None
Echinoderm Anatomy and Development Ontology
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
is a defining property chain axiom
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
database_cross_reference
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
https://github.com/information-artifact-ontology/ontology-metadata/issues/20
has exact synonym
has_exact_synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/20
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
BFO:0000050
quality
spatial
uberon
part_of
part_of
part of
part of
part_of
http://www.obofoundry.org/ro/#OBO_REL:part_of
https://wiki.geneontology.org/Part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
BFO:0000051
quality
spatial
uberon
has_part
has_part
has part
has part
has_part
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
BFO:0000062
uberon
preceded_by
preceded_by
preceded by
preceded by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
BFO:0000063
uberon
precedes
precedes
precedes
precedes
X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
BSPO:0000120
NCIT:C25229
spatial
uberon
in_left_side_of
in_left_side_of
in left side of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
BSPO:PATO_mtg_2009
X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
BSPO:0000121
NCIT:C25228
spatial
uberon
in_right_side_of
in_right_side_of
in right side of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
BSPO:PATO_mtg_2009
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
BSPO:0000126
spatial
uberon
in_lateral_side_of
in_lateral_side_of
in lateral side of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
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
UBERON:cjm
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
inheres_in
RO:0000052
characteristic_of
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
RO:0000053
has_characteristic
has characteristic
has characteristic
https://github.com/oborel/obo-relations/pull/284
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
RO:0000056
uberon
participates_in
participates_in
participates in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
RO:0000057
has_participant
has participant
has participant
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
RO:0000079
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
RO:0000080
quality_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
RO:0000081
role_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
RO:0000085
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
RO:0000086
uberon
has_quality
has_quality
has quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
RO:0000087
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
RO:0000091
has_disposition
has disposition
inverse of has disposition
RO:0000092
disposition_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.
disposition of
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
2017-05-24T09:30:46Z
RO:0002013
has_regulatory_component_activity
has regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
2017-05-24T09:31:01Z
RO:0002014
has_negative_regulatory_component_activity
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
2017-05-24T09:31:17Z
RO:0002015
has_positive_regulatory_component_activity
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
2017-05-24T09:44:33Z
RO:0002017
has_component_activity
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
2017-05-24T09:49:21Z
RO:0002018
has_component_process
has component process
2017-09-17T13:52:24Z
RO:0002022
directly_regulated_by
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
directly regulated by
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
2017-09-17T13:52:38Z
RO:0002023
directly_negatively_regulated_by
directly negatively regulated by
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
2017-09-17T13:52:47Z
RO:0002024
directly_positively_regulated_by
directly positively regulated by
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
2017-09-22T14:14:36Z
RO:0002025
has_effector_activity
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
David Osumi-Sutherland
<=
RO:0002081
before_or_simultaneous_with
Primitive instance level timing relation between events
before or simultaneous with
x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), 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 and '=' indicates the same instance in time.
David Osumi-Sutherland
RO:0002082
uberon
simultaneous_with
simultaneous_with
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
simultaneous with
David Osumi-Sutherland
RO:0002086
ends_after
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
David Osumi-Sutherland
starts_at_end_of
RO:0002087
uberon
immediately_preceded_by
immediately_preceded_by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
immediately preceded by
David Osumi-Sutherland
ends_at_start_of
meets
RO:0002090
immediately_precedes
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
x overlaps y if and only if there exists some z such that x has part z and z part of y
x overlaps y iff they have some part in common.
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO:0002131
spatial
uberon
overlaps
overlaps
"(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF []
overlaps
overlaps
true
x overlaps y iff they have some part in common.
BSPO:cjm
lactation SubClassOf 'only in taxon' some 'Mammalia'
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.
'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
RO:0002160
uberon
only_in_taxon
only_in_taxon
only in taxon
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
RO:0002162
uberon
in_taxon
in_taxon
Connects a biological entity to its taxon of origin.
in taxon
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO:0002180
uberon
has_component
has_component
has component
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
RO:0002202
uberon
develops_from
develops_from
This is the transitive form of the develops from relation
develops from
develops from
inverse of develops from
RO:0002203
uberon
develops_into
develops_into
develops into
develops into
p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
RO:0002211
regulates
regulates
regulates (processual)
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
negatively regulates (process to process)
RO:0002212
negatively_regulates
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
positively regulates (process to process)
RO:0002213
positively_regulates
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
has function realized in
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
RO:0002215
uberon
capable_of
capable_of
capable of
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
has function in
RO:0002216
uberon
capable_of_part_of
capable_of_part_of
capable of part of
capable of part of
true
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
RO:0002222
temporally_related_to
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
inverse of starts with
Chris Mungall
Allen
RO:0002223
uberon
starts
starts
starts
starts
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Chris Mungall
started by
RO:0002224
uberon
starts_with
starts_with
starts with
starts with
inverse of ends with
Chris Mungall
RO:0002229
uberon
ends
ends
ends
ends
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Chris Mungall
finished by
RO:0002230
uberon
ends_with
ends_with
ends with
ends with
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
consumes
RO:0002233
has_input
has input
https://wiki.geneontology.org/Has_input
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
RO:0002254
uberon
has_developmental_contribution_from
has_developmental_contribution_from
has developmental contribution from
has developmental contribution from
inverse of has developmental contribution from
RO:0002255
developmentally_contributes_to
developmentally contributes to
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
false
In general you should not use this relation to make assertions - use one of the more specific relations below this one
RO:0002258
developmentally_preceded_by
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.
RO:0002263
acts_upstream_of
acts upstream of
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
RO:0002264
affects
acts_upstream_of_or_within
acts upstream of or within
https://wiki.geneontology.org/Acts_upstream_of_or_within
Inverse of developmentally preceded by
RO:0002286
developmentally_succeeded_by
developmentally succeeded by
p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
RO:0002295
results_in_developmental_progression_of
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.
http://www.geneontology.org/GO.doc.development.shtml
RO:0002296
results_in_development_of
results in development of
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
RO:0002304
causally_upstream_of,_positive_effect
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
causally upstream of, positive effect
p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
RO:0002305
causally_upstream_of,_negative_effect
causally upstream of, negative effect
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
inheres in part of
RO:0002314
characteristic_of_part_of
characteristic of part of
true
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
GOC:mtg_berkeley_2013
RO:0002315
results_in_acquisition_of_features_of
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.
RO:0002320
evolutionarily_related_to
evolutionarily 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
RO:0002323
mereotopologically_related_to
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
RO:0002324
developmentally_related_to
developmentally related to
a particular instances of akt-2 enables some instance of protein kinase activity
c enables p iff c is capable of p and c acts to execute p.
catalyzes
executes
has
is catalyzing
is executing
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
RO:0002327
enables
enables
https://wiki.geneontology.org/Enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
RO:0002328
uberon
functionally_related_to
functionally_related_to
functionally related to
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
false
RO:0002329
part_of_structure_that_is_capable_of
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
actively involved in
enables part of
RO:0002331
involved_in
involved in
https://wiki.geneontology.org/Involved_in
inverse of enables
RO:0002333
enabled_by
enabled by
enabled by
https://wiki.geneontology.org/Enabled_by
inverse of regulates
regulated by (processual)
RO:0002334
regulated_by
regulated by
inverse of negatively regulates
RO:0002335
negatively_regulated_by
negatively regulated by
inverse of positively regulates
RO:0002336
positively_regulated_by
positively regulated by
inverse of has input
RO:0002352
uberon
input_of
input_of
input of
input of
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
RO:0002384
has_developmental_potential_involving
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
RO:0002385
uberon
has_potential_to_developmentally_contribute_to
has_potential_to_developmentally_contribute_to
has potential to developmentally contribute to
has potential to developmentally contribute to
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
RO:0002387
uberon
has_potential_to_develop_into
has_potential_to_develop_into
has potential to develop into
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
RO:0002388
has_potential_to_directly_develop_into
has potential to directly develop into
inverse of upstream of
RO:0002404
causally_downstream_of
causally downstream of
RO:0002405
immediately_causally_downstream_of
immediately causally downstream of
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
indirectly activates
RO:0002407
indirectly_positively_regulates
indirectly positively regulates
https://wiki.geneontology.org/Indirectly_positively_regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly inhibits
RO:0002409
indirectly_negatively_regulates
indirectly negatively regulates
https://wiki.geneontology.org/Indirectly_negatively_regulates
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative?
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
RO:0002410
causally_related_to
causally related to
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
https://en.wikipedia.org/wiki/Causality
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
RO:0002411
causally_upstream_of
causally upstream of
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
RO:0002412
immediately_causally_upstream_of
immediately causally upstream of
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
influences (processual)
RO:0002418
affects
causally_upstream_of_or_within
causally upstream of or within
inverse of causally upstream of or within
RO:0002427
causally_downstream_of_or_within
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
RO:0002428
involved_in_regulation_of
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
RO:0002429
involved_in_positive_regulation_of
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
RO:0002430
involved_in_negative_regulation_of
involved in negative regulation of
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
involved in or reguates
RO:0002431
involved_in_or_involved_in_regulation_of
involved in or involved in regulation of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
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.
RO:0002434
in pairwise interaction with
interacts_with
interacts with
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
http://purl.obolibrary.org/obo/MI_0914
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
binds
molecularly binds with
RO:0002436
molecularly_interacts_with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
Axiomatization to GO to be added later
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
RO:0002447
phosphorylates
phosphorylates
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
RO:0002448
molecularly controls
directly_regulates_activity_of
directly regulates activity of
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
directly inhibits
RO:0002449
molecularly decreases activity of
directly_negatively_regulates_activity_of
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
directly activates
RO:0002450
molecularly increases activity of
directly_positively_regulates_activity_of
directly positively regulates activity of
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
RO:0002464
helper_property_(not_for_use_in_curation)
helper property (not for use in curation)
RO:0002481
is_kinase_activity
is kinase activity
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.
RO:0002487
relation_between_physical_entity_and_a_process_or_stage
relation between physical entity and a process or stage
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).
RO:0002488
uberon
existence_starts_during
existence_starts_during
existence starts during
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).
RO:0002489
uberon
existence_starts_with
existence_starts_with
existence starts with
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))
RO:0002490
existence_overlaps
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.
existence overlaps
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).
RO:0002492
ceases_to_exist_during
uberon
existence_ends_during
existence_ends_during
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.
existence ends during
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
https://orcid.org/0000-0002-6601-2165
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).
RO:0002493
uberon
existence_ends_with
existence_ends_with
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.
existence ends with
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).
RO:0002496
uberon
existence_starts_during_or_after
existence_starts_during_or_after
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.
existence starts during or after
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.
RO:0002497
uberon
existence_ends_during_or_before
existence_ends_during_or_before
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.
existence ends during or before
A relationship between a material entity and a process where the material entity has some causal role that influences the process
RO:0002500
causal_agent_in_process
causal agent in process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
RO:0002501
causal_relation_between_processes
causal relation between processes
RO:0002502
depends_on
depends on
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
RO:0002506
causal_relation_between_entities
causal relation between entities
causally influenced by (entity-centric)
RO:0002559
causally_influenced_by
causally influenced by
RO:0002563
interaction_relation_helper_property
interaction relation helper property
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
RO:0002564
molecular_interaction_relation_helper_property
molecular interaction relation helper property
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
causally influences (entity-centric)
RO:0002566
causally_influences
causally influences
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
directly regulates (processual)
RO:0002578
directly_regulates
directly regulates
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
RO:0002584
has_part_structure_that_is_capable_of
has part structure that is capable of
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
RO:0002595
causal_relation_between_material_entity_and_a_process
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
RO:0002596
capable_of_regulating
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
RO:0002597
capable_of_negatively_regulating
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
RO:0002598
capable_of_positively_regulating
capable of positively regulating
Inverse of 'causal agent in process'
RO:0002608
process_has_causal_agent
process has causal agent
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
RO:0002629
directly_positively_regulates
directly positively regulates
https://wiki.geneontology.org/Directly_positively_regulates
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
RO:0002630
directly_negatively_regulates
directly negatively regulates
https://wiki.geneontology.org/Directly_negatively_regulates
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
2018-01-25T23:20:13Z
RO:0004031
enables_subfunction
enables subfunction
2018-01-26T23:49:30Z
RO:0004032
acts_upstream_of_or_within,_positive_effect
acts upstream of or within, positive effect
https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect
2018-01-26T23:49:51Z
RO:0004033
acts_upstream_of_or_within,_negative_effect
acts upstream of or within, negative effect
https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
2018-01-26T23:53:14Z
RO:0004034
acts_upstream_of,_positive_effect
acts upstream of, positive effect
https://wiki.geneontology.org/Acts_upstream_of,_positive_effect
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
2018-01-26T23:53:22Z
RO:0004035
acts_upstream_of,_negative_effect
acts upstream of, negative effect
https://wiki.geneontology.org/Acts_upstream_of,_negative_effect
2018-03-13T23:55:05Z
RO:0004046
causally_upstream_of_or_within,_negative_effect
causally upstream of or within, negative effect
https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect
2018-03-13T23:55:19Z
RO:0004047
causally_upstream_of_or_within,_positive_effect
causally upstream of or within, positive effect
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
RO:0011002
regulates_activity_of
regulates activity of
p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
2022-09-26T06:07:17Z
RO:0012011
indirectly_causally_upstream_of
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
2022-09-26T06:08:01Z
RO:0012012
indirectly_regulates
indirectly regulates
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
2021-11-08T12:00:00Z
utilizes
RO:0017001
device_utilizes_material
device utilizes material
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
RO:0019000
regulates_characteristic
regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
RO:0019001
positively_regulates_characteristic
positively regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
RO:0019002
negatively_regulates_characteristic
negatively regulates characteristic
p has anatomical participant c iff p has participant c, and c is an anatomical entity
2018-09-26T01:08:58Z
RO:0040036
results_in_changes_to_anatomical_or_cellular_structure
results in changes to anatomical or cellular structure
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
occurrent
Occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
processual entity (BFO)
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
per discussion with Barry Smith
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
anatomical entity (BFO)
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
process
Process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
disposition
Disposition
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
realizable
RealizableEntity
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable
realizable entity
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
quality
Quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
sdc
SpecificallyDependentContinuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
characteristic
specifically dependent continuant
https://github.com/OBOFoundry/COB/issues/65
https://github.com/oborel/obo-relations/pull/284
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
per discussion with Barry Smith
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
role
Role
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
gdc
GenericallyDependentContinuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
generically dependent continuant
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
function
Function
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
material
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
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.
spatial
CARO:0000000
anatomical entity
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
CARO:MAH
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CALOHA:TS-2035
FBbt:00007002
FMA:68646
GO:0005623
KUPO:0000002
MESH:D002477
VHOG:0001533
WBbt:0004017
XAO:0003012
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
cell
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CARO:mah
A cell that lacks a nucleus.
FMA:68647
non-nucleated cell
anucleate cell
A cell that lacks a nucleus.
FB:ma
A cell with a single nucleus.
single nucleate cell
A cell with a single nucleus.
FB:ma
GOC:tfm
binucleate cell
A cell with more than one nucleus.
AEO:0000203
WBbt:0008074
syncitium
syncytial cell
syncytium
multinucleate cell
A cell with more than one nucleus.
FB:ma
MESH:D005057
eukaryotic cell
fungal cell
A cell containing at least one nucleus.
2010-09-07T03:32:33Z
FMA:67513
nucleate cell
A cell containing at least one nucleus.
GOC:tfm
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.
precursor cell
A cell that, by division or terminal differentiation, can give rise to other cell types.
GOC:dos
root node
life cycle period
Biological process during which certain cells of a female or male individual (parent) are transformed into specialized reproductive cells (gametes) that will initiate development of a progeny individual (offspring) upon fertilization.
gametogenesis
ecao_developmental_stage
Period during which female gametes (or oocytes, or eggs) develop and mature from primordial female germ cells to generate cells competent to further development upon fertilization by a mature spermatozoid.
ovogenesis period
oogenesis period
ecao_developmental_stage
A female gamete that is small in size, i.e. about 10 microm in diameter, and that is at the previtellogenic stage.
previtellogenic primary oocyte stage
ecao_developmental_stage
A developing female gamete that started growing in size by accumulation of yolk proteins. At this stage, it is characterized by the presence of a large nucleus, the germinal vesicle, which contains a prominent nucleolus and occupies most of the cytoplasm.
not fully grown oocyte stage
ecao_developmental_stage
A developing female gamete that has reached its full size. It has grown up to ten times its original size, i.e. 80 to 100microm. It also displays a large germinal vesicle that is centered, but it is still not competent for fertilization.
fully grown oocyte with centered germinal vesicle stage
ecao_developmental_stage
A developing female gamete that has reached its full size and in which the germinal vesicle has moved asymmetrically to the cell periphery. The germinal vesicle is now close to the animal pole.
primary oocyte
fully grown oocyte with off-centered germinal vesicle stage
ecao_developmental_stage
A developing female gamete in which the germinal vesicle has broken down. The germinal vesicle is no longer visible. However, the female gamete is still not mature. It is undergoing meiotic maturation, extruding successively a first and a second polar body.
fully grown oocyte with no nucleus stage
ecao_developmental_stage
A mature female gamete that has achieved its meiotic maturation and in which the female pronucleus is visible. The mature oocyte is arrested in G1 phase and its average size is 80 to 100 µm. It is surrounded by a transparent jelly coat that is about 30 µm thick. It is competent to fertilization and it is located in the female gonad where it may be stored for weeks to months before its release in sea water by spawning. In the P. lividus species, the mature female gametes are characterized by the presence of pigment granules concentrated in a subequatorial band. This band is classically called the pigment band and allows to visualize the first embryonic axis, i.e. the animal-vegetal axis, which is perpendicular to the band.
spawned egg
unfertilized egg
mature oocyte stage
ecao_developmental_stage
Period during which male gametes (or spermatozoa, or spermatozoid) develop and mature from primordial male germ cells to generate cells competent to further development upon fertilization of a mature oocyte.
spermatogenesis period
ecao_developmental_stage
A developing, immature male gamete undergoing mitosis and meiosis to ultimately produce mature spermatozoa.
spermatid
developing spermatozoa stage
ecao_developmental_stage
A mature male gamete that is composed of a head, encompassing a compact nucleus, a neck, a middle piece, and a tail (or flagellum) that propels it towards the oocyte upon spawning.
spermatozoa
sperm
mature spermatozoid stage
ecao_developmental_stage
Biological process during which the embryo forms. This process starts with the fertilization of a mature oocyte by a mature spermatozoid. It is characterized by a succession of rapid mitotic divisions with no significant growth, but with axis establishment and cellular differentiation, thereby leading to the development of a multicellular embryo.
embryogenesis
ecao_developmental_stage
A fertilized egg, right after fertilization. The embryo is characterized morphologically by the fact that it is a single diploid cell surrounded by a fertilization envelope. This stage corresponds to an embryo of age 0 hour post-fertilization.
UBERON:0000106
fertilized egg
zygote stage
1-cell stage
ecao_developmental_stage
Period during which the fertilized egg undergoes a succession of rapid cell divisions with no significant growth.
UBERON:0000107
cleavage period
ecao_developmental_stage
An embryo that is composed of two cells and is surrounded by a fertilization envelope. The first cleavage plane took place meridionally (i.e. along the animal-vegetal axis), thereby generating two blastomeres of equal size, each containing both animal and vegetal cytoplasm.
UBERON:0007232
2c
2-cell stage
ecao_developmental_stage
An embryo that is composed of four cells and is surrounded by a fertilization envelope. The second cleavage plane was meridional and perpendicular to the first one, thereby producing four blastomeres of equal size, each containing both animal and vegetal cytoplasm.
UBERON:0007233
4c
4-cell stage
ecao_developmental_stage
An embryo that is composed of eight cells and is surrounded by a fertilization envelope. The third cleavage took place perpendicular to the first two cleavage planes and was equatorial. It thus generated an animal and a vegetal hemisphere each composed of a quartet of four cells of equal volume.
UBERON:0007236
8c
8-cell stage
ecao_developmental_stage
An embryo that is composed of 16 cells and is surrounded by a fertilization envelope. Note for euechinoid indirect developers: although the fourth cleavage occurred simultaneously in all cells, the pattern of cell division differed in the animal and vegetal blastomeres. In the animal hemisphere the four cells divided meridionally, producing eight blastomeres of equal volume arrayed in a single tier. These cells are called the mesomeres. In the vegetal hemisphere, the four cells underwent an unequal, equatorial cleavage, producing a tier of four large cells, the macromeres, and a tier of four small cells, the micromeres, located at the vegetal pole. At the 16-cell stage, the embryo is hence composed of three groups of cells with distinct sizes. In most sea urchin species,this is the first morphological indication of the animal-vegetal axis.
16c
16-cell stage
ecao_developmental_stage
An embryo that is composed of 28 cells and is surrounded by a fertilization envelope. Note for euechinoid indirect developers: In most sea urchin species, the fifth cleavage signed the end of cell division synchrony, with the mesomeres and macromeres dividing prior to the micromeres with a significant time difference. In the animal hemisphere, the mesomeres underwent an equal and equatorial cleavage, giving rise to two animal cell tiers, each composed of eight blastomeres of equal size: the an1 tier located at the animal pole and the an2 tier located below an1. In parallel, the macromeres divided meridionally, forming a ring of eight cells of equal volume located below the an2 tier. At that stage, the micromeres have not yet divided and are still at a number of four cells.
28c
28-cell stage
ecao_developmental_stage
An embryo that is composed of 32 cells and is surrounded by a fertilization envelope. Note for euechinoid indirect developers: The micromeres have undergone a fifth cleavage (and this has occurred prior to a subsequent division of the other cells). This cleavage was unequal and equatorial, thereby producing four large micromeres and four small micromeres, the smallest cells still marking the vegetal pole.
32c
32-cell stage
ecao_developmental_stage
An embryo that is composed of 56 cells and is surrounded by a fertilization envelope. Note for euechinoid indirect developers: In the animal hemisphere, cells of the an1 and an2 tiers underwent an additional meridional division, producing tiers composed of 16 cells. The macromeres divided equatorially and equally, generating two vegetal cell tiers, each composed of 8 cells of equal volume, namely the veg1 tier (located below an2) and the veg2 tier (located below veg1 and above the large micromeres). At that stage, the large and small micromeres (4 cells each) have not undergone yet a sixth division.
56c
56-cell stage
ecao_developmental_stage
An embryo that is composed of 60 cells and is surrounded by a fertilization envelope. Note for euechinoid indirect developers: The large micromeres have achieved a sixth cleavage, which was meridional, thereby generating a ring of 8 cells. At that stage, from the animal to the vegetal pole, the embryo is composed of: 16 an1-cells, 16 an2-cells, 8 veg1-cells, 8 veg2-cells, 8 large micromeres and 4 small micromeres.
60c
60-cell stage
ecao_developmental_stage
Period during which the embryo is transformed into a hollow sphere that is one cell layer thick and encompasses a central, fluid-filled cavity called the blastocoel. During this period, every cell of the embryo is in contact on the inside with the blastocoel and on the outside with the hyaline layer.
UBERON:0000307
blastula period
ecao_developmental_stage
The embryo is composed of 110-120 cells, as most blastomeres have completed an additional mitotic division after the 60-cell stage. The embryo is surrounded by a fertilization envelope. All cells are about the same size and there are no obvious morphological indications of embryonic polarity or embryonic territories. All cells have begun to acquire apico-basal polarity, and the embryo is beginning to transform into a hollow sphere with a wall that is one cell layer thick and a fluid-filled cavity (the blastocoel) in the center. Note for euechinoid indirect developers: the micromere progeny divide more slowly than other cells of the embryo. Molecular labelling typically indicates the presence of 8 large micromere descendants and 4 small micromeres at this stage .
120-cell stage
B1
vEB
very early blastula stage
ecao_developmental_stage
The embryo is composed of slightly more than 200 cells, as most blastomeres have completed an additional mitotic division after the very early blastula stage. The embryo is surrounded by a fertilization envelope. The embryo remains spherical and one cell layer thick, and the blastocoel has expanded slightly since the very early blastula stage, without increasing though the size of the embryo. The synchrony of cell divisions between animal and vegetal cell tiers, as well as within cell tiers, is becoming less pronounced. Note for euechinoid indirect developers: Molecular labeling typically indicates the presence of 16 large micromere descendants and 4 small micromeres at this stage .
B2
EB
early blastula stage
ecao_developmental_stage
The embryo is composed of about 300 cells and is surrounded by a fertilization envelope. Cell divisions are less synchronous than at earlier stages. The cells have flattened slightly on their inner (basal) surface, further contributing to the enlargement of the blastocoel. In some species, cells have started to form cilia on their outer surface. The embryo is still spherical and does not display any obvious morphological landmarks that indicate the primary or secondary embryonic axes. Note for euechinoid indirect developers: molecular labeling typically indicates the presence of 16 to 32 large micromere descendant cells and 4 to 8 small micromere descendants at this stage .
B3
midB
mid-B
mid-blastula stage
ecao_developmental_stage
The embryo is composed of about 400 cells and is surrounded by a fertilization envelope. The embryo is still spherical but the wall is thinner and smoother than at previous stages. The vegetal plate has not formed. Many cells are ciliated, and in some species (e.g. P. lividus) the embryo has begun to rotate within the fertilization envelope, while in others (e.g. S. purpuratus) it is still non-motile. Note for euechinoid indirect developers: molecular labeling typically indicates the presence of 32 large micromere descendants and 4 to 8 small micromere descendants at this stage .
B4
LB
pre-HB
prehatched blastula
Late-B
late blastula stage
ecao_developmental_stage
The embryo is composed of about 800 cells and is surrounded by a fertilization envelope. The fertilization envelope has started to break down due to the secretion by ectodermal cells of the hatching enzyme, a metalloprotease that digests the fertilization envelope and frees the embryo. The vegetal plate has not formed. The embryo rotates within the envelope or swims away as soon as it is free. At the animal pole, a tuft of long and immotile cilia has started growing.
B5
very late blastula stage
HB
hatched blastula stage
ecao_developmental_stage
The embryo has hatched from the fertilization envelope and swims freely. It is still a hollow sphere that is one cell layer thick, but the cells constituting the vegetal plate (i.e. located at the vegetal pole) have started thickening along the apico-basal axis, thereby creating a morphological landmark that enables orienting the embryo along the animal-vegetal axis. In addition, at the animal pole, the apical tuft composed of long and immotile cilia has continued expending.
SB
swimming blastula stage
ecao_developmental_stage
The embryo has started elongated along the animal-vegetal axis. Its vegetal region has further continued to thicken and it is marked by a characteristic 'V' shape formed by the blastocoel at the level of the cells constituting the vegetal plate, thereby pointing to the vegetal pole. At the animal pole, the embryo is characterized by the presence of an apical tuft.
late-SB
late swimming blastula stage
ecao_developmental_stage
Period during which complex and coordinated cellular movements take place and ultimately generate a three-layered embryo with inner tissues. A portion of cells will ingress, invaginate and/or migrate within the embryo and form the two inner layers (i.e. the endoderm and the mesoderm). The cells that remained outside will instead spread over the whole surface of the embryo and form the outer layer (i.e. the ectoderm).
UBERON:0000109
gastrula period
ecao_developmental_stage
The phase during which skeletogenic primary mesenchyme cells (PMCs) move from the vegetal plate into the blastocoel (ingress) but before the vegetal plate has started to invaginate.
mesenchyme blastula phase
ecao_developmental_stage
The vegetal plate is apparent and skeletogenic primary mesenchyme cells (PMCs) are in the process of ingression, a type of epithelial–mesenchymal transition (EMT). The epithelial wall of the embryo has thickened at the animal pole, where a tuft of long, non-motile cilia has formed.
eMB
early mesenchyme blastula stage
ecao_developmental_stage
All skeletogenic primary mesenchyme cells (PMCs) have ingressed into the blastocoel, leaving behind a reformed vegetal plate containing at its center the 8 small micromere descendants surrounded by non-skeletogenic mesoderm cells. The PMCs are organized in a mound on the vegetal plate but have not begun to disperse. The thickened apical pole domain with its tuft of long, non-motile cilia is still apparent.
mid-MB
mid-mesenchyme blastula stage
ecao_developmental_stage
The skeletogenic primary mesenchyme cells (PMCs) have migrated away from the vegetal plate by extending filopodia and moving along the blastocoel wall. The vegetal plate has flattened but has not started to invaginate. The apical pole domain still bears an apical tuft of long, non-motile cilia.
late mesenchyme blastula stage
ecao_developmental_stage
Period during which the inpocketing and elongation of the archenteron takes place.
invagination phase
ecao_developmental_stage
The embryo is characterized morphologically by a slight invagination of the vegetal plate and the dispersal of the skeletogenic primary mesenchyme cells (PMCs) along the blastocoel wall at the periphery of the invaginating region. The PMCs are just beginning to adopt a characteristic, ring-like arrangement near the equator of the embryo. Within the vegetal plate, the peripheral non-skeletogenic mesoderm cells have started to indent, undergoing important cell shape changes, but the center of the vegetal plate (composed of small micromeres) has not started to elevate. Invagination has generated the blastopore (an opening that will give rise to the larval anus) as well as the anterior portion of the archenteron (a region that will give rise to the coelomic pouches). At the animal pole, the apical pole domain is still marked by an enlarged epithelium bearing long and immotile cilia.
blastopore gastrula stage
blasto-G
blastopore formation stage
ecao_developmental_stage
The embryo is mainly characterized morphologically by the presence in the blastocoel of a small archenteron (i.e. primitive digestive tract) that is about a third of its finally size. Following the initial invagination of the vegetal plate, the archenteron has slightly been extended, within the blastocoel, by the subsequent invagination of additional non-skeletogenic mesoderm cells and of some endoderm cells. In parallel, the skeletogenic mesenchyme cells (or SM cells, primary mesenchyme cells or PMC) have by now started migrating along the blastocoel wall, towards the animal pole, thereby creating two lateral chains (one left and one right), while around the developing archenteron, they have gathered into two ventrolateral clusters separated by an oral (or ventral) and an aboral (or dorsal) chain defined by the remaining skeletogenic mesenchyme cells. Within the oral and aboral skeletogenic mesenchyme chains, the cells have further started to fuse to form syncytial filopodial cables within which skeletal calcification will subsequently take place. At the animal pole, the animal neuroectoderm territory is still marked by an enlarged epithelium bearing long and immotile cilia.
EG
eG
early gastrula stage
ecao_developmental_stage
The embryo is mainly characterized morphologically by the presence of an archenteron (i.e. primitive digestive tract) that has reached one-half its way into the blastocoel. A second phase of archenteron elongation has taken place by invagination of additional cells into the blastocoel, by cell division or by convergent-extension movements depending on the sea urchin species. Non-skeletogenic mesoderm cells that are present at the tip of the archenteron have further started ingressing into the blastocoel, generating the non-skeletogenic mesenchyme cells (or NSM cells, secondary mesenchyme cells or SMC). The oral ectoderm has also started to flatten and to become thicker, providing the first morphological indicator of the oral-aboral (or ventro-dorsal) axis of the embryo. As a consequence the oral chain formed by a portion of the skeletogenic mesenchyme cells has also flattened. Finally, skeletal calcification has further begun within the skeletogenic mesenchyme ventrolateral clusters, marked by the presence of the first calcified structures, which appear as small dots at that stage. At the animal pole, the animal neuroectoderm territory is still marked by an enlarged epithelium bearing long and immotile cilia.
mid-G
G
mid-gastrula stage
ecao_developmental_stage
The embryo is mainly characterized morphologically by the presence in the blastocoel of a fully extended archenteron (i.e. primitive digestive tract) that has now reached the roof of the blastocoel. The third and last extension phase of the archenteron has been ensured by pulling forces exerted by non-skeletogenic mesoderm cells that are still present at the tip of the archenteron. These cells have produced filopodia that extended towards the animal pole, attached the wall, and then shortened, thereby pulling up the archenteron. In some sea urchin species, this pulling force is already orienting the tip of the archenteron towards the oral ectoderm, where the future mouth of the larvae will form. In parallel, in the blastocoel, additional non-skeletogenic mesoderm cells continued ingressing from the tip of the archenteron and the skeletal calcified structures present in the skeletogenic mesenchyme ventrolateral clusters have further grown, forming now the primary triradiate skeletal rudiments (or spicules). At the animal pole, the animal neuroectoderm territory is still marked by an enlarged epithelium bearing long and immotile cilia.
late-G
LG
late gastrula stage
ecao_developmental_stage
To be written
organogenesis period
ecao_developmental_stage
The embryo is mainly characterized morphologically by a typical triangular shape, the beginning of the tripatition of the digestive tract and the presence of pigmented cells. The oral (or ventral) ectoderm has by now even more flattened, making an almost perfect right angle with the blastoporal side of the embryo. By contrast, on the opposite side, the aboral (or dorsal) ectoderm has round up and slightly elongated, thereby forming the primitive apex of the future larvae. These changes have conferred the embryo a typical and easy recognizable triangular shape. In the oral ectoderm, a small depression has further appeared, called the stomodeum, which will later fuse with the tip of the archenteron to form the mouth. In the blastocoel, the digestive tract has also by now bended toward the stomodeum and started to become tripartite. The cardiac sphincter has started forming, separating the future esophagus from the future stomach. The triradiate spicules have also continued elongating, thereby forming by now, towards the animal pole, the right and left dorsoventral connecting rods, towards the apex, the body rods, and along the vegetal, oral ectoderm the left and right ventral transverse rods. Moreover, some non-skeletogenic mesenchyme cells (or NSM cells, secondary mesenchyme cells or SMC) have started becoming pigmented and inserted into the aboral ectoderm. These cells represent part of the future immune system of the larvae along with other blastocoelar cells that are present in the blastocoel around the gut. In the vicinity of the future esophagus, other non-skeletogenic mesoderm descendant cells along with some endoderm cells have further arranged to form a single unpaired coelomic pouch. At the animal pole, the apical pole domain has also started to flatten making the embryo look like a square when viewed from the oral side, and it still arbors a tuft a long and immotile cilia. Finally, within the apical pole domain, but not yet in the ciliary band, molecular labeling surveys also start by this stage to reveal the presence of differentiating neuronal cells.
D
Pr
prism stage
ecao_developmental_stage
larval development
ecao_developmental_stage
Biological process during which the specific outcome is the progression of a free-living larva before the development of the adult. Indirect development represents the mainstream developmental mode of metazoans. This process usually starts with the emergence of a larva that is planktonic and stops at the end of metamorphosis once the animal assumes adult characters.
UBERON:0000069
early feeding larva period
ecao_developmental_stage
The embryo is by now a fully formed pluteus larva. The mouth has opened and the digestive tract is becoming functional. On the ventral side, the mouth is surrounded anteriorly by an oral hood and posteriorly by two postoral arms. On the dorsal side, the apex has lengthened. The skeleton has indeed continued extending, expending the dorsoventral connecting rods, the body rods, and the ventral transverse rods as well as developing the anterolateral rods and the postoral rods. Within the larva, the tripartition of the digestive tract has further progressed. The cardiac sphincter is now fully formed in between the esophagus and the stomach, and the pyloric sphincter in between the stomach and the intestine and the anal sphincter at the level of the anus have also started forming. Around the esophagus, the coelomic pouch has further developed into two bilobed sacs (or pouches), one on each side of the digestive tract. Finally, within the apical pole domain, as well as within the ciliary band, differentiated neurons with their extended axons can also now be distinguished by immunostaining. In parallel, the apical tuft of long and immotile cilia remains discernable at the tip of the oral hood, while in parallel the ciliary band has further started growing a concentrated number of intermediate size motile cilia, which will be used by the larva to swim directionally.
UBERON:0008265
2-arm pluteus stage
early pluteus stage
Eplut
early pluteus larva stage
ecao_developmental_stage
The 4-arm pluteus larva is mainly characterized morphologically by the presence, on the ventral side, of four extended arms (two anterolateral arms at the level of the oral hood and two postoral arms) and on the dorsal side by a sleeked apex. The larva now possesses a completely tripartite and functional digestive tract composed of an esophagus, a stomach, and an intestine, respectively limited by a cardiac sphincter, a pyloric sphincter, and an anal sphincter. Around the esophagus, the right and left coelomic pouches have further started to grow in size and elongate. The first morphological indicator of a left-right asymmetry becomes apparent at that stage, the left coelomic pouch being slightly more elongated than the right one. Furthermore, a thin protrusion of non-skeletogenic mesenchyme cells can be seen extending from the left coelomic pouch to the anterior ectoderm. This is the primary pore canal, which opens to the exterior environment by the hydropore. The larva further now possesses, all around the esophagus, a network of contractile muscles allowing it to swallow and feed. Finally, the apical tuft previously observed at the animal pole has by now disappeared, leaving behind only the concentrated stretch of intermediate size cilia borne by the ciliary band.
UBERON:0008265
P
Plut
Plut4a
pluteus larva
Pluteus
4-arm pluteus larva stage
ecao_developmental_stage
To be written
late feeding larva period
ecao_developmental_stage
The 6-arm pluteus larva is mainly characterized morphologically by the presence, on the ventral side, of six arms, and by the development, on the anterior midline of the esophagus, of the dorsal arch. The larva has indeed extended on the ventral side two additional posterodorsal arms and has developed on the anterior side an additional skeletal element called the dorsal arch. In addition, at the basis of the postoral and posterodorsal arms, four small patches of ciliary band have by now cut off and migrated toward the apex, forming four patches of ciliated structures called the epaulettes (one posterior and one anterior pair). The nervous system of the larva has also become more complex with cell bodies and axons being present all along the arms and for the latter as well throughout the apex. The left and right coelomic pouches have continued to elongate on each side of the digestive tract. As a note this stage is relatively fleeting.
UBERON:0008265
Plut6a
6-arm pluteus larva stage
ecao_developmental_stage
The 8-arm pluteus larva is mainly characterized morphologically by the presence on the ventral side of the larva of eight arms and by the development within the larva, on the left side of the stomach, of the adult rudiment. This stage is relatively long. It includes distinct changes occurring to the larva as well as within the larva, although the larva consistently exhibits 8 arms. In addition, it should be highlighted that the sequence of events taking place at the level of the larva compared to that occurring on the left side of the stomach to form the rudiment are heterochronic, meaning that differences are observed among individuals in the relative timing of these events. From the larval point of view, at that stage, on the anterior side, the dorsal arch has extended out of the oral hood, thereby forming two additional arms above the mouth, i.e. the preoral arms. In parallel, across the apex, the epaulettes have continued developing, thereby generating four large structures rich in cilia and perpendicular to the ventro-dorsal axis. At the tip of the apex, the suture of the body rods has also eventually ruptured, considerably enlarging the larval apex and reducing the angle between the postoral and posterodorsal arms. In parallel, inside the larva, the left coelomic pouch has also by now been partitioned into three parts: the axocoel (upper part, close to the esophagus), the hydrocoel (middle part) and the somatocoel (lower part, next to the stomach). Likewise, on the opposite side, the right coelomic pouch has also been partitioned into a right axohydrocoel and a right somatocoel, although the right axohydrocoel remains in a rudimentary state compared to its left counterparts. In addition, at the basis of the posterodorsal arm on the left side, a small portion of the ectoderm has thickened, invaginated, and came into contact with the left hydocoel. This structure is called the vestibule and together with the left hydrocoel and the left stomatocoel they have further subsequently fused to form the adult rudiment. The formation of the rudiment has overall taken some time, giving rise first to a pentaradial disc and then to a pentaradial complex structure harboring podia (i.e. tube feet) and spines. In parallel, on the right size of the larva, a variable number of pedicellariae (one to four) and endoskeletal elements (i.e. the five genital plates) have further formed, which will also later contribute to the composition of the adult body.
UBERON:0008265
Plut8a
8-arm pluteus larva stage
ecao_developmental_stage
The competent pluteus larva is mainly characterized morphologically by the presence, on the ventral size, of still 8 arms and by the presence on the left side of the stomach of the rudiment that is now the size of or even bigger than the stomach. The rudiment further harbors by now five long primary podia (i.e. tube feet), five quartets of definitive spines located between the primary podia and five pairs of immature spines at the basis of the primary podia, while on the opposite side, i.e. on the right side of the larva, five to seven immature spines have further developed, supported by the genital plates, along with one to four pedicaellariae. At the level of the larva, in parallel, the anterior and posterior pairs of epaulettes have also considerably increased in size by now and even fused dorsally to the hydropore and to the anus respectively, thereby leaving exempt of cilia two lateral fields in between them. At the center of the left lateral field, the vestibular roof has also by now ruptured and this opening has created the vestibular pore, through which some primary podia of the rudiment protrude outside the larva and scrutinize the substrate looking for the adequate cues to begin metamorphosis. At that stage, the larva is thus exhibiting a typical substrate-test behavior, going to the sea bottom and scrutinizing the substrate. This behavior is characteristic of a larva named competent to metamorphosis, which it will accomplish providing that it is adequately stimulated by environmental factors.
UBERON:0008265
Cpt8a
cPlut
competent pluteus larva stage
ecao_developmental_stage
The metamorphic larva stage consists essentially of the evagination of the echinoid rudiment. It is characterized by the execution of conspicuous and relatively abrupt physical changes that take place quite quickly, in about one hour, and during which the planktonic larva is transformed into a benthic juvenile. At that stage, the larva is settled on the substrate and is firmly attached to it by the primary podia of the rudiment. The ectodermal epithelium of its arms has started to collapse, making the spicules supporting the larval arms piercing through the epidermis. The larval mouth and anus have further closed, while in parallel, within the larva, the rudiment spines have lifted up thereby distending the vestibular wall and wide opening the vestibular pore. Following these movements, the rudiment has farther down accomplished and finalized its complete eversion, encapsulating the digestive tract and reaching the right side of the larval body. During this process, the genital plates and the associated pedicellariae and immature spines present on the right side of the larva have further completed the production of the aboral part of the adult body. At the end of metamorphosis, hence at the end of the metamorphic larva stage, the individual has thus become benthic, it is settled in the substrate, and it looks like an adult pentaradial sea urchin although it is smaller in size, deprived of a functional digestive system and sexually immature.
meta
metamorphosis
metamorphic larva stage
ecao_developmental_stage
Biological process during which changes occur in biological and psychological domains to generate a sexually mature animal.
adulthood
ecao_developmental_stage
Period during which a young individual, posing as a small adult, grows but remains unable to reproduce.
UBERON:0034919
juvenile period
ecao_developmental_stage
The early juvenile is morphologically similar to both the late rudiment and a miniature sea urchin adult. Like the rudiment, it harbors five primary podia (or tube feet), five quartet of definitive spines, five pairs of immature spines located at the basis of the primary podia, 5 to 7 immature spines supported by the genital plates as well as 1 to 4 pedicellariae. Like the adult, it displays a pentarial symmetry and is settled on the substrate. An early juvenile is about 300 µm in diameter. On its aboral side, it still exhibits some remaining larval rods and tissues, although these will soon disappear. In addition, the plates forming its endoskeleton are still rather light and porous making it looking relatively clear, although it bears lots of red-pigmented cells. However, the postlarva is still deprived of a mouth and an anus, hence of a functional digestive tract. The early juvenile is thus endotrophic, meaning that its growth and development solely relies on energy derived from internal sources. Furthermore, the early juvenile is sexually immature.
UBERON:0007021
endotrophic juvenile
postlarva
PLJuv
early juvenile stage
ecao_developmental_stage
The late juvenile really looks like a small adult. The plates of its endoskeleton have by now densified providing it with a dark shell. In addition, it has finally developed a functional digestive tract. The digestive tract inherited from the larva has indeed by now undergone a complete reorganization, progressively bending within the perivisceral cavity to form two successive loops. The buccal plates and the aristotle lantern have further finished developing, creating a new mouth that has opened on the oral side at the center of the aristotle's lantern, while a new anus has also opened in the periproct, i.e. at the center of the five genital plates. The late juvenile can thus feed and starts growing in size, by grazing on the substrate. The late juvenile is exotrophic, meaning that its growth and development rely on energy derived from external sources. In addition, the primary podia have started to regress by that stage and will eventually disappear, while secondary podia have emerged and are functional, allowing the juvenile to move. Similarly, the immature spines have also started to be lost and be replaced by definitive spines. The genital plate CD has further differentiated into the madreporite and sphaeridia have formed. However, this individual is still sexually immature.
UBERON:0007021
ExJuv
late juvenile stage
ecao_developmental_stage
Period during which the animal reaches sexual maturity.
UBERON:0000066
adult period
ecao_developmental_stage
This stage corresponds to a fully formed pentaradial sea urchin that has reached sexual maturity. The gonads have developed within the perivisceral cavity and are connected to the outside by the genital pores pierced into the genital plates. The young adult has grown up to about several centimeters in diameter and is now producing gametes. Time after fertilization is unknown, between several months to one year depending on the sea urchin species and the rate and type of feeding.
UBERON:0000113
gravid sea urchin
sexual mature sea urchin
adult stage
ecao_developmental_stage
The embryo is composed of about 800 cells and is surrounded by a fertilization envelope. The wall of the embryo is thinner and smoother than at previous stages. The vegetal plate has not formed. Many cells are ciliated but the embryo has not begun to rotate within the fertilization envelope. Note for euechinoid indirect developers: molecular labeling typically indicates the presence of 32 large micromere descendants and 4 small micromere descendants at this stage.
vLB
very late blastula stage
ecao_developmental_stage
Stage when the vegetal plate is apparent but primary mesenchyme cells (PMCs) have not started to ingress. Embryos are motile due ciliary beating but have not completed hatching.
VP
vegetal plate stage
ecao_developmental_stage
open mouth stage
open mouth stage
ecao_developmental_stage
early prism stage
early prism stage
ecao_developmental_stage
late prism stage
late prism stage
ecao_developmental_stage
early pluteus stage
early pluteus stage
ecao_developmental_stage
early organogenesis stage
early organogenesis stage
ecao_developmental_stage
mid-organogenesis stage
mid-organogenesis stage
ecao_developmental_stage
late organogenesis stage
late organogenesis stage
ecao_developmental_stage
very late organogenesis stage
very late organogenesis stage
ecao_developmental_stage
mesenchyme blastula stage
mesenchyme blastula stage
ecao_developmental_stage
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.
UBERON:0001062
echinoderm anatomy
echinoderm_anatomy
Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome
UBERON:0000061
anatomical structure
echinoderm_anatomy
A system that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity. Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function
UBERON:0000467
body system
connected anatomical system
organ system
anatomical system
echinoderm_anatomy
A region of the whole organism without well-defined compartmental boundaries
UBERON:0000475
organism subdivision
anatomical region
echinoderm_anatomy
UBERON:0000464
anatomical space
echinoderm_anatomy
Anatomical structure that is an individual member of a species and consists of one cell or more
whole organism
echinoderm_anatomy
Anatomical structure that is an individual member of a species and consists of more than one cell
UBERON:0000468
multicellular organism
echinoderm_anatomy
Anatomical entity that comprises the animal 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
UBERON:0000922
embryo
echinoderm_anatomy
UBERON:0002548
larva
echinoderm_anatomy
UBERON:0034919
juvenile
echinoderm_anatomy
UBERON:0007023
adult
echinoderm_anatomy
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
UBERON:0001007
digestive system
echinoderm_anatomy
The gastrointestinal tract that is being formed during embryonic development starting with the formation of the primitive gut tube (or archenteron)
embryonic digestive system
echinoderm_anatomy
Organ system responsible for the food uptake and processing in the larva
larval digestive system
echinoderm_anatomy
juvenile digestive system
echinoderm_anatomy
Anatomical system that processes ingested substances in the adult
adult digestive system
echinoderm_anatomy
UBERON:0002405
immune system
echinoderm_anatomy
embryonic immune system
echinoderm_anatomy
larval immune system
echinoderm_anatomy
juvenile immune system
echinoderm_anatomy
adult immune system
echinoderm_anatomy
Anatomical system that has as its parts the organs concerned with reproduction, i.e. the male and female gonads.
UBERON:0000990
reproductive system
echinoderm_anatomy
UBERON:0001016
nervous system
echinoderm_anatomy
The sum of all the structures in the embryo that will develop into the larval nervous system
embryonic nervous system
echinoderm_anatomy
The sum of all the neural structures present in the larva
larval nervous system
echinoderm_anatomy
juvenile nervous system
echinoderm_anatomy
UBERON:6003559
adult nervous system
echinoderm_anatomy
UBERON:0000383
muscular system
echinoderm_anatomy
larval muscular system
echinoderm_anatomy
juvenile muscular system
echinoderm_anatomy
UBERON:6003218
adult muscular system
echinoderm_anatomy
Internal support structure of an animal composed of mineralized tissue. It gives shape, support and protection to the body.
UBERON:0001434
endoskeleton
echinoderm_anatomy
embryonic endoskeleton
echinoderm_anatomy
larval endoskeleton
echinoderm_anatomy
skeletal rudiment
rudiment endoskeleton
echinoderm_anatomy
juvenile endoskeleton
echinoderm_anatomy
adult endoskeleton
echinoderm_anatomy
The water vascular system is a hydraulic system used by sea urchins for locomotion, food and waste transportation, and respiration. The system is composed of canals connecting numerous tube feet.
UBERON:0008251
water vascular system
echinoderm_anatomy
The hemal system contains the blood. It is composed of a complex network of vessels mainly located around the gut.
haemal system
hemal system
echinoderm_anatomy
Anatomical region that corresponds to the upper half of the embryo, which later is composed of the mesomeres, and ultimately encompasses the presumptive ectoderm
UBERON:0012284
upper half
upper hemisphere
animal half
animal hemisphere
echinoderm_anatomy
Anatomical region that corresponds to the lower half of the embryo, which later is composed of the macromeres and the micromeres, and ultimately encompasses the endoderm and mesoderm
UBERON:0012285
lower half
lower hemisphere
vegetal half
vegetal hemisphere
echinoderm_anatomy
cell cortex
echinoderm_anatomy
cleavage furrow
echinoderm_anatomy
Cell component comprising the outermost layer of the animal region of the oocyte. It consists of a phospholipid bilayer and associated proteins
animal cortex
echinoderm_anatomy
Cell component comprising the outermost layer of the vegetal region of the oocyte. It consists of a phospholipid bilayer and associated proteins
vegetal cortex
echinoderm_anatomy
The apical region of the animal hemisphere
animal pole
echinoderm_anatomy
The apical most region of the vegetal hemisphere. Once cleavages have started the vegetal pole is characterized by the presence of the micromeres initially and then that of the small micromeres
vegetal pole
echinoderm_anatomy
animal plate
anterior neuroectoderm
apical plate
neurogenic ectoderm
apical pole domain
animal pole domain
echinoderm_anatomy
UBERON:0000100
blastopore
echinoderm_anatomy
UBERON:3010455
blastopore lip
echinoderm_anatomy
bottle cell
echinoderm_anatomy
embryonic cell
echinoderm_anatomy
vegetal plate
echinoderm_anatomy
Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane
cell
echinoderm_anatomy
Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher.
cell part
echinoderm_anatomy
Any of the organs or elements that are part of the digestive system
UBERON:0013765
digestive system element
echinoderm_anatomy
UBERON:0004765
skeletal element
echinoderm_anatomy
Any anatomical structure that is part of an embryo
UBERON:0002050
embryonic structure
echinoderm_anatomy
Any anatomical structure that is part of a larva
larval structure
echinoderm_anatomy
Any anatomical structure that is part of a juvenile
juvenile structure
echinoderm_anatomy
Any anatomical structure that is part of an adult
adult structure
echinoderm_anatomy
UBERON:0000479
tissue
echinoderm_anatomy
imaginal adult rudiment
adult rudiment
rudiment
echinoderm_anatomy
rudiment structure
echinoderm_anatomy
non-rudiment adult structure
echinoderm_anatomy
intracellular part
echinoderm_anatomy
cytoskeleton
echinoderm_anatomy
microtubule
echinoderm_anatomy
A membrane-bounded organelle of in which chromosomes are housed and replicated. In most cells, it contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some specialized cell types, RNA metabolism or DNA replication may be absent
nucleus
echinoderm_anatomy
A female haploid germ cell.
oocyte
echinoderm_anatomy
The enlarged, fluid filled nucleus of a primary oocyte, the development of which is suspended in prophase I of the first meiotic division between embryohood and sexual maturity
germinal vesicle
echinoderm_anatomy
The subequatorial accumulation of pigment granules (the so-called ‘pigment band’) in eggs or early stage embryos, which constitutes an unambiguous marker of animal-vegetal polarity
pigmented band
pigment band
equatorial pigment band
echinoderm_anatomy
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures
cytoplasm
echinoderm_anatomy
centrosome
echinoderm_anatomy
mitotic spindle
echinoderm_anatomy
meiotic spindle
echinoderm_anatomy
A structure that lies outside the plasma membrane and surrounds the egg. The fertilization envelope forms from the vitelline membrane after fertilization as a result of cortical granule release
fertilization membrane
fertilization envelope
echinoderm_anatomy
A mature male germ cell
male gamete
mature sperm cell
spermatozoa
spermatozoan
sperm
spermatozoid
echinoderm_anatomy
mitotic aster
spindle aster
aster
echinoderm_anatomy
spermatozoid aster
sperm aster
echinoderm_anatomy
UBERON:0005764
acellular membrane
echinoderm_anatomy
UBERON:0003125
vitelline envelope
vitelline layer
vitelline membrane
echinoderm_anatomy
hyaline membrane
hyaline layer
echinoderm_anatomy
microvillus
echinoderm_anatomy
fibropellin layer
apical lamina
echinoderm_anatomy
secretory vesicle
echinoderm_anatomy
cilium
echinoderm_anatomy
filopodium
echinoderm_anatomy
UBERON:0000482
basal lamina
echinoderm_anatomy
basal vesicle
basal lamina vesicle
basal laminar vesicle
echinoderm_anatomy
apical vesicle
echinoderm_anatomy
cortical vesicle
cortical granule
echinoderm_anatomy
echinonectin granule
nectosome
echinonectin vesicle
echinoderm_anatomy
mitochondrion
echinoderm_anatomy
actin cytoskeleton
echinoderm_anatomy
F-actin filament
microfilament
actin filament
echinoderm_anatomy
nuclear part
echinoderm_anatomy
nucleoplasm
echinoderm_anatomy
nuclear envelope
echinoderm_anatomy
endoplasmic reticulum
echinoderm_anatomy
spermatozoid entry point
echinoderm_anatomy
cell membrane
plasma membrane
echinoderm_anatomy
A small cell formed by the meiotic division of an oocyte
polar body
echinoderm_anatomy
sperm part
spermatozoid part
echinoderm_anatomy
The part of the late spermatid or spermatozoon that contains the nucleus and acrosome.
spermatozoid head
echinoderm_anatomy
A microtubule-based flagellum (or cilium) that is part of a sperm, a mature male germ cell that develops from a spermatid
sperm tail
spermatozoid flagellum
echinoderm_anatomy
An organelle that develops over the anterior half of the head in the spermatozoa
acrosome
acrosomal vesicle
echinoderm_anatomy
presumptive primordial germ cell
small micromere descendant cell
echinoderm_anatomy
presumptive primordial germ cell
echinoderm_anatomy
primordial germ cell
echinoderm_anatomy
germ cell
echinoderm_anatomy
gamete
echinoderm_anatomy
immature egg
immature occyte
echinoderm_anatomy
A mature female gamet that has entered meiosis.
female gamete
female germ cell
unfertilized egg
egg
mature oocyte
echinoderm_anatomy
An undifferentiated cell produced by early cleavages of the fertilized egg (zygote)
blastoderm cell
blastomere
echinoderm_anatomy
blastomere of 2-cell embryo
echinoderm_anatomy
blastomere of 4-cell embryo
echinoderm_anatomy
Intermediate size blastomere forming the animal hemisphere of the cleaving embryo
mesomeres
mesomere
echinoderm_anatomy
Larger blastomere of the vegetal hemisphere of the cleaving embryo located below the equator
macromeres
macromere
echinoderm_anatomy
blastomere tier
cell tier
echinoderm_anatomy
macromere daughter cell tier
echinoderm_anatomy
Small blastomere of the vegetal hemisphere of the cleaving embryo located at to the vegetal pole
micromeres
micromere
echinoderm_anatomy
large micromere
echinoderm_anatomy
presumptive PMC
presumptive primary mesenchyme cell
presumptive skeletogenic mesenchyme cell
large micromere progeny
large micromere descendant cell
echinoderm_anatomy
SM
small micromere
echinoderm_anatomy
A progenitor cell of the nervous system that will develop into a neuron
neuronal progenitor cell
presumptive neuron
echinoderm_anatomy
animal pole domain neuronal progenitor cell
apical pole domain presumptive neuron
animal pole domain presumptive neuron
echinoderm_anatomy
ectoderm neuronal progenitor cell
ectoderm presumptive neuron
echinoderm_anatomy
ciliary band neuronal progenitor cell
ciliary band presumptive neuron
echinoderm_anatomy
endoderm associated neuronal progenitor cell
endoderm associated presumptive neuron
echinoderm_anatomy
nerve cell
neuron
echinoderm_anatomy
larval neuron
echinoderm_anatomy
serotonergic neuron
echinoderm_anatomy
synaptotagmin-B neuron
echinoderm_anatomy
dopaminergic neuron
echinoderm_anatomy
GABAergic neuron
echinoderm_anatomy
sensory cell
sensory neuron
echinoderm_anatomy
biopolar neuron
echinoderm_anatomy
multipolar neuron
echinoderm_anatomy
neuronal structure
neural structure
echinoderm_anatomy
UBERON:0001018
axon bundle
axonal tract
axon tract
echinoderm_anatomy
peripheral neuron
ciliary band neuron
echinoderm_anatomy
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
UBERON:0000924
ectoderm
echinoderm_anatomy
presumptive ciliary band cell
echinoderm_anatomy
endoderm associated neuron
echinoderm_anatomy
UBERON:0000045
ganglion
echinoderm_anatomy
apical organ
apical ganglion
echinoderm_anatomy
adult neuron
echinoderm_anatomy
circumoral nerve ring
echinoderm_anatomy
UBERON:0000429
digestive nerve plexus
enteric plexus
enteric nerve plexus
echinoderm_anatomy
radial nerve cord
echinoderm_anatomy
primary podia associated neuron
echinoderm_anatomy
secondary podia associated neuron
echinoderm_anatomy
definitive spine associated neuron
echinoderm_anatomy
pedicellaria associated neuron
echinoderm_anatomy
basiepidermal nerve plexus
echinoderm_anatomy
Group of four cells of equal size forming the animal hemisphere of an eight-cell stage embryo
animal quartet
echinoderm_anatomy
Group of four cells of equal size forming the vegetal hemisphere of an eight-cell stage embryo
vegetal quartet
echinoderm_anatomy
an1
animal tier 1
echinoderm_anatomy
an2
animal tier 2
echinoderm_anatomy
ectoendoderm
veg1
vegetal tier 1
echinoderm_anatomy
endomesoderm
veg2
vegetal tier 2
echinoderm_anatomy
presumptive vegetal ectoderm
veg1 upper
veg1U
vegetal tier 1 upper
echinoderm_anatomy
veg1 lower
veg1L
vegetal tier 1 lower
echinoderm_anatomy
veg2 upper
veg2U
vegetal tier 2 upper
echinoderm_anatomy
presumptive non-skeletogenic mesoderm
veg2 lower
veg2L
vegetal tier 2 lower
echinoderm_anatomy
UBERON:0000923
embryonic germ layer
primary germ layer
germ layer
echinoderm_anatomy
UBERON:0005291
embryonic tissue
echinoderm_anatomy
UBERON:0006601
presumptive ectoderm
echinoderm_anatomy
animal ectoderm
echinoderm_anatomy
vegetal ectoderm
echinoderm_anatomy
oral ectoderm
ventral ectoderm
echinoderm_anatomy
aboral ectoderm
dorsal ectoderm
echinoderm_anatomy
veg1
vegetal tier 1
ectoendoderm
echinoderm_anatomy
mesoendoderm
veg2
vegetal tier 2
endomesoderm
echinoderm_anatomy
inner apical pole domain
inner animal pole domain
echinoderm_anatomy
outer apical pole domain
outer animal pole domain
echinoderm_anatomy
central ectoderm
echinoderm_anatomy
BE
border ectoderm
echinoderm_anatomy
near-apical ectoderm
echinoderm_anatomy
apical ectoderm
echinoderm_anatomy
veg1-lateral ectoderm
echinoderm_anatomy
veg-1 oral ectoderm
echinoderm_anatomy
lateral ectoderm
echinoderm_anatomy
right lateral ectoderm
echinoderm_anatomy
left lateral ectoderm
echinoderm_anatomy
arm tip ectoderm
echinoderm_anatomy
dorsal arm tip ectoderm
echinoderm_anatomy
ventral arm tip ectoderm
echinoderm_anatomy
apical tuft
echinoderm_anatomy
larval tissue
echinoderm_anatomy
rudiment tissue
echinoderm_anatomy
juvenile tissue
echinoderm_anatomy
adult tissue
echinoderm_anatomy
presumptive stomodeum
echinoderm_anatomy
UBERON:0000930
presumptive mouth
stomodeum
echinoderm_anatomy
ciliary band
echinoderm_anatomy
oral hood ciliary band
echinoderm_anatomy
arm ciliary band
echinoderm_anatomy
animal pole ciliary band
echinoderm_anatomy
vegetal ciliary band
echinoderm_anatomy
lateral ciliary band
echinoderm_anatomy
PL
preoral lobe
oh
oral hood
echinoderm_anatomy
apex
echinoderm_anatomy
larval arm
echinoderm_anatomy
ALA
AL
right anterolateral arm
echinoderm_anatomy
ALA
AL
left anterolateral arm
echinoderm_anatomy
PO
right postoral arm
echinoderm_anatomy
PO
left postoral arm
echinoderm_anatomy
PD
right posterodorsal arm
echinoderm_anatomy
PD
left posterodorsal arm
echinoderm_anatomy
PRO
PR
right preoral arm
echinoderm_anatomy
PRO
PR
left preoral arm
echinoderm_anatomy
spicule rudiment
echinoderm_anatomy
spicule dot
spicule granule
echinoderm_anatomy
spicule primordium
triradiate spicule rudiment
echinoderm_anatomy
triradiate spicule
right ventrolateral triradiate spicule rudiment
echinoderm_anatomy
left ventrolateral triradiate spicule rudiment
echinoderm_anatomy
hexaradiate spicule
hexaradiate spicule rudiment
echinoderm_anatomy
A triradiate or hexaradiate minute calcareous skeletal element that initiates most if not all skeletal structures found within the sea urchin embryo, larva and adult.
primary triradiate skeletal rudiment
larval spicule
echinoderm_anatomy
The embryonic tissue made up of loosely connected mesoderm cells that will produce all of the skeletal elements.
primary mesenchyme
SM
embryonic skeletogenic mesenchyme
echinoderm_anatomy
spicule rod
skeletal rod
echinoderm_anatomy
anonymous rod
echinoderm_anatomy
right anonymous rod
echinoderm_anatomy
left anonymous rod
echinoderm_anatomy
right dorsoventral connecting rod
echinoderm_anatomy
right anterolateral rod
echinoderm_anatomy
left dorsoventral connecting rod
echinoderm_anatomy
left anterolateral rod
echinoderm_anatomy
right postoral rod
echinoderm_anatomy
left postoral rod
echinoderm_anatomy
right posterodorsal rod
echinoderm_anatomy
left posterodorsal rod
echinoderm_anatomy
dorsal arch
echinoderm_anatomy
right preoral rod
echinoderm_anatomy
left preoral rod
echinoderm_anatomy
right ventral transverse rod
echinoderm_anatomy
left ventral transverse rod
echinoderm_anatomy
posterior tip of body rod
echinoderm_anatomy
body rod end
scheitel
echinoderm_anatomy
body rod
echinoderm_anatomy
left body rod
echinoderm_anatomy
right body rod
echinoderm_anatomy
posterior tip of left body rod
echinoderm_anatomy
posteror tip of right body rod
echinoderm_anatomy
right recurrent rod
echinoderm_anatomy
left recurrent rod
echinoderm_anatomy
posterior transverse rod
echinoderm_anatomy
UBERON:0000165
mouth
echinoderm_anatomy
larval mouth
echinoderm_anatomy
UBERON:0001245
anus
echinoderm_anatomy
larval anus
echinoderm_anatomy
UBERON:0006595
prospective endoderm
presumptive endoderm
echinoderm_anatomy
UBERON:0000925
endoderm
echinoderm_anatomy
UBERON:0004735
primitive gut
embryonic gut
archenteron
echinoderm_anatomy
UBERON:0001046
hindgut
echinoderm_anatomy
dorsal hindgut
echinoderm_anatomy
ventral hindgut
echinoderm_anatomy
UBERON:0001045
midgut
echinoderm_anatomy
ventral midgut
echinoderm_anatomy
dorsal midgut
echinoderm_anatomy
anterior midgut
echinoderm_anatomy
posterior midgut
echinoderm_anatomy
anterior hindgut
echinoderm_anatomy
posterior hindgut
echinoderm_anatomy
UBERON:0001041
tip of the digestive tract
foregut
echinoderm_anatomy
ventral foregut
echinoderm_anatomy
dorsal foregut
echinoderm_anatomy
anterior foregut
echinoderm_anatomy
posterior foregut
echinoderm_anatomy
UBERON:3010432
archenteron roof
tip of archenteron
echinoderm_anatomy
UBERON:0006603
prospective mesoderm
presumptive mesoderm
echinoderm_anatomy
UBERON:0000926
mesoderm
echinoderm_anatomy
The subset of the embryonic mesoderm that will later give rise to the skeletogenic mesenchyme and embryonic skeleton.
embryonic skeletogenic mesoderm
echinoderm_anatomy
primary mesenchyme cell
PMC
embryonic skeletogenic mesenchyme cell
echinoderm_anatomy
multinucleated cell
syncytial cell
syncytium
multinucleate cell
syncytium
echinoderm_anatomy
Anatomical structure composed of skeletogenic mesenchyme cells that have fused to form a single syncytial network.
embryonic skeletogenic mesenchyme syncytium
echinoderm_anatomy
PMC ring
primary mesenchyme cell ring
subequatorial PMC ring
subequatorial SM ring
subequatorial primary mesenchyme cell ring
SM ring
subequatorial skeletogenic mesenchyme ring
echinoderm_anatomy
Subpopulation of skeletogenic mesenchyme forming a chain on the oral (i.e. ventral) side of the embryo.
ventral skeletogenic mesenchyme chain
echinoderm_anatomy
Subpopulation of skeletogenic mesenchyme forming a chain on the aboral (i.e. dorsal) side of the embryo.
dorsal skeletogenic mesenchyme chain
echinoderm_anatomy
Subpopulation of skeletogenic mesenchyme forming a cluster (i.e. a group of cells) in the ventrolateral region of the embryo.
right ventrolateral skeletogenic mesenchyme cluster
echinoderm_anatomy
left ventrolateral skeletogenic mesenchyme cluster
echinoderm_anatomy
Subpopulation of skeletogenic mesenchyme forming a chain on either side of the developing digestive tract, along the blastocoel wall and towards the animal pole.
lateral chain of skeletogenic mesenchyme
echinoderm_anatomy
Subpopulation of skeletogenic mesenchyme forming a chain along the blastocoel wall towards the animal pole on the right side of the embryo.
right lateral chain of skeletogenic mesenchyme
echinoderm_anatomy
Subpopulation of skeletogenic mesenchyme forming a chain along the blastocoel wall towards the animal pole on the left side of the embryo.
left lateral chain of skeletogenic mesenchyme
echinoderm_anatomy
embryonic non-skeletogenic mesoderm
echinoderm_anatomy
ventral non-skeletogenic mesoderm
echinoderm_anatomy
dorsal non-skeletogenic mesoderm
echinoderm_anatomy
NSM
secondary mesenchyme
embryonic non-skeletogenic mesenchyme
echinoderm_anatomy
secondary mesenchyme cell
SMC
embryonic non-skeletogenic mesenchyme cell
echinoderm_anatomy
larval non-skeletogenic mesenchyme
echinoderm_anatomy
larval non-skeletogenic mesenchyme cell
echinoderm_anatomy
presumptive blastocoelar cell
echinoderm_anatomy
presumptive immunocyte
presumptive pigmented cell
presumptive pigment cell
echinoderm_anatomy
a cell that contains red coloring matter
pigmented immunocyte
pigmented cell
pigment cell
echinoderm_anatomy
embryonic pigment cell
echinoderm_anatomy
larval pigment cell
echinoderm_anatomy
juvenile pigment cell
echinoderm_anatomy
rudiment pigment cell
echinoderm_anatomy
blastocoelar cell
echinoderm_anatomy
globular cell
echinoderm_anatomy
filopodial cell
echinoderm_anatomy
ovoid cell
echinoderm_anatomy
amoeboid cell
echinoderm_anatomy
presumptive muscle cell
muscle precursor cell
echinoderm_anatomy
muscle
echinoderm_anatomy
contractile muscle
larval muscle
echinoderm_anatomy
rudiment muscle
echinoderm_anatomy
juvenile muscle
echinoderm_anatomy
adult muscle
echinoderm_anatomy
UBERON:0000090
blastocoel
echinoderm_anatomy
sphincter
echinoderm_anatomy
midgut-hindgut constriction
pyloric sphincter
echinoderm_anatomy
foregut-midgut constriction
cardiac sphincter
echinoderm_anatomy
hindgut-ectoderm constriction
anal sphincter
echinoderm_anatomy
UBERON:0004590
sphincter muscle
echinoderm_anatomy
myoepithelial cell
sphincter muscle cell
echinoderm_anatomy
UBERON:0001202
pyloric sphincter
pyloric sphincteric muscle
echinoderm_anatomy
cardiac sphincter
cardiac sphincteric muscle
echinoderm_anatomy
UBERON:0004916
anal sphincter
anal sphincteric muscle
echinoderm_anatomy
larval esophagus
echinoderm_anatomy
circumesophageal muscle
echinoderm_anatomy
presumptive circumesophageal muscle cell
circumesophageal muscle cell
echinoderm_anatomy
larval stomach
echinoderm_anatomy
larval intestine
echinoderm_anatomy
The mesenchyme cells that produce new skeletal elements (i.e., the posterodorsal rods, dorsal arch, and preoral rods) in the larva after feeding begins
larval skeletogenic mesenchyme
echinoderm_anatomy
larval skeletogenic mesenchyme cell
echinoderm_anatomy
UBERON:0011997
coelom
echinoderm_anatomy
unpaired coelomic rudiment
unpaired coelomic pouch
echinoderm_anatomy
right coelomic pouch
echinoderm_anatomy
left coelomic sac
left coelomic pouch
echinoderm_anatomy
right coelomic constriction
echinoderm_anatomy
left coelomic constriction
echinoderm_anatomy
larval epithelium
echinoderm_anatomy
amniotic sac
vestibule
echinoderm_anatomy
UBERON:0002424
circumoral ectoderm
circumoral epithelium
oral epidermis
oral epithelium
echinoderm_anatomy
aboral epithelium
echinoderm_anatomy
The left lateral field is the lateral field located on the left side of the larva
left lateral field
echinoderm_anatomy
Opening located in the left lateral field
vestibular pore
echinoderm_anatomy
anterior coelom
axocoel
echinoderm_anatomy
left axocoel
echinoderm_anatomy
axial coelom
echinoderm_anatomy
central coelom
hydrocoel
echinoderm_anatomy
posterior coelom
somatocoel
echinoderm_anatomy
left hydrocoel
echinoderm_anatomy
left somatocoel
echinoderm_anatomy
anterior sac
right axohydrocoel
echinoderm_anatomy
right somatocoel
echinoderm_anatomy
axial complex
echinoderm_anatomy
stone canal
echinoderm_anatomy
ring canal
echinoderm_anatomy
radial canal
echinoderm_anatomy
hydropore canal
primary pore canal
echinoderm_anatomy
hydropore
echinoderm_anatomy
right axocoel
echinoderm_anatomy
right hydrocoel
echinoderm_anatomy
axial sinus
echinoderm_anatomy
axial organ
echinoderm_anatomy
dorsal sac
echinoderm_anatomy
ciliated epaulette
echinoderm_anatomy
anterior ciliated epaulette
echinoderm_anatomy
posterior ciliated epaulette
echinoderm_anatomy
The lateral field is located in the aboral ectoderm of the larva. It separates the anterior and posterior pairs of epaulettes
lateral field
echinoderm_anatomy
The right lateral field is the lateral field located on the right side of the larva
right lateral field
echinoderm_anatomy
ambulacral plate
echinoderm_anatomy
The mesenchyme cells that produce biomineralized elements (e.g., spines, test plates, and teeth) in the juvenile and adult.
adult skeletogenic mesenchyme
echinoderm_anatomy
int
interambulacral plate
echinoderm_anatomy
ambulacra
echinoderm_anatomy
interambulacra
echinoderm_anatomy
genital plate
echinoderm_anatomy
appendage
echinoderm_anatomy
UBERON:0008261
pedicellaria
echinoderm_anatomy
terminal plate
ocular plate
echinoderm_anatomy
buccal plate
echinoderm_anatomy
genital plate AB
echinoderm_anatomy
genital plate BC
echinoderm_anatomy
genital plate CD
echinoderm_anatomy
genital plate DE
echinoderm_anatomy
genital plate EA
echinoderm_anatomy
UBERON:0008247
tube foot
podia
echinoderm_anatomy
primary tube foot
primary podia
echinoderm_anatomy
disk of primary podia
echinoderm_anatomy
secondary tube foot
secondary podia
echinoderm_anatomy
disk of secondary podia
echinoderm_anatomy
buccal podia
echinoderm_anatomy
UBERON:0008260
spine appendage
spine
echinoderm_anatomy
splayed spines
juvenile spine
echinoderm_anatomy
adult spine
definitive spine
echinoderm_anatomy
sphaeridium
echinoderm_anatomy
UBERON:0008252
tube foot ampulla
ampulla
echinoderm_anatomy
adult mouth
echinoderm_anatomy
adult anus
echinoderm_anatomy
UBERON:0008253
Aristotles lantern
echinoderm_anatomy
tooth
echinoderm_anatomy
UBERON:0009476
madreporite
echinoderm_anatomy
genital pore
gonopore
echinoderm_anatomy
UBERON:0000991
gonad
echinoderm_anatomy
UBERON:0000992
ovary
echinoderm_anatomy
UBERON:0000473
testis
echinoderm_anatomy
juvenile digestive tract
echinoderm_anatomy
adult digestive tract
echinoderm_anatomy
UBERON:0002095
mesentery
echinoderm_anatomy
perivisceral cavity
echinoderm_anatomy
photoreceptor cell
photosensory cell
echinoderm_anatomy
A population of embryonic cells that share a common developmental fate or program of gene expression and comprising a region that lacks clear morphological boundaries
embryonic territory
echinoderm_anatomy
A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage.
UBERON:0007023
adult organism
echinoderm_anatomy
The muscle system of the embryo.
embryonic muscular system
echinoderm_anatomy
A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues.
extracellular matrix
echinoderm_anatomy
A blastomere of an 8-cell embryo.
blastomere of 8-cell embryo
echinoderm_anatomy
A blastomere of a 16-cell embryo.
blastomere of 16-cell embryo
echinoderm_anatomy
A cell that will develop into a neuron of the animal pole domain.
animal pole domain neuronal progenitor cell
apical pole domain presumptive neuron
presumptive animal pole domain neuron
echinoderm_anatomy
An ectodermal cell that will develop into a neuron.
ectoderm neuronal progenitor cell
presumptive ectoderm neuron
echinoderm_anatomy
A cell that will develop into a neuron of the ciliary band.
ciliary band neuronal progenitor cell
presumptive ciliary band neuron
echinoderm_anatomy
An endodermal cell that will develop into a neuron.
endoderm-ssociated neuronal progenitor cell
presumptive endodermal neuron
presumptive endoderm-associated neuron
echinoderm_anatomy
A neuron located near the base of an oral arm and outside the ciliary band.
postoral neuron
echinoderm_anatomy
A cell that will give rise to a postoral neuron.
presumptive postoral neuron
echinoderm_anatomy
A neuron that produces the synaptotagmin-B protein.
synaptotagmin-positive neuron
synaptotagmin- B neuron
synaptotagmin-B-expressing neuron
echinoderm_anatomy
A neuron that produces the nitric oxide synthase protein.
nitric oxide synthase-expressing neuron
echinoderm_anatomy
A neuron that uses acetylcholine as a vesicular neurotransmitter.
cholinergic neuron
echinoderm_anatomy
A neuron that uses both acetylcholine and catecholamines as vesicular neurotransmitters.
catecholaminergic/cholinergic neuron
echinoderm_anatomy
A neuron derived from endoderm.
endodermal neuron
endoderm-associated neuron
echinoderm_anatomy
One of two bilateral ganglia that arise in the oral ectoderm near the ciliary band.
lateral ganglion
echinoderm_anatomy
The lateral ganglion that forms on the right side of the embryo.
right lateral ganglion
echinoderm_anatomy
The lateral ganglion that forms on the left side of the embryo.
left lateral ganglion
echinoderm_anatomy
The part of the blastula that will give rise to ventral ectoderm.
presumptive oral ectoderm
presumptive ventral ectoderm
echinoderm_anatomy
The part of the blastula that will give rise to dorsal ectoderm.
presumptive aboral ectoderm
presumptive dorsal ectoderm
echinoderm_anatomy
A dynamic terriritory within the prospective ectoderm of the early embryo, located at the anterior (animal) end of the embryo and shaped by Wnt signaling, that contains cells with neurogenic potential.
ANE
animal ectoderm
anterior neuroectoderm
echinoderm_anatomy
A dynamic territory within the prospective ectoderm of the early embryo, located between the anterior neuroectoderm and the endomesoderm.
equatorial ectoderm
echinoderm_anatomy
The innermost part of the anterior neuroectoderm, immediately surrounding the animal pole.
inner apical pole domain
inner ANE
inner anterior neuroectoderm
echinoderm_anatomy
A torus shaped region comprising the outer part of the anterior neuroectoderm.
outer apical pole domain
outer ANE
outer anterior neuroectoderm
echinoderm_anatomy
A region of the ectoderm derived from the animal hemisphere (i.e., mesomere descendants) and located just above the equator on the ventral side of the embryo.
central oral ectoderm
central ventral ectoderm
echinoderm_anatomy
A region of the ectoderm derived from the animal hemisphere (i.e., mesomere descendants) and located between the central ventral ectoderm and the animal pole domain on the ventral side of the embryo.
near apical ectoderm
echinoderm_anatomy
A region of border ectoderm located on a lateral surface of the embryo.
lateral BE
veg1 lateral ectoderm
lateral border ectoderm
echinoderm_anatomy
A region of border ectoderm located on the ventral side of the embryo.
oral BE
oral border ectoderm
ventral BE
veg1 oral ectoderm
ventral border ectoderm
echinoderm_anatomy
A region of border ectoderm located on the dorsal side of the embryo.
aboral BE
aboral border ectoderm
dorsal BE
veg1 aboral ectoderm
dorsal border ectoderm
echinoderm_anatomy
A region of ectoderm derived from the animal hemisphere and located laterally at the boundary between hte ventral and dorsal ectoderm; this region overlaps with part of the prospective ciliary band.
animal lateral ectoderm
echinoderm_anatomy
The animal lateral ectoderm on the right side of the embryo.
right animal lateral ectoderm
echinoderm_anatomy
The animal lateral ectoderm on the left side of the embryo.
left animal lateral ectoderm
echinoderm_anatomy
A portion of the ectoderm located at the tip of a postoral arm.
postoral arm tip ectoderm
echinoderm_anatomy
A portion of the ectoderm located at the tip of the right postoral arm.
right postoral arm tip ectoderm
echinoderm_anatomy
A portion of the ectoderm located at the tip of the left postoral arm.
left postoral arm tip ectoderm
echinoderm_anatomy
The cells that will give rise to the ciliary band.
presumptive ciliated band
presumptive ciliary band
echinoderm_anatomy
An elongated extension of the embryo on the ventral side, supported by a simple or fenestrated skeletal rod and often covered in part by a ciliary band. Arms develop in bilaterally symmetrical pairs.
arm
echinoderm_anatomy
A type of arm that projects from the oral hood; forms after the postoral arms appear and prior to the appearance of the preoral and posterodorsal arms.
anterolateral arm
echinoderm_anatomy
A type of arm that forms between the equator and the posterior pole, near the position of the skeletal rudiment; the first type of arm to appear.
postoral arm
echinoderm_anatomy
A rod that forms by the branching or pronounced curving of the anterior tip of a dorsoventral connecting rod and that projects ventrally from the oral hood, supporting an anterolateral arm.
anterolateral rod
echinoderm_anatomy
A rod that forms by the branching of the anonymous rod and projects ventrally, supporting a postoral arm.
postoral rod
echinoderm_anatomy
A rod that initially forms as one of the three arms of the embryonic triradiate spicule rudiment; this rod extends toward the animal pole before branching or curving to form the anterolateral rod and, in some species, the recurrent rod.
dorsoventral connecting rod
echinoderm_anatomy
A rod that initially forms as one of the three arms of the embryonic triradiate spicule rudiment; this rod projects toward the ventral midline and ceases growth early in development without branching.
ventral transverse rod
echinoderm_anatomy
The growing tip of the body rod as it extends dorsally.
distal tip of body rod
echinoderm_anatomy
The distal tip of the body rod that forms on the right side of the embryo.
distal tip of right body rod
echinoderm_anatomy
The distal tip of the body rod that forms on the left side of the embryo..
distal tip of left body rod
echinoderm_anatomy
A rod that forms from the branching of a dorsoventral transverse rod and extends dorsally.
recurrent rod
echinoderm_anatomy
The part of the embryonic presumptive mesoderm that will later give rise to the skeletogenic mesenchyme and embryonic skeleton.
presumptive embryonic skeletogenic mesoderm
echinoderm_anatomy
A cluster of skeletogenic cell bodies that forms in the ventrolateral region of the subequatorial skeletogenic mesenchyme ring; one triradiate spicule rudiment will form in each of two ventrolateral clusters.
ventrolateral skeletogenic mesenchyme cluster
echinoderm_anatomy
Embryonic cells tin the epithelial wall of the vegetal plate or the archenteron that will give rise to mesodermal derivatives other than skeleton.
NSM
presumptive embryonic non-skeletogenic mesoderm
echinoderm_anatomy
The presumptive embryonic non-skeletogenic mesoderm on the ventral side of the embryo.
ventral presumptive embryonic non-skeletogenic mesoderm
echinoderm_anatomy
The presumptive embryonic non-skeletogenic mesoderm on the dorsal side of the embryo.
dorsal presumptive embryonic non-skeletogenic mesoderm
echinoderm_anatomy
A cell that will give rise to a muscle cell.
muscle precursor cell
presumptive muscle cell
echinoderm_anatomy
A cell that is part of a muscle.
muscle cell
echinoderm_anatomy
The inner, extracellular space between blastomeres of the cleavage stage embryo that will gradually expand and form the blastocoel.
presumptive blastocoel
echinoderm_anatomy
A cell that is part of the pyloric sphincter.
pyloric sphincter muscle cell
echinoderm_anatomy
A cell that is part of the cardiac sphincter.
cardiac sphincter muscle cell
echinoderm_anatomy
A cell that is part of the anal sphincter.
UBERON:0004916
anal pore muscle cell
anal sphincter muscle cell
echinoderm_anatomy
A strand of mesenchyme cells that extends from the left coelom to the ectoderm and that will give rise to the primary pore canal.
presumptive hydropore canal
primary pore canal rudiment
echinoderm_anatomy
An evagination of the midgut that will contribute to the coelom.
posterior enterocoel
echinoderm_anatomy
In species with a posterior enterocoel, the left coelomic pouch that evaginates from the unpaired coelomic pouch at the anterior end of the archenteron.
left anterior coelomic pouch
echinoderm_anatomy
In species with a posterior enterocoel, the right coelomic pouch that evaginates from the unpaired coelomic pouch at the anterior end of the archenteron.
right anterior coelomic pouch
echinoderm_anatomy
In species with two separate ciliary bands, a ciliary band that surrounds the anterior-ventral end of the embryo, anterior to the mouth.
preoral ciliary band
echinoderm_anatomy
In species with two separate ciliary bands, a ciliary band that surrounds the posterior-dorsal end of the embryo, posterior to the mouth.
postoral ciliary band
echinoderm_anatomy
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
GO:0005554
molecular function
molecular_function
GO:0003674
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
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.
This is the same as GO molecular function
gene product or complex activity
molecular_function
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
GOC:pdt
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Wikipedia:Enzyme
enzyme activity
molecular_function
GO:0003824
catalytic activity
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GOC:vw
ISBN:0198506732
enzyme activity
GOC:dph
GOC:tb
A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).
https://github.com/geneontology/go-ontology/issues/17729
GO:0008372
NIF_Subcellular:sao1337158144
cell or subcellular entity
cellular component
cellular_component
subcellular entity
GO:0005575
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
cellular_component
A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).
GOC:pdt
subcellular entity
NIF_Subcellular:nlx_subcell_100315
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.
https://github.com/geneontology/go-ontology/issues/17776
Wikipedia:Intracellular
internal to cell
intracellular
protoplasm
cellular_component
nucleocytoplasm
protoplast
GO:0005622
intracellular anatomical structure
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.
ISBN:0198506732
nucleocytoplasm
GOC:mah
protoplast
GOC:mah
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
NIF_Subcellular:sao1702920020
Wikipedia:Cell_nucleus
cell nucleus
horsetail nucleus
cellular_component
GO:0005634
nucleus
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
GOC:go_curators
horsetail nucleus
GOC:al
GOC:mah
GOC:vw
PMID:15030757
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
GO:0005636
Wikipedia:Nuclear_envelope
cellular_component
GO:0005635
nuclear envelope
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
ISBN:0198547684
The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
https://github.com/geneontology/go-ontology/issues/23023
Wikipedia:Cytoplasm
cellular_component
GO:0005737
cytoplasm
The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
ISBN:0198547684
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
Wikipedia:Vacuole
cellular_component
vacuolar carboxypeptidase Y
GO:0005773
vacuole
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
GOC:mtg_sensu
ISBN:0198506732
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0005887
GO:0005904
juxtamembrane
NIF_Subcellular:sao1663586795
Wikipedia:Cell_membrane
cell membrane
cellular membrane
cytoplasmic membrane
plasmalemma
bacterial inner membrane
inner endospore membrane
integral component of plasma membrane
integral to plasma membrane
plasma membrane lipid bilayer
cellular_component
GO:0005886
plasma membrane
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
ISBN:0716731363
cellular membrane
NIF_Subcellular:sao6433132645
plasma membrane lipid bilayer
GOC:mah
The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
https://github.com/geneontology/go-ontology/issues/26298
Wikipedia:Cell_cortex
ectoplasm
cellular_component
cell periphery
peripheral cytoplasm
GO:0005938
cell cortex
The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
GOC:mah
ISBN:0815316194
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
https://github.com/geneontology/go-ontology/issues/21234
biological_process
GO:0007275
Note that this term was 'developmental process'.
multicellular organism development
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
GOC:dph
GOC:ems
GOC:isa_complete
GOC:tb
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
https://github.com/geneontology/go-ontology/issues/24968
jl
2012-09-19T15:05:24Z
GO:0000004
GO:0007582
GO:0044699
Wikipedia:Biological_process
biological process
physiological process
biological_process
single organism process
single-organism process
GO:0008150
A biological process is an evolved process
Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological process
biological_process
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
GOC:pdt
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
GO:0009795
embryogenesis and morphogenesis
Wikipedia:Embryogenesis
embryogenesis
embryonal development
biological_process
GO:0009790
embryo development
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
GOC:go_curators
GOC:isa_complete
GOC:mtg_sensu
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.
biological_process
GO:0009791
post-embryonic development
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.
GOC:go_curators
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
jl
2012-12-11T16:56:55Z
GO:0008151
GO:0044763
GO:0050875
cell physiology
cellular physiological process
cell growth and/or maintenance
biological_process
single-organism cellular process
GO:0009987
This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
cellular process
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:go_curators
GOC:isa_complete
A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
Wikipedia:Endomembrane_system
cellular_component
GO:0012505
endomembrane system
A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
GOC:lh
A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
2014-03-06T11:37:54Z
GO:0016021
GO:0098589
GO:0098805
Wikipedia:Biological_membrane
Wikipedia:Transmembrane_protein
integral component of membrane
integral to membrane
membrane region
region of membrane
whole membrane
cellular_component
transmembrane
GO:0016020
membrane
A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GOC:dos
GOC:mah
ISBN:0815316194
transmembrane
GOC:mah
true
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Reactome:R-HSA-6788855
Reactome:R-HSA-6788867
phosphokinase activity
molecular_function
GO:0016301
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
kinase activity
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
ISBN:0198506732
Reactome:R-HSA-6788855
FN3KRP phosphorylates PsiAm, RibAm
Reactome:R-HSA-6788867
FN3K phosphorylates ketosamines
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
EC:2.-.-.-
Reactome:R-HSA-1483089
Reactome:R-HSA-1483186
Reactome:R-HSA-5668414
Reactome:R-HSA-8868783
molecular_function
GO:0016740
transferase activity
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
ISBN:0198506732
Reactome:R-HSA-1483089
PE is converted to PS by PTDSS2
Reactome:R-HSA-1483186
PC is converted to PS by PTDSS1
Reactome:R-HSA-5668414
TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK
Reactome:R-HSA-8868783
TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
EC:2.7.-.-
molecular_function
GO:0016772
Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
transferase activity, transferring phosphorus-containing groups
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
GOC:jl
ISBN:0198506732
The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
https://github.com/geneontology/go-ontology/issues/24390
Wikipedia:Cellular_differentiation
biological_process
GO:0030154
cell differentiation
The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
ISBN:0198506732
A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
NIF_Subcellular:sao830981606
cellular_component
intracellular membrane
GO:0031090
organelle membrane
A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
GOC:dos
GOC:mah
intracellular membrane
NIF_Subcellular:sao830981606
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
NIF_Subcellular:sao1687101204
cellular_component
GO:0031965
nuclear membrane
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
GOC:mah
GOC:pz
A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes.
cellular_component
GO:0031967
organelle envelope
A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes.
GOC:mah
GOC:pz
A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers.
cellular_component
GO:0031975
envelope
A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers.
GOC:mah
GOC:pz
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
jl
2012-09-19T16:07:47Z
GO:0044707
GO:0050874
organismal physiological process
biological_process
single-multicellular organism process
GO:0032501
multicellular organismal process
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
GOC:curators
GOC:dph
GOC:isa_complete
GOC:tb
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
jl
2012-12-19T12:21:31Z
GO:0044767
development
biological_process
single-organism developmental process
GO:0032502
developmental process
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
GOC:isa_complete
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
NIF_Subcellular:sao1539965131
Wikipedia:Organelle
cellular_component
GO:0043226
organelle
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
NIF_Subcellular:sao414196390
membrane-enclosed organelle
cellular_component
GO:0043227
membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
cellular_component
GO:0043229
intracellular organelle
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
intracellular membrane-enclosed organelle
cellular_component
GO:0043231
intracellular membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
GOC:go_curators
The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place.
https://github.com/geneontology/go-ontology/issues/24390
biological_process
terminal differentiation
GO:0048468
cell development
The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place.
GOC:go_curators
terminal differentiation
GOC:dph
GOC:tb
Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
https://github.com/geneontology/go-ontology/issues/25943
Wikipedia:Organogenesis
development of an organ
organogenesis
biological_process
GO:0048513
animal organ development
Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
GOC:dph
GOC:jid
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
https://github.com/geneontology/go-ontology/issues/26424
development of an anatomical structure
biological_process
GO:0048856
anatomical structure development
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
GO_REF:0000021
A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
biological_process
GO:0048869
cellular developmental process
A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
GOC:isa_complete
The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures.
mah
2010-10-04T01:51:47Z
cellular_component
GO:0071944
cell periphery
The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures.
GOC:pdt
A membrane that is a (regional) part of the plasma membrane.
dos
2014-03-06T11:55:32Z
region of plasma membrane
cellular_component
GO:0098590
Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass.
plasma membrane region
A membrane that is a (regional) part of the plasma membrane.
GOC:dos
Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.
cellular_component
GO:0099568
cytoplasmic region
Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.
GOC:dos
The complete extent of cell cortex that underlies some some region of the plasma membrane.
perimembrane region
cellular_component
GO:0099738
cell cortex region
The complete extent of cell cortex that underlies some some region of the plasma membrane.
GOC:dos
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
https://github.com/geneontology/go-ontology/issues/24200
https://github.com/geneontology/go-ontology/issues/26424
kmv
2019-08-12T18:01:37Z
cellular_component
GO:0110165
cellular anatomical entity
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
GOC:kmv
data item
data item
information content entity
information content entity
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
obsolescence reason specification
denotator type
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
denotator type
GC_ID:1
PMID:30365038
PMID:32761142
ncbi_taxonomy
all
NCBITaxon:1
root
all
GC_ID:1
ncbi_taxonomy
biota
NCBITaxon:131567
cellular organisms
biota
GC_ID:1
true yeasts
ncbi_taxonomy
NCBITaxon:147537
Saccharomycotina
true yeasts
GC_ID:1
ncbi_taxonomy
Archiascomycota
NCBITaxon:147554
Schizosaccharomycetes
Archiascomycota
GC_ID:11
PMID:10425795
PMID:10425796
PMID:10425797
PMID:10490293
PMID:10843050
PMID:10939651
PMID:10939673
PMID:10939677
PMID:11211268
PMID:11321083
PMID:11321113
PMID:11411719
PMID:11540071
PMID:11542017
PMID:11542087
PMID:11760965
PMID:12054223
PMID:2112744
PMID:270744
PMID:32628106
PMID:36748408
PMID:7520741
PMID:8123559
PMID:8186100
PMID:8590690
PMID:9103655
PMID:9336922
eubacteria
ncbi_taxonomy
Monera
Procaryotae
Prokaryota
Prokaryotae
bacteria
prokaryote
prokaryotes
NCBITaxon:2
Bacteria
eubacteria
Monera
Procaryotae
Prokaryota
Prokaryotae
bacteria
prokaryote
prokaryotes
GC_ID:11
PMID:10425795
PMID:10425796
PMID:10425797
PMID:10490293
PMID:10843050
PMID:10939651
PMID:10939673
PMID:10939677
PMID:11211268
PMID:11321083
PMID:11321113
PMID:11411719
PMID:11540071
PMID:11541975
PMID:11542064
PMID:11542149
PMID:11760965
PMID:12054223
PMID:2112744
PMID:25527841
PMID:270744
PMID:32628106
PMID:36748408
PMID:8123559
PMID:8590690
PMID:9103655
PMID:9336922
ncbi_taxonomy
Archaebacteria
Mendosicutes
Metabacteria
Monera
Procaryotae
Prokaryota
Prokaryotae
archaea
prokaryote
prokaryotes
NCBITaxon:2157
Archaea
Archaebacteria
Mendosicutes
Metabacteria
Monera
Procaryotae
Prokaryota
Prokaryotae
archaea
prokaryote
prokaryotes
GC_ID:1
PMID:23020233
PMID:30257078
eucaryotes
eukaryotes
ncbi_taxonomy
Eucarya
Eucaryotae
Eukarya
Eukaryotae
eukaryotes
NCBITaxon:2759
Eukaryota
eucaryotes
eukaryotes
Eucarya
Eucaryotae
Eukarya
Eukaryotae
eukaryotes
GC_ID:1
ncbi_taxonomy
Fungi/Metazoa group
opisthokonts
NCBITaxon:33154
Opisthokonta
Fungi/Metazoa group
opisthokonts
GC_ID:1
metazoans
multicellular animals
ncbi_taxonomy
Animalia
animals
NCBITaxon:33208
Metazoa
metazoans
multicellular animals
Animalia
animals
GC_ID:1
ncbi_taxonomy
NCBITaxon:33213
Bilateria
GC_ID:1
ncbi_taxonomy
NCBITaxon:34346
Schizosaccharomycetales
GC_ID:1
PMID:15689432
PMID:16151185
PMID:17010206
PMID:17051209
PMID:17572334
ncbi_taxonomy
NCBITaxon:451864
Dikarya
GC_ID:1
ncbi_taxonomy
NCBITaxon:451866
Taphrinomycotina
GC_ID:1
PMID:11062127
PMID:12684019
ncbi_taxonomy
Mycota
fungi
NCBITaxon:4751
Fungi
Mycota
fungi
GC_ID:1
PMID:17572334
ascomycetes
sac fungi
ncbi_taxonomy
ascomycete fungi
NCBITaxon:4890
Ascomycota
ascomycetes
sac fungi
ascomycete fungi
GC_ID:1
ncbi_taxonomy
Hemiascomycetes
NCBITaxon:4891
Saccharomycetes
Hemiascomycetes
GC_ID:1
ncbi_taxonomy
Endomycetales
budding yeasts
NCBITaxon:4892
Saccharomycetales
Endomycetales
budding yeasts
NCBITaxon:221665
NCBITaxon:44280
GC_ID:1
ncbi_taxonomy
NCBITaxon:4893
Saccharomycetaceae
GC_ID:1
fission yeasts
ncbi_taxonomy
Schizosaccharomycetoideae
NCBITaxon:4894
Schizosaccharomycetaceae
fission yeasts
Schizosaccharomycetoideae
GC_ID:1
ncbi_taxonomy
NCBITaxon:4895
Schizosaccharomyces
NCBITaxon:45042
GC_ID:1
fission yeast
ncbi_taxonomy
Schizosaccharomyces malidevorans
NCBITaxon:4896
Schizosaccharomyces pombe
fission yeast
Schizosaccharomyces malidevorans
NCBITaxon:36915
GC_ID:1
ncbi_taxonomy
Pachytichospora
NCBITaxon:4930
Saccharomyces
Pachytichospora
NCBITaxon:41870
GC_ID:1
Saccharomyces cerevisiae 'var. diastaticus'
baker's yeast
brewer's yeast
ncbi_taxonomy
Candida robusta
Mycoderma cerevisiae
Saccharomyces capensis
Saccharomyces diastaticus
Saccharomyces italicus
Saccharomyces oviformis
Saccharomyces uvarum var. melibiosus
NCBITaxon:4932
Saccharomyces cerevisiae
Saccharomyces cerevisiae 'var. diastaticus'
baker's yeast
brewer's yeast
Candida robusta
Mycoderma cerevisiae
Saccharomyces capensis
Saccharomyces diastaticus
Saccharomyces italicus
Saccharomyces oviformis
Saccharomyces uvarum var. melibiosus
GC_ID:1
ncbi_taxonomy
NCBITaxon:6072
Eumetazoa
GC_ID:1
ncbi_taxonomy
NCBITaxon:716545
saccharomyceta
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATO:0000072
quality
PATO:0000001
quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATOC:GVG
A quality which inheres in a continuant.
PATO:0001237
PATO:0001238
snap:Quality
monadic quality of a continuant
multiply inhering quality of a physical entity
quality of a continuant
quality of a single physical entity
quality of an object
quality of continuant
monadic quality of an object
monadic quality of continuant
quality
PATO:0001241
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
physical object quality
A quality which inheres in a continuant.
PATOC:GVG
A monadic quality of continuant that exists at the cellular level of organisation.
quality
PATO:0001396
cellular quality
A monadic quality of continuant that exists at the cellular level of organisation.
PATOC:GVG
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
quality
PATO:0001404
nucleate quality
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
PATOC:GVG
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
quality
PATO:0001405
anucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
Biology-online:Biology-online
A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.
quality
PATO:0001406
binucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.
Biology-online:Biology-online
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
quality
PATO:0001407
mononucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
Biology-online:Biology-online
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
quality
PATO:0001908
multinucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
PATOC:GVG
An organismal quality inhering in a bearer by virtue of the bearer's consisting cells.
quality
PATO:0001992
cellularity
An organismal quality inhering in a bearer by virtue of the bearer's consisting cells.
PATOC:GVG
A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell.
quality
PATO:0001993
multicellular
A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell.
PATOC:GVG
A quality that inheres in an entire organism or part of an organism.
quality
PATO:0001995
organismal quality
A quality that inheres in an entire organism or part of an organism.
PATOC:CJM
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
2013-10-21T05:44:34Z
quality
PATO:0002505
nucleated
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
PATOC:GVG
A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components.
http://orcid.org/0000-0001-7258-9596
quality
PATO:0070044
anatomical structure quality
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
BFO:0000003
uberon
UBERON:0000000
processual entity
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
span:ProcessualEntity
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
EMAPA:0
FBbt:00007001
FMA:305751
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:D000825
SCTID:362889002
TAO:0000037
TGMA:0001823
VHOG:0001759
XAO:0003000
ZFA:0000037
http://dbpedia.org/ontology/AnatomicalStructure
biological structure
connected biological structure
uberon
UBERON:0000061
anatomical structure
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
CARO:0000003
FBbt:00007001
connected biological structure
CARO:0000003
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
adult stage
BTO:0001043
BilaDO:0000004
EFO:0001272
FBdv:00005369
WBls:0000041
XtroDO:0000084
fully formed animal stage
juvenile-adult stage
uberon
UBERON:0000066
fully formed stage
https://github.com/obophenotype/uberon/issues/566
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
https://orcid.org/0000-0002-6601-2165
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
BilaDO:0000002
EV:0300001
FBdv:00005289
FMA:72652
HsapDv:0000002
MmusDv:0000002
OGES:000000
OGES:000022
SCTID:296280003
WBls:0000003
WBls:0000092
WBls:0000102
XAO:1000012
embryonic stage
uberon
embryogenesis
UBERON:0000068
embryo stage
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
http://orcid.org/0000-0002-6601-2165
End of the life of an organism.
ncit:Death is an outcome
XAO:0000437
XtroDO:0000085
uberon
death
UBERON:0000071
death stage
End of the life of an organism.
XAO:0000437
ncit:Death is an outcome
ncit
Stage succeeding embryo, including mature structure.
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
BilaDO:0000003
OGES:000010
OGES:000014
OGES:000024
WBls:0000022
WBls:0000093
WBls:0000103
postembryonic stage
post-hatching stage
uberon
postembryonic
UBERON:0000092
post-embryonic stage
https://github.com/obophenotype/uberon/issues/344
Stage succeeding embryo, including mature structure.
https://orcid.org/0000-0002-6601-2165
An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism.
FBdv:00000000
HsapDv:0000001
MmusDv:0000001
OGES:000011
ncithesaurus:Life
entire life cycle
entire lifespan
life
lifespan
uberon
UBERON:0000104
life cycle
https://github.com/obophenotype/uberon/issues/532
An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism.
https://orcid.org/0000-0002-6601-2165
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
BILS:0000105
EFO:0000399
FBdv:00007012
FMA:24120
HsapDv:0000000
MESH:D008018
MmusDv:0000000
OlatDv:0000010
PdumDv:0000090
WBls:0000002
XAO:1000000
ZFS:0000000
ZFS:0100000
ncithesaurus:Developmental_Stage
developmental stage
stage
uberon
UBERON:0000105
life cycle stage
A spatiotemporal region encompassing some part of the life cycle of an organism.
https://orcid.org/0000-0002-6601-2165
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
BILS:0000106
BilaDO:0000005
EFO:0001322
EHDAA:27
FBdv:00005288
IDOMAL:0000302
NCIT:C12601
PdumDv:0000100
VHOG:0000745
Wikipedia:Zygote
XAO:1000001
ZFS:0000001
1-cell stage
fertilized egg stage
one cell stage
uberon
fertilized egg stage
one-cell stage
zygote
zygotum
UBERON:0000106
zygote stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
Wikipedia:Zygote
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
2012-09-17
VHOG:0000745
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107
http://bgee.unil.ch/
IDOMAL:0000302
https://github.com/biopragmatics/biomappings
fertilized egg stage
BTO:0000854
one-cell stage
VHOG:0000745
zygote
VHOG:0000745
zygotum
Wikipedia:Zygote
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
BILS:0000111
BilaDO:0000010
HsapDv:0000015
MmusDv:0000018
OGES:000005
OGES:000032
Wikipedia:Organogenesis
uberon
segmentation stage
UBERON:0000111
organogenesis stage
https://github.com/obophenotype/developmental-stage-ontologies/issues/84
https://github.com/obophenotype/uberon/issues/533
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
Wikipedia:Organogenesis
Anatomical entity that has mass.
AAO:0010264
AEO:0000006
BILA:0000006
CARO:0000006
EHDAA2:0003006
FBbt:00007016
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
VHOG:0001721
uberon
UBERON:0000465
material anatomical entity
Anatomical entity that has mass.
http://orcid.org/0000-0001-9114-8737
FBbt:00007016
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
organismal
organism
AAO:0010026
AEO:0000191
BILA:0000012
BIRNLEX:18
BSA:0000038
BTO:0000042
CARO:0000012
EFO:0002906
EHDAA2:0003103
EHDAA2:0003191
EHDAA:1
EMAPA:25765
EV:0100016
FBbt:00000001
FMA:256135
HAO:0000012
NCIT:C13041
SCTID:243928005
TADS:0000001
TAO:0001094
TGMA:0001832
VHOG:0000671
WBbt:0007833
Wikipedia:Multi-cellular_organism
XAO:0003004
ZFA:0001094
galen:Organism
ncithesaurus:Whole_Organism
multi-cellular organism
uberon
Koerper
body
whole body
whole organism
UBERON:0000468
multicellular organism
Anatomical structure that is an individual member of a species and consists of more than one cell.
CARO:0000012
Wikipedia:Multi-cellular_organism
http://orcid.org/0000-0001-9114-8737
organism
FBbt:00000001
VHOG:0000671
WBbt:0007833
FBbt:00000001
multi-cellular organism
CARO:0000012
Koerper
BTO:0001489
body
AEO:0000103
BIRNLEX:18
FMA:256135
NCIT:C13041
whole body
BTO:0001489
whole organism
FBbt:00000001
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
embryonic
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
AAO:0011035
AEO:0000169
BILA:0000056
BSA:0000039
BTO:0000379
CALOHA:TS-0229
EFO:0001367
EHDAA2:0000002
EHDAA2_RETIRED:0003236
EHDAA:38
EMAPA:16039
FBbt:00000052
FMA:69068
GAID:963
IDOMAL:0000646
MAT:0000226
MESH:D004622
MIAA:0000019
NCIT:C28147
OGEM:000001
SCTID:57991002
UMLS:C0013935
VHOG:0001766
Wikipedia:Embryo
XAO:0000113
ZFA:0000103
http://neurolex.org/wiki/Category:Embryonic_organism
embryonic organism
uberon
developing organism
developmental tissue
UBERON:0000922
embryo
https://github.com/obophenotype/uberon/issues/503
https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
BTO:0000379
FB:FBrf0039741
FB:FBrf0041814
GO:0009790
Wikipedia:Embryo
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
ZFA
FBbt:00000052
IDOMAL:0000646
https://github.com/biopragmatics/biomappings
UMLS:C0013935
ncithesaurus:Embryo
embryonic organism
BILA:0000056
developing organism
BILA:0000056
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
AAO:0010841
AEO:0000000
BFO:0000004
BILA:0000000
BIRNLEX:6
CARO:0000000
EHDAA2:0002229
FBbt:10000000
FMA:62955
HAO:0000000
MA:0000001
NCIT:C12219
TAO:0100000
TGMA:0001822
UMLS:C1515976
WBbt:0000100
XAO:0000000
ZFA:0100000
uberon
UBERON:0001062
anatomical entity
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
FMA:62955
http://orcid.org/0000-0001-9114-8737
FBbt:10000000
UMLS:C1515976
ncithesaurus:Anatomic_Structure_System_or_Substance
A multicellular organism that existence_starts_with a post-embryonic stage.
MA:0002405
postnatal organism
TS28 mouse
post-hatching organism
post-natal organism
postnatal mouse
uberon
UBERON:0009953
post-embryonic organism
https://github.com/obophenotype/uberon/issues/667
A multicellular organism that existence_starts_with a post-embryonic stage.
OBOL:automatic
TS28 mouse
MA:0002405
post-hatching organism
https://orcid.org/0000-0002-6601-2165
post-natal organism
https://orcid.org/0000-0002-6601-2165
postnatal mouse
MA:0002405
An anatomical structure that has more than one cell as a part.
CARO:0010000
FBbt:00100313
multicellular structure
uberon
UBERON:0010000
multicellular anatomical structure
An anatomical structure that has more than one cell as a part.
CARO:0010000
FBbt:00100313
multicellular structure
FBbt:00100313
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.
uberon
UBERON:0015212
lateral structure
Any structure that is placed on one side of the left-right axis of a bilaterian.
http://orcid.org/0000-0002-6601-2165
example to be eventually removed
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
Person:Alan Ruttenberg
failed exploratory term
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
ready for release
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
pending final vetting
placeholder removed
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term imported
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
term split
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
Alan Ruttenberg
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
universal
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
Alan Ruttenberg
defined class
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
Alan Ruttenberg
named class expression
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI
requires discussion
The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
https://github.com/information-artifact-ontology/ontology-metadata/issues/77
https://orcid.org/0000-0001-5208-3432
out of scope
2
2
1
2
true
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
infer input from direct reg
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
enabling an MF enables its parts
true
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
involved in BP
This can't be added as a property chain because it causes a circularity violation for 'part of'.
This can't be added as a property chain because it causes a circularity violation for 'part of'.
This can't be added as a property chain because it causes a circularity violation for 'part of'.
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).