoderm.
merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
Mesenchyme that is part of a mandibular prominence.
An anatomical space that surrounded_by a digestive tract.
The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]
An epithelium characterised by its most superficial layer consisting of squamous epithelial cells.
FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium
Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA].
A squamous epithelium that is part of a esophagus.
MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass
A squamous epithelium that is part of a stomach.
A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands.
we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland.
Any gland that is part of the digestive system.
Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA].
Stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region.
stomach glandular region glandular mucous membrane
Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue.
note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical
The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis.
The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA].
A capillary that is part of the coronary system.
A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n
Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.
The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
consider FBbt:00005541 ! cardiogenic mesoderm
A multicellular organism that is at the juvenile stage.
Whole organism that is not fully grown or sexually mature.[TAO]
A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage.
Whole organism that is fully grown or sexually mature.[TAO]
The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis
Cranial neural crest that migrates into the mandibular arch.
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
GO uses blood circulation generically to include the haemolymphatic fluid of arthropods
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]
A mesothelium that is part of a serous pericardium.
The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis.
Multicellular organism that can produce both male and female gametes.
The vasculature consisting of brachiocephalic arteries and veins.
Mesenchyme that develops_from a cranial neural crest.
head mesenchyme from cranial neural crest
mesenchyme derived from head neural crest
Mesenchyme that develops_from a trunk neural crest.
mesenchyme derived from trunk neural crest
relationship to Meckel's cartilage to be added
A tunica media that is part of a artery.
A tunica adventitia that is part of a artery.
A tunica adventitia that is part of a vein.
Gray matter of the central nervous system which is a collection of clustered nuclei.
Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei.
this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future.
Any collection of muscles that is part of a pectoral appendage.
Any collection of muscles that is part of a pelvic appendage.
Musculature that is part of the pelvic fin.[TAO]
Any collection of muscles that is part of an appendage.
Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle.
The collection of all skeletal elements in a pelvic appendage region.
The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.
The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR].
Portion of tissue that is part of the heart tube and will become the sinus venosus.
A presumptive structure that has the potential to develop into a endocardium.
Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]
Embryonic structure that gives rise to the midbrain hindbrain boundary.
A presumptive structure that has the potential to develop into a presomitic mesoderm.
A presumptive structure that has the potential to develop into a neural plate.
Region of the gastrula which gives rise to the neural plate.[TAO]
The part of the blastula that has the potential to develop into a paraxial mesoderm.
A blood vessel that is part of a pectoral appendage.
A blood vessel that is part of a limb/fin.
A vasculature that is part of a pectoral appendage.
A vasculature that is part of a chordate pharynx.
A vasculature that is part of a limb/fin.
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
this grouping class exists primarily to align with GO - see GO:0008544.
Outermost layer of cells surrounding the embryo.
Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]
relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]
Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.
A cartilage tissue that is part of a paired limb or fin.
Cartilage which is part of one of the paired fins.[TAO]
A cartilage tissue that is part of a pectoral appendage.
Cartilage which is part of the pectoral fin.[TAO]
A cartilage tissue that is part of a pelvic appendage.
Cartilage which is part of the pelvic fin.[TAO]
A nucleus of brain that spans a midbrain tegmentum.
this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species
A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified.
An epithelial tube that is open at one end only.
An epithelial tube open at both ends that allows fluid flow.
Mesenchyme with little extracellular matrix.
this class will be an important part of the NC reorganization
Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA].
In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system
Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html]
Epithelium bearing vibratile cilia on the free surface.
A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO].
An anatomical cavity that surrounded_by a synovial joint.
cavitas articularis (junctura synovialis)
Epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules.
A neural nucleus that is part of a medulla oblongata.
The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP].
in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate.
An anatomical structure that connects two structures
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm'
A bone that is part of a reproductive organ.
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces
characteristically low in protein and cellular content (unless there has been secondary concentration)
Anatomical system that consists of all blood and lymph vessels.
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots.
The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]
A bone that is part of a appendage girdle region.
A bone that is part of a pectoral girdle region.
A bone element or fused bone that is part of pelvic girdle.
check sacrum, coccyx (MA does NOT include these)
typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone
A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons.
Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO]
Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO]
Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO]
The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG]
Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.336 and Figure 9.18
Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.
need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)
Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]
Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]
Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]
The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]
Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333
Bone element that arises as a result of intramembranous ossification.
Bone element that arises as a result of intramembranous ossification.[VSAO]
Intramembranous bone that forms deep in the organism.[TAO]
Skeletal element that is composed of cartilage tissue and may be permanent or transient.
Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue.
the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification).
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]
Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]
dense regular collagenous connective tissue
typus regularis (textus connectivus collagenosus compactus)
A bone that is part of a craniocervical region.
A skeletal joint that is part of a appendage girdle region.
An anatomical surface that is part of a cartilage element.
Any muscle organ that is part of a pectoral girdle region.
EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate
The part of the ventral body cavity that is within the pelvis.
Musculature system of the pharyngeal and head regions.
in MA this is restricted to skeletal muscles
Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax.
A muscle of back that is part of a dorsal thoracic segment of trunk.
An endothelium that is part of a heart [Automatically generated definition].
this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class.
A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified].
Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing
A brain that develops_from a neural tube.
a reasoner should automatically classify all the vertebrate ontology brain classes here
Any skeletal muscle organ in the hypodermis / superficial fascia.
We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this
The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins.
Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA]
Subdivision of endoskeleton derived from pharyngeal arches
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]
The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]
The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]
VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton.
many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235
Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
Intramembranous bone that forms superficially in the organism.[TAO]
other AOs are not yet in sync with this classification
Bone element that is adjacent to the notochord.
We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA
Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]
System pertaining to blood vessels in the brain.
A zone of skin that is part of a dorsal thoracic segment of trunk.
Vein that drains left lung and returns blood to the heart.
A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein].
Vein that drains right lung and returns blood to the heart.
A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein].
An organism containing a developing embryo, fetus, or unborn offspring within the body.
A gonad prior to differentiating into a definitive testis or ovary.
typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321]
Cranial ganglion which develops from an epibranchial placode.
Epibranchial ganglia orchestrate the development of the cranial neurogenic crest
Endocardium that is part of the right atrium.
A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities.
A vein that is part of a craniocervical region.
consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)
An ectoderm that is part of a buccopharyngeal membrane.
An endoderm that is part of a buccopharyngeal membrane.
A portion of mesenchymal tissue associated with an individual pharyngeal arch.
this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures.
A sulcus limitans of neural tube that is part of a future spinal cord.
spinal cord lateral wall sulcus limitans
A sulcus limitans of neural tube that is part of a future medulla oblongata.
A sulcus limitans of neural tube that is part of a future metencephalon.
A sulcus limitans of neural tube that is part of a future myelencephalon.
Mesenchyme that is part of a 1st arch mandibular component.
mesenchymal region of mandibular component of first pharyngeal arch
Mesenchyme that is part of a developing left lung.
Mesenchyme that is part of a developing right lung.
A neural plate that develops_from a presumptive midbrain.
A neural plate that develops_from a presumptive hindbrain.
TODO - developmental relationships for lines
midbrain-hindbrain boundary neural plate
midbrain hindbrain boundary neural plate
A presumptive structure that has the potential to develop into a midbrain.
Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles.
A major contributor to neurocranium [PMID:16313393]
Any endocardium that is part of the right ventricle of the heart.
Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk.
Any endocardium that is part of the left ventricle of the heart.
Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta.
An anatomical cavity that surrounded_by a stomodeum.
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures
decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts
A ganglion that is part of a abdominal segment of trunk.
A serous sac that has the pleura and the pleural cavity as parts.
despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
Branch or outpocketing of the digestive tract.
A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland.
We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach
A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract).
extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708].
In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested
in mouse has left ventricular identity[PMID:22855565]
Mesenchyme that is part of a developing face.
A multicellular organism that existence_starts_with a post-embryonic stage.
Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia.
Includes: trigeminal, otic, lateral line and epibranchial placodes.
While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000)
An anatomical structure that has more than one cell as a part.
A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function.
Mesenchyme that is part of a pharyngeal arch 6.
An organ of the digestive tract that is capable of retaining and storing food.
This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates
Mesenchyme that is part of a pharyngeal arch 1.
The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells.
associated mesenchyme of pharyngeal region
entire branchial arch associated mesenchyme
entire pharyngeal arch associated mesenchyme
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa
An epithelium consisting of cuboidal epithelial cells.
TODO - coordinate with CL, add cuboidal cell
Mesenchyme that has the potential to develop into a dermis.
A structure that will develop into a diaphragm.
A developing anatomical structure that has the potential to develop into a metencephalon.
A developing anatomical structure that has the potential to develop into a myelencephalon.
A gray matter that has the potential to develop into a superior salivatory nucleus.
Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers.
Any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli.
An epithelial sheet is a flat surface consisting of closely packed epithelial cells.
An anatomical cavity that surrounded_by a blood vessel.
The paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation.
One of the laterally paired arteries that supply the gonads.
An anatomical boundary that corresponds to some physical discontinuity.
One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)
Multi-tissue structure that is part of the heart tube and will become the cardiac atrium.
The core globe-shaped component of the camera-type eye.
An exocrine gland whose secretions are excreted via exocytosis from secretory cells into an epithelial-walled duct or ducts and thence onto a bodily surface or into the lumen; the gland releases its product and no part of the gland is lost or damaged.
Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme.
1st arch mandibular mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme.
4th pharyngeal arch mesenchyme derived from neural crest
mesenchyme derived from neural crest of mesenchyme of 4th arch
pharyngeal arch 4 mesenchyme from neural crest
branchial arch 4 mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme.
pharyngeal arch 6 mesenchyme from neural crest
branchial arch 6 mesenchyme from neural crest
Mesenchyme that develops_from a rhombencephalon neural crest.
mesenchyme from rhombencephalic neural crest
Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme.
mesenchyme derived from neural crest of mesenchyme of 1st arch
pharyngeal arch 1 mesenchyme from neural crest
branchial arch 1 mesenchyme from neural crest
Portion of tissue that is dorsolateral to the floor plate and part of the midbrain.
Portion of neural tube that gives rise to the midbrain.
we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed
An endothelium that is part of a sclera.
Mesenchyme surrounding the developing optic cup which develops into the sclera.
The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288
An epithelium that is part of a extraembryonic structure.
Developing anatomical structure that develops into the eyeball and associated structures.
Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]
An anatomical structure that develops from the neural crest.
An anatomical structure that has some part that develops from the neural crest.
structure with developmental contribution from neural crest
A skeletal element that is part of a orbital region.
Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)
that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium
Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]
Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]
Mesenchyme that is part of a limb/fin bud.
Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme.
mandibular process mesenchyme from neural crest
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme.
mandibular process mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme.
1st arch mandibular mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme.
mesenchyme derived from head mesoderm of mesenchyme of 1st arch
1st arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme.
head mesenchyme derived arch 4 mesenchyme
mesenchyme derived from head mesoderm of mesenchyme of 4th arch
pharyngeal arch 4 mesenchyme from head mesenchyme
branchial arch 4 mesenchyme from head mesenchyme
4th arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme.
head mesenchyme derived arch 6 mesenchyme
pharyngeal arch 6 mesenchyme from head mesenchyme
branchial arch 6 mesenchyme from head mesenchyme
6th arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme.
branchial arch mesenchyme from neural crest
Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
pharyngeal arch mesenchyme from neural crest
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme.
branchial arch mesenchyme from head mesenchyme
pharyngeal arch mesenchyme from head mesenchyme
Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues.
An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements.
This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
Mesenchyme that develops_from a somatopleure.
the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives
Mesenchyme that develops_from a splanchnopleure.
The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms.
The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens.
A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow.
In an adult mammal, most red blood cells are formed in flat bones
Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment
Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs
A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels.
Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia.
glandular in NCIT; we consider the two NCIT terms synonymous
Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile.
epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)
pseudostratified ciliated columnar epithelium
Skeletal element that forms as a replacement or substitution of another element or tissue.
A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses.
An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]
Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]
note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)
Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle.
Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO]
note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region)
pectoral girdle plus anterior limb or fin
pectoral girdle plus pectoral limb or fin
Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle.
Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]
note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here
pelvic girdle plus posterior limb or fin
The subdivision of the skeleton of either the pectoral or pelvic girdle.
Skeletal subdivision that is part of the appendage girdle region.[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle).
A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin.
considering adding pectoral and pelvic complex skeleton classes
note that the MA class includes girdle parts so it belongs here;
bone of forelimb or pectoral fin or pectoral girdle
A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle.
the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle
Muscles of the pelvic girdle, hindlimb or pelvic fin.
Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO]
A muscle of a pectoral girdle, pectoral fin or anterior limb.
the MA class belongs here, based on its current child classes
Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO]
Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.
Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]
Any muscle organ that is part of either the head or the neck.
A cartilage element that is part of a splanchnocranium.
A skeleton of pelvic girdle that is part of a right pelvic girdle region.
A skeleton of pelvic girdle that is part of a left pelvic girdle region.
A pelvic girdle region that is in the right side of a multicellular organism.
A pelvic girdle region that is in the left side of a multicellular organism.
A synovial joint that is part of a pelvic girdle region.
A synovial joint that is part of a pectoral girdle region.
in FMA, these are part of the bony pectoral girdle
Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis.
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.
Subdivision of skull that consists of the facial bones.
The skull can be divided into two: the neurocranium and the facial skeleton
primary subdivision of cranial skeletal system
A bone that is part of a neurocranium [Automatically generated definition].
A multi cell part structure that is part of a central nervous system.
central nervous system cell part cluster
Muscles within the eye (bulbus oculi).[AAO]
Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa.
Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath]
synovial membrane of synovial tendon sheath
fibrous membrane of synovial tendon sheath
Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints.
Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]
The part of the trunk that is in the dorsum[cjm].
In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]
compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'
A blood vasculature that is part of a head.
Blood vessel part of cranial vasculature.[TAO]
An anatomical cavity that is part of a esophagus.
The collection of all skeletal elements in an individual limb or fin.
Skeletal subdivision that is part of the paired limb/fin.[VSAO]
Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
consider obsoleting, coordinate with VSAO
A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions.
An epithelium that develops_from a ectoderm and is part of a oral epithelium.
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem
subdivision of organism along main body axis
A cardiovascular system that is part of a conceptus.
An anatomical space that is part of a bone of lower jaw.
A neural nucleus that is part of the spinal cord.
Ectodermal placode that does not develop into a component of the nervous system.
An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart.
Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]
typus irregularis (textus connectivus collagenosus compactus)
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets
our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid.
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.
An acinus that is part of a exocrine gland.
the FMA class specifically refers to ureter
The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity.
The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity.
The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity.
The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity.
The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity.
Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris.
Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous.
The Epimysium also protects muscles from friction against other muscles and bones
A region of the stomach that is lined with glandular epithelium.
as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus
The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.
EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining.
The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6
Bone that forms as a replacement of another structural tissue.
Bone that forms as a replacement of another structural tissue.[TAO]
This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.
Anatomical system that consists of the integumental system plus all mucosae and submucosae.
A primordium that has the potential to develop into a stomach.
A zone of skin that is part of a craniocervical region.
The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins.
An artery that originates from the abdominal aorta.
An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified].
Epithelium that derives from the mesoderm. [Automatically generated definition].
One of five swellings formed during the development of the face
The deep cervical artery (Profunda cervicalis) is an artery of the neck.
The transverse cervical artery (transverse artery of neck, transversa colli artery) is a branch of the thyrocervical trunk, running at a higher level than the suprascapular artery.
Unclear if MA class belongs here or in parent
descending branch of the transverse cervical
A bone element that is part of a jaw region.
A layer of tissue between the muscularis and serosa.
Contains nerves, blood vessels, lymphatics and lymph nodes
respiratory system arterial smooth muscle
A smooth muscle tissue that is part of a respiratory system venous blood vessel.
Blood-forming tissue, consisting of reticular fibers and cells.
Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue
The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth.
An anatomical space with no opening to another space or to the exterior.
The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle.
skeleton of anterior limb/fin and girdle
The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle.
skeleton of posterior limb/fin and girdle
An adventitia that is part of a esophagus.
TODO mirror representation of abdominal aorta
this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein
Any vein within the general circulation that transports blood back to the right atrium of the heart.
The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells.
Anatomical cavity that is the lumen of the skull and contains the brain.
A blood vessel endothelium that is part of a lung [Automatically generated definition].
The anatomical space that is enclosed by a stomach.
Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585].
Anatomical space that is an opening in a bone of the skull.
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
Vascular endothelium found in blood vessels of the blood-brain-barrier.
Musculature of the head and neck, spine, and ribs.
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
The region of the organism associated with the visceral organs.
Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].
A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily.
Fluid contained within the notochordal canal
A organ component layer that is part of a integumental system.
An organ component layer that is part of a integumental system.
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart.
Groupings may vary - typically pulmonary vessels and aorta and vena cavae
Mesenchyme that develops_from the neural crest[Automatically generated definition].
Muscle that is part of the respiratory system.
this class may be merged with 'respiratory system muscle'; check intercostals
An anatomical space that is enclosed by a sinusoid.
A part of the body present only in a specific gender.
A part of the body present only in females.
Subcutaneous adipose tissue that is located in the peritoneal cavity.
Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041].
Subcutaneous adipose tissue that is located in the abdominal region.
Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.
A ventral horn of spinal cord that is part of a thoracic spinal cord.
A gray matter of spinal cord that is part of a cervical spinal cord.
A ventral horn of spinal cord that is part of a cervical spinal cord.
A gray matter of spinal cord that is part of a thoracic spinal cord.
An anatomical space that is enclosed by a pleuroperitoneal canal.
A neuromere that is part of the presumptive midbrain
A neuromere that is part of the presumptive spinal cord
Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin.
Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin.
Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin).
Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin).
A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles).
A portion of tissue that will develop into vasculature.
One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites.
Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4].
consider merging into myocardial compact layer
perimysial connective tissue of subepicardium
Visceral intrapericardial fat contiguous with the myocardial surface.
A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands.
the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104]
the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648]
An eye consisting of multiple light-sensing organs
present on mantle edge in arcacean Bivalvia
The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species
A region of somite adjacent to presomitic mesoderm.
Epithelium located in the intersomitic region.
Any structure that is placed on one side of the left-right axis of a bilaterian.
This class is primarily to implement taxon constraints. It may be removed in the future.
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
A basement membrane of epithelium that is part of a respiratory system.
A smooth muscle tissue that is part of a hypodermis.
muscle layer in fatty layer of subcutaneous tissue
stratum musculosum panniculi adiposi telae subcutaneae
smooth muscle layer in fatty layer of subcutaneous tissue
A epithelium that is part of a camera-type eye.
An epithelium that is part of a camera-type eye.
An epithelium that is part of a foregut.
A hole in the diaphragm through which the esophagus passes.
Is the sensory system for the sense of hearing.
Auditory system is general anatomical term in FMA
Luminal space of the right ventricle of the heart.
Luminal space of the left atrium of the heart.
Luminal space of the left ventricle of the heart.
Luminal space of the right atrium of the heart.
The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches.
A layer of of the central nervous system that is part of gray matter.
central nervous system gray matter layer
Primordium that develops into the central nervous system
Primordium that develops into the nervous system
The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.
An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
A zone of skin that is part of a lower lip.
Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104
Any portion of submucosa that lines the digestive tract.
Any organ component layer that consists of muscle tissue.
NCITA class may refer to smooth muscle only
Muscle innervated by the trigeminal nerve (Cranial Nerve V).
muscle innervated by the trigeminal nerve
muscles innervated by the trigeminal nerve
An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart.
Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes.
Any region of epithelium that is part of a skin region.
The part of the eye that consists of both the retina and the optic choroid
An exocrine gland that is part of a integumental system.
A portion of organism substance that is secreted by a reproductive gland.
Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].
this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer
Serous membrane layer that is adjacent to and lines an organ.
Serous membrane layer that lines to a body cavity.
A specific region of the foregut into the area in which the lung will develop.
An embryonic or larval epithelium that is committed to form part of the nervous system.
An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.
A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.
spinal cord lateral wall ventricular layer
Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain.
The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa.
Any substance in the body or expelled from the body that is in a gaseous state.
Any portion of gas located in a part of the respiratory system that is composed primarily of air.
The area of axial mesoderm that develops into the prechordal plate.
Endocardium that is part of the left atrium.
Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein.
An multicellular anatomical structure that has subparts of multiple organs as a part.
A cluster of cells, largely surrounded by a morphological boundary.
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures.
Any organ component layer that consists of smooth muscle tissue.
organ region with floating fiat boundary
Any portion of gas located in a part of the respiratory system.
Mesenchyme that is part of a developing jaw [Automatically generated definition].
Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included.
Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat
Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface.
Any of several arteries that arise from the aorta and supply blood to the esophagus.
The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin.
Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers.
The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin.
A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery.
Any chamber of the left side of the heart.
Any chamber of the right side of the heart.
The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva
The primordial mouth region of the developing head.
The sum of epicardial and paracardial fat deposits.
Fat deposits in the mediastinum outside the parietal pericardium .
Any fat deposit surrounding a visceral organ.
The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity.
A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity.
respiratory primordium associated mesenchyme
An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.
Material anatomical entity that forms the outermost boundary of an anatomical structure.
A bodily fluid that is located in the coelom.
he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid]
Any gland that is part os the respiratory system.
A notochord that has persisted beyond the embryonic stage.
The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit.
ramus zygomaticotemporalis (Nervus zygomaticus)
ramus zygomaticotemporalis nervus zygomatici
zygomaticotemporal branch of zygomatic nerve
Wall of ventricle which is continuous with the wall of aorta.
Wall of ventricle which is continuous with the wall of pulmonary trunk.
Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle.
myocardium of anterior wall of left ventricle
myocardium of anterior wall of right ventricle
A mucosa that is part of a lip region [Automatically generated definition].
vasculature of central nervous system plus retina
Wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees.
A zone of skin that is part of the face.
An anatomical junction between two parts of the digestive tract.
Cartilage which is part of the axial skeleton.
This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse.
the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences
Blood vessel endothelium that has pores that allow passage small molecules and proteins[ZFA].
Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes.
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.
This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305
Dermal, epidermal, glandular and pigment structures of the external head integument.
Dermal, epidermal, glandular and pigment structures of the body integument.
An anatomical surface that is part of a bone.
Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane.
Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane.
A collection of Purkinje fibers that receives signals from the right and left bundle branches and innervates the ventricular cardiac muscle. The Purkinje fiber network creates synchronized contractions of the heart ventricles.
A heterotroph that consumes plant and animal matter either in whole or in part via ingestion through a type of "mouth". Animal and plant matter is broken down through an internal digestion process
An environmental zone which an animal consistently defends against conspecifics or, occasionally, animals of other species
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
conservatively place at deuterostome, excluding acoelomates
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
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'
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'
This can't be added as a property chain because it causes a circularity violation for 'part of'.
This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps"
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).