PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.
CARO part_of NCBITaxon:79327; CL part_of NCBITaxon:79327
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Melanie Courtot
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
Add as annotation triples in the granting ontology
Relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
Notes on the homology status of this class.
Notes on the how instances of this class vary across species.
Notes on how similar or equivalent classes are represented in other ontologies.
synonym typically used in the context of human anatomy
synonym typically used in the context of vertebrate anatomy
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
has exact synonym
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
has narrow synonym
An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
has related synonym
treat-xrefs-as-genus-differentia
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
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.
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
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
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole.
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
Direcly opposite to. i.e. on the opposite side through the axis.
X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure
x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross.
x immediately deep to y iff x deep_to y and x is contiguous with y.
A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. If s finishes axis x, and x has end point p, then x overlaps p
A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. . If s starts axis x, and x has start point p, then x overlaps p
placeholder. used for relation between anatomical surface and an anatomical side.
x immediately superficial to y iff x superficial to y and x is contiguous with y.
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
has_specified_output
The inverse property of is_specified_output_of
PERSON: Alan Ruttenberg
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
Alan Ruttenberg
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
disposition of
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
contained_in
contains
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
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)
"(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF []
overlaps
A is spatially_disjoint_from B if and only if they have no parts in common
There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
Chris Mungall
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
This is the transitive form of the develops from relation
develops from
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.
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
negatively regulates (process to process)
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
positively regulates (process to process)
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
adjacent to
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
has developmental contribution from
inverse of has developmental contribution from
developmentally contributes to
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
developmentally succeeded by
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
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.
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
characteristic of part of
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
a particular instances of akt-2 enables some instance of protein kinase activity
c enables p iff c is capable of p and c acts to execute p.
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
part of structure that is capable of
c involved_in p if and only if c enables some process p', and p' is part of p
involved in
enabled by
regulated by
negatively regulated by
positively regulated by
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).
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
has potential to developmentally contribute to
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
has potential to directly develop into
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 positively regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly negatively regulates
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
causally upstream of
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
immediately causally upstream of
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
inverse of causally upstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
directly positively regulates activity of
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
relation between physical entity and a process or stage
x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
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).
x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
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
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
a produced_by b iff some process that occurs_in b has_output a.
produced by
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
acts upstream of or within, positive effect
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
causally upstream of or within, negative effect
causally upstream of or within, positive effect
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
p 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.
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
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
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.
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
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
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
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]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
immaterial entity
A 2D surface of an anatomical continuant.
A straight line through space, intersecting an anatomical entity.
Axis directions are defined in terms of axes.
An axis that extends through an organism from head end to opposite end of body or tail.
In sponges, AP is used to indicate the direction of movement [in larval stage] (as it is in other metazoans that move, e.g., the basal bilaterians). [PM]
An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure.
An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal).
In some communities, proximal and distal are used when specifying the position of parts of elements that are contained within the body, such as gill arches or vertebral spines. In these cases, use of the classes medial-lateral axis or medial-external axis are more appropriate.
An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body.
An axis that bisects an organism from left to right sides of body, through a sagittal plane.
Anatomical plane that divides body into anterior and posterior parts.
Anatomical plane that divides bilateral body into dorsal and ventral parts.
Anatomical region that overlaps the anterior and dorsal regions of a body or body part.
Anatomical region that overlaps the anterior and ventral regions of a body or body part.
Anatomical region that overlaps the posterior and lateral regions of the body or body part.
Anatomical region that overlaps the anterior and lateral regions of a body or body part.
Anatomical region that overlaps the posterior and dorsal regions of the body or body part.
Anatomical region that overlaps the posterior and ventral regions of a body or body part.
An anatomical region bounded by a plane perpendicular to an axis through the middle.
An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane.
An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane.
Anatomical side that is located on the apical end of an organism or structure.
Anatomical side that is located on the basal end of an organism or structure.
The part of the organism attached to a substrate. Axis of symmetry.
An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane.
An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane.
A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm.
Anatomical region anteriorly located on the body or body part.
Anatomical region posteriorly located on the body or body part.
Anatomical region located on the apical end on the body or body part.
Anatomical region located basally on the body or body part.
Anatomical region dorsally located on the body or body part.
Anatomical region that overlaps the dorsal and lateral regions of a body or body part.
Anatomical region laterally located on the body or body part.
Anatomical region ventrally located on the body or body part.
Anatomical region that overlaps the ventral and lateral regions of a body or body part.
This is an example of a composition of two axis positions.
An anatomical axis that extends from the center of the body outwards or externally.
The medial-external axis could apply to a sphere-shaped body.
An axis that extends from the oral opening to the furthest point in an organism that is directly opposite.
Anatomical surface that is located on the anterior side of the body or body part.
Anatomical surface that is located on the posterior side of the body or body part.
Anatomical surface that is located on the apical side of the body or body part.
Anatomical surface that is located on the basal side of the body or body part.
Anatomical surface that located on the dorsal side of the body or body part.
Anatomical surface that located on the lateral side of the body or body part.
Anatomical surface that is located on the ventral side of the body or body part.
A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions.
These anatomical sections are applicable to most bilaterally symmetrical animals, but bipedal animals such as humans have more complex usage of these terms. For example, in post-embryonic humans a coronal plane is vertical and a transverse plane is horizontal, but for embryos and quadrupeds a coronal plane is horizontal and a transverse plane is vertical.
Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size.
An axis that extends from the center of organism to one or other side.
Properly, the ML axis is a half axis; practically, its usage is less clumsy and less linguistically biased than "left-right". The terms may still be used relatively to describe locations along the LR axis. The gills are medial to the operculum, but lateral to the heart.
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
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.
Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.
anatomical entity
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
connected anatomical structure
material anatomical entity
A one dimensional, immaterial anatomical entity.
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis.
Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle.
The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis.
A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle.
The cell cycle phase which is the first stage of M phase of mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell.
The cell cycle phase, following prophase, during which chromosomes become aligned on the equatorial plate of the cell as part of a mitotic cell cycle.
The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of a mitotic cell cycle.
The cell cycle phase which follows anaphase during M phase of mitosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts.
The cell cycle phase which is the first stage of prophase I in meiosis, and during which the chromosomes first become visible.
The cell cycle phase which follows leptotene during prophase I of meiosis, and during which each chromosome pairs with its homolog; the two become aligned and crossing over may occur.
The cell cycle phase which follows zygotene during prophase I of meiosis, and during which crossing over occurs between a chromatid in one partner and another chromatid in the homologous chromosome.
The cell cycle phase which follows pachytene during prophase I of meiosis, during which the homologous chromosomes begin to separate and the synaptonemal complex dissolves.
The cell cycle phase which follows diplotene during prophase I of meiosis, the separation of homologous chromosomes is complete and crossing over has occurred.
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.
A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase.
The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring.
developmental process involved in reproduction
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
The cell cycle phase which is the first stage of meiosis I and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell.
The cell cycle phase, following prophase I, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis I.
The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis I.
The cell cycle phase which follows anaphase I of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts.
The cell cycle phase which is the first stage of meiosis II and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell.
The cell cycle phase, following prophase II, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis II.
The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis II.
The cell cycle phase which follows anaphase II of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts.
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 biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
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.
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.
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
transferase activity, transferring phosphorus-containing groups
A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid).
Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.
The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.
One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events.
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
A distinct period or stage in a biological process or cycle.
Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase.
The creation of two or more organelles by division of one organelle.
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.
The cell cycle 'gap' phase which is the interval between the completion of DNA segregation (usually by mitosis or meiosis) and the beginning of DNA synthesis.
The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation (usually by mitosis or meiosis).
The cell cycle phase, following G1, during which DNA synthesis takes place.
Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
Note that this term should not be confused with 'GO:0140013 ; meiotic nuclear division'. 'GO:0051321 ; meiotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140013 meiotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.
The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle.
The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell.
The cell cycle phase which is the first stage of M phase of meiosis and mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell.
The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs.
The cell cycle phase which follows anaphase during M phase of mitosis and meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts.
A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a meiotic cell cycle.
The cell cycle phase which begins after cytokinesis and ends when meiotic prophase begins. Meiotic cells have an interphase after each meiotic division, but only interphase I involves replication of the cell's DNA.
The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs.
The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by meiosis and the beginning of DNA synthesis.
The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by meiosis.
The cell cycle phase, following G1, during which DNA synthesis takes place as part of a meiotic cell cycle.
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation or biogenesis
cellular component organisation or biogenesis at cellular level
cellular component organization or biogenesis at cellular level
cellular component organization or biogenesis
One of the distinct periods or stages into which the meiotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events.
This term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation should be to 'regulation of x/y phase transition' or to a process which occurs during the reported phase (e.g. mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events.
A meiotic cell cycle phase prior to a during which some part of meiosis I nuclear division or the proceeding cytokinesis occurs.
A meiotic cell cycle phase that occurs after meiosis I (the first meiotic nuclear division).
One of the two nuclear divisions that occur as part of the meiotic cell cycle.
A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.
A process that is part of the meiotic cell cycle.
A process that is part of the mitotic cell cycle.
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
based on Oxford English Dictionary
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Melanie Courtot
denotator type
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Barry Smith, Werner Ceusters
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
PERSON: Bjoern Peters
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
centrally registered identifier
PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles.
A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.
Justin Whorton
centrally registered identifier registry
identifier
An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
Mathias Brochhausen
proper name
Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)
A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
dubbing process
naming
identifier creating process
An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things.
code map
code system
codeset
coding system
controlled vocabulary
Code sets might include non-entities/things (e.g. missing thumbs).
Does not imply absence vs. presence of any taxonomy.
Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.
Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).
For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).
For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.
Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.
The information content entities do not denote each other.
code set
planned process
A process that realizes a plan which is the concretization of a plan specification.
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.
A spatial quality inhering in a bearer by virtue of the bearer's placement which is defined by the angle between the bearer and an axis, or the angle between the bearer and another object.
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
A shape quality inhering in a bearer by virtue of the bearer's having three angles.
A shape quality inhering in a bearer by virtue of the bearer's being narrowly triangular, wider at the apex and tapering toward the base.
A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed along the longitudinal or anterior-posterior axis.
A shape that is in the form of a plug, being tube-like and expanded on one end.
A stage of Smed embryonic development, 0 - 2 days post-egg capsule deposition at 20˚C. Zygote and dispersed blastomere cleavage in a yolk syncytium.
A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 3 days post-egg capsule deposition at 20˚C. Sphere formation. A fraction of the blastomeres differentiate into temporary embryonic tissues that provide form and function to the embryo. Undifferentiated blastomeres remain in the embryonic wall.
Depicted by field contains hematoxylin and eosin staining section of a stage 2 embryo. Scale bar = 100um
A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 4 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity.
Depicted by field contains hematoxylin and eosin staining section of a stage 3 embryo. Scale bar = 100um
A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 3 - 5 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation.
Depicted by field contains hematoxylin and eosin staining section of a stage 4 embryo. Scale bar = 100um
A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 5-7 days post-egg capsule deposition at 20˚C. Organogenesis onset. Downregulation of early embryo enriched transcripts and birth of adult lineages within the blastomere population. Early embryonic gut formation continues. Yolk ingestion into the gut cavity.
Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo. Scale bar = 100um
A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 7 - 9 days post-egg capsule deposition at 20˚C. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation.
Depicted by field contains hematoxylin and eosin staining section of a stage 6 embryo. Scale bar = 100um
A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 9 - 11 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility.
Depicted by field contains hematoxylin and eosin staining section of a stage 7 embryo. Scale bar = 100um
A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 13 - 15 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Hatching.
Depicted by field contains hematoxylin and eosin staining section of a stage 8 embryo. Scale bar = 100um
A heterogeneous subpopulation of neoblasts with enriched expression of SoxP-1 and SoxP-2 thought to contain both pluripotent stem cells and tissue-specific progenitors.
Neoblasts and post-mitotic, differentiating daughters coexpressing POU2-3, six1/2-2, Sal1, Eya and Osr,required for maintenance and regeneration of protonephridial cell types.
Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system.
Musculature surrounding internal organs of the body.
Image is an electron micrograph depicting the visceral musculature (arrowheads) that lies beneath the gut. The gut is identifiable by the collection of darkly stained lipid droplets in the top right corner and the white of the lumen at the top of the image. Scale bar is 10um
An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s).
Image is an electron micrograph of the dorsal side of the animal where there is a transition from nonciliated epidermal cells to ciliated ones. On the left side of the image are the ciliated cells and on the right are the nonciliated. A few nonciliated have been marked with arrowheads. Scale bar is 10um.
A plicate and protrusible organ that is the sole point of entry and exit for the Triclad gut. It contains epithelial, muscular, secretory and neuronal cell types.
Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain.
Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells.
Progenitor neoblasts implicated in the maintenance and regeneration of muscle fibers.
Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct.
http://purl.obolibrary.org/obo/Depicted by field contains a whole-mount acetylated tubulin (AcTub) staining. Scale bars_ 500 um. Inset to right shows depth-coded projection of AcTub staining. Superficial structures are in blue and deeper structures are in red. Scale bars: 50 um
Organisms sharing a specified genotype or karyotype.
An innervated, muscular pump that ingests yolk cells into the gut cavity. The embryonic pharynx is an extraembryonic tissue that forms during Stage 2, functions during Stages 3-5, and degenerates during Stages 6-7.
Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo that zooms in on the embryonic pharynx.
Asexual animal strains that reproduce solely through fission followed by whole body regeneration. Asexual Smed are stable diploids that harbor a chromosome translocation, making them karyotypically distinct from sexual Smed.
Image is an scanning electron micrograph of the dorsal side of an entire animal. This is an adult asexual Schmidtea mediterranea. Anterior is to the right and posterior is to the left. Scale bar is 500um.
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organisms, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
The planarian triclad gut contains a central anterior gut branch connected to two posterior gut branches arranged around the pharynx. Secondary gut branches extend laterally from the primary gut branches, while tertiary gut branches extend from the secondary branches. Food and waste enter and exit the gut through the pharynx.
Strains of cross-fertilizing hemaphrodites that reproduce sexually and do not undergo fission. After mating, each parent lays an egg capsule containing one or more embryos. Sexual Smed are stable diploids.
Depicted by field contains light micrscope image of asexual and sexual biotypes of Schmidtea meditteranea with their respective karyotypes. Note that the asexual bioptype has a chromosome inversion compared to the sexual.
Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts.
A single cell layer of extraembryonic, post-mitotic ectodermal cells bounding the embryo. The primitive ectoderm forms during Stage 2 and is thought to degenerate as the definitive epidermis forms during Stages 5-7.
The median line/ plane of bilateral symmetry along the anteroposterior axis.
Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup.
The median line/plane of bilateral symmetry along the anteroposterior axis on the dorsal surface of the animal.
Illustration of the dorsal midline (in green).
Mitotically active zeta neoblasts and their post-mitotic descendants which undergo progressive differentiation and outward directed movement through the mesenchyme prior to incorporation into the epidermis, where terminal differentiation occurs.
A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal.
At present, this definition does not apply to epithelial structures other than the dorsal and ventral epidermis (i.e., the pharyngeal epithelium).
Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells.
Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The eyes are indicated by arrows. Scale bar = 250um
we will move forward using "tissue" instead. We have not listed anything as a regenerating or developing tissue, so this seems unnecessary
The median line/ plane of bilateral symmetry along the anteroposterior axis on the ventral surface of the animal.
Illustration of the ventral midline (in green).
An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut.
this term is not needed. All previous children of this term (Stage 1, Sage 2, etc) are now children of GO life cycle stage or zygote stage
obsolete Schmidtea mediterranea developmental stage
Stage 3-5 embryo hemisphere centered around the pole opposite the embryonic pharynx.
The single, central gut branch of the triclad gut anterior to the pharynx.
Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. Anterior primary gut branch indicated by arrows. Scale bar = 250um
Region along the edge of the animal where the dorsal and ventral surfaces meet.
dorsal/ventral compartment boundary of whole organism
dorsal ventral margin of the whole animal
The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head.
Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema.
Image is an electron micrograph depicting the body wall musculature beneath the dorsal epidermis. The first layer of muscle cells beneath the basal lamina (BL), circular muscle, have been colored and labeled with arrowheads. Circular muscle = magenta; longitudinal muscle = green; diagonal muscle = red. Scale bar is 2um.
Pluripotent piwi-1+ stem cells that self-renew, form expanding colonies and produce differentiating daughters that contribute to multiple organ systems. cNeoblasts are predicted to be broadly distributed across the anteroposterior axis of the adult worm.
Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis.
Image is an electron micrograph depicting a collecting duct (arrowheads) passing through the basal lamina (BL). Dorsal is up and the scale bar is 5 um.
Body wall muscle fibers arrayed diagonally along the anteroposterior axis.
Image is an electron micrograph depicting the body wall musculature beneath the dorsal epidermis. The third layer of cells beneath the basement membrane, diagonal muscle cells, have been colored and labeled with arrowheads. Circular muscle = magenta; longitudinal muscle = green; diagonal muscle = red. Scale bar is 2um.
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
removing all processes. may bring back if PLANA expanded to cover processes.
Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells.
Depicted by field contains a diagram representing the protonephrida unit (top) as well as a 3D rendering of confocal data depicting the same. In the diagram, terminal flame cells and their corresponding cilia are in blues, the proximal tubule is in reds, the distal tubule is in greens while thecollecting duct is in purple. In the 3D rendering below the cilia (AcTub) are in blue, portions of the proximal tubule (slc6a-13) are in red while the distal tubule (slc6a-12) is in green.
Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe.
Image is an electron micrograph depicting the dorsal epidermis (arrowheads). Also visible in this micrograph, immediately deep to the epidermis is the basal lamina and beneath that is a photoreceptor. Scale bar is 10 um.
Ciliated epithelial cells along the dorsal midline.
Image is an electron micrograph showing the dorsal side of the head of an adult worm. Arrowheads mark where the ciliated cells of the dorsal stripe can be seen. Anterior is up and scale bar is 100um.
Turbellarian (freshwater flatworm) embryos that undergo a modified form of cleavage due to separation of oocyte and yolk. Yolk is not contained within oocytes, and is produced by somatic vitellogenic gland cells.
A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the embryonic pharynx and primitive gut cells. Embryonic gut cells, likely produced from blastomeres, form a phagocytic tissue layer surrounding the inner gut cavity during Stages 4-6. It is not known whether the embryonic gut is temporary embryonic tissue or a definitive tissue. For convenience, the embryonic gut is currently designated as an extraembryonic structure because cell type specific markers for the embryonic gut do not stain the definitive gut in hatchlings or adult animals.
Dispersed, phagocytic gut cells that appear during Stage 4 and ultimately generate a honeycomb-like lattice surrounding the central gut cavity in Stage 5 embryos. Early embryonic gut cell specific transcripts are expressed from Stage 4-6, and are downregulated during Stage 7.
The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos.
Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo with anatomical feature noted with black indicators.
Image is an electron micrograph depicting the enteric musculature (arrowheads) surrounding the gut, which extends across the top of the image. These cells are very small compared to the layer of medial muscle underneath them. Scale bar is 1um.
Attachment between the triclad gut and the proximal end of the pharynx.
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
Terminal structure of protonephridia unit; consists of flame cells.
Image is an electron micrograph depicting a flame cell (outlined), which is a part of the flame bulb. "N" marks this cell's nucleus and the cilia are noted by an arrowhead. Scale bar is 1um.
Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the filtration weir‚ or filtration diaphragm, which consists of closely apposed strands of cytoplasm surrounding a central cilia bundle, and by numerous microvilli between weir and cilia. Positive for acetyated tubulin.
The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle.
Secretory cells that release digestive enzymes into the lumen of the intestine.
Image is an electron micrograph showing part of the gastrodermis. A goblet cell, a type of gastrodermal cell is labeled with arrowheads. Note the large, dark mucus granules contained in the cell body. The lumen of the gut can be seen on the right side of the image and has been labeled with "L." Scale bar is 1 um.
Cavity encompassed by the embryonic digestive tract, prior to formation of the branched defintive gut.
Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole.
Absorptive digestive cells that engulf food particles for intracellular digestion.
Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers.Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole.
Image is an electron micrograph depicting the body wall musculature beneath the dorsal epidermis. The longitudinal muscle cells (arrowheads) sit behind both the circular muscle and the diagonal muscle. Circular muscle = magenta; longitudinal muscle = green; diagonal muscle = red. Scale bar is 2um.
The sole point of entry and exit for the Triclad planarian flatworm gut. The mouth is connected to the pharyngeal pouch to allow for exit and re-entry of the pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells.
Image is an electron micrograph of the mouth (arrowheads), which is located on the ventral side of the animal. Note the heavily ciliated pharynx that is peeking out. Scale bar is 10um.
A female germ cell that has entered meiosis.
A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons.
Stage 3-5 embryo hemisphere centered around the embryonic pharynx.
Illustration of the oral hemispshere (in green).
Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers.
Muscles that are present through the mesenchyme, inclusing dorsal-ventral muscles, intestinal muscles and pharynx muscles.
Image is an electron micrograph of the parenchyma. Three muscle cells have been notated with an arrowhead. Scale bar is 2 um.
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
An epithelial structure housing the pharynx, connected to the esophagus and mouth.
racing stripe is now a synonym of PLANA:0000055 dorsal stripe
The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch.
Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The posterior primary gut branch is indicated by arrows. Scale bar = 250um
A phagocytic cell closely associated with the embryonic pharynx.
Ciliated epithelial cells form tubules, generating coiled, branching units terminating in flame bulbs. Tubules are formed via intercellular junctions between two epithelial cells. Proximal tubules are connected to non-ciliated distal tubules within the parenchyma.
Image is an electron micrograph depicting a proximal tubule (arrowheads) of the protonephridia structure. Note the cilia and the characteristic way the cell membrane connects with other proximal tubule epithelial cells. Scale bar is 2um.
The renal system is an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.
Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge.
Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The secondary gut branch is indicated by arrows. Scale bar = 250um
A mature male germ cell that develops from a spermatid.
Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2.
Gut branches originating from and connected to the secondary gut branches.
Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The tertiary gut branch indicated is by arrows. Scale bar = 250um
Ovo+ neoblasts and post-mitotic eye progenitors that simultaneously migrate and differentiate into photoreceptor neurons and non-neuronal pigment cup cells comprising the optic cup.
Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells
The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO].
Diploid cell resulting from the fusion of male and female gametes at fertilization. [The_Dictionary_of_Cell_and_Molecular_Biology:Third_Edition ].
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where the apical part is directed towards the lumen and the basal part to the basal lamina.
A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
Image is an electron micrograph depicting a muscle cell (arrowheads) cut in a transverse orientation with respect to the fiber length. Note the texture of the cytoplasm that comes from the organization of myofibrils. Scale bar is 1um.
A subdivision of an anatomical compartment.
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
Straight or curved rod-like structures within the epidermal cells, oriented with long axis at right angles to the epidermal surface, that are discharged into mucous secretions.
Image is an electron micrograph depicting the epidermis. Inside of the epidermal cells, rhabdites (arrowheads) can be seen in various stages of expansion. Scale bar is 5 um.
A cell that specializes in controlled release of one or more substances.
Image is an electron micrograph of a viscid gland cell (arrowheads) passing across the basal lamina (BL). This cell secretes a specialized type of mucus. The secretory duct transports mucus to the outside of the animal, through the secretory pore. Ventral is down and scale bar is 5um.
An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo.
extra layer of complexity not needed upon further examination
obsolete anatomical compartment subdivision feature
foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the pharynx.
Ciliated epithelial cells that assemble into proximal tubules.
Image is an electron micrograph of a proximal tubule epithelial cell (arrowheads). N = nucleus. Note the way the cell is wrapped around the cilia, creating the lumen in the middle. Scale bar is 2um.
obsolete Schmidtea mediterranea developmental term
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
Nonciliated epithelial cells that assemble into protonephridial distal tubules.
Image is an electron micrograph showing a cell (outlined) that is part of the collecting duct. Note how much more stained this cell is, compared to the surrounding ones. Also note the visible lumen of the collecting duct inside the cell where it is white and wrinkled. Scale bar is 1um.
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.
Anatomical structure that is part of an embryo.
Nonciliated epithelial cells that assemble into collecting ducts.
A post-mitotic, terminally differentiated cell type found in planarian embryos, juveniles and/or adult animals.
A cycling neoblast and/or post-mitotic cell that is primed or irreversibly committed to a tissue-specific differentation program
A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
A mature sexual reproductive cell having a single set of unpaired chromosomes.
The sensory system subserving the sense of vision.
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
Anatomical system that has as its parts the organs concerned with reproduction.
Ciliated epithelial cells that assemble into the oviduct.
Ciliated epithelial cells comprising the sperm ducts.
piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers.
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue.
A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers.
Cells expressing nanos that are located ventrally in the location that the ovaries form. Primordial germ cells are present in both asexual adults and sexual hermaphrodites. This term may be redundant with oogonial stem cell.
Anatomical structure that is an individual member of Schmidtea mediterranea or any other flatworm of the class Turbellaria.
The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass).
PROG-2-5 positive granules that range in size from 0.5um to 1um present in epithelia and epithelia progenitor cells. These are distinct from rhabdites.
Image is an immunoelectron micrograph depicting hyman vesicles in the apical side of an epidermal cell. Scale bar is 1um.
Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus.
Illustration of the anterior region of the whole animal (in green).
Three dimensional compartment along the dorsoventral axis that is above the anteroposterior axis, containing the eyes.
Illustration of the dorsal region of the whole animal (in green).
Three dimensional compartment along the anteroposterior axis that is closer to the tail rather than the head, from the anterior boundary of the pharyngeal pouch to the tip of the tail.
posterior compartment of the whole animal
Illustration of the posterior compartement of the whole animal (in green).
Compartment along the dorsoventral axis that is below the anteroposterior axis.
Illustration of the ventral region of the whole animal (in green).
The passageway connecting the genital atrium to the copulatory bursa. Part of the copulatory apparatus. During mating, sperm from a partner is deposited into the bursal canal, where it collects in the copulatory bursa before travelling up the oviducts to the tuba.
The gonopore, a component of the copulatory apparatus, is an opening located on the ventral side of the animal posterior to the pharynx. The gonopore is the sole point of exit and entry for the reproductive system, allowing from reciprocal exchange of sperm during copulation and egg capsule laying.
A gonad containing female germline stem cells which fuel oocyte production. Two ovaries are located ventally, underneath the body wall musculature, immediately posterior to the cephalic ganglia (brain) and adjacent to the ventral nerve cords. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuel formation of the ovaries during juvenile development.
Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium.
A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal.
A network of tubes that transport sperm from the testes to the seminal vesicles. Tubes connect each testis to ducts that run along the ventral nerve cords. The ducts bifurcate immediately posterior to the pharynx, where they connect to the seminal vesicles.
A gonad containing male germline stem cells which fuel sperm production. Testes are located dorsolaterally, and are excluded from the head. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuels formation of testes during juvenile development and regeneration.
obsolete developing anatomical structure
Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2.
A postnatal stage of Smed development that initiates with hatching and proceeds until sexual maturity is reached. Reproductive structures develop during the juvenile stage.
Products of the reproductive system include gametes, zygotes, yolk cells and egg capsules.
A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos.Egg capsules are anchored to a substrate via a stalk.
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
Cells coexpressing piwi-1 and nanos that are required for male gonad formation. Primordial germ cells are present in both asexual adults and sexual hermaphrodites. This term may be redundant with spermatogonial stem cell.
gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm.
An euploid male germ cell of an early stage of spermatogenesis. In planaria, the gh4+ stem cell daughter exiting the niche undergoes three rounds of transit amplifying division with incomplete cytokinesis prior to transitioning to terminal differentiation.
A tektin-1+ male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids.
A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa.
A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes.
Glands surrounding the genital atrium that are required for production of the proteinaceous egg capsule shell and stalk.
1. A gamete (as an egg or sperm cell) or one of its antecedent cells. 2. A mature male or female germ cell usually possessing a haploid chromosome set and capable of initiating formation of a new diploid individual by fusion with a gamete of the opposite sex.
A male germ cell is a germ cell that supports male gamete production.
Female germ cell is a germ cell that supports female gamete production.
A sperm storage organ located immediately posterior to the ovary, at the anterior end of the oviduct. Oocytes exiting the ovary are fertilized in the tuba as they enter the oviduct.
Glands surrounding the oviducts which produce yolk cells. Yolk cells deposited into the oviducts travel to the genital atrium where they are packaged, along with one or more zygotes, into developing egg capsules.
Accessory reproductive structures involved in copulation, egg capsule development and laying.
An organ that receives and stores sperm from mating partners.
Glandular pouches adjoining the sperm ducts which produce seminal fluid.
A cyst of 8 interconnected spermatocytes undergoes meiosis, producing 32 haploid round spermatids. Round spermatids express protein kinase A, andundergo morphogenesis to produce mature sperm.
Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm.
An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes.
Any collection of muscles that is part of a body wall [Automatically generated definition].
http://purl.obolibrary.org/obo/Image is an electron micrograph of the dorsal epidermis, basal lamina (BL), and underlying body wall musculature. Three types of muscle cells have been color coded form superficial to deep_ Circular muscle = magenta; longitudinal muscle = green; diagonal muscle = red. Scale bar is 2um.
Pharynx muscle fibers running anteroposterior (proximal to distal).
Image is an electron micrograph of a transverse section through the pharynx. The inner longitudinal muscle (arrowheads) is immediately deep to the inner circular muscle of the pharynx. Magenta = circular; green = longitudinal; red = radial. Scale bar is 2 um.
Anatomical space enclosed by the pharynx inner epithelium.
Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. Cavity of pharynx is indicated by arrows. Scale bar = 250um
An anatomical space that is surrounded by a digestive tract.
Depicted by field contains hematoxylin and eosin staining on a coronal section of a asexual adult animal. The lumen of the digestive tract is indicated by arrows. Scale bar = 250um
The orifice that connects the mouth to the exterior of the body.
Anatomical space between the pharynx and the epithelial cells comprising parapharyngeal pouch.
Depicted by field contains hematoxylin and eosin stainingcoronal section section of a asexual adult animal. Parapharyngeal pouch cavity is indicated by arrows. Scale bar = 250um
The apical surface of the single layered epidermis that is in contact with the environment.
Electron micrograph of the dorsal epidermis in a transverse plane from an asexual adult animal. The apical epidermis surface is noted with magenta arrows. Scale bar is 5um.
The basal surface of the epidermis in direct contact with the basal lamina.
Electron micrograph of the dorsal epidermis in a transverse plane. The basal epidermis surface is noted with magenta arrows. Scale bar is 5um.
The surface of the gastrodermis in contact with the gut lumen.
The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the anterior primary gut branch. The lumen gut surface is marked by black arrows. Scale bar is 200um.
The epithelial surface lining the interior of the pharynx, facing the lumen.
Image is an electron micrograph of a transverse section through the pharynx. An epidermal cell, a part of the inner epithelial layer, has been marked with arrowheads. Immediately deep to the inner epithelial layer of the pharynx is musculature that has been colored. Magenta = circular; blue = longitudinal; yellow = radial. Scale bar is 5 um.
Epithelial surface covering the outside of the pharynx.
Image is an electron micrograph of a transverse section through the pharynx. The pharynx pouch cavity is at the top. The outer epithelium has been labeled with arrowheads. Immediately deep to the outer epithelial layer of the pharynx is musculature that has been colored. Red = circular; blue = longitudinal. Scale bar is 2 um.
The surface of the parapharyngeal pouch facing the pharynx.
The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the pharynx and surrounding tissues. Anterior is up. The parapharyngeal pouch surface is marked by black arrows. Scale bar is 200um.
Anatomical structure which is a subdivision of a whole adult or juvenile organism, consisting of components of multiple anatomical systems.
The head is the anterior-most division of the body [GO]. A three dimensional compartment bounded by the anterior margin or the head and the posterior boundary of the cephalic ganglia (brain).
Depicted by field contains diagram representation of body region.
Region of the juvenile or adult animal between the posterior end of the cephalic ganglia and the anterior end of the pharynx.
Region of the animal lateral to and surrounding the pharynx.
Trunk is a synonym here because the parapharyngeal region is always contained in a trunk fragment. However, a trunk fragment may also contain some neck and some tail.
Caudal region, beginning at the mouth and ending at posterior pole.
Medial region of the tail; the parenchymal space between the posterior primary gut branches.
Anatomical structure which is a subdivision of a whole developing/ embryonic organism, consisting of components of multiple anatomical systems.
obsolete definitive anatomical structure
An anatomical structure that has more than one cell as a part.
Total musculature of the planarian body.
A heterogeneous population of pluripotent, somatic adult stem cells and lineage primed progenitors that are required for maintenance and regeneration of all cell types in planaria, including the germline.
Image is an electron micrograph showing a neoblast undergoing mitotic telophase (outlined). The condensed chromatin is visible toward the left side of the cell and has been outlined by the nuclear envelope. Scale bar is 1um.
Anatomical structure that performs a specific function or group of functions.
obsolete regenerating anatomical structure
A decussation of the diencephalon where the fibers of the optic nerve cross
A bundle of nerve fibers connecting the two cephalic ganglia.
Nerve branches that extend from the lateral side of each cephalic ganglia lobe. Each lobe has nine lateral branches which terminate in sensory organs. Evidence suggests they play a role in chemosensation.
A cell that performs a sensory function.
Neurons that express choline acetyltransferase.
Neurons that express glutamine decarboxylase.
Plexus of nerves located in the pharynx comprised of inner and outer wall rings.
Plexus of nerves located just between the epidermis and the body wall musculature.
Plexus of nerves that innervate the body wall musculature.
A thin net of single nerve fibers located around the gut.
A cluster of neurites that is part of a nervous system and forms a network of dendrites and axons where synapses are present and in which neuronal somata do not occur.
Heavily ciliated epidermal cells covering the outer surface of the pharynx shaft. These are "insunk" epidermal cells in which the nuclei reside behind the layers of longitudinal and circumferential muscles and the epithelial cell body sends out a ciliated projection to the surface to cover and encase the shaft.
Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles.
Image is an electron micrograph of a transverse section through the pharynx. The pharynx pouch cavity is at the top. The outer circular muscle (arrowheads) is immediately deep to the outer longitudinal muscle of the pharynx. Red = circular; blue = longitudinal. Scale bar is 2 um.
Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers.
Image is an electron micrograph of a transverse section through the pharynx. The pharynx lumen it to the left. The inner circular muscle (arrowheads) is immediately deep to the inner epithelial layer of the pharynx. Magenta = circular; green = longitudinal; red = radial. Scale bar is 2 um.
Pharynx muscle fibers running anteroposterior which lie beneath both the inner circular muscle fibers and the apical, ciliated portion of the epithium lining the lumenal surface.
pharyngeal inner longitudinal muscle cell
pharyngeal inner longitudinal muscle fiber
Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium.
pharyngeal outer longitudinal muscle cell
pharyngeal outer longitudinal muscle fiber
Image is an electron micrograph of a transverse section through the pharynx. The pharynx pouch cavity is at the top. The outer longitudinal muscle (arrowheads) is immediately deep to the outer epithelium of the pharynx. Red = circular; blue = longitudinal. Scale bar is 2 um.
Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts.
Image is an electron micrograph of a transverse section through the pharynx. Immediately deep to the inner epithelial layer of the pharynx is musculature that has been colored. Magenta = circular; blue = longitudinal; yellow = radial. Scale bar is 5 um.
The total musculature within the pharynx.
Ring of the pharynx nerve plexus that is proximal to the lumen.
Image is an electron micrograph of a transverse section through the pharynx. Neuronal cells/tissue are marked with arrowheads. The inner nerve plexus is immediately deep to the inner longitudinal musculature. Magenta = circular; blue = longitudinal; yellow = radial. Scale bar is 5 um.
Ring of the pharynx nerve plexus that is proximal to the exterior surface.
Image is an electron micrograph of a transverse section through the pharynx.The pharynx pouch cavity is at the top. The outer nerve plexus (arrowheads) is immediately deep to the outer circular muscle of the pharynx. Red = circular; blue = longitudinal. Scale bar is 2 um.
Neurons that express the neurotransmitter serotonin.
A neuron that expresses the neurotransmitter dopamine.
Neurons that express the biogenic amine octopamine.
Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus.
Specialized insunk epithelial cells located in the mesenchyme that participate in mucus secretion. They are characterized by elongated cell bodies with long cytoplasmic projections that terminate between, or penetrate directly throughepithelial cells and form a secretory pore at the surface.
Image is an electron micrograph depicting a portion of a gland cell (arrowheads). Note the nucleus surrounded by endoplasmic reticulum and the dark mucus granules that fill the long cytoplasmic projection. Scale bar is 2 um.
The opening by which the gland cells secrete mucus to the exterior of the animal.
Image is an electron micrograph of a viscid gland cell passing across the basal lamina (BL). This cell secretes a specialized type of mucus. The secretory duct transports mucus to the outside of the animal, through the secretory pore (arrowhead). Ventral is down and scale bar is 5um.
One of two distinct histochemical classes of gland cells, these can be found throughout the body but primarily form clusters of subepidermal marginal adhesive glands along the dorsoventral border of the animal.
One of two distinct histochemical classes of gland cells, these are found near the ventral mesenchyme, the pharynx and in the dorsal region of the head. May also be called cyanophilic gland cells.
Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA].
we will just use commissural neuron moving forward
any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain
A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise.
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
PLANA:0000500 child terms moved to cellular component (GO:0005575) term and we think better serves interoperability and searchability
A prolongation or process extending from a cell.
A cell projection supported by an assembly of actin filaments.
inadvertently duplicated, going with ID that is best annotated
Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments.
Image is an electron micrograph depicting a portion of the outer epithelium of the pharynx. Microvilli on the left hand of the image have been labeled with arrowheads. To the right of the microvilli are larger cilia. Note the difference in width and length. Scale bar is 2 um.
Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions.
A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
Image is an electron micrograph of two outer epidermal cells of the pharynx. There is an adherens junction (arrowheads) between two cells. Scale bar is 0.5 um.
A cell junction that forms a connection between two or more cells in a multicellular organism; this excludes direct cytoplasmic junctions such as ring canals.
The attachment of one cell to another cell via adhesion molecules.
Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures
Image is an electron micrograph depicting a portion of a cell. Outside of the nucleus (N), the arrowheads mark areas of cytoplasm, which appears as a mottled gray filling. Scale bar is 0.5um.
Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell.
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.
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes
intracellular non-membrane-bounded organelle
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes.
Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound 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.
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
Organized structure of distinctive morphology and function, 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-bounded organelle
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
Image is an electron micrograph showing golgi bodies (arrowheads). Many secretory vesicles can be seen, as well as rough endoplasmic reticulum on the right side of the micrograph. Scale bar is 0.2 um.
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.
Image is an electron micrograph of several nuclei (N) close to and a part of the dorsal epidermis. Note how the epidermal cell nuclei appear more wrinkled and have stained differently than the cells lying beneath the basal lamina (BL). Scale bar is 2 um.
A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space.
Image is an electron micrograph depicting two golgi bodies and accompanying secratory vesicles. A few have been labeled with arrowheads. Scale bar is 200 nm.
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.
Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
Image is an electron micrograph depicting a nucleus. Inside, the nucleolus has been labeled with arrowheads. Scale bar is 1 um.
The ordered and organized complex of DNA, protein (histones), and sometimes RNA, that forms the chromosome.
Image is an electron micrograph showing a mitotic cell with condensed chromatin (arrowhead). Scale bar is 1um.
A compact and highly condensed form of chromatin.
A dispersed and relatively uncompacted form of chromatin.
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ https://www.worldcat.org/search?q=bn%3A0198506732 ]
Image is an electron micrograph depicting ribosomes (arrowheads) in two separate cells. They can be seen as small dots in the cytoplasm and associating with the rough endoplasmic reticulum in the cell in the bottom of the micrograph. Scale bar is 200 nm.
A group of axons linking two or more neuropils and having a common origin, termination
A cell whose function is determined by its response to an electric signal.
A cell that initiates an electrical signal and passes that signal to another cell.
An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
A neuron which conveys sensory information centrally from the periphery.
A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.
A neuron that has an axon which crosses the midline.
A neuron which sends impulses peripherally to activate muscles or secretory cells.
A motor neuron that is capable of directly inducing muscle contraction.
In vertebrates, all motor neurons are excitatory, but various types of inhibitory motor neurons exist in invertebrates.
Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.
Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement.
Neuronal cells which synthesize, store and release neurohormones.
Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides.
Neuron with one neurite that extends from the cell body.
Neuron with an axon and two or more dendrites.
Cells that are in close proximity to neurons.
neuron associated cell (sensu Nematoda and Protostomia)
Any neuron that is part of a central nervous system.
Any neuron that is part of a peripheral nervous system.
A neruon whose cell body is within an autonomic ganglion.
A neruon contained within with the enteric nervous system (gastrodermal plexus).
Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue.
this class represents a continuous sheet of basal lamina which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal lamina' represents a portion of substance on the scale of a single cell.
Image is an electron micrograph showing the dorsal epidermis. Epidermal cells can be seen above (superfical to) the basal lamina (BL) and the body wall musculature can be seen below. Scale bar is 2um.
Rhabdites that are located basally to the epidermis, in the mesenchyme. In Smed these are present in cells likely on their way to becoming part of the mature epidermis.
http://purl.obolibrary.org/obo/part_of 'dorsal epidermis progenitor cell' (PLANA_0003501), 'ventral epidermis progenitor cell' (PLANA:0003503)because EM data we can see immature adenal rhbadites in cells just underneath the basal lamina dorsally and ventrally.
Image is an electron micrograph showing the dorsal epidermis and underlying basal lamina at the top. Adenal rhabdites are marked with "Rh" and can be seen in cells underneath or medial to the basal lamina. Scale bar is 2um.
A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
Finger-like processes at the terminal pore of adhesive gland cells around the marginal adhesive zone. They protrude past the epidermis and are longer microvilli, and shorter than cilia.
Image is an electron micrograph of the outside of an animal at the marginal adhesive zone. The adhesive papilla (arrowheads) are colored in blue and surround each secretory pore (yellow). Mucus and cilia are both green. Scale bar is 2um.
A wound resulting in two or more separate tissue fragments.
A branch of the triclad gut located anterior to the pharynx.
The anterior-medial region of the head margin.
Illustration of the anterior tip in green.
A sense organ located along the dorsolateral head margin. The auricular groove is highly innervtated by ciliated sensory neurons, and has an altered epidermis devoid of rhabdites and gland cells.
Image is a scanning electron micrograph of the dorsal side of the head of an adult worm. The auricles (arrowheads) appear as a short groove on each side of the head. Anteror is down and scale bar is 100um.
The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
Image is an electron micrograph showing a cross section of an axon (arrowheads), right underneath or medial to the dorsal body wall musculature. Dorsal is up and the scale bar is 2um.
The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
Image is an electron micrograph of several cilia where a cross-section reveals the axoneme with a 9+2 arrangement of microtubles. Arrowheads denote microtubules. Scale bar is 100nm.
A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport.
Image is an electron micrograph showing a cross-section of a cilium, revealing the basal body (arrowhead). Scale bar is 0.5um.
Region of the cephalic ganglia innervated by the optic nerve (posterior-projecting photoreceptor neuron fasiculated axons).
An enlarged portion of the seminal vesicle, comprised of secretory epithelial cells, that connects to the ejaculatory duct within the penis papilla.
Irradiation-sensitive, mesenchymal cells that are absent from the head region anterior to the eyes and the pharynx. The Category 1 designation encompasses the neoblast population.
The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
One of two bilaterally symmetric structures comprising the planarian brain.
A central nervous system neuron located within the planarian brain.
Amputation carried out by application of chemicals.
Amputation of the phaynx, including the esophagus, by treatment with Sodium Azide.
Any neuron that capable of some detection of chemical stimulus involved in sensory perception.
A membrane-less, cytoplasmic ribonucleoprotein granule present in neoblasts and germ cells implicated in post-transcriptional regulation. The RNA helicase DHH1/RCK, Tudor, SmB, methylated substrates of PRMT5, PIWI-3 and Germinal Histone H4 localize to chromatoid bodies in neoblasts.
Image is an electron micrograph showing a chromatoid body (arrowhead) next to the cell's nucleus (N) which takes up the bottom left corner. Scale bar is 200nm.
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
Image is an electron micrograph showing a mitotic cell. An arrowhead marks the long arm of a chromosome. Scale bar is 1um.
Under the microscope chromosomes appear as thin, thread-like structures. They all have a short arm and long arm separated by a primary constriction called the centromere. The short arm is designated as p and the long arm as q.
Epithelium bearing vibratile cilia on the free surface.
Image is an electron micrograph of an outer epidermal cell of the pharynx. These cells are heavily ciliated. Scale bar is 2um.
A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. The longitudinal array of microtubules are almost always in a 9+2 array with 2 microtubles in the central cilia bundle and 9 sets of doublet microtubules around the perimeter. The exception to this arrangement is spermatazoa flagella, which have a 9+1 array in planarians.
Image is an electron micrograph depicting several cilia (arrowheads) emerging from a ventral epidermis cell. Scale bar is 0.5um.
A bundle of nerve fibers crossing from one side to the other side of the brain or spinal cord.
A wound or cleft resulted from tissue separation into parts or laid open or penetrated with a sharp edge or instrument.
A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conduct nerve impulses towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
A muscle cell that runs in the transverse plane that connects the dorsal and ventral sides of the animal.
Image is an electron micrograph depicting multiple dorsal-ventral muscle cells (arrowheads). The ventral epidermis is at the bottom of this image. Scale bar is 10um.
A premeiotic female germ cell (i.e., a diploid female germline stem cell or transit amplifying oogonial cell).
A premeiotic male germ cell (i.e., a spermatogonial stem cell or transit amplifying spermatogonial cell).
A cryptic digestive cavity comprised of phagocytic embryonic gut cells.
An epithelial cell of the integument (the outer layer of an organism).
Image is an electron micrograph depicting the dorsal epidermis. A single cell has been labeled with arrowheads. Immediately deep to the epidermis is the basal lamina, labeled with "BL." Scale bar is 2um.
Rhabdites located within epidermal cells.
http://purl.obolibrary.org/obo/part of 'dorsal epidermal cell' (PLANA_0003105) and 'ventral epidermal cell' (PLANA:0003101) added because we see rhabdites in both in EM data
Image is an electron micrograph depicting the epidermis. Rhabdites (arrowheads) can be seen in various stages of expansion inside of the epidermal cells. Scale bar is 5 um.
The lipid bilayer surrounding the endoplasmic reticulum.
Image is an electron micrograph depicting (rough) endoplasmic reticulum adjacent tp the nucleus (N). The arrowheads mark the ER membrane. Note the ribosomes (small dots) that can be seen both in the cytoplasm and lining the ER membrane. Scale bar is 0.2um.
The black pigment that gives non-neuronal pigment cells of the optic cup their characteristic color.
A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids.
Image is an electron micrograph showing a cell that is part of the collecting duct. An arrowhead marks the nucleus of this cell. Note the visible lumen of the collecting duct extending out and passing through the basal lamina. This cell is involved in excretion. Scale bar is 2 um.
A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues.
Image is an electron micrograph showing the extracellular matrix (arrowheads) between two cells. Scale bar is 0.2um.
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
A form of asexual reproduction resulting in self-amputation of posterior tissue, generating an anterior fragment and a fission fragment.
Planarian undulipodia consisting of spermatazoa cell posterior protrusions. Planarian spermatozoa contain two flagella and are composed of 9 + 1 axonemal microtubule arrangements in their flagella (markedly different from the 9 + 2 structures generally observed in sperm of other animals).
A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins.
A chamber where egg capsules are formed. One or more zygotes and yolk cells produced by the vitelline glands collect in the genital atrium; glands surrounding the genital atrium produce the egg capsule shell.
A clonally-related group of interconnected spermatogonial or oogonial cells, enveloped by somatic gonadal cells.
Stem cell that is the precursor of gametes.
Cytoplasmic bead-like structures of animal cells, visible by electron microscope. Each granule is a functional unit with the biosynthesis and catabolism of glycogen being catalyzed by enzymes bound to the granule surface.
Image is an electron micrograph depicting glycogen granules (arrowheads) within the cytoplasm of a cell. Scale bar is 200 nm.
A surgical cut that breaches the epidermis, made with a defined edge.
Epithelial cells lining the inside of the pharynx. In Smed, distally located cells are heavily ciliated.
Image is an electron micrograph of a transverse section through the pharynx. The phayrnx lumen is to the bottom left. An epidermal cell, a part of the inner epithelial layer, has been marked with arrowheads. Immediately deep to the inner epithelial layer of the pharynx is musculature that has been colored. Magenta = circular; blue = longitudinal; yellow = radial. Scale bar is 5 um.
Gland or secretory cells sandwiched between muscle and epidermal layers in the pharynx.
Image is an electron micrograph depicting a transverse section through the pharynx. Arrowheads label the inner zone of gland cells. They can be identified by the mucus granules the cell body is filled with. Scale bar is 5um.
A cell junction that forms a connection between two or more cells in a multicellular organism.
An amputation performed with a transverse, oblique or longitudinal cut.
A breach of the epidermis and optionally down into other structures though an insult with a knife or other instrument, such that the movement includes the z direction and one or more of the x y direction.
An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
Image is an electron micrograph depicting two lipid droplets (arrowheads) within two different cells. Note the mostly round shape of the droplets. Often, mitochondria can be seen clumped around lipids. Scale bar is 1um.
The cavity or channel within a tube or tubular organ such as a blood vessel or the intestine.
Zone present along the lateral dorsoventral boundary that sits just underneath the animal, in contact with substrates. It is comprised of bunches of adhesion gland cells whose terminal pores form pore rosettes through the dorsal ventral boundary epidermis.This region of is devoid of rhabdites.
Image is an electron micrograph depicting the lateral dorsoventral boundary. Several adhesion gland cells have been labeled with arrowheads to visualize the line of the marginal adhesive zone. Scale bar is 10um.
Any neuron that is capable of some detection of mechanical stimulus involved in sensory perception.
Subset of dorsal-ventral muscle cells located in the medial body region.
Image is an electron micrograph depicting multiple medial dorsal-ventral muscle cells (arrowheads). At the bottom of this image is the ventral epidermi, to the left is the dark staining of the gut tissue. Scale bar is 10um.
A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
A secreted, mucin-rich extracellular substance coating the epidermal surface of the animal implicated in gliding locomotion, substrate adhesion, innate immunity and predator avoidance.
Image is an electron micrograph of the outside of an animal at the marginal adhesive zone. The adhesive papilla are colored in blue and surround each secretory pore (yellow). Mucus (arrowheads) and cilia are both green. Scale bar is 2um.
The external opening and terminus of a protonephridium made by a terminal cell.
Cell appendage of the neuron which includes the axon and the dendrite.
A neuron that produces and releases neuropeptides at chemical synapses.
Differentiating, immature epidermal cells lacking cilia.
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).
Image is an electron micrograph depicting the nuclear envelope (arrowheads). The nucleus takes up the top left corner of the image and the nuclear envelope encloses it. Scale bar is 200 nm.
The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
Image is an electron micrograph depicting the nuclear envelope. The nucleus takes up the top left corner of the image and the inner nuclear membrane has been labeled with arrowheads. Scale bar is 200 nm.
The volume enclosed by the nuclear inner membrane.
The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.
Image is an electron micrograph depicting the nuclear envelope. The nucleus takes up the top left corner of the image and the outer nuclear membrane has been labeled with arrowheads. Scale bar is 200 nm.
The portion of the nuclear lumen proximal to the inner nuclear membrane.
Parenchymal cells that synthesize and contain brown ommonchrome pigment.
A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila.
Heavily ciliated, insunk epithelial cells bounding the outside of the pharynx. Outer pharynx epithelial cell nuclei are positioned beneath the pharynx musculature.
Image is an electron micrograph of a transverse section through the pharynx. The pharynx pouch cavity is at the top. An epidermal cell, a part of the outer epithelium, has been labeled with arrowheads. Immediately deep to the outer epithelial layer of the pharynx is musculature that has been colored. Red = circular; blue = longitudinal. Scale bar is 2 um.
A cell that engulfs large particles or cells via invagination of the plasma membrane and creation of a phagosome.
The distal-most end of the pharnyx containing an opening to the pharynx lumen.
Image is an electron micrograph of the tip of the pharynx. Many gland cells can be seen inside, filled with mucus. Scale bar is 5um.
A pigment cell is a cell that contains pigment granules.
A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes.
A wound resulting from an amputation of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch.
Illustration of an example of a plug amputation showing resultant fragment and donor wound.
A breach of the epidermis made with a sharp pointed object, like a needle or an insect pin.
An anatomical space that is an opening, usually at the end of a canal or duct, on the surface of the integument or the lining of an internal anatomical space.
A haploid gamete undergoing terminal differentiation.
A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
A diploid germline stem cell or transit amplifying germ cell that has not committed to undergoing meiotic DNA replication, reductive divisions or terminal differentiation.
The part of a synapse that is part of the presynaptic cell.
Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.
A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
The largest branch of the triclad intestine. It is comprised of the gastrodermis, a columnar epithelium, surrounded by basal lamina and visceral musculature.
Four large phagocytic cells associated with the embryonic pharynx.
Gut branches originating from and connected to the tertiary gut branches.
Any anatomical structure that is part of the reproductive system.
The light sensing structure consisting of photoreceptor neuron dendrites that project into the optic lumen and show close associations with eumelanin-containing pigment cup cells.
The dendritic process of a bipolar photoreceptor neuron that projects into the optic cup lumen and senses light.
A tubular structure that transports secreted or excreted substances.
Image is an electron micrograph of a viscid gland cell passing across the basal lamina (BL). This cell secretes a specialized type of mucus. The secretory duct (arrowhead) transports mucus to the outside of the animal, through the secretory pore. Ventral is down and scale bar is 5um.
A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
One of the cells of the body that compose the tissues, organs, and parts of that individual other than the germ cells.
A non-germline cell within the ovary or testis.
A presumptive progenitor cell that expresses both pan-neoblast markers and pro-differentiation gene(s), frequently developmental transcription factors, implicated in lineage commitment and tissue-specific differentiation programs.
A thin, flexible rod that anchors an egg capsule to a solid substrate.
A wound produced by non-autonomous physical means.
The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released.
Vesicles that store various neurotransmitters that are released at the synapse. The release is regulated by a voltage-dependent calcium channel. Vesicles are essential for propagating nerve impulses between neurons and are constantly recreated by the cell. [Wikipedia]
A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element.
The posterior-medial region of the tail margin.
Illustration of the tail tip (in green).
The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
A cell-cell junction in invertebrates that seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other.
Image is an electron micrograph depicting the inner epithelium of the pharynx. Septate junctions (arrowheads) can be clearly seen between cells. Scale bar is 200 nm.
A wound resulting from a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
Illustration of a wedge amputation depicting the resultant donor wound and wedge fragment.
A sorted cell population enriched for irradiation-sensitive, cycling cells (4n cells, with high levels of Hoescht 33342 staining) with scant cytoplasm (low levels of calcein-AM staining). X1 cells are enriched for cycling neoblasts.
A heterogeneous sorted cell population of unstained planarian cells with similar size and complexity to irradiation-sensitive, cycling cells contained in the X1 gate. Unlike X1 cells, X1(FS) cells are amenable to cell transplantation.
A sorted cell population containing irradiation-sensitive and irradiation-insensitive cells, characterized by weak Hoescht 33342 and calcein-AM staining. X2 cell populations contain neoblasts as well as a variety of lineage-dedicated post-mitotic progenitor cells.
A sorted cell population of irradiation-insensitive cells that contains a variety of post-mitotic, differentiated cell types.
Adjacent to blastema, or proximal to blastema.
Illustration of the post-blastema region(in green) in the anterior region of a regenerating tail fragment.
A fragment derived from a spontaneous or induced fission event.
The avascular cellular layers that cover body surfaces and cavities and may form glands.
Image is an electron micrograph of a transverse section of a planarian through the pharyngeal region depicting 3 different epithelial layers (arrowheads). At the top is the dorsal epidermis, in the middle is the epithelium of the pharyngeal pouch, and at the bottom of the image, the outer epithelium of the pharynx. Scale bar is 5um.
The triclad planarian gut is serially bifrucated into connected lumens where each bifrucation is a branch.
Organ that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.
An event or occurrence that causes damage to a tissue or organ.
structural element of a chromosome, for example, a telomere and a centromere
A longitudinal fragment containing the preexisting midline and medial structures.
Illustration of a thick fragment (in green).
A longitudinal fragment lacking a midline and medial structures.
Illustration of a thin fragment (in green).
A piece of tissue isolated from the body.
A region bounded by any sagittal plane though the animal and the left or right side of the animal. NOTE: sagittal plane is an anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size
Illustration of a longitudinal region (green).
An intentional wound produced by non-autonomous chemical means.
A wound resulting from the removal of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch.
Illustration of a wound left in a donor animal resulting from a plug amputation.
A wound resulting from the removal of a piece of tissue from the lateral margin at any given point that extends interiorly to more medial structures.
A fragment that has undergone wound healing and is undergoing tissue replacement and morphallaxis.
An orientation quality inhering in a bearer by virtue of the bearer having a position that is in the sagittal plane. This plane runs longitudinally and is not necessarily medial.
An orientation quality inhering in a bearer by virtue of the bearer having a position that is in the parasagittal plane, which runs longitudinally, and is never medial.
An anatomical entity consisting of a single or a few multinucleated structures
Cytoplasmic part which forms a distinctive granular particle, which may or may not be visible using light microscopy.
Image is an electron micrograph depicting a cell with many intracellular granules (arrowheads) visible in the cytoplasm. The scale bar is 1um.
Any number of cells from dissociated planarian tissue sorted via a FACS sorter for any parameter.
Cells isolated from dissociated planarian tissue.
An epithelial monolayer lining the pharynx pouch cavity.
Image is an electron micrograph of a transverse slice through the parapharyngeal region. It includes the dorsal epidermis, pharynx pouch epithelium (arrowheads), and a portion of the pharynx. Dorsal is up and the lumen of the pouch is visible as the white stripe in the middle of the micrograph. Scale bar is 5um.
Epithelial surface lining the sperm duct.
A loosely organized collection of connective tissue and cells, including neoblasts and their immediate progeny, located in the space outside of the organs between the body wall musculature and the gut.
Illustration of the dorsal region of the tail (in green).
The lateral region of the medio-lateral axis of the whole animal.
The center-most region just anterior to the pharynx
cell which is part of the ventral epidermis
cell which is part of the enteric musculature
cell which is part of the dorsal region of the epidermis
cell which is part of the adhesion gland
cell which is part of the body wall musculature
epithelial cell which is part of the pharynx
muscle cell which is part of the pharynx
epithelial cell which is part of the pharynx pouch
pigment granule which is part of the eumelanin
pigment granule which is part of the ommochrome pigment cell
cell which is part of the parapharyngeal region
cell which is part of the prepharyngeal region
Image is an electron micrograph showing a neoblast undergoing mitotic prophase (outlined). Note the difference in appearance compared to neighboring cells, nuclei labeled "N." Scale bar is 2 um.
Image is an electron micrograph depicting cells in the mesenchyme, near the regeneration blastema. In the middle of the image, outlined, a cell is undergoing mitotic metaphase. This cell's chromosomes can be seen in a vertical arrangement. Scale bar is 2um.
Image is an electron micrograph showing a neoblast undergoing mitotic anaphase. The entire cell has been outlined and the condensed chromatin is visible inside. Scale bar is 2um.
Image is an electron micrograph showing a neoblast undergoing mitotic telophase (outlined). The condensed chromatin is visible inside and has been partially outlined by the nuclear envelope. Scale bar is 1um.
spermatogonial stem cell undergoing mitotic G1 phase
spermatogonial stem cell undergoing mitotic S phase
spermatogonial stem cell undergoing mitotic G2 phase
spermatogonial stem cell undergoing mitotic prophase
spermatogonial stem cell undergoing mitotic metaphase
spermatogonial stem cell undergoing mitotic anaphase
spermatogonial stem cell undergoing mitotic telophase
oogonial stem cell undergoing mitotic G1 phase
oogonial stem cell undergoing mitotic S phase
oogonial stem cell undergoing mitotic G2 phase
oogonial stem cell undergoing mitotic prophase
oogonial stem cell undergoing mitotic metaphase
oogonial stem cell undergoing mitotic anaphase
oogonial stem cell undergoing mitotic telophase
spermatogonium undergoing mitotic G1 phase
spermatogonium undergoing mitotic S phase
spermatogonium undergoing mitotic G2 phase
spermatogonium undergoing mitotic prophase
spermatogonium undergoing mitotic metaphase
spermatogonium undergoing mitotic anaphase
spermatogonium undergoing mitotic telophase
oogonial cell undergoing mitotic G1 phase
oogonial cell undergoing mitotic S phase
oogonial cell undergoing mitotic G2 phase
oogonial cell undergoing mitotic prophase
oogonial cell undergoing mitotic metaphase
oogonial cell undergoing mitotic anaphase
oogonial cell undergoing mitotic telophase
germ cell cyst undergoing mitotic G1 phase
germ cell cyst undergoing mitotic S phase
germ cell cyst undergoing mitotic G2 phase
germ cell cyst undergoing mitotic prophase
germ cell cyst undergoing mitotic metaphase
germ cell cyst undergoing mitotic anaphase
germ cell cyst undergoing mitotic telophase
spermatocyte undergoing meiotic G1 phase
spermatocyte undergoing meiotic G2 phase
spermatocyte undergoing meiotic prophase I
spermatocyte undergoing meiotic metaphase I
spermatocyte undergoing meiotic anaphase I
spermatocyte undergoing meiotic telophase I
spermatocyte undergoing meiosis II cell cycle phase
spermatocyte undergoing meiotic prophase II
spermatocyte undergoing meiotic metaphase II
spermatocyte undergoing meiotic anaphase II
spermatocyte undergoing meiotic telophase II
This primordium develops into cephalic ganglia
lumen which is part of the protonephridia
A progenitor cell that gives rise to one or more of the cell type(s) in the nervous system.
A progenitor cell that gives rise to one or more of the cell type(s) in the dorsal epidermis.
A progenitor cell that gives rise to optic cup cells of the eye.
A progenitor cell that gives rise to one or more of the cell type(s) in the epidermis.
This progenitor cell develops into testis somatic gonadal cell
testis somatic gonadal cell progenitor cell
A fragment derived from a prepharyngeal amputation encompassing the head.
A fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region.
Illustration of a trunk fragment (in green).
A fragment derived from a postpharyngeal amputation encompassing the tail.
A fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal.
Illustration of a prepharyngeal fragment (in green).
A fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip.
Illustration of a postpharyngeal fragment (in green).
A fragment encompassing all or part of the anterior region of the animal.
A fragment encompassing all or part of the posterior region of the animal.
Illustration of an example of a posterior fragment (in green).
A fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region. [SMR: a fragment that encompasses the side of the animal, not necessarily longituduinal, or parallel to the midline]
http://purl.obolibrary.org/obo/A fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region. [SMR_ a fragment that encompasses the side of the animal, not necessarily longituduinal, or parallel to the midline]
a fragment derived from an amputation parallel to the midline.
A 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch.
Illustration of an example plug fragment in green.
A piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
Illustration of an example wedge fragment in green.
The dorsal region of a fragment derived from a prepharyngeal amputation encompassing the head.
Illustration of the dorsal region of a head fragment (green).
The ventral region of a fragment derived from a prepharyngeal amputation encompassing the head.
Illustration of the ventral region of a head fragment (green).
The anterior region of a fragment derived from a prepharyngeal amputation encompassing the head.
Illustration of the anterior region of a head fragment (green).
The posterior region of a fragment derived from a prepharyngeal amputation encompassing the head.
Illustration of the posterior region of a head fragment (green).
The dorsal region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region.
Illustration of the dorsal region of a trunk fragment (green).
The ventral region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region.
Illustration of the ventral region of a trunk fragment (green).
The anterior region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region.
Illustration of the anterior region of a trunk fragment (green).
The posterior region of a fragment derived from pre- and post-pharyngeal amputations, encompassing the pharynx and parapharyngeal region.
Illustration of the posterior region of a trunk fragment (green).
The dorsal region of a fragment derived from a postpharyngeal amputation encompassing the tail.
Illustration of the dorsal region of a tail fragment (green).
The ventral region of a fragment derived from a postpharyngeal amputation encompassing the tail.
Illustration of the ventral region of a tail fragment (green).
The anterior region of a fragment derived from a postpharyngeal amputation encompassing the tail.
Illustration of the anterior region of a tail fragment (green).
The posterior region of a fragment derived from a postpharyngeal amputation encompassing the tail.
Illustration of the posterior region of a tail fragment (green).
The dorsal region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal.
Illustration of the dorsal region of a prepharyngeal fragment (green).
The ventral region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal.
ventral region of prepharyngeal fragment
Illustration of the ventral region of a prepharyngeal fragment (green).
The anterior region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal.
anterior region of prepharyngeal fragment
Illustration of the anterior region of a prepharyngeal fragment (green).
The posterior region of a fragment derived from two prepharyngeal amputations, removing the head and posterior regions of the animal.
posterior region of prepharyngeal fragment
Illustration of the posterior region of a prepharyngeal fragment (green).
The dorsal region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip.
dorsal region of postpharyngeal fragment
Illustration of the dorsal region of a postpharyngeal fragment (green).
The ventral region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip.
ventral region of postpharyngeal fragment
Illustration of the ventral region of a postpharyngeal fragment (green).
The anterior region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip.
anterior region of postpharyngeal fragment
Illustration of the anterior region of a postpharyngeal fragment (green).
The posterior region of a fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip.
posterior region of postpharyngeal fragment
Illustration of the posterior region of a postpharyngeal fragment (green).
The dorsal region of a fragment encompassing all or part of the anterior region of the animal.
Illustration of the dorsal region of an anterior fragment (green).
The ventral region of a fragment encompassing all or part of the anterior region of the animal.
Illustration of the ventral region of an anterior fragment (green).
The anterior region of a fragment encompassing all or part of the anterior region of the animal.
Illustration of the anterior region of an anterior fragment (green).
The posterior region of a fragment encompassing all or part of the anterior region of the animal.
Illustration of the posterior region of an anterior fragment (green).
The dorsal region of a fragment encompassing all or part of the posterior region of the animal.
Illustration of the dorsal region of a posterior fragment (green).
The ventral region of a fragment encompassing all or part of the posterior region of the animal.
Illustration of the ventral region of a posterior fragment (green).
The anterior region of a fragment encompassing all or part of the posterior region of the animal.
Illustration of the anterior region of a posterior fragment (green).
The posterior region of a fragment encompassing all or part of the posterior region of the animal.
Illustration of the posterior region of a posterior fragment (green).
The dorsal region of a fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region.
Illustration of the dorsal region of a lateral fragment (green).
The ventral region of a fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region.
Illustration of the ventral region of a lateral fragment (green).
The anterior region of a fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region.
Illustration of the anterior region of a lateral fragment (green).
The posterior region of a fragment derived from an amputation parallel to or along any edge, which overlaps the lateral region, dorso-lateral region, ventro-lateral region, antero-lateral margin, lateral margin, ventro-lateral margin, postero-lateral margin, dorso-lateral margin, antero-lateral region, postero-lateral region.
Illustration of the posterior region of a lateral fragment (green).
The dorsal region of a fragment derived from an amputation parallel to the midline.
Illustration of the dorsal region of a longitudinal fragment (green).
The ventral region of a fragment derived from an amputation parallel to the midline.
Illustration of the ventral region of a longitudinal fragment (green).
The anterior region of a fragment derived from an amputation parallel to the midline.
anterior region of longitudinal fragment
Illustration of the anterior region of a longitudinal fragment (green).
The posterior region of a fragment derived from an amputation parallel to the midline.
posterior region of longitudinal fragment
Illustration of the posterior region of a longitudinal fragment (green).
The dorsal region of a 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch.
Illustration of the dorsal region of a plug fragment (green).
The ventral region of a 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch.
Illustration of the ventral region of a plug fragment (green).
The anterior region of a 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch.
Illustration of the anterior region of a plug fragment (green).
The posterior region of a 3D piece of tissue, usually though the whole depth of the animal encompassing both dorsal and ventral sides, often made with a biopsy punch.
Illustration of the posterior region of a plug fragment (green).
The dorsal region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
The ventral region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
The anterior region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
Illustration of the anterior region of a wedge fragment (green).
The posterior region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
Illustration of the posterior region of a wedge fragment (green).
photoreceptor neuron is contained in the anterior region of the eye
photoreceptor neuron contained in anterior region of the eye
photoreceptor neuron is contained in the posterior region of the eye
photoreceptor neuron contained in posterior region of the eye
muscle cell is contained in the lateral region
muscle cell is contained in the anterior region
muscle cell contained in anterior region
muscle cell is contained in the posterior region
muscle cell contained in posterior region
blastema which develops into head region
blastema which develops into tail region
a prepharyngeal fragment that is regenerating
a postpharyngeal fragment that is regenerating
a anterior fragment that is regenerating
a posterior fragment that is regenerating
a longitudinal fragment that is regenerating
A fully formed, sexually mature organism that reproduces through cross-fertilization.
Depcited by field shows a light microscopy image of a sexually mature adult with a scale bar of 2 mm.
Asexually reproducing Schmidtea mediterranea exist as constitutive adults, undergoing successive cycles of fission and whole animal regeneration. Asexual Schmidtea mediterranea contain primordial germ cells, but do not possess a reproductive system.
Depicted by field shows an asexual adult with a scale bar of 500um
dmd-1+ expressing somatic cells within the testis that promote male GSC maintenance. dmd-1+, ophis-1+ somatic gonadal cells ensheath germ cells via long cytoplasmic processes and promote differentiation.
ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia.
Axis that runs from the oral pole and to the aboral pole of the spherical embryo (Stage 3 through early Stage 6). The oral pole is centered around the embryonic pharynx; the aboral pole is located opposite the embryonic pharynx.
Illustration noting the oral-aboral axis in cyan double headed arrow. It starts at the embryonic pharynx and extends to opposite pole.
The apical surface of the single layered primitive ectoderm that is in contact with the environment.
The surface of the primitive gut cells in contact with the embryonic wall.
The surface of phagocytic embryonic gut cells in contact with ingested yolk cells.
The epithelial cell surface lining the embryonic pharynx lumen.
embryonic pharynx lumen epithelial surface
An undifferentiated, cycling embryonic cell in Stage 1-5 embryos that expresses piwi-1, numerous adult asexual neoblast enriched genes, and early embryo enriched genes. Blastomeres give rise to temporary embryonic tissues during Stage 2, continue dividing asynchronously in the embryonic wall, and ultimately give rise to neoblasts and adult lineage progenitors beginning in Stage 5.
Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues.
A neuronal cell innervating the embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening.
Differentiated radial muscle cell present in the embryonic pharynx.
foxA1+ epithelial cell contained in the embryonic pharynx.
Differentiated muscle cell present in a circular muscle fiber of the embryonic pharynx.
Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus.
Epithelia associated with the pharynx organ.
Image is an electron micrograph of a transverse section through the pharynx. Outlined, is the outer epithium, which is an "insunk" epithelium where the nuclei are set back medially away from the epithelium surface. Here, just the surface is outlined.. Scale bar is 2um.
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
Anatomical space enclosed by the oviduct epithelium.
Anatomical space enclosed by the sperm duct epithelium.
Ciliated epithelium lining the sperm duct.
Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct.
Anatomical plane which divides the body into right and left parts. This plane passes through the midline at the midline but does not always the midline.
Illustration of a sagittal plane of the whole animal (in green).
now using patterned term ventral region PLANA:0000143
now using patterned term anterior region
choosing to use UBERON:0000476, acellular anatomical structure instead
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
Image is an electron micrograph showing several cells. Arrowheads label the plasma membrane, the boundary between cells. Scale bar is 1um.
Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi.
A spherical to rod shaped organelle that generates the majority of a cell's supply of ATP via cellular respiration. Mitochondria have their own genome and consist of outer and inner membranes, the latter folds inward to form cristae. This folding increases the surface area of the membrane and thus increases the space available to produce ATP. The inner and outer membranes are separated by an intermembrane space, and the inner membrane encloses the matrix.
Image is an electron micrograph depicting a couple different cells. A few mitochondria have been labeled with arrowheads. Note the variation in shape from spherical to rod-like. This is dependent on cutting orientation at fission/fusion state of the mitochondria. Scale bar is 1 um.
Network of interconnected, flattened, and/or tubular membrane, known as cisternae. This membrane is contiguous with the outer nuclear membrane. The endoplasmic reticulum is involved in both protein and lipid synthesis.
Image is an electron micrograph depicting endoplasmic reticulum (magenta) in multiple cells. Scale bar is 0.5um.
Network of interconnected, flattened, and/or tubular membrane, known as cisternae. This membrane is contiguous with the outer nuclear membrane. The endoplasmic reticulum is involved in both protein and lipid synthesis. The outer surface is studded with protein-synthesizing particles known as ribosomes.
Image is an electron micrograph depicting the rough endoplasmic reticulum (arrowheads) of a cell. Ribosomes can be seen associating with the ER membrane creating a rough ER, as well as free within the cytoplasm of the cell. Scale bar is 200 nm.
Endoplamic reticulum that does not contain ribosomes, which synthesizes lipids, phospholipids, and steroids.
Image is an electron micrograph depicting smooth ER (arrowheads) in a cell, next to the nucleus (N). Ribosomes can be seen within the cytoplasm, but not associating with the ER membrane. Scale bar is 200 nm.
Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
Image is an electron micrograph depicting the nuclear envelope. The nucleus takes up the top left corner of the image and two nuclear pores have been labeled with arrowheads. Scale bar is 200 nm.
The digestive component of the cell. They are homogenous, dense, membrane bound organelles filled with acid hydrolases which break down polymers.
Image is an electron micrograph depicting two lysosomes (arrowheads) within a cell. The nucleus sits in the bottom left corner. Lysosomes can sometimes be identified by the swirling material they are breaking down inside. Scale bar is 0.5um.
Axis that runs along the long axis of the animal from anterior (head) to posterior (tail). It is perpendicular to the dorsoventral axis and as such, it splits dorsal and ventral regions of the animal to either side.
anterior-posterior axis of whole organism
anterior-posterior axis of the whole animal
Depiction shows an asexual adult with the term annotated in yellow. Scale bar =500um
Axis that runs along the short axis of the animal, perpendicular to the anteroposterior axis, running from the dorsal (back) side of the animal to the ventral (belly) side of the animal. This axis splits anterior and posterior regions of the animal to either side.
Axis perpendicular to both the anteroposterior and dorsoventral axis that runs from the left side of the animal, through the medial region (center) and out to the right side.
Axis that runs from the center of the body, starting at the anteroposterior axis and out to the lateral (left, right, dorsal or ventral) surface of the animal.
Axis that starts at the distal part of an appendage, closest to the body, and runs to the proximal part of an appendage, farthest from the body.
proximal-distal axis of the whole animal
Pharynx of an asexual adult exposed by tricaine treatment. The proximodistal axis is denoted with the double headed magenta arrow.
Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD.
Illustration of the anterior pole (green).
Distinct posterior cluster of muscle cells located at the midline which express wnt1.
Illustration of the posterior pole (in green).
A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu, guide neuronal migration during development, and exchange metabolites with neurons.
Image is an electron micrograph depicting a section of the ventral nerve cord. The arrowheads point at a likely glial cell. Note the difference in darkness of cytoplasm in the cell body of the glial cell compared to the surrounding axons. Scale bar is 2um.
A biological tissue mass of nerve cell bodies.
Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft.
epithelium lining the lumen of the pharynx
Pharynx muscle fibers running circumferentially about the pharynx.
Groupings of specialized epithelial cells located along the dorsal ventral margin. Adhesion glands are comprised of three cell types, the viscid and releasing gland cells which penetrate through an epithelial anchor cell and terminate at the epidermal surface.
Image is an electron micrograph showing the multicellular total adhesion gland structure (outlined) embedded in the epidermis. Note that the gland cells cross the basal lamina into the epithelium. Ventral is up and scale bar is 2um.
Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells.
Image is an electron micrograph showing the total multicellualr adhesion gland structure. The anchor cell has been outlined, though mucus-filled projections of gland cells can be seen densely packed inside. Nucleus is that of the anchor cell. Ventral is up and scale bar is 2um.
A specialized insunk epithelial cell that is part of the adhesion glands which is responsible for production and excretion of the viscid substance allowing adherence to a substrate.
Image is an electron micrograph showing the whole adhesion gland structure, specifically outlining a single cell (viscid gland cell) associated with this multicelluar structure. Ventral is up and scale bar is 2um.
Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance.
Image is an electron micrograph showing the whole adhesion gland structure. Arrowheads mark releasing gland cells which are associated with this multicelluar structure. The releasing gland cells have very small excretory particles compared to the neighboring viscid gland. Ventral is up and scale bar is 1um.
A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2.
A subset of sensory neurons located along the dorsal head margin.
no longer designating mediolateral regions using the contained_in object property
piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons.
piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole.
Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords.
obsolete body wall musculature compartment
piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons.
piwi-1+, klf+ progenitor neoblasts required for production of cintillo+ sensory neurons.
A population of piwi-2+, ston-2+, elav-2+, ptprd-9+ and msi-1+ progenitors that give rise to one or more neuronal (pc-2+, synapsin+) lineages.
A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus.
piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons.
A lumen enclosed by the embryonic pharynx epithelial cells through which yolk cells are transported into the embryonic gut cavity.
Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs.
Neurons that express the biogenic amine glutamate.
An individual member of the sexual biotype of Schmidtea mediterranea.
An individual member of the asexual biotype of Schmidtea mediterranea.
A cell present near the brain and eye where photoreceptor axons form a bundle projecting out from the eye that are near axon choice points. Guidepost cells are positive for Arrestin, notum, fz5/8-4+, 6G10, and low levels of troponin, tropomyosin, colF-2 and mp-1.
Guidepost cell associated with the visual circuit that are present near the eye, located along axons just anterior and ventral to the eye. Name acronym stands for notum+ muscle cell near eye.
Guidepost cell assocaited with the visual circuit, present at the axon choice point ventral, posterior to and slightly medial to the eye. Name acronym stands for notum+ muscle cells at the choice point.
Guidepost cell present at the medial brain, ventral to the optic chiasm. Closely associated with photoreceptor axons during regneration. Name acronym stands for notum+ brain cells.
A sexually immature member of the Schmidtea mediterranea sexuallly reproducing biotype
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
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
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
An anatomical structure that is undergoing regeneration.
we define this in terms of active participation in regeneration, rather that capabilities. In this sense it is different from the AEO structure.
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
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.
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
This can't be added as a property chain because it causes a circularity violation for 'part of'.
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