PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.
Planarian Anatomy Ontology (PLANA)
Planarian_Anatomy
1.2
CARO part_of NCBITaxon:79327; CL part_of NCBITaxon:79327
2023-03-13
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
editor note
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
Person:Alan Ruttenberg
Add as annotation triples in the granting ontology
term replaced by
term replaced by
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
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
is indirect form of
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
is a defining property chain axiom
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
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.
external_definition
Notes on the homology status of this class.
homology_notes
has_relational_adjective
Notes on the how instances of this class vary across species.
taxon_notes
Notes on how similar or equivalent classes are represented in other ontologies.
external_ontology_notes
IAO:0100001
synonym typically used in the context of human anatomy
IAO:0100001
synonym typically used in the context of vertebrate anatomy
http://purl.org/dc/elements/1.1/creator
uberon
dc-creator
true
dc-creator
creator
http://purl.org/dc/elements/1.1/description
uberon
dc-description
true
dc-description
description
http://purl.org/dc/elements/1.1/title
uberon
dc-title
true
dc-title
title
http://purl.org/dc/terms/license
uberon
dcterms-license
true
dcterms-license
license
IAO:0100001
namespace-id-rule
IAO:0100001
synonym_type_property
has_alternative_id
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
https://github.com/information-artifact-ontology/ontology-metadata/issues/18
has broad synonym
has_broad_synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/18
IAO:0100001
database_cross_reference
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
https://github.com/information-artifact-ontology/ontology-metadata/issues/20
IAO:0100001
has exact synonym
has_exact_synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/20
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
https://github.com/information-artifact-ontology/ontology-metadata/issues/19
IAO:0100001
has narrow synonym
has_narrow_synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/19
IAO:0100001
has_obo_format_version
IAO:0100001
has_obo_namespace
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.
https://github.com/information-artifact-ontology/ontology-metadata/issues/21
IAO:0100001
has related synonym
has_related_synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/21
IAO:0100001
has_scope
IAO:0100001
has_synonym_type
in_subset
IAO:0100001
shorthand
Sofia Robb
2017-07-26T18:19:59Z
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
BFO:0000050
external
quality
spatial
uberon
part_of
part_of
part of
part of
part_of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
BFO:0000051
external
quality
spatial
uberon
has_part
has_part
has part
has part
has_part
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
preceded by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
precedes
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
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.
BSPO:0000096
rostral_to
spatial
anterior_to
anterior_to
anterior to
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.
BSPO:cjm
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).
BSPO:0000098
spatial
dorsal_to
dorsal_to
dorsal to
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).
BSPO:cjm
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.
BSPO:0000099
caudal to
spatial
posterior_to
posterior_to
posterior to
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.
BSPO:cjm
caudal to
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).
BSPO:0000102
spatial
ventral_to
ventral_to
ventral to
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).
BSPO:cjm
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.
BSPO:0000104
spatial
approximately_perpendicular_to
approximately_perpendicular_to
approximately perpendicular to
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.
BSPO:cjm
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
BSPO:0000107
spatial
deep_to
deep_to
deep to
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
BSPO:cjm
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
BSPO:0000108
spatial
superficial_to
superficial_to
superficial to
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
BSPO:cjm
Direcly opposite to. i.e. on the opposite side through the axis.
BSPO:0000113
spatial
opposite_to
opposite_to
opposite to
Direcly opposite to. i.e. on the opposite side through the axis.
BSPO:cjm
X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
BSPO:0000120
spatial
in_left_side_of
in_left_side_of
in left side of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
BSPO:PATO_mtg_2009
X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
BSPO:0000121
spatial
in_right_side_of
in_right_side_of
in right side of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
BSPO:PATO_mtg_2009
X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure
BSPO:0000126
spatial
in_lateral_side_of
in_lateral_side_of
in lateral side of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure
UBERON:cjm
x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross.
spatial
parallel_to
parallel to
x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross.
BSPO:curators
x immediately deep to y iff x deep_to y and x is contiguous with y.
BSPO:0001107
spatial
immediately_deep_to
immediately_deep_to
immediately deep to
x immediately deep to y iff x deep_to y and x is contiguous with y.
BSPO:curators
BSPO:0015001
spatial
finishes_axis
finishes_axis
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
finishes axis
crossing at right angles
BSPO:0015005
spatial
orthogonal_to
orthogonal_to
orthogonal to
crossing at right angles
BSPO:cjm
Intersects at two points.
BSPO:0015006
spatial
passes_through
passes_through
passes through
Intersects at two points.
BSPO:cjm
BSPO:0015007
spatial
starts_axis
starts_axis
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
starts axis
BSPO:0015008
spatial
surface_of
surface_of
placeholder. used for relation between anatomical surface and an anatomical side.
surface of
x immediately superficial to y iff x superficial to y and x is contiguous with y.
BSPO:0015014
spatial
immediately_superficial_to
immediately_superficial_to
immediately superficial to
x immediately superficial to y iff x superficial to y and x is contiguous with y.
BSPO:curators
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
person:Alan Ruttenberg
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
has_specified_output
The inverse property of is_specified_output_of
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
is_specified_output_of
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
PERSON:Bjoern Peters
is_specified_output_of
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
disposition of
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
contained in
contains
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.
dos
2017-05-24T09:30:46Z
has regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
dos
2017-05-24T09:31:01Z
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
dos
2017-05-24T09:31:17Z
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
dos
2017-05-24T09:44:33Z
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
dos
2017-05-24T09:49:21Z
has component process
dos
2017-09-17T13:52:24Z
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
directly regulated by
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
GOC:dos
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
dos
2017-09-17T13:52:38Z
directly negatively regulated by
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
GOC:dos
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
dos
2017-09-17T13:52:47Z
directly positively regulated by
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
GOC:dos
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
dos
2017-09-22T14:14:36Z
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
GOC:dos
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
David Osumi-Sutherland
starts_at_end_of
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
David Osumi-Sutherland
ends_at_start_of
meets
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
RO:0002092
external
happens_during
happens_during
happens during
RO:0002093
external
ends_during
ends_during
ends during
x overlaps y if and only if there exists some z such that x has part z and z part of y
x overlaps y iff they have some part in common.
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO:0002131
spatial
overlaps
overlaps
"(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF []
overlaps
overlaps
true
x overlaps y iff they have some part in common.
BSPO:cjm
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
BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
spatially disjoint from
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
This is the transitive form of the develops from relation
develops from
inverse of develops from
develops into
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.
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
regulates
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
Chris Mungall
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.
Chris Mungall
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.
Chris Mungall
has function realized in
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
Chris Mungall
has function in
capable of part of
true
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
Chris Mungall
RO:0002220
spatial
adjacent_to
adjacent_to
adjacent to
adjacent to
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
Chris Mungall
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
Chris Mungall
consumes
has input
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
has developmental contribution from
inverse of has developmental contribution from
developmentally contributes to
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
false
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
acts upstream of
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
affects
acts upstream of or within
Inverse of developmentally preceded by
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.
cjm
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
causally upstream of, positive effect
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.
cjm
causally upstream of, negative effect
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
Chris Mungall
inheres in part of
characteristic of part of
true
A mereological relationship or a topological relationship
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
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.
Chris Mungall
catalyzes
executes
has
is catalyzing
is executing
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
Chris Mungall
false
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
Chris Mungall
actively involved in
enables part of
involved in
inverse of enables
Chris Mungall
enabled by
inverse of regulates
Chris Mungall
regulated by (processual)
regulated by
inverse of negatively regulates
Chris Mungall
negatively regulated by
inverse of positively regulates
Chris Mungall
positively regulated by
inverse of has input
Chris Mungall
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
inverse of upstream of
Chris Mungall
causally downstream of
Chris Mungall
immediately causally downstream of
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
Chris Mungall
indirectly activates
indirectly positively regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
Chris Mungall
indirectly inhibits
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.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
https://en.wikipedia.org/wiki/Causality
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
Chris Mungall
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.
Chris Mungall
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
Chris Mungall
influences (processual)
affects
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
Chris Mungall
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
Chris Mungall
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
Chris Mungall
involved in negative regulation of
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
Chris Mungall
involved in or reguates
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
executes activity in
enables activity in
is active in
true
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
GOC:cjm
GOC:dos
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Considering relabeling as 'pairwise interacts with'
Chris Mungall
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
http://purl.obolibrary.org/obo/MI_0914
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
Chris Mungall
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
Axiomatization to GO to be added later
Chris Mungall
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
Chris Mungall
Vasundra Touré
molecularly controls
directly regulates activity of
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly inhibits
molecularly decreases activity of
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly activates
molecularly increases activity of
directly positively regulates activity of
Chris Mungall
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
has part that occurs in
true
Chris Mungall
is kinase activity
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
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.
existence overlaps
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).
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence starts during or after
x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends during or before
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
Chris Mungall
depends on
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between entities
Chris Mungall
causally influenced by (entity-centric)
causally influenced by
Chris Mungall
interaction relation helper property
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
Chris Mungall
molecular interaction relation helper property
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
Chris Mungall
Vasundra Touré
causally influences (entity-centric)
causally influences
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.
GOC:cjm
lumen of
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
luminal space of
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
Chris Mungall
directly regulates (processual)
directly regulates
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
Chris Mungall
has part structure that is capable of
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
capable of positively regulating
Inverse of 'causal agent in process'
process has causal agent
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
directly positively regulates
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
directly negatively regulates
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.
cjm
2018-01-25T23:20:13Z
enables subfunction
cjm
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
cjm
2018-01-26T23:49:51Z
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
cjm
2018-01-26T23:53:14Z
acts upstream of, positive effect
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
cjm
2018-01-26T23:53:22Z
acts upstream of, negative effect
cjm
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
cjm
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
Vasundra Touré
regulates activity of
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.
pg
2022-09-26T06:07:17Z
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
pg
2022-09-26T06:08:01Z
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.
https://orcid.org/0000-0001-9625-1899
https://orcid.org/0000-0003-2620-0345
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
2021-11-08T12:00:00Z
utilizes
device utilizes material
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
positively regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
negatively regulates characteristic
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
occurrent
Occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
per discussion with Barry Smith
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
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
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
process
Process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
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
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
disposition
Disposition
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
realizable
RealizableEntity
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
quality
Quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
sdc
SpecificallyDependentContinuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
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
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
per discussion with Barry Smith
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
role
Role
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
gdc
GenericallyDependentContinuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
function
Function
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
material
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
immaterial entity
A 2D surface of an anatomical continuant.
FMA:24137
surface
spatial
BSPO:0000005
to be merged into CARO
anatomical surface
A 2D surface of an anatomical continuant.
BSPO:cjm
A straight line through space, intersecting an anatomical entity.
http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG
spatial
BSPO:0000010
Axis directions are defined in terms of axes.
anatomical axis
A straight line through space, intersecting an anatomical entity.
BSPO:cjm
An axis that extends through an organism from head end to opposite end of body or tail.
A-P axis
AP axis
anteroposterior axis
cephalocaudal axis
craniocaudal axis
rostral/caudal
rostrocaudal axis
spatial
longitudinal axis
BSPO:0000013
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]
anterior-posterior axis
An axis that extends through an organism from head end to opposite end of body or tail.
BSPO:cjm
cephalocaudal axis
http://en.wikipedia.org/wiki/Anatomical_terms_of_location
craniocaudal axis
rostral/caudal
rostrocaudal axis
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.
apical/basal
spatial
longitudinal axis
BSPO:0000014
apical-basal axis relative to substrate
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.
BSPO:mah
An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal).
proximal/distal
proximodistal
spatial
BSPO:0000015
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.
proximal-distal axis
An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal).
BSPO:curators
http://en.wikipedia.org/wiki/Anatomical_terms_of_location
An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body.
D-V axis
DV axis
dorsoventral axis
anterior-posterior axis
spatial
BSPO:0000016
dorsal-ventral axis
An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body.
BSPO:curators
anterior-posterior axis
An axis that bisects an organism from left to right sides of body, through a sagittal plane.
L-R axis
LR axis
R-L axis
RL axis
dextro-sinister axis
left to right axis
right to left axis
right-left axis
spatial
BSPO:0000017
left-right axis
An axis that bisects an organism from left to right sides of body, through a sagittal plane.
BSPO:cjm
Anatomical plane that divides body into anterior and posterior parts.
FMA:12247
axial plane
axial section
transverse section
spatial
cross-section
BSPO:0000018
transverse plane
Anatomical plane that divides body into anterior and posterior parts.
BSPO:mah
Anatomical plane that divides bilateral body into dorsal and ventral parts.
FMA:52810
frontal plane
horizontal anatomical plane
horizontal section
spatial
coronal section
frontal section
BSPO:0000019
horizontal plane
Anatomical plane that divides bilateral body into dorsal and ventral parts.
BSPO:mah
horizontal anatomical plane
FMA:52810
Anatomical region that overlaps the anterior and dorsal regions of a body or body part.
Melissa Haendel
2009-06-15T01:01:38Z
anterodorsal region
spatial
BSPO:0000026
antero-dorsal region
Anatomical region that overlaps the anterior and dorsal regions of a body or body part.
BSPO:wd
Anatomical region that overlaps the anterior and ventral regions of a body or body part.
Melissa Haendel
2009-06-15T01:04:59Z
anteroventral region
spatial
BSPO:0000027
antero-ventral region
Anatomical region that overlaps the anterior and ventral regions of a body or body part.
BSPO:wd
Anatomical region that overlaps the posterior and lateral regions of the body or body part.
Melissa Haendel
2009-06-15T01:06:01Z
posterolateral region
spatial
BSPO:0000028
postero-lateral region
Anatomical region that overlaps the posterior and lateral regions of the body or body part.
BSPO:wd
Anatomical region that overlaps the anterior and lateral regions of a body or body part.
Melissa Haendel
2009-06-15T01:07:18Z
anterolateral region
spatial
BSPO:0000029
antero-lateral region
Anatomical region that overlaps the anterior and lateral regions of a body or body part.
BSPO:wd
Anatomical region that overlaps the posterior and dorsal regions of the body or body part.
Melissa Haendel
2009-06-15T01:08:13Z
posterodorsal region
spatial
BSPO:0000030
postero-dorsal region
Anatomical region that overlaps the posterior and dorsal regions of the body or body part.
BSPO:wd
Anatomical region that overlaps the posterior and ventral regions of a body or body part.
Melissa Haendel
2009-06-15T01:08:38Z
posteroventral region
spatial
BSPO:0000035
postero-ventral region
Anatomical region that overlaps the posterior and ventral regions of a body or body part.
BSPO:wd
An anatomical region bounded by a plane perpendicular to an axis through the middle.
FBql:00005841
spatial
BSPO:0000054
anatomical side
An anatomical region bounded by a plane perpendicular to an axis through the middle.
BSPO:cjm
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.
FBcv:0000053
FBql:00005848
anterior
rostral
spatial
BSPO:0000055
anterior side
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.
BSPO:RW
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.
FBcv:0000065
FBql:00005849
posterior
caudal
spatial
BSPO:0000056
posterior side
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.
BSPO:RW
BSPO:wd
caudal
Anatomical side that is located on the apical end of an organism or structure.
FBcv:0000054
FBql:00005854
apical
spatial
BSPO:0000057
apical side
Anatomical side that is located on the apical end of an organism or structure.
BSPO:wd
Anatomical side that is located on the basal end of an organism or structure.
FBcv:0000055
FBql:00005855
basal
spatial
BSPO:0000058
The part of the organism attached to a substrate. Axis of symmetry.
basal side
Anatomical side that is located on the basal end of an organism or structure.
BSPO:wd
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.
FBcv:0000059
FBql:00005842
dorsal
spatial
BSPO:0000063
dorsal side
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.
BSPO:wd
FBcv:0000063
FBql:00005844
lateral
spatial
BSPO:0000066
lateral side
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.
FBcv:0000070
FBql:00005843
ventral
spatial
BSPO:0000068
ventral side
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.
BSPO:RW
BSPO:wd
A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm.
FBql:00005841
spatial
BSPO:0000070
to be merged into CARO
anatomical region
A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm.
BSPO:cjm
Anatomical region anteriorly located on the body or body part.
FBql:00005848
spatial
BSPO:0000071
anterior region
Anatomical region anteriorly located on the body or body part.
BSPO:wd
Anatomical region posteriorly located on the body or body part.
FBql:00005849
spatial
BSPO:0000072
posterior region
Anatomical region posteriorly located on the body or body part.
BSPO:wd
Anatomical region located on the apical end on the body or body part.
FBql:00005854
spatial
BSPO:0000073
apical region
Anatomical region located on the apical end on the body or body part.
BSPO:wd
Anatomical region located basally on the body or body part.
FBql:00005855
spatial
BSPO:0000074
basal region
Anatomical region located basally on the body or body part.
BSPO:wd
Anatomical region dorsally located on the body or body part.
FBql:00005842
spatial
BSPO:0000079
dorsal region
Anatomical region dorsally located on the body or body part.
BSPO:wd
Anatomical region that overlaps the dorsal and lateral regions of a body or body part.
FBql:00005845
dorsolateral region
spatial
BSPO:0000080
dorso-lateral region
Anatomical region that overlaps the dorsal and lateral regions of a body or body part.
BSPO:wd
Anatomical region laterally located on the body or body part.
FBql:00005844
spatial
BSPO:0000082
lateral region
Anatomical region laterally located on the body or body part.
BSPO:wd
Anatomical region ventrally located on the body or body part.
FBql:00005843
spatial
BSPO:0000084
ventral region
Anatomical region ventrally located on the body or body part.
BSPO:wd
Anatomical region that overlaps the ventral and lateral regions of a body or body part.
FBql:00005846
ventrolateral region
spatial
BSPO:0000085
This is an example of a composition of two axis positions.
ventro-lateral region
Anatomical region that overlaps the ventral and lateral regions of a body or body part.
BSPO:wd
FBql:00005873
FMA:9647
spatial
BSPO:0000086
to be merged into CARO
anatomical compartment
FBql:00005881
spatial
BSPO:0000092
to be merged into CARO
anatomical compartment boundary
FBcv:0000034
FBql:00005879
spatial
BSPO:0000094
dorsal/ventral compartment boundary
An anatomical axis that extends from the center of the body outwards or externally.
wasila.dahdul
2013-07-02T11:21:42Z
spatial
proximal-distal axis
BSPO:0000196
The medial-external axis could apply to a sphere-shaped body.
medial-external axis
An anatomical axis that extends from the center of the body outwards or externally.
BSPO:curators
An axis that extends from the oral opening to the furthest point in an organism that is directly opposite.
wasila.dahdul
2013-07-02T11:29:33Z
spatial
BSPO:0000198
oral-aboral axis
An axis that extends from the oral opening to the furthest point in an organism that is directly opposite.
BSPO:PM
Anatomical surface that is located on the anterior side of the body or body part.
FBql:00005848
spatial
BSPO:0000371
anterior surface
Anatomical surface that is located on the anterior side of the body or body part.
BSPO:wd
Anatomical surface that is located on the posterior side of the body or body part.
FBql:00005849
spatial
BSPO:0000372
posterior surface
Anatomical surface that is located on the posterior side of the body or body part.
BSPO:wd
Anatomical surface that is located on the apical side of the body or body part.
FBql:00005854
spatial
BSPO:0000373
apical surface
Anatomical surface that is located on the apical side of the body or body part.
BSPO:wd
Anatomical surface that is located on the basal side of the body or body part.
FBql:00005855
spatial
BSPO:0000374
basal surface
Anatomical surface that is located on the basal side of the body or body part.
BSPO:wd
Anatomical surface that located on the dorsal side of the body or body part.
FBql:00005842
spatial
BSPO:0000379
dorsal surface
Anatomical surface that located on the dorsal side of the body or body part.
BSPO:wd
Anatomical surface that located on the lateral side of the body or body part.
FBql:00005844
spatial
BSPO:0000382
lateral surface
Anatomical surface that located on the lateral side of the body or body part.
BSPO:wd
Anatomical surface that is located on the ventral side of the body or body part.
FBql:00005843
spatial
BSPO:0000384
ventral surface
Anatomical surface that is located on the ventral side of the body or body part.
BSPO:wd
A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions.
FMA:242982
anatomical cross-section
anatomical section
plane
section
spatial
cross-section
BSPO:0000400
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
A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions.
BSPO:cjm
Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size.
FMA:11361
left/right plane
median plane
sagittal section
spatial
BSPO:0000417
sagittal plane
Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size.
BSPO:DOS
BSPO:cjm
BSPO:mah
An axis that extends from the center of organism to one or other side.
http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG
M-L axis
ML axis
medio-lateral axis
mediolateral axis
spatial
proximal-distal axis
BSPO:0001001
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.
medial-lateral axis
An axis that extends from the center of organism to one or other side.
BSPO:cjm
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.
spatial
CARO:0000000
Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.
anatomical entity
anatomical entity
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
CAROC:Brownsville2014
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
CARO:MAH
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
spatial
CARO:0000003
anatomical structure
connected anatomical structure
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
CC:DOS
An anatomical entity that has mass.
spatial
CARO:0000006
material anatomical entity
material anatomical entity
An anatomical entity that has mass.
CC:DOS
An anatomical entity that has no mass.
spatial
CARO:0000007
immaterial anatomical entity
An anatomical entity that has no mass.
CC:DOS
A one dimensional, immaterial anatomical entity.
spatial
CARO:0000008
anatomical line
A one dimensional, immaterial anatomical entity.
CC:DOS
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
spatial
CARO:0000010
anatomical boundary
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
CC:DOS
biological entity
The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
GO:0019952
GO:0050876
Wikipedia:Reproduction
reproductive physiological process
biological_process
GO:0000003
reproduction
The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
GOC:go_curators
GOC:isa_complete
GOC:jl
ISBN:0198506732
The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis.
G1 phase of mitotic cell cycle
biological_process
GO:0000080
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).
mitotic G1 phase
The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis.
GOC:mtg_cell_cycle
The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle.
S phase of mitotic cell cycle
S-phase of mitotic cell cycle
biological_process
GO:0000084
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).
mitotic S phase
The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle.
GOC:mtg_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.
G2 phase of mitotic cell cycle
biological_process
GO:0000085
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).
mitotic G2 phase
The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis.
GOC:mtg_cell_cycle
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.
M phase of mitotic cell cycle
M-phase of mitotic cell cycle
biological_process
GO:0000087
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).
mitotic M phase
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.
GOC:mtg_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.
biological_process
GO:0000088
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).
mitotic prophase
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.
GOC:mtg_cell_cycle
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.
biological_process
GO:0000089
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).
mitotic metaphase
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.
GOC:mtg_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.
biological_process
GO:0000090
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).
mitotic anaphase
The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of a mitotic cell cycle.
GOC:mtg_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.
biological_process
GO:0000093
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).
mitotic telophase
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.
GOC:mtg_cell_cycle
The cell cycle phase which is the first stage of prophase I in meiosis, and during which the chromosomes first become visible.
Wikipedia:Leptotene
Wikipedia:Meiosis#Leptotene
biological_process
GO:0000237
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).
leptotene
The cell cycle phase which is the first stage of prophase I in meiosis, and during which the chromosomes first become visible.
GOC:mtg_cell_cycle
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.
Wikipedia:Meiosis#Zygotene
Wikipedia:Zygotene
biological_process
GO:0000238
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).
zygotene
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.
GOC:mtg_cell_cycle
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.
Wikipedia:Meiosis#Pachytene
Wikipedia:Pachytene
biological_process
GO:0000239
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).
pachytene
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.
GOC:mtg_cell_cycle
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.
Wikipedia:Diplotene
Wikipedia:Meiosis#Diplotene
biological_process
GO:0000240
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).
diplotene
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.
GOC:mtg_cell_cycle
The cell cycle phase which follows diplotene during prophase I of meiosis, the separation of homologous chromosomes is complete and crossing over has occurred.
Wikipedia:Diakinesis
Wikipedia:Meiosis#Diakinesis
biological_process
GO:0000241
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).
diakinesis
The cell cycle phase which follows diplotene during prophase I of meiosis, the separation of homologous chromosomes is complete and crossing over has occurred.
GOC:mtg_cell_cycle
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
GO:0007067
Wikipedia:Mitosis
biological_process
mitosis
GO:0000278
Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.
mitotic cell cycle
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
GOC:mah
ISBN:0815316194
Reactome:69278
A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase.
Wikipedia:M_phase
M-phase
biological_process
GO:0000279
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).
M phase
A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase.
GOC:mtg_cell_cycle
The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
biological_process
karyokinesis
GO:0000280
nuclear division
The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
GOC:mah
A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring.
puberty
biological_process
reproductive developmental process
GO:0003006
developmental process involved in reproduction
A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring.
GOC:dph
GOC:isa_complete
puberty
GOC:dph
reproductive developmental process
GOC:dph
GOC:tb
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
molecular process
molecular function
GO:0003674
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
molecular_function
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
GOC:pdt
catalytic activity
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
GO:0008372
NIF_Subcellular:sao1337158144
cell or subcellular entity
cellular component
cellular_component
subcellular entity
GO:0005575
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
cellular_component
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
GOC:pdt
NIF_Subcellular:sao1337158144
subcellular entity
NIF_Subcellular:nlx_subcell_100315
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
jl
2013-12-19T15:25:51Z
GO:1902589
organelle organisation
single organism organelle organization
biological_process
organelle organization and biogenesis
single-organism organelle organization
GO:0006996
organelle organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
GOC:mah
single organism organelle organization
GOC:TermGenie
organelle organization and biogenesis
GOC:dph
GOC:jl
GOC:mah
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
Wikipedia:Cell_cycle
cell-division cycle
biological_process
GO:0007049
cell cycle
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
GOC:go_curators
GOC:mtg_cell_cycle
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.
biological_process
GO:0007128
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).
meiotic prophase I
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.
GOC:mtg_cell_cycle
The cell cycle phase, following prophase I, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis I.
biological_process
GO:0007132
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).
meiotic metaphase I
The cell cycle phase, following prophase I, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis I.
GOC:mtg_cell_cycle
The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis I.
biological_process
GO:0007133
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).
meiotic anaphase I
The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis I.
GOC:mtg_cell_cycle
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.
biological_process
GO:0007134
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).
meiotic telophase 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.
GOC:mtg_cell_cycle
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.
biological_process
GO:0007136
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).
meiotic prophase II
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.
GOC:mtg_cell_cycle
The cell cycle phase, following prophase II, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis II.
biological_process
GO:0007137
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).
meiotic metaphase II
The cell cycle phase, following prophase II, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis II.
GOC:mtg_cell_cycle
The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis II.
biological_process
GO:0007138
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).
meiotic anaphase II
The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis II.
GOC:mtg_cell_cycle
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.
biological_process
GO:0007139
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).
meiotic telophase 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.
GOC:mtg_cell_cycle
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.
https://github.com/geneontology/go-ontology/issues/24968
jl
2012-09-19T15:05:24Z
GO:0000004
GO:0007582
GO:0044699
Wikipedia:Biological_process
biological process
physiological process
biological_process
single organism process
single-organism process
GO:0008150
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological_process
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
GOC:pdt
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
GOC:pdt
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
jl
2012-12-11T16:56:55Z
GO:0008151
GO:0044763
GO:0050875
cell physiology
cellular physiological process
cell growth and/or maintenance
biological_process
single-organism cellular process
GO:0009987
This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
cellular process
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:go_curators
GOC:isa_complete
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
GO:0044235
GO:0071842
cell organisation
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
biological_process
cell organization and biogenesis
GO:0016043
cellular component organization
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
GOC:ai
GOC:jl
GOC:mah
cellular component organisation at cellular level
GOC:mah
cellular component organisation in other organism
GOC:mah
cell organization and biogenesis
GOC:mah
true
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Reactome:R-HSA-6788855
Reactome:R-HSA-6788867
phosphokinase activity
GO:0016301
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
kinase activity
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
ISBN:0198506732
Reactome:R-HSA-6788855
FN3KRP phosphorylates PsiAm, RibAm
Reactome:R-HSA-6788867
FN3K phosphorylates ketosamines
transferase activity
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).
https://github.com/geneontology/go-ontology/issues/22929
Wikipedia:Sexual_reproduction
biological_process
GO:0019953
Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.
sexual reproduction
A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid).
Wikipedia:Sexual_reproduction
The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.
biological_process
GO:0022402
cell cycle process
The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.
GOC:isa_complete
GOC:mtg_cell_cycle
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.
biological_process
GO:0022403
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).
cell cycle phase
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.
GOC:mtg_cell_cycle
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
jl
2012-09-19T15:56:06Z
GO:0044702
biological_process
single organism reproductive process
GO:0022414
reproductive process
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
GOC:dph
GOC:isa_complete
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
jl
2012-12-19T12:21:31Z
GO:0044767
development
biological_process
single-organism developmental process
GO:0032502
developmental process
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
GOC:isa_complete
The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
biological_process
GO:0043473
pigmentation
The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
GOC:jl
A distinct period or stage in a biological process or cycle.
jl
2014-07-16T13:12:40Z
biological_process
GO:0044848
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.
biological phase
A distinct period or stage in a biological process or cycle.
GOC:jl
The creation of two or more organelles by division of one organelle.
biological_process
GO:0048285
organelle fission
The creation of two or more organelles by division of one organelle.
GOC:jid
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
development of an anatomical structure
biological_process
GO:0048856
anatomical structure development
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
GO_REF:0000021
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
Wikipedia:Cell_division
biological_process
GO:0051301
Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.
cell division
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
GOC:di
GOC:go_curators
GOC:pr
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.
Wikipedia:G1_phase
biological_process
GO:0051318
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).
G1 phase
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.
GOC:mtg_cell_cycle
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).
Wikipedia:G2_phase
biological_process
GO:0051319
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).
G2 phase
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).
GOC:mtg_cell_cycle
The cell cycle phase, following G1, during which DNA synthesis takes place.
Wikipedia:S_phase
S-phase
biological_process
GO:0051320
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).
S phase
The cell cycle phase, following G1, during which DNA synthesis takes place.
GOC:mtg_cell_cycle
Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
https://github.com/geneontology/go-ontology/issues/24599
GO:0007126
Wikipedia:Meiosis
biological_process
meiosis
GO:0051321
Note that this term should not be confused with 'GO:0140013 ; meiotic nuclear division'. 'GO:0051321 ; meiotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140013 meiotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.
meiotic cell cycle
Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
GOC:ai
The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle.
Wikipedia:Anaphase
biological_process
GO:0051322
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).
anaphase
The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle.
GOC:mtg_cell_cycle
The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell.
Wikipedia:Metaphase
biological_process
GO:0051323
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).
metaphase
The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell.
GOC:mtg_cell_cycle
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.
Wikipedia:Prophase
biological_process
GO:0051324
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).
prophase
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.
GOC:mtg_cell_cycle
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.
resting phase
Wikipedia:Interphase
karyostasis
biological_process
GO:0051325
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).
interphase
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.
GOC:mtg_cell_cycle
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.
Wikipedia:Telophase
biological_process
GO:0051326
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).
telophase
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.
GOC:mtg_cell_cycle
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.
M phase of meiotic cell cycle
biological_process
GO:0051327
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).
meiotic M phase
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.
GOC:mtg_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.
interphase of meiotic cell cycle
biological_process
GO:0051328
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).
meiotic interphase
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.
GOC:mtg_cell_cycle
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.
interphase of mitotic cell cycle
biological_process
GO:0051329
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).
mitotic interphase
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.
GOC:mtg_cell_cycle
The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by meiosis and the beginning of DNA synthesis.
G1 phase of meiotic cell cycle
biological_process
GO:0051330
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).
meiotic G1 phase
The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by meiosis and the beginning of DNA synthesis.
GOC:mtg_cell_cycle
The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by meiosis.
G2 phase of meiotic cell cycle
biological_process
GO:0051331
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).
meiotic G2 phase
The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by meiosis.
GOC:mtg_cell_cycle
The cell cycle phase, following G1, during which DNA synthesis takes place as part of a meiotic cell cycle.
S phase of meiotic cell cycle
S-phase of meiotic cell cycle
premeiotic S-phase
biological_process
GO:0051332
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).
meiotic S phase
The cell cycle phase, following G1, during which DNA synthesis takes place as part of a meiotic cell cycle.
GOC:mtg_cell_cycle
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
mah
2010-09-10T01:39:16Z
GO:0071841
cellular component organisation or biogenesis
cellular component organisation or biogenesis at cellular level
cellular component organization or biogenesis at cellular level
biological_process
GO:0071840
cellular component organization or biogenesis
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
GOC:mah
cellular component organisation or biogenesis
GOC:mah
cellular component organisation or biogenesis at cellular level
GOC:mah
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.
biological_process
GO:0098762
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).
meiotic cell cycle phase
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.
GOC:dos
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.
biological_process
GO:0098763
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).
mitotic cell cycle phase
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.
GOC:dos
A meiotic cell cycle phase prior to a during which some part of meiosis I nuclear division or the proceeding cytokinesis occurs.
biological_process
GO:0098764
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).
meiosis I cell cycle phase
A meiotic cell cycle phase prior to a during which some part of meiosis I nuclear division or the proceeding cytokinesis occurs.
GOC:dos
A meiotic cell cycle phase that occurs after meiosis I (the first meiotic nuclear division).
biological_process
GO:0098765
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).
meiosis II cell cycle phase
A meiotic cell cycle phase that occurs after meiosis I (the first meiotic nuclear division).
GOC:dos
One of the two nuclear divisions that occur as part of the meiotic cell cycle.
https://github.com/geneontology/go-ontology/issues/19910
pg
2017-03-23T09:40:00Z
meiosis
biological_process
GO:0140013
meiotic nuclear division
One of the two nuclear divisions that occur as part of the meiotic cell cycle.
PMID:9334324
A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.
https://github.com/geneontology/go-ontology/issues/19910
pg
2017-03-23T14:44:23Z
mitosis
biological_process
GO:0140014
mitotic nuclear division
A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.
ISBN:0198547684
A process that is part of the meiotic cell cycle.
jl
2014-05-22T14:22:28Z
biological_process
GO:1903046
meiotic cell cycle process
A process that is part of the meiotic cell cycle.
GOC:TermGenie
GOC:mtg_cell_cycle
GO_REF:0000060
A process that is part of the mitotic cell cycle.
jl
2014-05-22T14:22:34Z
biological_process
GO:1903047
mitotic cell cycle process
A process that is part of the mitotic cell cycle.
GOC:TermGenie
GOC:mtg_cell_cycle
GO_REF:0000060
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: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
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
PERSON: Jonathan Rees
based on Oxford English Dictionary
symbol
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.
PERSON: Chris Stoeckert
OBI_0000142
information content entity
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
obsolescence reason specification
denotator type
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
denotator type
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: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
CRID symbol
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
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.
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.
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
CRID
Original proposal from Bjoern, discussions at IAO calls
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
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
CRID registry
Original proposal from Bjoern, discussions at IAO calls
https://github.com/information-artifact-ontology/IAO/issues/237
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.
Justin Whorton
Mathias Brochhausen
proper name
https://github.com/information-artifact-ontology/IAO/issues/237
Mathias Brochhausen
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)
identifier
A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
Justin Whorton
Mathias Brochhausen
dubbing process
naming
https://github.com/information-artifact-ontology/IAO/issues/237
Mathias Brochhausen
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.
Alan Ruttenberg
Justin Whorton
Mathias Brochhausen
code map
code system
codeset
coding system
controlled vocabulary
https://github.com/information-artifact-ontology/IAO/issues/237
Alan Ruttenberg
Clint Dowland
Matt Diller
Sarah Bost
William R. Hogan
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.
planned process
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
quality (PATO)
PATO:0000072
quality
PATO:0000001
quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATOC:GVG
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
quality
PATO:0000051
morphology
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
PATOC:GVG
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
PATO:0001647
relational shape quality
quality
PATO:0000052
Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.
shape
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
PATOC:GVG
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.
PATO:0000137
angular placement
quality
amount of rotation
angle
angular magnitude
plane angle
PATO:0000133
orientation
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.
PATOC:JE
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
PATO:0001032
PATO:0001631
location
placement
relational spatial quality
quality
PATO:0000140
position
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
PATOC:GVG
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
PATO:0002079
Wikipedia:Physical_property
relational physical quality
quality
PATO:0001018
physical quality
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
PATOC:GVG
A quality which inheres in a continuant.
PATO:0001237
PATO:0001238
snap:Quality
monadic quality of a continuant
multiply inhering quality of a physical entity
quality of a continuant
quality of a single physical entity
quality of an object
quality of continuant
monadic quality of an object
monadic quality of continuant
quality
PATO:0001241
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
physical object quality
A quality which inheres in a continuant.
PATOC:GVG
A shape quality inhering in a bearer by virtue of the bearer's having three angles.
deltoid
quality
delta shaped
triangle
triangle-shaped
PATO:0001875
triangular
A shape quality inhering in a bearer by virtue of the bearer's having three angles.
wordreference:wordreference
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.
wedge-shaped
quality
PATO:0001955
cuneate
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.
wordreference:wordreference
A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
quality
2-D projection
cross-sectional
PATO:0002006
2-D shape
A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
PATOC:CJM
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.
2014-10-17T14:24:19Z
quality
PATO:0005024
longitudinal orientation
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.
PATOC:WD
A shape that is in the form of a plug, being tube-like and expanded on one end.
2018-11-12T18:24:41Z
plug like
quality
PATO:0040012
plug shaped
A shape that is in the form of a plug, being tube-like and expanded on one end.
https://orcid.org/0000-0003-3162-7490
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Schmidtea_mediterranea_Developmental_Stages
Stage 1
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.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
protosphere
Schmidtea_mediterranea_Developmental_Stages
Stage 2
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.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Schmidtea_mediterranea_Developmental_Stages
Stage 3
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.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Schmidtea_mediterranea_Developmental_Stages
Stage 4
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.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Schmidtea_mediterranea_Developmental_Stages
Stage 5
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.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Schmidtea_mediterranea_Developmental_Stages
Stage 6
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.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
PMID:28812561
Schmidtea_mediterranea_Developmental_Stages
Stage 7
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.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
hatchling
newborn hatchling
Schmidtea_mediterranea_Developmental_Stages
Stage 8
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.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:15972844
PMID:25017721
PMID:25956527
PMID:26457503
PMID:26651295
PMID:27013241
PMID:27150006
PMID:27542689
PMID:28287248
PMID:28686611
PMID:28757112
PMID:29557542
PMID:29674432
PMID:29906446
sigma class neoblast
sigma-class neoblast
Planarian_Anatomy
sigma neoblast
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.
PMID:25017721
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.
Planarian_Anatomy
PLANA:0000011
protonephridial progenitor cell
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.
PMID:24523458
PMID:28072387
Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system.
neural committed stem cell
neural precursor cell
neural progenitor cell
neuronal progenitor
Planarian_Anatomy
PLANA:0000012
neural progenitor cell
Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system.
PMID:21282632
PMID:24173799
PMID:25356635
PMID:26057828
PMID:26525673
PMID:28072387
PMID:29674432
Musculature surrounding internal organs of the body.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
FBbt:00005070
PMID:26904543
PMID:30471994
visceral muscle
Planarian_Anatomy
visceral musculature
Musculature surrounding internal organs of the body.
PMID:26904543
PMID:30471994
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).
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:25017721
PMID:25956527
PMID:26457503
PMID:26651295
PMID:27013241
PMID:27150006
PMID:27542689
PMID:28292427
PMID:28757112
PMID:28807897
PMID:29158443
PMID:29557542
PMID:29674431
PMID:29674432
PMID:29906446
zeta
zeta class
zeta class neoblast
zeta-class neoblast
zeta-neoblast
Planarian_Anatomy
zeta neoblast
An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s).
PMID:25017721
An epithelial cell lacking cilia.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
XAO:0004225
Planarian_Anatomy
non ciliated epithelial cell
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
OCLC:16809160
PMID:15866156
PMID:16033796
PMID:16311336
PMID:16890156
PMID:17251262
PMID:17376870
PMID:17390146
PMID:17670787
PMID:17905225
PMID:17942485
PMID:18063755
PMID:18063757
PMID:18202849
PMID:18287199
PMID:18456843
PMID:18786419
PMID:19048075
PMID:19174194
PMID:19211673
PMID:19247960
PMID:19766622
PMID:19852954
PMID:19933103
PMID:20215344
PMID:20223763
PMID:20422023
PMID:20511647
PMID:20599901
PMID:20707997
PMID:20865784
PMID:20967238
PMID:21179478
PMID:21282632
PMID:21295483
PMID:21356107
PMID:21458439
PMID:21664348
PMID:21747960
PMID:21806978
PMID:21828097
PMID:21852957
PMID:21894189
PMID:21937596
PMID:22125640
PMID:22339734
PMID:22371573
PMID:22385657
PMID:22411224
PMID:22439894
PMID:22451003
PMID:22543868
PMID:22884275
PMID:23079596
PMID:23123964
PMID:23250205
PMID:23297191
PMID:23318635
PMID:23405188
PMID:23629965
PMID:23652002
PMID:23954785
PMID:24040508
PMID:24063805
PMID:24120894
PMID:24131630
PMID:24173799
PMID:24238224
PMID:24704339
PMID:24737865
PMID:24922054
PMID:25017721
PMID:25254346
PMID:25356635
PMID:25558068
PMID:25725068
PMID:25956527
PMID:26062938
PMID:26114597
PMID:26457503
PMID:26459857
PMID:26525673
PMID:26711341
PMID:27034770
PMID:27063937
PMID:27074666
PMID:27122174
PMID:27150006
PMID:27163480
PMID:27240733
PMID:27441386
PMID:27501047
PMID:27551436
PMID:27612382
PMID:27612384
PMID:27654173
PMID:28072387
PMID:28126842
PMID:28171748
PMID:28245923
PMID:28287248
PMID:28292427
PMID:28434803
PMID:28461239
PMID:28495872
PMID:28686611
PMID:28807897
PMID:28893948
PMID:29291981
PMID:29674431
PMID:29906446
PMID:30194301
PMID:30237141
PMID:30282036
PMID:30383829
PMID:30399335
PMID:30471994
PMID:30485821
PMID:30729158
PMID:30962434
https://doi.org/10.1101/279364
definitive pharynx
Planarian_Anatomy
pharynx
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.
OCLC:16809160
Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:16033796
PMID:17251262
PMID:17390146
PMID:17553481
PMID:17905225
PMID:17942485
PMID:18202849
PMID:19048075
PMID:20967238
PMID:21282632
PMID:21852957
PMID:22339734
PMID:22411224
PMID:22427692
PMID:22445864
PMID:22549959
PMID:22884275
PMID:23250205
PMID:23318641
PMID:24063805
PMID:24922054
PMID:25254346
PMID:25356635
PMID:25493551
PMID:25772472
PMID:26017970
PMID:26618653
PMID:27068018
PMID:27606067
PMID:27612384
PMID:27800171
PMID:28137894
PMID:28216315
PMID:28245923
PMID:28495872
PMID:28976975
PMID:29547123
PMID:29674431
PMID:29674432
PMID:30143032
PMID:30399335
PMID:30471994
PMID:30485821
UBERON:0006562
PRN
neuronal photoreceptive cell
optical neuron
photoreceptive neuron
photoreceptor cell
photosensitive cell
visual neuron
Planarian_Anatomy
photoreceptor neuron
Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain.
PMID:21852957
PMID:22884275
Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:18786419
PMID:22439894
PMID:25017721
PMID:26457503
PMID:28072387
Planarian_Anatomy
Category 4 cell
Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells.
PMID:25017721
PMID:26457503
Progenitor neoblasts implicated in the maintenance and regeneration of muscle fibers.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:29674431
PMID:29674432
PMID:30471994
Planarian_Anatomy
muscle progenitor cell
Progenitor neoblasts implicated in the maintenance and regeneration of muscle fibers.
PMID:25017721
Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
OCLC:16809160
PMID:19852954
PMID:19933103
PMID:21828097
PMID:21937596
PMID:22479207
PMID:23318635
PMID:23318641
PMID:23954785
PMID:24063805
PMID:24523458
PMID:24737865
PMID:24992682
PMID:25017721
PMID:25254346
PMID:26057828
PMID:26457503
PMID:26651295
PMID:26711341
PMID:27068018
PMID:27150006
PMID:27501047
PMID:27551436
PMID:27612384
PMID:28245923
PMID:28292427
PMID:28807897
PMID:29100657
PMID:29158443
PMID:29674431
PMID:29674432
UBERON:0006973
excretory organ
nephridia
osmoregulatory duct
protonephridial tubule
Planarian_Anatomy
protonephridia
Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct.
OCLC:16809160
PMID:21828097
PMID:26057828
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
biotype
Post-mitotic, ciliated epidermal cells.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:25017721
PMID:28072387
Planarian_Anatomy
Category 5 cell
Post-mitotic, ciliated epidermal cells.
PMID:25017721
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
FBbt:00001866
ISBN:9780070316607
PMID:28072387
temporary embryonic pharynx
Planarian_Anatomy
embryonic pharynx
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.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:11972158
PMID:28812561
asexual
asexual adult
asexual biotype
Planarian_Anatomy
Smed asexual biotype
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.
PMID:11972158
PMID:17376870
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].
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:16033796
PMID:16311336
PMID:17251262
PMID:18202849
PMID:19048075
PMID:19211673
PMID:19247960
PMID:20223763
PMID:20707997
PMID:20967238
PMID:21806978
PMID:22339734
PMID:22427692
PMID:22445864
PMID:22549959
PMID:22696458
PMID:23079596
PMID:23250205
PMID:23297191
PMID:23318641
PMID:23903188
PMID:24131630
PMID:24173799
PMID:24737865
PMID:24950970
PMID:25254346
PMID:25278423
PMID:25725068
PMID:26062938
PMID:26114597
PMID:26556349
PMID:27013241
PMID:27068018
PMID:27163480
PMID:27501047
PMID:27523733
PMID:27551436
PMID:27612384
PMID:27864883
PMID:28292427
PMID:29357350
PMID:29557542
PMID:29674431
PMID:30399335
UBERON:0001016
nerve system
Planarian_Anatomy
nervous system
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].
UBERON:0001016
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:17553481
PMID:17942485
PMID:18063757
PMID:18287199
PMID:19174194
PMID:19247960
PMID:19933103
PMID:20707997
PMID:20865784
PMID:20967238
PMID:21179478
PMID:21282632
PMID:21356107
PMID:21458439
PMID:21566185
PMID:21566195
PMID:21664348
PMID:21806978
PMID:21828097
PMID:22411224
PMID:22439894
PMID:22451003
PMID:22899852
PMID:23079596
PMID:23235145
PMID:23250205
PMID:23318635
PMID:23318641
PMID:23405188
PMID:23903188
PMID:23954785
PMID:24040508
PMID:24063805
PMID:24120894
PMID:24173799
PMID:24238224
PMID:24415944
PMID:24737865
PMID:24950970
PMID:24992682
PMID:25017721
PMID:25254346
PMID:25356635
PMID:25558068
PMID:25956527
PMID:26062938
PMID:26114597
PMID:26457503
PMID:26556349
PMID:26651295
PMID:27034770
PMID:27063937
PMID:27074666
PMID:27122174
PMID:27150006
PMID:27163480
PMID:27240733
PMID:27441386
PMID:27501047
PMID:27542689
PMID:27551436
PMID:27612382
PMID:27612384
PMID:27864883
PMID:28072387
PMID:28216315
PMID:28245923
PMID:28287248
PMID:28292427
PMID:28461239
PMID:28686611
PMID:28807897
PMID:29100657
PMID:29158443
PMID:29547123
PMID:29674431
PMID:29674432
PMID:29906446
PMID:30143032
PMID:30194301
PMID:30282036
PMID:30297872
PMID:30383829
PMID:30471994
PMID:30962434
UBERON:0000160
https://doi.org/10.1101/279364
adult gut
blind gut
definitive gut
digestive tract
gastrovascular digestive tract
gastrovascular tract
intestinal tract
intestine
three-branched gut
triclad gut
Planarian_Anatomy
gut
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.
PMID:3490491
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:11972158
PMID:19022767
PMID:28812561
hermaphroditic biotype
sexual
sexual hermaphrodite
Planarian_Anatomy
Smed sexual biotype
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.
PMID:11972158
PMID:19022767
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:18786419
PMID:20040488
PMID:21894189
PMID:22385657
PMID:22427692
PMID:22439894
PMID:22899852
PMID:23318635
PMID:23629965
PMID:24063805
PMID:24173799
PMID:24367277
PMID:25017721
PMID:26114597
PMID:26651295
PMID:27013241
PMID:27068018
PMID:27542689
PMID:28072387
PMID:29674431
Category 2 gene expressing cell
NB.21.11e expressing cell
Smed-NB.21.11e+ cell
early division progeny
early epidermal progenitor
early neoblast progeny
early post-mitotic progeny
early progeny
prog-1+ epidermal progenitor cell
Planarian_Anatomy
Category 2 cell
Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts.
PMID:18786419
PMID:20040488
PMID:22385657
PMID:25017721
PMID:26114597
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:20423827
OCLC:464776945
OCLC:82522822
PMID:28072387
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md
Planarian_Anatomy
primitive ectoderm
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.
OCLC:20423827
OCLC:464776945
OCLC:82522822
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md
The median line/ plane of bilateral symmetry along the anteroposterior axis.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
NCIT:C81170
Planarian_Anatomy
midline
Illustration of the midline (in green).
Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17251262
PMID:17390146
PMID:17553481
PMID:17905225
PMID:20967238
PMID:21282632
PMID:21458439
PMID:21852957
PMID:22339734
PMID:22445864
PMID:22884275
PMID:23250205
PMID:23318641
PMID:24063805
PMID:25254346
PMID:25493551
PMID:26017970
PMID:27122174
PMID:27551436
PMID:27606067
PMID:28137894
PMID:28245923
PMID:28287248
PMID:28495872
PMID:28976975
PMID:29158443
PMID:29674431
PMID:29674432
PMID:30471994
eye pigment cell
eye pigment cup cell
eye pigment producing cell
eye pigmented cell
melanin pigment cell
optic cup cell
photoceptor pigmented cell
Planarian_Anatomy
pigment cup cell
Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup.
PMID:21852957
PMID:22884275
The median line/plane of bilateral symmetry along the anteroposterior axis on the dorsal surface of the animal.
dorsal region of midline
Planarian_Anatomy
PLANA:0000032
dorsal midline
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.
epithelial progenitor
Planarian_Anatomy
PLANA:0000033
epidermal progenitor cell
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.
PMID:27150006
PMID:27606067
PMID:29674432
PMID:30282036
A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
OCLC:16809160
PMID:15866156
PMID:16311336
PMID:18786419
PMID:19048075
PMID:19247960
PMID:19852954
PMID:20215344
PMID:20511647
PMID:20599901
PMID:20865784
PMID:21179478
PMID:21282632
PMID:21295483
PMID:22252539
PMID:22549959
PMID:23235145
PMID:23297191
PMID:23954785
PMID:24120894
PMID:24173799
PMID:24922054
PMID:24950970
PMID:25558068
PMID:25772472
PMID:26114597
PMID:26457503
PMID:26651295
PMID:26711341
PMID:27034770
PMID:27074666
PMID:27150006
PMID:27163480
PMID:27240733
PMID:27501047
PMID:27612384
PMID:28137894
PMID:28216315
PMID:28245923
PMID:28292427
PMID:28686611
PMID:28757112
PMID:28976975
PMID:29100657
PMID:29158443
PMID:29273738
PMID:29674431
PMID:29674432
PMID:29906446
PMID:30194301
PMID:30282036
PMID:30962434
UBERON:0001003
definitive epidermis
epidermal layer
epidermis
epithelium
mature epidermis
tegument
Planarian_Anatomy
At present, this definition does not apply to epithelial structures other than the dorsal and ventral epidermis (i.e., the pharyngeal epithelium).
epidermis
A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal.
OCLC:16809160
Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:18786419
PMID:20040488
PMID:21894189
PMID:22252539
PMID:22427692
PMID:22439894
PMID:22899852
PMID:23297191
PMID:23318635
PMID:23629965
PMID:23954785
PMID:24063805
PMID:24173799
PMID:24367277
PMID:26114597
PMID:26457503
PMID:26651295
PMID:27013241
PMID:27068018
PMID:28072387
AGAT-1 expressing cell
AGAT1 expressing cell
Category 3 gene expressing cell
Smed-AGAT-1+ cell
late division progeny
late epidermal progenitor
late neoblast progeny
late postmitotic progeny
late progeny
Planarian_Anatomy
Category 3 cell
Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells.
PMID:18786419
PMID:20040488
PMID:26114597
PMID:26457503
An organ that detects light.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:15866156
PMID:15972844
PMID:16311336
PMID:16890156
PMID:17251262
PMID:17553481
PMID:17905225
PMID:17942485
PMID:18063755
PMID:18063757
PMID:18202849
PMID:18287199
PMID:18456843
PMID:18786419
PMID:19048075
PMID:19174194
PMID:19211673
PMID:19247960
PMID:19766622
PMID:19805089
PMID:19852954
PMID:20040488
PMID:20215344
PMID:20223763
PMID:20422023
PMID:20599901
PMID:20707997
PMID:20865784
PMID:20967238
PMID:21179478
PMID:21282632
PMID:21295481
PMID:21295483
PMID:21356107
PMID:21458439
PMID:21566185
PMID:21566195
PMID:21747960
PMID:21806978
PMID:21828097
PMID:21852957
PMID:21894189
PMID:21937596
PMID:22125640
PMID:22318224
PMID:22339734
PMID:22385657
PMID:22411224
PMID:22439894
PMID:22445864
PMID:22479207
PMID:22549959
PMID:22884275
PMID:22899852
PMID:23235145
PMID:23297191
PMID:23318635
PMID:23318641
PMID:23405188
PMID:23629965
PMID:23903188
PMID:24063805
PMID:24120894
PMID:24131630
PMID:24173799
PMID:24238224
PMID:24415944
PMID:24704339
PMID:24737865
PMID:24922054
PMID:24950970
PMID:24992682
PMID:25017721
PMID:25254346
PMID:25356635
PMID:25493551
PMID:25558068
PMID:25725068
PMID:25772472
PMID:25956527
PMID:26017970
PMID:26062938
PMID:26114597
PMID:26457503
PMID:26525673
PMID:26556349
PMID:26618653
PMID:26711341
PMID:26884331
PMID:27034770
PMID:27063937
PMID:27150006
PMID:27240733
PMID:27542689
PMID:27551436
PMID:27606067
PMID:27654173
PMID:27800171
PMID:28171748
PMID:28216315
PMID:28287248
PMID:28292427
PMID:28495872
PMID:28686611
PMID:28893948
PMID:28976975
PMID:29100657
PMID:29158443
PMID:29273738
PMID:29291974
PMID:29291981
PMID:29357350
PMID:29547123
PMID:29674431
PMID:30237141
PMID:30282036
PMID:30297872
PMID:30383829
PMID:30485821
PMID:30962434
UBERON:0000970
https://doi.org/10.1101/279364
cerebral eye
eye spot
eye-spot
eyespot
ocelli
photoreceptor
Planarian_Anatomy
Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The eyes are indicated by arrows. Scale bar = 250um
eye
An organ that detects light.
UBERON:0000970
we will move forward using "tissue" instead. We have not listed anything as a regenerating or developing tissue, so this seems unnecessary
obsolete definitive tissue
true
The median line/ plane of bilateral symmetry along the anteroposterior axis on the ventral surface of the animal.
ventral region of midline
Planarian_Anatomy
PLANA:0000038
ventral midline
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:25017721
PMID:26651295
PMID:27013241
PMID:27150006
PMID:27542689
PMID:28287248
PMID:28757112
PMID:28807897
PMID:29674431
PMID:29674432
PMID:29906446
gamma
gamma class neoblast
gamma-neoblast
gut progenitor cell
Planarian_Anatomy
gamma neoblast
An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut.
PMID:25017721
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
true
Stage 3-5 embryo hemisphere centered around the pole opposite the embryonic pharynx.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
UBERON:0008259
Planarian_Anatomy
aboral hemisphere
Stage 3-5 embryo hemisphere centered around the pole opposite the embryonic pharynx.
PMID:28072387
The single, central gut branch of the triclad gut anterior to the pharynx.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21664348
PMID:3490491
Planarian_Anatomy
anterior primary gut branch
The single, central gut branch of the triclad gut anterior to the pharynx.
PMID:3490491
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.
D/V boundary
DV border
DV boundary
DV domain
DV margin
body edge
body margin
body periphery
dorsal ventral boundary
dorsal-ventral boundary
dorsal/ventral compartment boundary of whole organism
dorsoventral margin
edge
Planarian_Anatomy
PLANA:0000043
dorsal ventral margin of the whole animal
Region along the edge of the animal where the dorsal and ventral surfaces meet.
ISBN:9780070316607
PMID:17905225
PMID:19174194
PMID:20865784
PMID:21295481
PMID:21295483
PMID:21458439
PMID:22549959
PMID:22696458
PMID:24415944
PMID:26457503
PMID:28216315
PMID:29357350
PMID:29674431
PMID:29674432
PMID:30399335
PMID:30485821
The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
OCLC:16809160
PMID:15866156
PMID:16033796
PMID:16344473
PMID:16890156
PMID:17251262
PMID:17376870
PMID:17553481
PMID:17670787
PMID:17905225
PMID:17942485
PMID:17999079
PMID:18063755
PMID:18063757
PMID:18202849
PMID:18287199
PMID:19048075
PMID:19174194
PMID:19211673
PMID:19247960
PMID:19766622
PMID:20215344
PMID:20422023
PMID:20844018
PMID:20967238
PMID:21179478
PMID:21282632
PMID:21295481
PMID:21458439
PMID:21566195
PMID:21806978
PMID:22074376
PMID:22125640
PMID:22339734
PMID:22411224
PMID:22445864
PMID:22451003
PMID:22549959
PMID:23235145
PMID:23297191
PMID:23318635
PMID:23318641
PMID:23405188
PMID:23652002
PMID:24131630
PMID:24173799
PMID:24238224
PMID:24415944
PMID:24950970
PMID:25254346
PMID:25278423
PMID:25356635
PMID:25404302
PMID:25725068
PMID:25772472
PMID:25956527
PMID:26017970
PMID:26884331
PMID:27013241
PMID:27074666
PMID:27163480
PMID:27612382
PMID:27612384
PMID:27800171
PMID:28072387
PMID:28126842
PMID:28216315
PMID:28287248
PMID:29291974
PMID:29291981
PMID:29547123
PMID:29674431
PMID:30194301
PMID:30237141
UBERON:0000955
https://doi.org/10.1101/279364
bi-lobed brain
bi-lobed cephalic ganglia
brain
cerebral ganglia
Planarian_Anatomy
cephalic ganglia
Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:26904543
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md
circular muscle fiber
Planarian_Anatomy
circular muscle cell
Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema.
PMID:26904543
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:16344473
PMID:19247960
PMID:20215344
PMID:21566185
PMID:21852957
PMID:21937596
PMID:22318224
PMID:22385657
PMID:22411224
PMID:22543868
PMID:22549959
PMID:22884275
PMID:22899852
PMID:23079596
PMID:23297191
PMID:23318641
PMID:23652002
PMID:23954785
PMID:24040508
PMID:24120894
PMID:24173799
PMID:25017721
PMID:25254346
PMID:25356635
PMID:26711341
PMID:27063937
PMID:27074666
PMID:27149082
PMID:27150006
PMID:27502555
PMID:27523733
PMID:27551436
PMID:28434803
PMID:29357350
PMID:29674431
PMID:29674432
PMID:29906446
PMID:30962434
adult pluripotent stem cell
cNeoblast
clonogenic stem cell
pluripotent stem cell
Planarian_Anatomy
clonogenic neoblast
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.
PMID:21566185
Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:26057828
PMID:27068018
PMID:29674431
UBERON:0001232
collection duct
Planarian_Anatomy
collecting duct
Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis.
PMID:26057828
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:23903188
PMID:26904543
PMID:27068018
PMID:28461239
PMID:28807897
PMID:30471994
diagonal fiber
diagonal muscle
diagonal muscle fiber
Planarian_Anatomy
diagonal muscle cell
Body wall muscle fibers arrayed diagonally along the anteroposterior axis.
PMID:26904543
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:15866156
PMID:16311336
PMID:16344473
PMID:17390146
PMID:17553481
PMID:17905225
PMID:18063757
PMID:18287199
PMID:19048075
PMID:19247960
PMID:19766622
PMID:19933103
PMID:20040488
PMID:20215344
PMID:20707997
PMID:21356107
PMID:21664348
PMID:21806978
PMID:22451003
PMID:22479207
PMID:23079596
PMID:24737865
PMID:24922054
PMID:25254346
PMID:25558068
PMID:26556349
PMID:27068018
PMID:27501047
PMID:29357350
UBERON:0001007
gastrointestinal system
gastrovascular system
Planarian_Anatomy
digestive system
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
UBERON:0001007
removing all processes. may bring back if PLANA expanded to cover processes.
obsolete direct development
true
removing all processes. may bring back if PLANA expanded to cover processes.
obsolete dispersed cleavage
true
Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21828097
PMID:27068018
UBERON:0004135
Planarian_Anatomy
distal tubule
Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells.
PMID:21828097
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.
dorsal epithelium
dorsal region of epidermis
Planarian_Anatomy
PLANA:0000054
dorsal region of the epidermis
Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe.
ISBN:9780070316607
PMID:17942485
PMID:19048075
PMID:19852954
PMID:20599901
PMID:20844018
PMID:22385657
PMID:22479207
PMID:26457503
PMID:27612382
PMID:28292427
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17553481
racing stripe
Planarian_Anatomy
dorsal stripe
Ciliated epithelial cells along the dorsal midline.
PMID:17553481
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:22074376
PMID:27149082
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000002.md
Planarian_Anatomy
ectolecithal embryo
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.
PMID:22074376
PMID:27149082
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000002.md
removing all processes. may bring back if PLANA expanded to cover processes.
obsolete embryonic cleavage
true
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
UBERON:6001842
Planarian_Anatomy
embryonic digestive system
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.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Planarian_Anatomy
embryonic gut cell
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.
PMID:28072387
The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:16809160
PMID:12888018
PMID:28072387
Planarian_Anatomy
embryonic wall
The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos.
OCLC:16809160
PMID:12888018
Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo with anatomical feature noted with black indicators.
Visceral muscle surrounding the gut.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21664348
PMID:22411224
PMID:23079596
PMID:26904543
PMID:30471994
PMID:30962434
UBERON:2001324
enteric muscle
intestinal muscle
Planarian_Anatomy
enteric musculature
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
OCLC:16809160
PMID:18063757
PMID:20707997
PMID:21806978
PMID:24737865
PMID:27063937
PMID:29674431
PMID:30485821
UBERON:0001043
gut pharynx intersection
pharynx root
root of pharynx
Planarian_Anatomy
esophagus
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0000478
Planarian_Anatomy
extraembryonic structure
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
UBERON:0000478
Terminal structure of protonephridia unit; consists of flame cells.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21828097
PMID:26057828
Planarian_Anatomy
flame bulb
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
OCLC:16809160
PMID:17670787
PMID:19247960
PMID:19852954
PMID:21828097
PMID:21937596
PMID:24523458
PMID:26057828
PMID:26711341
PMID:27068018
PMID:27542689
PMID:29674431
PMID:29674432
Planarian_Anatomy
flame cell
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.
OCLC:16809160
PMID:21828097
PMID:26057828
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.
The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0000509
ISBN:9780070316607
PMID:21282632
PMID:21664348
PMID:24120894
PMID:25558068
PMID:27441386
PMID:27501047
PMID:28287248
PMID:30608231
gut epithelia
gut epithelium
intestinal epithelium
Planarian_Anatomy
gastrodermis
The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle.
PMID:3490491
Secretory cells that release digestive enzymes into the lumen of the intestine.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0001540
PMID:20865784
PMID:21664348
PMID:23079596
PMID:27501047
PMID:28137894
PMID:28287248
PMID:29674431
PMID:29674432
Planarian_Anatomy
goblet cell
Secretory cells that release digestive enzymes into the lumen of the intestine.
PMID:3490491
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Planarian_Anatomy
embryonic gut cavity
Cavity encompassed by the embryonic digestive tract, prior to formation of the branched defintive gut.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:26904543
PMID:30962434
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md
inner longitudinal muscle fiber
inner longitudinal muscle layer
Planarian_Anatomy
inner longitudinal muscle cell
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.
PMID:26904543
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md
Absorptive digestive cells that engulf food particles for intracellular digestion.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:19933103
PMID:21664348
PMID:23079596
PMID:27542689
PMID:28072387
PMID:29674431
PMID:29674432
enterocyte
gut enterocyte
gut phagocyte
intestinal epithelial cell
Planarian_Anatomy
intestinal phagocyte
Absorptive digestive cells that engulf food particles for intracellular digestion.
PMID:3490491
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:23903188
PMID:26904543
PMID:27551436
PMID:28461239
PMID:28807897
PMID:30471994
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md
BW longitudinal fiber
body wall longitudinal fiber
longitudinal fiber
longitudinal muscle
longitudinal muscle cell
longitudinal muscle fiber
Planarian_Anatomy
longitudinal muscle cell
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.
PMID:26904543
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
OCLC:16809160
PMID:17251262
PMID:17905225
PMID:18287199
PMID:19174194
PMID:19211673
PMID:20707997
PMID:21295481
PMID:21458439
PMID:21806978
PMID:23954785
PMID:26457503
PMID:26556349
PMID:27034770
PMID:27063937
PMID:27074666
PMID:27122174
PMID:28807897
PMID:29674431
PMID:30399335
PMID:30471994
PMID:30485821
UBERON:0000165
anus
manus
Planarian_Anatomy
mouth
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.
OCLC:16809160
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000023
PMID:25278423
PMID:27149082
PMID:27163480
PMID:27304889
PMID:27330085
PMID:27501047
PMID:28072387
PMID:28434803
PMID:28812561
egg
female gamete
ovum
Planarian_Anatomy
oocyte
A female germ cell that has entered meiosis.
CL:0000023
A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:15866156
PMID:20707997
PMID:20865784
PMID:21458439
PMID:21828097
PMID:21852957
PMID:22411224
PMID:22427692
PMID:22445864
PMID:22549959
PMID:22884275
PMID:25493551
PMID:26017970
PMID:26618653
PMID:27068018
PMID:27240733
PMID:27542689
PMID:27606067
PMID:27800171
PMID:28495872
PMID:29547123
PMID:30143032
PMID:30194301
UBERON:0003072
eye cup
photoreceptor pigment cup
photoreceptor pigmentation
pigment cup
pigmented cell cup
pigmented optic cup
Planarian_Anatomy
optic cup
A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons.
PMID:21852957
PMID:22884275
Stage 3-5 embryo hemisphere centered around the embryonic pharynx.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Planarian_Anatomy
oral hemisphere
Stage 3-5 embryo hemisphere centered around the embryonic pharynx.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:26904543
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md
outer longitudinal muscle layer
Planarian_Anatomy
outer longitudinal muscle cell
Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers.
PMID:26904543
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md
Muscles that are present through the mesenchyme, inclusing dorsal-ventral muscles, intestinal muscles and pharynx muscles.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
OCLC:16809160
PMID:30962434
dorsoventral muscle fibers
parenchymal muscle
Planarian_Anatomy
parenchymal musculature
Muscles that are present through the mesenchyme, inclusing dorsal-ventral muscles, intestinal muscles and pharynx muscles.
OCLC:16809160
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:20967238
PMID:22339734
PMID:23903188
PMID:26017970
PMID:26884331
PMID:27150006
PMID:27612382
PMID:29674431
UBERON:0000010
Planarian_Anatomy
peripheral nervous system
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.
UBERON:0000010
An epithelial structure housing the pharynx, connected to the esophagus and mouth.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:16809160
pharyngeal pocket
pharyngeal pouch
Planarian_Anatomy
pharynx pouch
An epithelial structure housing the pharynx, connected to the esophagus and mouth.
OCLC:16809160
racing stripe is now a synonym of PLANA:0000055 dorsal stripe
obsolete racing stripe
true
The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21664348
PMID:23318641
PMID:24063805
major posterior gut branch
primary posterior intestinal branch
Planarian_Anatomy
posterior primary gut branch
The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch.
PMID:3490491
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Planarian_Anatomy
primitive gut cell
A phagocytic cell closely associated with the embryonic pharynx.
PMID:28072387
removing all processes. may bring back if PLANA expanded to cover processes.
obsolete protosphere
true
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21828097
PMID:21937596
PMID:26057828
PMID:27068018
UBERON:0004134
Planarian_Anatomy
proximal tubule
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.
PMID:21828097
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:17670787
PMID:19048075
PMID:19247960
PMID:19852954
PMID:20707997
PMID:21828097
PMID:21937596
PMID:22427692
PMID:23079596
PMID:23235145
PMID:23903188
PMID:24173799
PMID:24523458
PMID:24737865
PMID:25254346
PMID:26057828
PMID:26711341
PMID:27068018
PMID:27542689
PMID:28461239
PMID:29674431
PMID:30297872
UBERON:0001008
excretory system
protonephridial system
Planarian_Anatomy
renal system
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.
UBERON:0001008
Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21664348
PMID:27122174
PMID:28287248
PMID:30471994
Planarian_Anatomy
secondary gut branch
Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge.
PMID:3490491
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000019
PMID:17390146
PMID:20844018
PMID:22074376
PMID:25278423
PMID:27149082
PMID:27163480
PMID:27304889
PMID:28072387
PMID:29095551
https://doi.org/10.1101/279364
mature sperm
spermatozoa
Planarian_Anatomy
sperm
A mature male germ cell that develops from a spermatid.
CL:0000019
removing all processes. may bring back if PLANA expanded to cover processes.
obsolete sphere formation
true
Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:15599763
syncytial yolk cell
Planarian_Anatomy
yolk syncytium
Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2.
PMID:15599763
Gut branches originating from and connected to the secondary gut branches.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21664348
PMID:23250205
PMID:27122174
PMID:28137894
PMID:28287248
PMID:30194301
PMID:30471994
tertiary branch
tertiary intestinal branch
Planarian_Anatomy
tertiary gut branch
Gut branches originating from and connected to the secondary gut branches.
PMID:3490491
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
removing all processes. may bring back if PLANA expanded to cover processes.
obsolete tissue morphogenesis
true
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21852957
PMID:22884275
PMID:23250205
PMID:24040508
PMID:27606067
PMID:28072387
PMID:28245923
PMID:29674431
PMID:30485821
eye progenitor
eye progenitor cell
ovo+ eye progenitor
Planarian_Anatomy
trail cell
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.
PMID:22884275
Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells
cilated ventral epidermis
ciliated ventral epithelium
ventral epidermin
ventral epithelia
ventral epithelium
ventral region of epidermis
Planarian_Anatomy
PLANA:0000096
ventral epidermis
Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells
ISBN:9780070316607
PMID:15866156
PMID:17942485
PMID:19852954
PMID:20599901
PMID:21282632
PMID:23144623
PMID:23903188
PMID:24523458
PMID:25017721
PMID:26457503
PMID:26912790
PMID:27068018
PMID:28292427
PMID:29100657
PMID:30383829
PMID:30962434
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].
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0002328
EFO:0000896
FBbt:00001102
ISBN:9780070316607
MAT:0000339
MIAA:0000339
PMID:16033796
PMID:16890156
PMID:17251262
PMID:17390146
PMID:17553481
PMID:17905225
PMID:18063755
PMID:18063757
PMID:18202849
PMID:18287199
PMID:19174194
PMID:19211673
PMID:19247960
PMID:20215344
PMID:20223763
PMID:20422023
PMID:20599901
PMID:20707997
PMID:20967238
PMID:21179478
PMID:21282632
PMID:21566185
PMID:21806978
PMID:21828097
PMID:22074376
PMID:22125640
PMID:22339734
PMID:22479207
PMID:23250205
PMID:23297191
PMID:23318635
PMID:23954785
PMID:24063805
PMID:24120894
PMID:24131630
PMID:24173799
PMID:24950970
PMID:25254346
PMID:25356635
PMID:25558068
PMID:25772472
PMID:25956527
PMID:26017970
PMID:26062938
PMID:26457503
PMID:26556349
PMID:27013241
PMID:27034770
PMID:27150006
PMID:27163480
PMID:27612382
PMID:28072387
PMID:28126842
PMID:28245923
PMID:28807897
PMID:29291974
PMID:29674431
PMID:30143032
PMID:30471994
UBERON:0000934
WBbt:0005829
http://en.wikipedia.org/wiki/Ventral:nerve:cord
nlx:146329
VNC
nerve cord
ventral cord
Planarian_Anatomy
ventral nerve cord
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].
UBERON:0000934
Diploid cell resulting from the fusion of male and female gametes at fertilization. [The_Dictionary_of_Cell_and_Molecular_Biology:Third_Edition ].
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0000854
CL:0000365
PMID:28812561
UBERON:0000106
Planarian_Anatomy
zygote
Diploid cell resulting from the fusion of male and female gametes at fertilization. [The_Dictionary_of_Cell_and_Molecular_Biology:Third_Edition ].
CL:0000365
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0000938
CL:0000540
NCIT:C12623
PMID:16033796
PMID:16890156
PMID:17553481
PMID:17905225
PMID:18202849
PMID:18287199
PMID:19048075
PMID:19174194
PMID:19211673
PMID:20215344
PMID:21566185
PMID:22411224
PMID:22439894
PMID:22479207
PMID:22549959
PMID:23297191
PMID:23903188
PMID:23954785
PMID:24040508
PMID:24131630
PMID:24173799
PMID:24737865
PMID:24922054
PMID:24950970
PMID:25254346
PMID:25356635
PMID:25558068
PMID:26457503
PMID:26525673
PMID:27013241
PMID:27063937
PMID:27150006
PMID:27163480
PMID:27542689
PMID:27612382
PMID:27612384
PMID:27864883
PMID:28072387
PMID:28126842
PMID:28137894
PMID:28245923
PMID:28292427
PMID:28461239
PMID:28807897
PMID:29100657
PMID:29184198
PMID:29291974
PMID:29291981
PMID:29357350
PMID:29674432
PMID:30143032
PMID:30399335
WBbt:0003679
differentiated neuron
nerve cell
neural cell
neuronal cell
Planarian_Anatomy
neuron
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
CL:0000540
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000066
PMID:18202849
PMID:19048075
PMID:20865784
PMID:22479207
PMID:24737865
PMID:26114597
PMID:28072387
PMID:28461239
epidermis cell
Planarian_Anatomy
epithelial cell
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.
CL:0000066
A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000187
PMID:15972844
PMID:18202849
PMID:19174194
PMID:20422023
PMID:20511647
PMID:21458439
PMID:21828097
PMID:22252539
PMID:22479207
PMID:23318641
PMID:23405188
PMID:23954785
PMID:24415944
PMID:24737865
PMID:25254346
PMID:25558068
PMID:26062938
PMID:27063937
PMID:27523733
PMID:28216315
PMID:28287248
PMID:28292427
PMID:28461239
PMID:28686611
PMID:28807897
PMID:28893948
PMID:30471994
PMID:30962434
muscle fiber
myocyte
Planarian_Anatomy
muscle cell
A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
CL:0000187
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BSPO:0000070
PMID:28292427
PMID:29547123
body region
Planarian_Anatomy
anatomical region
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:16033796
PMID:16344473
PMID:16890156
PMID:17251262
PMID:17553481
PMID:17670787
PMID:17905225
PMID:17942485
PMID:18063757
PMID:18202849
PMID:18287199
PMID:19174194
PMID:19247960
PMID:19933103
PMID:20865784
PMID:20967238
PMID:21282632
PMID:21295481
PMID:21458439
PMID:21664348
PMID:21806978
PMID:21828097
PMID:22125640
PMID:22252539
PMID:22339734
PMID:22385657
PMID:22411224
PMID:22427692
PMID:22439894
PMID:22445864
PMID:23297191
PMID:23318635
PMID:23318641
PMID:23903188
PMID:24063805
PMID:24173799
PMID:24367277
PMID:24704339
PMID:24737865
PMID:24922054
PMID:24950970
PMID:25356635
PMID:25493551
PMID:25772472
PMID:25956527
PMID:26017970
PMID:26459857
PMID:26711341
PMID:26884331
PMID:27013241
PMID:27063937
PMID:27068018
PMID:27074666
PMID:27150006
PMID:27163480
PMID:27240733
PMID:27523733
PMID:27542689
PMID:27612382
PMID:27612384
PMID:27800171
PMID:27864883
PMID:28126842
PMID:28434803
PMID:28461239
PMID:28807897
PMID:28976975
PMID:29273738
PMID:29291981
PMID:30399335
PMID:30471994
PMID:30729158
PMID:30962434
UBERON:0001017
https://doi.org/10.1101/279364
CNS
head-restricted nervous system
Planarian_Anatomy
central nervous system
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.
UBERON:0001017
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:16809160
Planarian_Anatomy
rhabdite
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.
OCLC:16809160
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000151
NCIT:C13055
Planarian_Anatomy
secretory cell
A cell that specializes in controlled release of one or more substances.
CL:0000151
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 epithelial cell that has cilia.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000067
PMID:24737865
PMID:28461239
PMID:28807897
ciliated epidermal cell
Planarian_Anatomy
ciliated epithelial cell
An epithelial cell that has cilia.
CL:0000067
An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000428
ISBN:9780070316607
PMID:22074376
PMID:27149082
PMID:28072387
PMID:28434803
PMID:29674431
vitellocyte
Planarian_Anatomy
yolk cell
An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo.
PMID:27149082
extra layer of complexity not needed upon further examination
obsolete anatomical compartment subdivision feature
true
foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the pharynx.
Planarian_Anatomy
PLANA:0000110
pharynx progenitor cell
foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the pharynx.
PMID:24737865
PMID:25254346
Ciliated epithelial cells that assemble into proximal tubules.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0006154
PMID:21828097
PMID:29674431
proximal tubule cell
Planarian_Anatomy
proximal tubule epithelial cell
Ciliated epithelial cells that assemble into proximal tubules.
PMID:21828097
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.
removing all processes. may bring back if PLANA expanded to cover processes.
obsolete Schmidtea mediterranea developmental term
true
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0000479
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000000.md
Planarian_Anatomy
tissue
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.
UBERON:0000479
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0000467
Planarian_Anatomy
anatomical system
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
UBERON:0000467
Nonciliated epithelial cells that assemble into protonephridial distal tubules.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21828097
PMID:29674431
distal tubule cell
Planarian_Anatomy
distal tubule epithelial cell
Nonciliated epithelial cells that assemble into protonephridial distal tubules.
PMID:21828097
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0000922
Planarian_Anatomy
embryo
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.
UBERON:0000922
Anatomical structure that is part of an embryo.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0000174
UBERON:0002050
Planarian_Anatomy
embryonic structure
Anatomical structure that is part of an embryo.
UBERON:0002050
Nonciliated epithelial cells that assemble into collecting ducts.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:26057828
Planarian_Anatomy
collecting duct epithelial cell
Nonciliated epithelial cells that assemble into collecting ducts.
PMID:26057828
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.
A post-mitotic, terminally differentiated cell type found in planarian embryos, juveniles and/or adult animals.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:29674432
Planarian_Anatomy
terminally differentiated cell
A cycling neoblast and/or post-mitotic cell that is primed or irreversibly committed to a tissue-specific differentation program
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21852957
PMID:29674432
https://doi.org/10.1101/279364
precursor cell
Planarian_Anatomy
progenitor cell
A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000034
PMID:17376870
PMID:19805089
PMID:20422023
PMID:20707997
PMID:21937596
PMID:22385657
PMID:23123964
PMID:23318635
PMID:24063805
PMID:24173799
PMID:26062938
PMID:26651295
PMID:26711341
PMID:27013241
PMID:27034770
PMID:27501047
PMID:29124009
https://doi.org/10.1101/279364
Planarian_Anatomy
stem cell
A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
CL:0000034
A mature sexual reproductive cell having a single set of unpaired chromosomes.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000300
PMID:20844018
PMID:23652002
PMID:27149082
PMID:27163480
PMID:27304889
PMID:28434803
Planarian_Anatomy
gamete
A mature sexual reproductive cell having a single set of unpaired chromosomes.
CL:0000300
A cell of the embryo.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0002321
Planarian_Anatomy
embryonic cell
A cell of the embryo.
CL:0002321
The sensory system subserving the sense of vision.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0002104
Planarian_Anatomy
visual system
The sensory system subserving the sense of vision.
UBERON:0002104
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0001032
Planarian_Anatomy
sensory system
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
UBERON:0001032
Anatomical system that has as its parts the organs concerned with reproduction.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0000990
Planarian_Anatomy
reproductive system
Anatomical system that has as its parts the organs concerned with reproduction.
UBERON:0000990
Ciliated epithelial cells that assemble into the oviduct.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:22074376
Planarian_Anatomy
oviduct epithelial cell
Ciliated epithelial cells that assemble into the oviduct.
PMID:22074376
Ciliated epithelial cells comprising the sperm ducts.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:19022767
PMID:22074376
Planarian_Anatomy
sperm duct epithelial cell
Ciliated epithelial cells comprising the sperm ducts.
PMID:19022767
PMID:22074376
replacing with UBERON term
obsolete anatomical structure
true
piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:29168507
Planarian_Anatomy
circular muscle progenitor cell
piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers.
PMID:29168507
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0001048
Planarian_Anatomy
primordium
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue.
UBERON:0001048
removing all processes. may bring back if PLANA expanded to cover processes.
obsolete gametogenesis
true
A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:18202849
PMID:7466176
mechanoreceptor
Planarian_Anatomy
mechanoreceptor cell
A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
PMID:18202849
PMID:7466176
piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:29168507
Planarian_Anatomy
longitudinal muscle progenitor cell
piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers.
PMID:29168507
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17390146
Planarian_Anatomy
female primordial germ cell
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.
PMID:17390146
Anatomical structure that is an individual member of Schmidtea mediterranea or any other flatworm of the class Turbellaria.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17251262
PMID:26711341
PMID:27502555
PMID:28976975
PMID:29906446
UBERON:0000468
WW
intact animal
intact planarian
whole animal
whole body
whole worm
Planarian_Anatomy
whole organism
Anatomical structure that is an individual member of Schmidtea mediterranea or any other flatworm of the class Turbellaria.
UBERON:0000468
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).
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0031099
GOC:mah
GOC:pr
Wikipedia:Regeneration:(biology)
regernative development
Planarian_Anatomy
regeneration
The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass).
GO:0031099
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:29100657
Planarian_Anatomy
Hyman vesicle
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.
PMID:29100657
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.
anterior region of whole organism
Planarian_Anatomy
PLANA:0000140
anterior region of the whole animal
Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus.
ISBN:9780070316607
OCLC:16809160
PMID:16033796
PMID:16311336
PMID:17251262
PMID:17376870
PMID:17390146
PMID:18063757
PMID:18456843
PMID:18786419
PMID:19048075
PMID:19174194
PMID:19211673
PMID:19247960
PMID:19766622
PMID:19805089
PMID:19852954
PMID:19933103
PMID:20215344
PMID:20422023
PMID:21282632
PMID:21295481
PMID:21356107
PMID:21566185
PMID:21806978
PMID:21828097
PMID:21852957
PMID:21894189
PMID:21937596
PMID:22339734
PMID:22385657
PMID:22439894
PMID:22479207
PMID:22696458
PMID:22899852
PMID:23250205
PMID:23297191
PMID:23318635
PMID:23405188
PMID:23629965
PMID:23903188
PMID:24040508
PMID:24063805
PMID:24367277
PMID:24415944
PMID:24523458
PMID:24950970
PMID:25017721
PMID:25278423
PMID:25356635
PMID:25493551
PMID:25558068
PMID:26062938
PMID:26114597
PMID:26556349
PMID:26651295
PMID:26884331
PMID:27013241
PMID:27034770
PMID:27063937
PMID:27074666
PMID:27150006
PMID:27240733
PMID:27612382
PMID:27612384
PMID:27800171
PMID:28072387
PMID:28287248
PMID:28893948
PMID:29273738
PMID:29547123
PMID:29557542
PMID:29906446
PMID:30143032
PMID:30471994
PMID:30485821
PMID:30962434
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.
dorsal region of whole organism
Planarian_Anatomy
PLANA:0000141
dorsal region of the whole animal
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
posterior region of whole organism
Planarian_Anatomy
PLANA:0000142
posterior region 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.
ventral region of whole organism
Planarian_Anatomy
PLANA:0000143
ventral region of the whole animal
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:20967238
PMID:22074376
PMID:25278423
PMID:27149082
Planarian_Anatomy
bursal canal
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.
PMID:22074376
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:16344473
PMID:19247960
PMID:20967238
PMID:21566185
PMID:22074376
PMID:22899852
PMID:25278423
PMID:27149082
PMID:28072387
PMID:28434803
https://doi.org/10.1101/279364
common gonopore
genital pore
Planarian_Anatomy
gonopore
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.
PMID:22074376
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
NCIT:C12404
PMID:16344473
PMID:17376870
PMID:17390146
PMID:18456843
PMID:19247960
PMID:20844018
PMID:20967238
PMID:22074376
PMID:22318224
PMID:22371573
PMID:23652002
PMID:25278423
PMID:25404302
PMID:27149082
PMID:27163480
PMID:27330085
PMID:28072387
PMID:28434803
PMID:28812561
https://doi.org/10.1101/279364
female gonad
Planarian_Anatomy
ovary
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.
PMID:17376870
Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:16344473
PMID:17376870
PMID:19247960
PMID:20844018
PMID:20967238
PMID:22074376
PMID:23652002
PMID:25278423
PMID:27149082
PMID:27163480
PMID:28072387
https://doi.org/10.1101/279364
ovovitilline duct
Planarian_Anatomy
oviduct
Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium.
PMID:22074376
A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:20967238
PMID:22074376
PMID:23652002
PMID:25278423
PMID:27074666
PMID:28072387
PMID:28434803
https://doi.org/10.1101/279364
penis
penis bulb
Planarian_Anatomy
penis papilla
A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal.
PMID:22074376
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:17390146
PMID:19022767
PMID:19247960
PMID:20844018
PMID:20967238
PMID:22074376
PMID:23652002
PMID:25278423
PMID:27149082
PMID:27304889
PMID:28072387
PMID:28434803
ZFA:0001268
https://doi.org/10.1101/279364
seminal duct
sperm ductule
Planarian_Anatomy
sperm duct
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.
PMID:19022767
PMID:22074376
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:16344473
PMID:17376870
PMID:18456843
PMID:19022767
PMID:19247960
PMID:20844018
PMID:20967238
PMID:22074376
PMID:22318224
PMID:22371573
PMID:23629965
PMID:23652002
PMID:25278423
PMID:25404302
PMID:27149082
PMID:27163480
PMID:27304889
PMID:27330085
PMID:28072387
PMID:28434803
PMID:28812561
PMID:29095551
UBERON:0000473
https://doi.org/10.1101/279364
male gonad
testis lobe
testis lobule
Planarian_Anatomy
testis
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.
PMID:19022767
replacing with UBERON term
obsolete developing anatomical structure
true
Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:20423827
OCLC:464776945
OCLC:82522822
PMID:28072387
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md
Planarian_Anatomy
primitive ectoderm cell
Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2.
OCLC:20423827
OCLC:464776945
OCLC:82522822
PMID:28072387
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md
replace with blastomere only
obsolete blastomere compartment
true
A postnatal stage of Smed development that initiates with hatching and proceeds until sexual maturity is reached. Reproductive structures develop during the juvenile stage.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0034919
Planarian_Anatomy
juvenile stage
Products of the reproductive system include gametes, zygotes, yolk cells and egg capsules.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
reproductive system product
A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos.Egg capsules are anchored to a substrate via a stalk.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:16344473
PMID:17376870
PMID:18942102
PMID:20967238
PMID:22074376
PMID:22371573
PMID:25278423
PMID:27149082
PMID:28072387
PMID:28434803
PMID:28812561
https://doi.org/10.1101/279364
capsule
cocoon
Planarian_Anatomy
egg capsule
A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos.Egg capsules are anchored to a substrate via a stalk.
PMID:18942102
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:16344473
PMID:17376870
PMID:17390146
PMID:20844018
PMID:22074376
PMID:22252538
PMID:22371573
PMID:23652002
PMID:27149082
PMID:27163480
PMID:28434803
PMID:28976975
UBERON:0000991
https://doi.org/10.1101/279364
Planarian_Anatomy
gonad
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
UBERON:0000991
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17376870
PMID:17390146
Planarian_Anatomy
male primordial germ cell
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.
PMID:17376870
PMID:17390146
gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:19022767
PMID:20844018
PMID:27163480
PMID:27330085
SSC
male germline stem cell
Planarian_Anatomy
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.
PMID:19022767
PMID:20844018
PMID:27163480
PMID:27330085
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000020
PMID:23629965
PMID:27163480
PMID:27330085
https://doi.org/10.1101/279364
spermatogonial cell
Planarian_Anatomy
spermatogonium
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.
PMID:27163480
PMID:27330085
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000017
PMID:17376870
PMID:20844018
PMID:22074376
PMID:25278423
PMID:25404302
PMID:27163480
PMID:27304889
PMID:27330085
PMID:29095551
primary spermatocyte
Planarian_Anatomy
spermatocyte
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.
PMID:27330085
A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000018
PMID:17376870
PMID:20844018
PMID:22074376
PMID:25278423
PMID:25404302
PMID:27163480
PMID:27304889
PMID:27330085
Planarian_Anatomy
spermatid
A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa.
CL:0000018
A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:23652002
PMID:25278423
PMID:27149082
PMID:27163480
PMID:27330085
female germ cell
female germline cell
female germline stem cell
oogonial stem cell
ovarian germline stem cell
Planarian_Anatomy
oogonial stem cell
A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes.
PMID:19022767
PMID:20844018
Glands surrounding the genital atrium that are required for production of the proteinaceous egg capsule shell and stalk.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ASIN:B000M4NK9M
ISBN:9780070316607
PMID:18942102
PMID:20967238
PMID:22074376
PMID:23652002
PMID:25278423
PMID:27149082
shell gland
Planarian_Anatomy
cement gland
Glands surrounding the genital atrium that are required for production of the proteinaceous egg capsule shell and stalk.
ASIN:B000M4NK9M
PMID:18942102
PMID:22074376
PMID:27149082
removing all processes. may bring back if PLANA expanded to cover processes.
obsolete oviparity
true
removing all processes. may bring back if PLANA expanded to cover processes.
obsolete cross-fertilization
true
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0000535
Planarian_Anatomy
germ cell
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.
BTO:0000535
A male germ cell is a germ cell that supports male gamete production.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000015
PMID:23652002
PMID:27304889
PMID:27330085
Planarian_Anatomy
male germ cell
A male germ cell is a germ cell that supports male gamete production.
CL:0000015
Female germ cell is a germ cell that supports female gamete production.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000021
Planarian_Anatomy
female germ cell
Female germ cell is a germ cell that supports female gamete production.
CL:0000021
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:19022767
PMID:20844018
PMID:22074376
PMID:25278423
PMID:27149082
PMID:27163480
PMID:28434803
Planarian_Anatomy
tuba
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.
PMID:19022767
PMID:20844018
PMID:22074376
PMID:27149082
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:16344473
PMID:16932928
PMID:17390146
PMID:18942102
PMID:19247960
PMID:22074376
PMID:23652002
PMID:27149082
PMID:27163480
PMID:27501047
PMID:28072387
PMID:28434803
https://doi.org/10.1101/279364
vitellaria
vitellarium
yolk gland
Planarian_Anatomy
vitelline gland
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.
PMID:16932928
PMID:18942102
PMID:27149082
Accessory reproductive structures involved in copulation, egg capsule development and laying.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:16344473
PMID:17376870
PMID:17390146
PMID:19247960
PMID:20967238
PMID:22074376
PMID:23652002
PMID:27149082
PMID:27163480
PMID:28434803
copulatory complex
Planarian_Anatomy
copulatory apparatus
Accessory reproductive structures involved in copulation, egg capsule development and laying.
PMID:22074376
An organ that receives and stores sperm from mating partners.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:20967238
PMID:22074376
PMID:25278423
https://doi.org/10.1101/279364
bursa
male antrum
Planarian_Anatomy
copulatory bursa
An organ that receives and stores sperm from mating partners.
PMID:22074376
Glandular pouches adjoining the sperm ducts which produce seminal fluid.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
NCIT:C12787
PMID:19022767
PMID:22074376
UBERON:0000998
Planarian_Anatomy
seminal vesicle
Glandular pouches adjoining the sperm ducts which produce seminal fluid.
PMID:19022767
PMID:22074376
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:20844018
PMID:27163480
PMID:27304889
PMID:27330085
PMID:29095551
https://doi.org/10.1101/279364
Planarian_Anatomy
round spermatid
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.
PMID:27163480
PMID:27330085
Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:20844018
PMID:27163480
PMID:27304889
PMID:27330085
PMID:29095551
elongating spermatid
Planarian_Anatomy
elongate spermatid
Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm.
PMID:27163480
PMID:27330085
An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
FMA:83673
Planarian_Anatomy
oogonial cell
An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes.
FMA:83673
Any collection of muscles that is part of a body wall [Automatically generated definition].
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BSA:0000058
BTO:0001863
FMA:86931
PMID:19048075
PMID:19174194
PMID:21828097
PMID:22385657
PMID:24992682
PMID:27063937
PMID:27074666
PMID:28171748
PMID:29100657
PMID:29547123
PMID:29674431
PMID:29674432
PMID:30471994
PMID:30962434
UBERON:0004462
WBbt:0005813
BWM
body muscle
body wall muscle
body wall muscles
body-wall muscle
body-wall musculature
muscle layer surrounding the body wall
Planarian_Anatomy
body wall musculature
Any collection of muscles that is part of a body wall [Automatically generated definition].
UBERON:0004462
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).
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ASIN:B000M4NK9M
pharyngeal longitudinal muscle cell
pharyngeal longitudinal muscle fiber
pharynx longitudinal muscle fiber
Planarian_Anatomy
pharynx longitudinal muscle cell
Pharynx muscle fibers running anteroposterior (proximal to distal).
ASIN:B000M4NK9M
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.
replacing with UBERON term
obsolete anatomical cavity
true
replacing with UBERON term
obsolete anatomical entity
true
replacing with UBERON term
obsolete immaterial anatomical entity
true
replacing with UBERON term
obsolete anatomical point
true
replacing with UBERON term
obsolete anatomical space
true
Anatomical space enclosed by the pharynx inner epithelium.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17251262
PMID:26711341
PMID:27502555
PMID:28976975
PMID:29906446
UBERON:0000468
cavity of pharynx
pharyngeal lumen
pharynx cavity
Planarian_Anatomy
pharynx lumen
Anatomical space enclosed by the pharynx inner epithelium.
UBERON:0000468
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17553481
PMID:21664348
PMID:21828097
PMID:28072387
UBERON:0006909
digestive system lumen
gut cavity
lumen of digestive tract
Planarian_Anatomy
digestive tract lumen
An anatomical space that is surrounded by a digestive tract.
PMID:21664348
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17670787
PMID:29674431
PMID:30399335
UBERON:0000166
pharyngeal mouth opening
pharynx opening
Planarian_Anatomy
oral opening
The orifice that connects the mouth to the exterior of the body.
UBERON:0000166
Anatomical space between the pharynx and the epithelial cells comprising parapharyngeal pouch.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:16809160
pharnygeal cavity
pharyngeal pouch cavity
Planarian_Anatomy
pharynx pouch cavity
Anatomical space between the pharynx and the epithelial cells comprising parapharyngeal pouch.
OCLC:16809160
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.
apical surface of epidermis
Planarian_Anatomy
PLANA:0000409
apical surface of the epidermis
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.
basal surface of epidermis
Planarian_Anatomy
PLANA:0000410
basal surface of the epidermis
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21664348
lumen gut surface
Planarian_Anatomy
gastrodermis surface
The surface of the gastrodermis in contact with the gut lumen.
PMID:21664348
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0001731
pharyngeal inner epidermis surface
pharyngeal inner epithelial surface
pharyngeal lumen epithelial surface
pharynx inner epidermis surface
pharynx lumen epithelial surface
Planarian_Anatomy
pharynx inner epithelium surface
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:24120894
PMID:29865769
doi:10.1002/jmor.1052060308
pharyngeal outer epidermis surface
pharyngeal outer epithelial surface
pharynx outer epidermis surface
pharynx outer side
Planarian_Anatomy
pharynx outer epithelium surface
Epithelial surface covering the outside of the pharynx.
PMID:29865769
doi:10.1002/jmor.1052060308
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:16809160
pharyngeal pouch surface
pharynx pouch surface
Planarian_Anatomy
pharynx pouch epithelial surface
The surface of the parapharyngeal pouch facing the pharynx.
OCLC:16809160
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.
replacing with UBERON term
obsolete organism subdivision
true
Anatomical structure which is a subdivision of a whole adult or juvenile organism, consisting of components of multiple anatomical systems.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
definitive organism subdivision
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).
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0000033
head
Planarian_Anatomy
head region
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:16809160
PMID:17251262
PMID:18202849
PMID:18287199
PMID:21295481
PMID:21852957
PMID:22339734
PMID:23318641
PMID:24120894
PMID:24922054
PMID:26556349
PMID:27063937
PMID:27150006
PMID:28216315
PMID:28245923
PMID:28287248
PMID:28893948
PMID:29547123
PMID:29674431
https://doi.org/10.1101/279364
neck
pre-pharyngeal region
pre-pharynx region
Planarian_Anatomy
prepharyngeal region
Region of the juvenile or adult animal between the posterior end of the cephalic ganglia and the anterior end of the pharynx.
OCLC:16809160
Depicted by field contains diagram representation of body region.
Region of the animal lateral to and surrounding the pharynx.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:22125640
PMID:25956527
PMID:26651295
PMID:28807897
PMID:29674431
PMID:30143032
para-pharyngeal
parapharyngeal
peri-pharyngeal
peripharyngeal region
trunk
Planarian_Anatomy
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.
parapharyngeal region
Depicted by field contains diagram representation of body region.
Caudal region, beginning at the mouth and ending at posterior pole.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0002415
tail
Planarian_Anatomy
tail region
Depicted by field contains diagram representation of body region.
Medial region of the tail; the parenchymal space between the posterior primary gut branches.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
tail stripe
Medial region of the tail; the parenchymal space between the posterior primary gut branches.
PMID:29906446
Anatomical structure which is a subdivision of a whole developing/ embryonic organism, consisting of components of multiple anatomical systems.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
embryonic subdivision
replacing with UBERON term
obsolete material anatomical entity
true
extra layer of complexity not needed upon further examination
obsolete definitive anatomical structure
true
replacing with UBERON term
obsolete acellular anatomical structure
true
An anatomical structure that has more than one cell as a part.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0010000
Planarian_Anatomy
multicellular anatomical structure
An anatomical structure that has more than one cell as a part.
UBERON:0010000
Total musculature of the planarian body.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:15866156
PMID:17942485
PMID:20707997
PMID:24950970
PMID:27068018
PMID:28137894
UBERON:0001015
muscular system
musculature
Planarian_Anatomy
musculature system
Total musculature of the planarian body.
UBERON:0001015
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0006347
PMID:15866156
PMID:15972844
PMID:16033796
PMID:16311336
PMID:16344473
PMID:16890156
PMID:17251262
PMID:17376870
PMID:17390146
PMID:17553481
PMID:17670787
PMID:17905225
PMID:18063755
PMID:18202849
PMID:18287199
PMID:18456843
PMID:18786419
PMID:19048075
PMID:19174194
PMID:19247960
PMID:19564616
PMID:19766622
PMID:19805089
PMID:20040488
PMID:20215344
PMID:20223763
PMID:20599901
PMID:20844018
PMID:21179477
PMID:21179478
PMID:21282632
PMID:21356107
PMID:21458439
PMID:21566185
PMID:21664348
PMID:21747960
PMID:21806978
PMID:21852957
PMID:21894189
PMID:21937596
PMID:22125640
PMID:22223737
PMID:22252538
PMID:22252539
PMID:22318224
PMID:22339734
PMID:22371573
PMID:22385657
PMID:22411224
PMID:22427692
PMID:22439894
PMID:22445864
PMID:22451003
PMID:22479207
PMID:22543868
PMID:22549959
PMID:22696458
PMID:22884275
PMID:22899852
PMID:23079596
PMID:23235145
PMID:23250205
PMID:23297191
PMID:23318635
PMID:23318641
PMID:23405188
PMID:23629965
PMID:23903188
PMID:23954785
PMID:24040508
PMID:24063805
PMID:24120894
PMID:24131630
PMID:24173799
PMID:24238224
PMID:24367277
PMID:24415944
PMID:24523458
PMID:24704339
PMID:24737865
PMID:24903754
PMID:24922054
PMID:24992682
PMID:25017721
PMID:25254346
PMID:25278423
PMID:25356635
PMID:25956527
PMID:26057828
PMID:26114597
PMID:26457503
PMID:26459857
PMID:26516985
PMID:26525673
PMID:26556349
PMID:26618653
PMID:26651295
PMID:26884331
PMID:27013241
PMID:27063937
PMID:27068018
PMID:27122174
PMID:27149082
PMID:27150006
PMID:27163480
PMID:27304889
PMID:27441386
PMID:27501047
PMID:27502555
PMID:27523733
PMID:27542689
PMID:27551436
PMID:27606067
PMID:27612384
PMID:27654173
PMID:27864883
PMID:28072387
PMID:28137894
PMID:28171748
PMID:28216315
PMID:28287248
PMID:28292427
PMID:28461239
PMID:28686611
PMID:28757112
PMID:28893948
PMID:29095551
PMID:29100657
PMID:29124009
PMID:29273738
PMID:29291974
PMID:29364871
PMID:29547123
PMID:29557542
PMID:29674431
PMID:29674432
PMID:29906446
PMID:30143032
PMID:30194301
PMID:30237141
PMID:30282036
PMID:30297872
PMID:30471994
PMID:30485821
PMID:30729158
PMID:30962434
https://doi.org/10.1101/279364
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md
ASC
adult somatic stem cell
adult stem cell
cycling cell
irradiation-sensitive cell
neoblast compartment
pASC
planarian adult stem cell
planarian stem cell
somatic stem cell
Planarian_Anatomy
neoblast
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.
PMID:16311336
PMID:21566185
PMID:22899852
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md
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.
A part of an epithelial cell.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
epithelial cell component
Anatomical structure that performs a specific function or group of functions.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:29547123
UBERON:0000062
Planarian_Anatomy
organ
Anatomical structure that performs a specific function or group of functions.
UBERON:0000062
replacing with UBERON term
obsolete regenerating anatomical structure
true
replacing with GO term
obsolete cellular component
true
A decussation of the diencephalon where the fibers of the optic nerve cross
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
AAO:0010622
BAMS:DC
BAMS:OC
BAMS:och
BAMS:ox
BM:Tel-OCX
C90609
DHBA:10644
DMBA:17783
EHDAA2:0001302
EHDAA:10227
EMAPA:17603
FMA:62045
GAID:832
HBA:9310
MA:0001098
MBA:117
MESH:D009897
NCIT:C90609
Optic:chiasm
PMID:15866156
PMID:16033796
PMID:17553481
PMID:17905225
PMID:18202849
PMID:18466009
PMID:19048075
PMID:19211673
PMID:21282632
PMID:22339734
PMID:22445864
PMID:25356635
PMID:25493551
PMID:26618653
PMID:27800171
PMID:28495872
PMID:30194301
PMID:30962434
TAO:0000556
UBERON:0000959
UMLS:C0029126
VHOG:0000190
XAO:0004071
ZFA:0000556
birnlex:1416
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=459
http://linkedlifedata.com/resource/umls/id/C0029126
http://www.snomedbrowser.com/Codes/Details/244453006
chiasm
chiasma
chiasma nervorum opticorum
chiasma opticum
decussation of optic nerve fibers
optic chiasm (Rufus of Ephesus)
optic chiasma
optic chiasmata
Planarian_Anatomy
optic chiasm
A decussation of the diencephalon where the fibers of the optic nerve cross
PMID:18466009
A bundle of nerve fibers connecting the two cephalic ganglia.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0000935
anterior brain commissure
Planarian_Anatomy
anterior commissure
A bundle of nerve fibers connecting the two cephalic ganglia.
UBERON:0000935
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:12128224
PMID:18287199
PMID:18466009
PMID:20422023
PMID:21282632
PMID:21806978
PMID:24922054
PMID:25254346
PMID:27612384
PMID:29674431
PMID:30399335
PMID:4452894
PMID:9493832
bilateral cephalic ganglia branch
brain branch
cephalic brain branch
cephalic branch
lateral brain branch
Planarian_Anatomy
lateral branch
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.
PMID:12128224
PMID:18466009
PMID:27612384
PMID:4452894
PMID:9493832
A cell that performs a sensory function.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0001037
ISBN:9780070316607
NCIT:C12628
PMID:17251262
PMID:17942485
Planarian_Anatomy
sensory cell
Neurons that express choline acetyltransferase.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:20338223
PMID:21566185
PMID:23652002
PMID:23903188
PMID:24131630
PMID:24173799
PMID:24950970
PMID:25356635
PMID:26525673
PMID:27163480
PMID:27612382
PMID:27864883
PMID:28126842
PMID:28137894
PMID:29291981
PMID:30143032
PMID:30194301
acetylcholinergic neuron
Planarian_Anatomy
cholinergic neuron
Neurons that express choline acetyltransferase.
PMID:20338223
Neurons that express glutamine decarboxylase.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000617
FBbt:00007228
PMID:18440152
PMID:23903188
PMID:24131630
PMID:24173799
PMID:24922054
PMID:24950970
PMID:25356635
PMID:26525673
PMID:27864883
PMID:28216315
PMID:29291981
PMID:30194301
PMID:30485821
WBbt:0005190
ZFA:0009276
GABA neuron
GABAergic cell
gabanergic neuron
inhibitory neuron
Planarian_Anatomy
GABAergic neuron
Neurons that express glutamine decarboxylase.
PMID:18440152
Plexus of nerves located in the pharynx comprised of inner and outer wall rings.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:16033796
PMID:17905225
PMID:20967238
PMID:23250205
PMID:23297191
nerve ganglia of pharynx
neural plexus of the pharynx
pharyngeal nerve plexus
pharyngeal nerve ring
pharyngeal nervous system
pharyngeal neural plexus
pharynx nerve ring
Planarian_Anatomy
pharynx nerve plexus
Plexus of nerves located just between the epidermis and the body wall musculature.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:27612384
doi:10.1002/jmor.1051550208
Planarian_Anatomy
subepidermal nerve plexus
Plexus of nerves that innervate the body wall musculature.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
submuscular nerve plexus
A thin net of single nerve fibers located around the gut.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17999079
doi.org/10.1002/jmor.1051550208
Planarian_Anatomy
gastrodermal plexus
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0005268
C12617
CALOHA:TS-2403
FBbt:00005139
FMA:261269
GAID:740
MESH:D019581
NIF:Subcellular:sao205380252
PMID:16033796
PMID:17553481
PMID:24173799
PMID:24950970
PMID:25356635
PMID:27612382
PMID:27612384
PMID:29291974
PMID:29291981
UBERON:0002606
UMLS:C0228081
birnlex:1142
http://en.wikipedia.org/wiki/Neuropil
http://linkedlifedata.com/resource/umls/id/C0228081
http://www.snomedbrowser.com/Codes/Details/67146008
central neuropil
cephalic ganglia neuropil
neuropilus
Planarian_Anatomy
neuropil
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.
PMID:27612384
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ASIN:B000M4NK9M
PMID:29674431
epithelial pharynx lining
outer pharyngeal epidermis
outer pharyngeal epithelium
outer pharynx epidermis
outer pharynx epithelium
Planarian_Anatomy
pharynx outer epithelium
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.
ASIN:B000M4NK9M
Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ASIN:B000M4NK9M
ISBN:9780070316607
outer circular muscle layer
pharyneal outer circular muscle fiber
pharyngeal outer circular muscle cell
pharynx outer circular muscle fiber
Planarian_Anatomy
pharynx outer circular muscle cell
Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles.
ASIN:B000M4NK9M
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ASIN:B000M4NK9M
inner circular muscle layer
pharyngeal inner circular muscle cell
pharyngeal inner circular muscle fiber
pharynx inner circular muscle fiber
Planarian_Anatomy
pharynx inner circular muscle cell
Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers.
ASIN:B000M4NK9M
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ASIN:B000M4NK9M
ISBN:9780070316607
inner longitudinal muscle layer
pharyngeal inner longitudinal muscle cell
pharyngeal inner longitudinal muscle fiber
pharynx inner longitudinal muscle fiber
Planarian_Anatomy
pharynx inner longitudinal muscle cell
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.
ASIN:B000M4NK9M
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.
Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ASIN:B000M4NK9M
pharyngeal outer longitudinal muscle cell
pharyngeal outer longitudinal muscle fiber
pharynx outer longitudinal muscle fiber
Planarian_Anatomy
pharynx outer longitudinal muscle cell
Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium.
ASIN:B000M4NK9M
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ASIN:B000M4NK9M
PMID:28072387
pharyngeal radial muscle cell
pharyngeal radial muscle fiber
pharynx radial muscle fiber
radial muscle cell
radial muscle fiber
Planarian_Anatomy
pharynx radial muscle cell
Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts.
ASIN:B000M4NK9M
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:26904543
PMID:29674432
UBERON:0004467
pharyngeal musculature
pharynx muscle
pharynx musculature
Planarian_Anatomy
pharynx musculature
The total musculature within the pharynx.
PMID:26904543
Ring of the pharynx nerve plexus that is proximal to the lumen.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
inner pharyngeal nerve ring
inner pharynx nerve ring
pharynx inner nerve plexus
Planarian_Anatomy
pharynx inner nerve plexus
Ring of the pharynx nerve plexus that is proximal to the lumen.
ISBN:9780070316607
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:27612384
doi:10.1002/jmor.1051550208
outer pharyngeal nerve ring
outer pharynx nerve plexus
outer pharynx nerve ring
Planarian_Anatomy
pharynx outer nerve plexus
Ring of the pharynx nerve plexus that is proximal to the exterior surface.
ISBN:9780070316607
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000850
FBbt:00005133
PMID:23903188
PMID:24131630
PMID:24173799
PMID:24922054
PMID:24950970
PMID:25356635
PMID:26525673
PMID:27864883
PMID:28137894
PMID:29357350
PMID:30194301
WBbt:0006837
ZFA:0009361
serotonergic cell
Planarian_Anatomy
serotonergic neuron
Neurons that express the neurotransmitter serotonin.
PMID:17624455
A neuron that expresses the neurotransmitter dopamine.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000700
FBbt:00005131
PMID:17565705
PMID:21458439
PMID:23250205
PMID:23903188
PMID:24131630
PMID:24173799
PMID:24950970
PMID:25356635
PMID:27864883
PMID:30194301
WBbt:0006746
ZFA:0009301
Planarian_Anatomy
dopaminergic neuron
A neuron that expresses the neurotransmitter dopamine.
PMID:17565705
Neurons that express the biogenic amine octopamine.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
FBbt:00007364
PMID:18926867
Planarian_Anatomy
octopaminergic neuron
Neurons that express the biogenic amine octopamine.
PMID:18926867
Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:20865784
WBbt:0006850
Planarian_Anatomy
secretory system
Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus.
PMID:20865784
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CLYH:1000090
ISBN:9780070316607
PMID:19247960
PMID:20865784
PMID:23318635
PMID:24737865
PMID:28807897
PMID:29674431
PMID:30962434
WBbt:0003670
secretory gland cell
Planarian_Anatomy
gland cell
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.
PMID:20865784
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:20865784
pore
Planarian_Anatomy
secretory pore
The opening by which the gland cells secrete mucus to the exterior of the animal.
PMID:20865784
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:20865784
eosinophilic gland cell
erythrophilous gland cell
Planarian_Anatomy
acidophilic gland cell
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.
PMID:20865784
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:20865784
PMID:23405188
cyanophilic gland cell
cyanophilic secretory cell
cyanophilous gland
Planarian_Anatomy
basophilic gland cell
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.
PMID:20865784
replacing with CARO term
obsolete anatomical line
true
replacing with BSPO term
obsolete anatomical plane
true
let odk import from BSPO if needed
replacing with UBERON term
obsolete plane of autonomy
obsolete plane of autotomy
true
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].
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
AEO:0000138
BTO:0000205
C12929
EHDAA2:0003138
EHDAA:3780
FMA:5901
ISBN:9780070316607
MA:0002407
PMID:16311336
PMID:21566185
PMID:22899852
UBERON:0001810
UMLS:C0501403
http://en.wikipedia.org/wiki/Nervous:system:plexus
http://linkedlifedata.com/resource/umls/id/C0501403
http://www.snomedbrowser.com/Codes/Details/122455009
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md
neural network
neural plexus
plexus
Planarian_Anatomy
nerve plexus
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].
UBERON:0001810
we will just use commissural neuron moving forward
obsolete nervous system commissure
true
any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0005970
Planarian_Anatomy
brain commissure
any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain
UBERON:0005970
A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
AEO:0000192
BTO:0001638
CARO:0000010
EFO:0003658
FMA:50705
PMID:15866156
PMID:15972844
PMID:16033796
PMID:16890156
PMID:17251262
PMID:17553481
PMID:17670787
PMID:17905225
PMID:17942485
PMID:18063755
PMID:18202849
PMID:18456843
PMID:19048075
PMID:19174194
PMID:19247960
PMID:19766622
PMID:19852954
PMID:20040488
PMID:20215344
PMID:20223763
PMID:20422023
PMID:20599901
PMID:21179478
PMID:21295481
PMID:21295483
PMID:21356107
PMID:21458439
PMID:21566195
PMID:21664348
PMID:21806978
PMID:21937596
PMID:22125640
PMID:22252539
PMID:22318224
PMID:22411224
PMID:22439894
PMID:22451003
PMID:22479207
PMID:22549959
PMID:22884275
PMID:22899852
PMID:23235145
PMID:23250205
PMID:23318641
PMID:23405188
PMID:23629965
PMID:23652002
PMID:24040508
PMID:24063805
PMID:24120894
PMID:24173799
PMID:24415944
PMID:24523458
PMID:24704339
PMID:24922054
PMID:25254346
PMID:25558068
PMID:25725068
PMID:25772472
PMID:25956527
PMID:26062938
PMID:26459857
PMID:26525673
PMID:26711341
PMID:26884331
PMID:27013241
PMID:27068018
PMID:27240733
PMID:27542689
PMID:27551436
PMID:27606067
PMID:27612382
PMID:27612384
PMID:28126842
PMID:28137894
PMID:28171748
PMID:28216315
PMID:28461239
PMID:28757112
PMID:28807897
PMID:28893948
PMID:29158443
PMID:29273738
PMID:29291974
PMID:29291981
PMID:29357350
PMID:30194301
PMID:30237141
PMID:30282036
PMID:30297872
PMID:30471994
PMID:30485821
PMID:30729158
TAO:0001270
UBERON:0005306
XAO:0004060
https://doi.org/10.1101/279364
ncithesaurus:Blastemal_Cell
regeneration blastema
regenerative blastema
Planarian_Anatomy
blastema
A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise.
UBERON:0005306
replacing with UBERON term
obsolete anatomical boundary
true
replacing with UBERON term
obsolete anatomical junction
true
replacing duplicate PLANA term
obsolete main body axis
true
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CALOHA:TS-2035
CL:0000000
FMA:68646
GO:0005623
KUPO:0000002
VHOG:0001533
WBbt:0004017
XAO:0003012
Planarian_Anatomy
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
cell
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CL:0000000
PLANA:0000500 child terms moved to cellular component (GO:0005575) term and we think better serves interoperability and searchability
obsolete cell part
true
A prolongation or process extending from a cell.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0042995
Planarian_Anatomy
cell projection
A prolongation or process extending from a cell.
GO:0042995
A cell projection supported by an assembly of actin filaments.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0098858
Planarian_Anatomy
actin-based cell projection
A cell projection supported by an assembly of actin filaments.
GO:0098858
inadvertently duplicated, going with ID that is best annotated
obsolete cilium
true
Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005902
Planarian_Anatomy
microvillus
Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments.
GO:0005902
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0044291
Planarian_Anatomy
cell-cell contact zone
Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions.
GO:0044291
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0030054
PMID:20511647
PMID:21458439
Planarian_Anatomy
cell junction
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.
GO:0030054
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005911
Planarian_Anatomy
cell-cell junction
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.
GO:0005911
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.
The attachment of one cell to another cell via adhesion molecules.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0098609
Planarian_Anatomy
cell-cell adhesion
The attachment of one cell to another cell via adhesion molecules.
GO:0098609
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.
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0044424
Planarian_Anatomy
intracellular part
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.
GO:0044424
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005737
PMID:16890156
PMID:28976975
Planarian_Anatomy
cytoplasm
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures
GO:0005737
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.
term is not needed.
obsolete acidophilic cytoplasm
true
term is not needed.
obsolete basophilic cytoplasm
true
Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0044444
Planarian_Anatomy
cytoplasmic part
Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0044444
Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0044433
Planarian_Anatomy
cytoplasmic vesicle part
Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell.
GO:0044433
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005773
Planarian_Anatomy
vacuole
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
GO:0005773
term is not needed.
obsolete cytoskeleton organization
true
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0043229
Planarian_Anatomy
intracellular organelle
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
GO:0043229
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
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0043232
Planarian_Anatomy
intracellular non-membrane-bounded organelle
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes
GO:0043232
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0016020
Planarian_Anatomy
membrane
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
GO:0016020
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0098588
Planarian_Anatomy
bounding membrane of organelle
Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes.
GO:0098588
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0044425
Planarian_Anatomy
membrane part
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.
GO:0044425
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0044459
Planarian_Anatomy
plasma membrane part
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.
GO:0044459
A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0031090
Planarian_Anatomy
organelle membrane
A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
GO:0031090
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0043226
Planarian_Anatomy
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.
GO:0043226
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0043227
Planarian_Anatomy
membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
GO:0043227
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0043231
Planarian_Anatomy
intracellular membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
GO:0043231
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005794
Planarian_Anatomy
Golgi apparatus
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.
GO:0005794
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005634
ISBN:9780070316607
PMID:23405188
PMID:25404302
PMID:26457503
PMID:28976975
PMID:29100657
PMID:29357350
Planarian_Anatomy
nucleus
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
GO:0005634
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0099503
Planarian_Anatomy
secretory vesicle
A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space.
GO:0099503
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0043228
Planarian_Anatomy
non-membrane-bounded organelle
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.
GO:0043228
Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0044428
Planarian_Anatomy
nuclear part
Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.
GO:0044428
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0044428
Planarian_Anatomy
nucleolus
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.
GO:0044428
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0000785
Planarian_Anatomy
chromatin
The ordered and organized complex of DNA, protein (histones), and sometimes RNA, that forms the chromosome.
GO:0000785
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0000792
Planarian_Anatomy
heterochromatin
A compact and highly condensed form of chromatin.
GO:0000792
A dispersed and relatively uncompacted form of chromatin.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0000791
Planarian_Anatomy
euchromatin
A dispersed and relatively uncompacted form of chromatin.
GO:0000791
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 ]
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005840
Planarian_Anatomy
ribosome
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 ]
GO:0005840
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
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:22884275
PMID:24950970
PMID:28137894
UBERON:0001018
axon bundle
axon bundles
axon tracts
Planarian_Anatomy
axon tract
A group of axons linking two or more neuropils and having a common origin, termination
UBERON:0001018
A cell whose function is determined by its response to an electric signal.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000393
Planarian_Anatomy
electrically responsive cell
A cell whose function is determined by its response to an electric signal.
CL:0000393
A cell that initiates an electrical signal and passes that signal to another cell.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000404
Planarian_Anatomy
electrically signaling cell
A cell that initiates an electrical signal and passes that signal to another cell.
CL:0000404
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:27612382
PMID:27800171
UBERON:0001021
nerve bundle
nerves
neural subtree
peripheral nerve
Planarian_Anatomy
nerve
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.
UBERON:0001021
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CARO:0001001
UBERON:0000122
Planarian_Anatomy
neuron projection bundle
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
CARO:0001001
A neuron which conveys sensory information centrally from the periphery.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000526
FMA:87653
input neuron
Planarian_Anatomy
afferent neuron
A neuron which conveys sensory information centrally from the periphery.
CL:0000526
A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000103
FMA:67282
ISBN:9780070316607
PMID:16033796
PMID:18202849
PMID:21458439
PMID:22445864
PMID:24173799
PMID:25493551
bipolar nerve cell
Planarian_Anatomy
bipolar neuron
A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.
CL:0000103
A neuron that has an axon which crosses the midline.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000678
PMID:22339734
Planarian_Anatomy
commissural neuron
A neuron that has an axon which crosses the midline.
CL:0000678
A neuron which sends impulses peripherally to activate muscles or secretory cells.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000527
output neuron
Planarian_Anatomy
efferent neuron
A neuron which sends impulses peripherally to activate muscles or secretory cells.
CL:0000527
A motor neuron that is capable of directly inducing muscle contraction.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0008014
PMID:25356635
excitatory neuron
Planarian_Anatomy
In vertebrates, all motor neurons are excitatory, but various types of inhibitory motor neurons exist in invertebrates.
excitatory motor neuron
A motor neuron that is capable of directly inducing muscle contraction.
CL:0008014
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0003811
CL:0000099
FBbt:00005125
FMA:67313
WBbt:0005113
Planarian_Anatomy
interneuron
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.
CL:0000099
Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0001037
CL:0000101
FBbt:00005124
FMA:84649
WBbt:0005759
Planarian_Anatomy
sensory neuron
Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
CL:0000101
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0000312
CL:0000100
FMA:83617
WBbt:0005409
motoneuron
Planarian_Anatomy
motor neuron
An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement.
CL:0000100
Neuronal cells which synthesize, store and release neurohormones.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000381
FBbt:00005130
PMID:24173799
neurosecretory cell
Planarian_Anatomy
neurosecretory neuron
Neuronal cells which synthesize, store and release neurohormones.
CL:0000381
Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0011103
Planarian_Anatomy
sympathetic neuron
Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides.
CL:0011103
Neuron with one neurite that extends from the cell body.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000106
FMA:67278
ISBN:9780070316607
PMID:18499291
PMID:24173799
unipolar nerve cell
Planarian_Anatomy
unipolar neuron
Neuron with one neurite that extends from the cell body.
CL:0000106
Neuron with an axon and two or more dendrites.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000104
FMA:67287
ISBN:9780070316607
PMID:18499291
multipolar nerve cell
Planarian_Anatomy
multipolar neuron
Neuron with an axon and two or more dendrites.
CL:0000104
Cells that are in close proximity to neurons.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000130
Planarian_Anatomy
neuron associated cell (sensu Nematoda and Protostomia)
Cells that are in close proximity to neurons.
CL:0000130
Any neuron that is part of a central nervous system.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:2000029
Planarian_Anatomy
central nervous system neuron
Any neuron that is part of a central nervous system.
CL:2000029
Any neuron that is part of a peripheral nervous system.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:2000032
PMID:23123964
PMID:23954785
PMID:25254346
PMID:26711341
PMID:29184198
peripheral neuron
Planarian_Anatomy
peripheral nervous system neuron
Any neuron that is part of a peripheral nervous system.
CL:2000032
A neruon whose cell body is within an autonomic ganglion.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000107
FMA:80121
Planarian_Anatomy
autonomic neuron
A neruon whose cell body is within an autonomic ganglion.
CL:0000107
A neruon contained within with the enteric nervous system (gastrodermal plexus).
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0007011
Planarian_Anatomy
enteric neuron
A neruon contained within with the enteric nervous system (gastrodermal plexus).
CL:0007011
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
AAO:0010269
AEO:0000065
BILA:0000065
C32186
CARO:0000065
EHDAA2:0003065
FMA:62918
HAO:0000065
ISBN:9780070316607
MESH:D001485
NIF_Subcellular:sao1397492660
PMID:18786419
PMID:19048075
PMID:21664348
PMID:21828097
PMID:22479207
PMID:23079596
PMID:23405188
PMID:23903188
PMID:25017721
PMID:26057828
PMID:26457503
PMID:27551436
PMID:29100657
PMID:30383829
PMID:30962434
TAO:0001485
TGMA:0001850
UMLS:C0085872
VHOG:0001592
WBbt:0005756
XAO:0003163
ZFA:0001485
basal lamina
basal lamina of epithelium
basement membrane
Planarian_Anatomy
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.
basal lamina of epidermis
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.
CARO:0000065
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
Planarian_Anatomy
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.
adenal rhabdite
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.
ISBN:9780070316607
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005912
PMID:26556349
Planarian_Anatomy
adherens junction
A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
GO:0005912
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.
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
adhesive papillae
Planarian_Anatomy
adhesive papilla
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.
ISBN:9780070316607
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
amputation
A branch of the triclad gut located anterior to the pharynx.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:18063757
PMID:18287199
PMID:19174194
PMID:20707997
PMID:21458439
PMID:21664348
PMID:21806978
PMID:22451003
PMID:22479207
PMID:23318635
PMID:24063805
PMID:28287248
PMID:30194301
anterior branch
anterior intestinal branch
Planarian_Anatomy
anterior gut branch
A branch of the triclad gut located anterior to the pharynx.
PMID:21664348
The anterior-medial region of the head margin.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:15866156
PMID:18063755
PMID:22479207
PMID:24415944
PMID:24992682
PMID:27063937
PMID:28126842
PMID:28216315
PMID:29547123
PMID:30962434
head tip
Planarian_Anatomy
anterior tip
The anterior-medial region of the head margin.
PMID:22479207
Illustration of the anterior tip in green.
A chamber formation in an organ.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
NCIT:C97102
Planarian_Anatomy
antrum
A chamber formation in an organ.
ISBN:9780070316607
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:27800171
PMID:28495872
PMID:30399335
PMID:30485821
Planarian_Anatomy
auricle
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.
ISBN:9780070316607
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0030424
PMID:16033796
PMID:17251262
PMID:17553481
PMID:18202849
PMID:20707997
PMID:21566185
PMID:22445864
PMID:23318641
PMID:23903188
PMID:25254346
PMID:25356635
PMID:25493551
PMID:25772472
PMID:27800171
PMID:28495872
nerve fiber
Planarian_Anatomy
axon
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.
GO:0030424
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005930
PMID:23144623
PMID:26057828
PMID:26912790
Planarian_Anatomy
axoneme
The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
GO:0005930
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0036064
ISBN:9780070316607
PMID:21282632
PMID:21828097
PMID:21937596
Planarian_Anatomy
basal body
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.
GO:0036064
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).
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:16033796
PMID:26618653
visual center
Planarian_Anatomy
brain visual center
Region of the cephalic ganglia innervated by the optic nerve (posterior-projecting photoreceptor neuron fasiculated axons).
PMID:16033796
An enlarged portion of the seminal vesicle, comprised of secretory epithelial cells, that connects to the ejaculatory duct within the penis papilla.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
https://doi.org/10.1101/279364
bulbar lumen
Planarian_Anatomy
bulbar cavity
An enlarged portion of the seminal vesicle, comprised of secretory epithelial cells, that connects to the ejaculatory duct within the penis papilla.
ISBN:9780070316607
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:18786419
PMID:21894189
PMID:22439894
Category 1 gene expressing cell
Planarian_Anatomy
Category 1 cell
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.
PMID:18786419
The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0044297
PMID:15866156
PMID:16033796
PMID:20865784
PMID:27612384
PMID:28495872
Planarian_Anatomy
cell body
The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
GO:0044297
One of two bilaterally symmetric structures comprising the planarian brain.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:15866156
PMID:16033796
PMID:16890156
PMID:17251262
PMID:17553481
PMID:17670787
PMID:17905225
PMID:17999079
PMID:18063757
PMID:18202849
PMID:18287199
PMID:19211673
PMID:19247960
PMID:19766622
PMID:19852954
PMID:20223763
PMID:20422023
PMID:20707997
PMID:20967238
PMID:21179478
PMID:21282632
PMID:21566185
PMID:21806978
PMID:21828097
PMID:21852957
PMID:22074376
PMID:22125640
PMID:22318224
PMID:22371573
PMID:22427692
PMID:22439894
PMID:22445864
PMID:22451003
PMID:22479207
PMID:22884275
PMID:23123964
PMID:23250205
PMID:23297191
PMID:23318635
PMID:23652002
PMID:23903188
PMID:24040508
PMID:24063805
PMID:24120894
PMID:24131630
PMID:24173799
PMID:24238224
PMID:24523458
PMID:24704339
PMID:24950970
PMID:24992682
PMID:25017721
PMID:25254346
PMID:25356635
PMID:25493551
PMID:25558068
PMID:25772472
PMID:26062938
PMID:26114597
PMID:26457503
PMID:26525673
PMID:26556349
PMID:26618653
PMID:27013241
PMID:27034770
PMID:27063937
PMID:27074666
PMID:27149082
PMID:27150006
PMID:27163480
PMID:27523733
PMID:27606067
PMID:27612382
PMID:27612384
PMID:27800171
PMID:27864883
PMID:28126842
PMID:28137894
PMID:28171748
PMID:28245923
PMID:28287248
PMID:28434803
PMID:28686611
PMID:28807897
PMID:28893948
PMID:29100657
PMID:29158443
PMID:29291974
PMID:29291981
PMID:29357350
PMID:29547123
PMID:29557542
PMID:29674431
PMID:29674432
PMID:30143032
PMID:30194301
PMID:30282036
PMID:30383829
PMID:30399335
PMID:30485821
PMID:30729158
bi-lobed brain
bi-lobed cephalic ganglia
brain ganglia
brain lobe
Planarian_Anatomy
cephalic ganglia lobe
One of two bilaterally symmetric structures comprising the planarian brain.
PMID:17999079
A central nervous system neuron located within the planarian brain.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17999079
PMID:24173799
PMID:27612382
brain neuron
Planarian_Anatomy
cephalic ganglia neuron
A central nervous system neuron located within the planarian brain.
PMID:17999079
Amputation carried out by application of chemicals.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:24737865
Planarian_Anatomy
chemical amputation
Amputation carried out by application of chemicals.
PMID:24737865
Amputation of the phaynx, including the esophagus, by treatment with Sodium Azide.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:24737865
chemical pharyngeal amputation
Planarian_Anatomy
chemical pharynx amputation
Amputation of the phaynx, including the esophagus, by treatment with Sodium Azide.
PMID:24737865
Any neuron that capable of some detection of chemical stimulus involved in sensory perception.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
FBbt:00005922
PMID:18202849
PMID:26525673
PMID:27612382
PMID:28126842
PMID:28686611
PMID:29547123
chemoreceptive neuron
chemoreceptor neuron
Planarian_Anatomy
chemosensory neuron
Any neuron that capable of some detection of chemical stimulus involved in sensory perception.
FBbt:00005922
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0033391
PMID:19247960
PMID:20215344
PMID:21356107
PMID:22318224
PMID:22385657
PMID:22439894
PMID:22543868
PMID:24120894
PMID:24367277
PMID:24903754
PMID:25017721
PMID:27523733
nuage
Planarian_Anatomy
chromatoid body
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.
PMID:22318224
PMID:24903754
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005694
PMID:25404302
PMID:28757112
PMID:28812561
PMID:29364871
PMID:30143032
Planarian_Anatomy
chromosome
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
GO:0005694
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
NCIT:C13355
PMID:25404302
SO:0000105
Planarian_Anatomy
chromosome arm
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.
NCIT:C13355
Image is an electron micrograph showing a mitotic cell. An arrowhead marks the long arm of a chromosome. Scale bar is 1um.
Epithelium bearing vibratile cilia on the free surface.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:26457503
PMID:26711341
PMID:28216315
PMID:28292427
UBERON:0007601
Planarian_Anatomy
ciliated epithelium
Epithelium bearing vibratile cilia on the free surface.
UBERON:0007601
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005929
Planarian_Anatomy
cilium
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.
GO:0005929
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
NCIT:C32349
Planarian_Anatomy
commissure
A bundle of nerve fibers crossing from one side to the other side of the brain or spinal cord.
NCIT:C32349
A wound or cleft resulted from tissue separation into parts or laid open or penetrated with a sharp edge or instrument.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
NCIT:C50518
Planarian_Anatomy
cut
A wound or cleft resulted from tissue separation into parts or laid open or penetrated with a sharp edge or instrument.
NCIT:C50518
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0030425
PMID:16033796
PMID:17553481
PMID:22445864
PMID:25493551
PMID:28495872
cell dendrite
dendritic process
dendritic projection
Planarian_Anatomy
dendrite
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.
GO:0030425
A muscle cell that runs in the transverse plane that connects the dorsal and ventral sides of the animal.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:30471994
PMID:30962434
DVM
dorsal-ventral muscle
dorsal-ventral muscle fibers
dorsoventral muscle
dorsoventralmuscle fibers
Planarian_Anatomy
dorsal-ventral muscle cell
A muscle cell that runs in the transverse plane that connects the dorsal and ventral sides of the animal.
PMID:30962434
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).
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
early female germ cell
A premeiotic male germ cell (i.e., a spermatogonial stem cell or transit amplifying spermatogonial cell).
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:27330085
Planarian_Anatomy
early male germ cell
A premeiotic male germ cell (i.e., a spermatogonial stem cell or transit amplifying spermatogonial cell).
PMID:27330085
A cryptic digestive cavity comprised of phagocytic embryonic gut cells.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Planarian_Anatomy
embryonic gut
A cryptic digestive cavity comprised of phagocytic embryonic gut cells.
PMID:28072387
An epithelial cell of the integument (the outer layer of an organism).
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000362
PMID:21458439
PMID:24922054
PMID:25017721
PMID:26457503
PMID:28292427
PMID:28686611
PMID:28807897
PMID:29100657
PMID:29357350
PMID:30399335
Planarian_Anatomy
epidermal cell
An epithelial cell of the integument (the outer layer of an organism).
CL:0000362
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
Planarian_Anatomy
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
epidermal rhabdite
Rhabdites located within epidermal cells.
ISBN:9780070316607
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005789
Planarian_Anatomy
ER membrane
The lipid bilayer surrounding the endoplasmic reticulum.
GO:0005789
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CHEBI:24009
PMID:25356635
PMID:26017970
PMID:27240733
eye cell pigment
eye pigment
Planarian_Anatomy
eumelanin
The black pigment that gives non-neuronal pigment cells of the optic cup their characteristic color.
PMID:15760337
PMID:26017970
PMID:8812261
A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000424
PMID:21566185
PMID:24173799
Planarian_Anatomy
excretory cell
A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids.
CL:0000424
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0031012
PMID:19048075
PMID:28126842
PMID:28137894
PMID:28807897
PMID:30962434
ECM
Planarian_Anatomy
extracellular matrix
A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues.
GO:0031012
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005615
PMID:21828097
Planarian_Anatomy
extracellular space
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
GO:0005615
A form of asexual reproduction resulting in self-amputation of posterior tissue, generating an anterior fragment and a fission fragment.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
fission
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).
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:29095551
PMID:4190073
Planarian_Anatomy
flagellum
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).
PMID:4190073
A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005921
PMID:17670787
PMID:22125640
Planarian_Anatomy
gap junction
A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins.
GO:0005921
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID: 22074376
atrium
female antrum
Planarian_Anatomy
genital atrium
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.
PMID:22074376
A clonally-related group of interconnected spermatogonial or oogonial cells, enveloped by somatic gonadal cells.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17376870
PMID:22318224
germ cell cluster
Planarian_Anatomy
germ cell cyst
A clonally-related group of interconnected spermatogonial or oogonial cells, enveloped by somatic gonadal cells.
PMID:17376870
Stem cell that is the precursor of gametes.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000014
FBbt:00004861
PMID:16344473
PMID:17376870
PMID:17390146
PMID:18456843
PMID:19247960
PMID:20215344
PMID:20844018
PMID:22074376
PMID:22252538
PMID:22318224
PMID:22385657
PMID:22543868
PMID:23652002
PMID:24173799
PMID:24367277
PMID:25278423
PMID:27013241
PMID:28434803
PMID:28812561
https://doi.org/10.1101/279364
germ cell
germ stem cell
germline cell
Planarian_Anatomy
germline stem cell
Stem cell that is the precursor of gametes.
FBbt:00004861
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0042587
PMID:30608231
Planarian_Anatomy
glycogen granule
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.
GO:0042587
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
incision
Epithelial cells lining the inside of the pharynx. In Smed, distally located cells are heavily ciliated.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:20511647
inner pharynx epidermal cell
Planarian_Anatomy
pharynx inner epidermal cell
Epithelial cells lining the inside of the pharynx. In Smed, distally located cells are heavily ciliated.
ISBN:9780070316607
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
Planarian_Anatomy
inner zone of gland cells
Gland or secretory cells sandwiched between muscle and epidermal layers in the pharynx.
ISBN:9780070316607
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005911
Planarian_Anatomy
intercellular junction
A cell junction that forms a connection between two or more cells in a multicellular organism.
GO:0005911
An amputation performed with a transverse, oblique or longitudinal cut.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
linear amputation
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
scratch
Planarian_Anatomy
linear incision
An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005811
PMID:30608231
https://doi.org/10.1101/279364
Planarian_Anatomy
lipid droplet
An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
GO:0005811
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
NCIT:C94478
Planarian_Anatomy
lumen
The cavity or channel within a tube or tubular organ such as a blood vessel or the intestine.
NCIT:C94478
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:20865784
Planarian_Anatomy
marginal adhesive zone
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.
ISBN:9780070316607
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
FBbt:00005919
PMID:25725068
PMID:28216315
WBbt:0008431
mechanosensory cell
Planarian_Anatomy
mechanosensory neuron
Any neuron that is capable of some detection of mechanical stimulus involved in sensory perception.
FBbt:00005919
Subset of dorsal-ventral muscle cells located in the medial body region.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:29674431
PMID:30962434
Planarian_Anatomy
medial muscle cell
Subset of dorsal-ventral muscle cells located in the medial body region.
PMID:30962434
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 germ cell undergoing meiosis.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:27330085
Planarian_Anatomy
meiotic germ cell
A germ cell undergoing meiosis.
PMID:27330085
A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0042470
Planarian_Anatomy
melanosome
A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
GO:0042470
A secreted, mucin-rich extracellular substance coating the epidermal surface of the animal implicated in gliding locomotion, substrate adhesion, innate immunity and predator avoidance.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21282632
PMID:22653920
UBERON:0000912
Planarian_Anatomy
mucus
A secreted, mucin-rich extracellular substance coating the epidermal surface of the animal implicated in gliding locomotion, substrate adhesion, innate immunity and predator avoidance.
PMID:22653920
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:21828097
UBERON:0006972
Planarian_Anatomy
nephridiopore
The external opening and terminus of a protonephridium made by a terminal cell.
ISBN:9780070316607
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.
Cell appendage of the neuron which includes the axon and the dendrite.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
FBbt:00005113
FMA:61814
ISBN:9780070316607
PMID:27612382
PMID:29547123
neuronal process
Planarian_Anatomy
neurite
Cell appendage of the neuron which includes the axon and the dendrite.
FMA:61814
A neuron that produces and releases neuropeptides at chemical synapses.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:24173799
PMID:25356635
PMID:27163480
cns peptidergic cell
peptidergic neuron
Planarian_Anatomy
neuropeptidergic neuron
A neuron that produces and releases neuropeptides at chemical synapses.
PMID:24173799
Differentiating, immature epidermal cells lacking cilia.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:26457503
PMID:28292427
Planarian_Anatomy
non-ciliated epidermis
Differentiating, immature epidermal cells lacking cilia.
PMID:26457503
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).
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005635
https://doi.org/10.1101/279364
Planarian_Anatomy
nuclear envelope
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
GO:0005635
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005637
inner leaflet
Planarian_Anatomy
nuclear inner membrane
The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
GO:0005637
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0031981
Planarian_Anatomy
nuclear lumen
The volume enclosed by the nuclear inner membrane.
GO:0031981
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005640
outer leaflet
Planarian_Anatomy
nuclear outer 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.
GO:0005640
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0034399
PMID:25404302
Planarian_Anatomy
nuclear periphery
The portion of the nuclear lumen proximal to the inner nuclear membrane.
GO:0034399
Parenchymal cells that synthesize and contain brown ommonchrome pigment.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:27240733
non-melanin pigment cell
Planarian_Anatomy
ommochrome pigment cell
Parenchymal cells that synthesize and contain brown ommonchrome pigment.
PMID:27240733
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:27800171
UBERON:0004904
Planarian_Anatomy
optic nerve
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.
UBERON:0004904
Heavily ciliated, insunk epithelial cells bounding the outside of the pharynx. Outer pharynx epithelial cell nuclei are positioned beneath the pharynx musculature.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
PMID:20511647
outer pharynx epidermal cell
Planarian_Anatomy
pharynx outer epidermal cell
Heavily ciliated, insunk epithelial cells bounding the outside of the pharynx. Outer pharynx epithelial cell nuclei are positioned beneath the pharynx musculature.
ISBN:9780070316607
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000234
ISBN:9780070316607
PMID:25956527
PMID:27501047
PMID:30471994
phagocyte
Planarian_Anatomy
phagocytic cell
A cell that engulfs large particles or cells via invagination of the plasma membrane and creation of a phagosome.
ISBN:9780070316607
PMID:30471994
The distal-most end of the pharnyx containing an opening to the pharynx lumen.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
pharynx tip
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000147
PMID:26618653
pigment producing cell
pigmented cell
Planarian_Anatomy
pigment cell
A pigment cell is a cell that contains pigment granules.
CL:0000147
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0048770
ISBN:9780070316607
PMID:27551436
Planarian_Anatomy
pigment granule
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.
GO:0048770
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
plug amputation
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
poke
Planarian_Anatomy
point incision
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0008915
Planarian_Anatomy
pore
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.
UBERON:0008915
A haploid gamete undergoing terminal differentiation.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
post-meiotic germ cell
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0045211
PMID:24950970
post-synaptic cell
Planarian_Anatomy
postsynaptic cell
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.
GO:0045211
A diploid germline stem cell or transit amplifying germ cell that has not committed to undergoing meiotic DNA replication, reductive divisions or terminal differentiation.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
premeiotic germ cell
The part of a synapse that is part of the presynaptic cell.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0098793
PMID:24950970
pre-synaptic cell
Planarian_Anatomy
presynaptic cell
The part of a synapse that is part of the presynaptic cell.
GO:0098793
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0043195
PMID:23903188
pre-synaptic terminal
Planarian_Anatomy
presynaptic terminal
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.
GO:0043195
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0008021
PMID:23903188
pre-synaptic vesicle
Planarian_Anatomy
presynaptic vesicle
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.
GO:0008021
The largest branch of the triclad intestine. It is comprised of the gastrodermis, a columnar epithelium, surrounded by basal lamina and visceral musculature.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17553481
PMID:20865784
PMID:21664348
PMID:27122174
PMID:28137894
PMID:29674431
main gut branch
primary intestine branch
Planarian_Anatomy
primary gut branch
The largest branch of the triclad intestine. It is comprised of the gastrodermis, a columnar epithelium, surrounded by basal lamina and visceral musculature.
PMID:21664348
Four large phagocytic cells associated with the embryonic pharynx.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
primitive endoderm
Planarian_Anatomy
primitive gut
Four large phagocytic cells associated with the embryonic pharynx.
PMID:28072387
Gut branches originating from and connected to the tertiary gut branches.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21664348
Planarian_Anatomy
quarternary gut branch
Gut branches originating from and connected to the tertiary gut branches.
PMID:21664348
An organ involved in reproduction
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:16344473
PMID:17376870
PMID:20844018
PMID:22074376
PMID:25278423
PMID:27074666
UBERON:0003133
https://doi.org/10.1101/279364
Planarian_Anatomy
reproductive organ
An organ involved in reproduction
UBERON:0003133
Any anatomical structure that is part of the reproductive system.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17376870
UBERON:0005156
Planarian_Anatomy
reproductive structure
Any anatomical structure that is part of the reproductive system.
UBERON:0005156
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:15760337
PMID:16033796
PMID:21852957
PMID:26017970
Planarian_Anatomy
rhabdome
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.
PMID:15760337
PMID:16033796
PMID:21852957
The dendritic process of a bipolar photoreceptor neuron that projects into the optic cup lumen and senses light.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0016028
PMID:15760337
PMID:16033796
PMID:18202849
PMID:20865784
PMID:21282632
PMID:21852957
PMID:22445864
PMID:25772472
PMID:26618653
PMID:27800171
Planarian_Anatomy
rhabdomere
The dendritic process of a bipolar photoreceptor neuron that projects into the optic cup lumen and senses light.
PMID:15760337
PMID:16033796
PMID:21852957
A tubular structure that transports secreted or excreted substances.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:30383829
UBERON:0000058
secretory canal
Planarian_Anatomy
secretory duct
A tubular structure that transports secreted or excreted substances.
UBERON:0000058
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0030141
PMID:29100657
Planarian_Anatomy
secretory granule
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.
GO:0030141
One of the cells of the body that compose the tissues, organs, and parts of that individual other than the germ cells.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
BTO:0001268
CL:0002371
PMID:20599901
PMID:21852957
PMID:22074376
PMID:22371573
PMID:22385657
PMID:25404302
PMID:27606067
PMID:28757112
Planarian_Anatomy
somatic cell
One of the cells of the body that compose the tissues, organs, and parts of that individual other than the germ cells.
BTO:0001268
A non-germline cell within the ovary or testis.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:27163480
PMID:27330085
WBbt:0007815
gonadal niche cell
somatic gonadal niche cell
somatic gonadal support cell
Planarian_Anatomy
somatic gonadal cell
A non-germline cell within the ovary or testis.
PMID:27163480
PMID:27330085
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:25254346
PMID:26651295
PMID:27542689
PMID:29674432
PMID:30962434
Planarian_Anatomy
specialized neoblast
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.
PMID:23404104
A thin, flexible rod that anchors an egg capsule to a solid substrate.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
Planarian_Anatomy
stalk
A thin, flexible rod that anchors an egg capsule to a solid substrate.
ISBN:9780070316607
A wound produced by non-autonomous physical means.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
surgical wound
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0045202
PMID:18202849
PMID:18287199
PMID:21282632
neural synapse
neuronal synapse
Planarian_Anatomy
synapse
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.
GO:0045202
The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0043083
PMID:23903188
Planarian_Anatomy
synaptic cleft
The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released.
GO:0043083
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]
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0008021
PMID:24950970
Planarian_Anatomy
synaptic vesicle
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]
GO:0008021
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0000795
PMID:25404302
Planarian_Anatomy
synaptonemal complex
The posterior-medial region of the tail margin.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
tail tip
Illustration of the tail tip (in green).
The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0000781
PMID:22371573
PMID:25404302
https://doi.org/10.1101/279364
Planarian_Anatomy
telomere
The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
GO:0000781
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0070160
Planarian_Anatomy
septate junction
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.
GO:0070160
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
wedge amputation
Illustration of a wedge amputation depicting the resultant donor wound and wedge fragment.
An injury that breaches the epidermis.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
injury
Planarian_Anatomy
wound
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:16872450
PMID:17670787
PMID:18456843
PMID:18786419
PMID:19048075
PMID:20215344
PMID:20223763
PMID:21937596
PMID:22385657
PMID:22427692
PMID:22543868
PMID:22549959
PMID:23235145
PMID:23629965
PMID:24120894
PMID:24367277
PMID:24992682
PMID:25254346
PMID:25558068
PMID:25956527
PMID:26114597
PMID:26457503
PMID:26711341
PMID:27013241
PMID:27068018
PMID:27150006
PMID:27502555
PMID:27523733
PMID:27551436
PMID:28137894
PMID:29100657
PMID:29557542
PMID:29674432
PMID:29906446
PMID:30194301
X1
X1 cell population
X1 neoblast
X1 population
Planarian_Anatomy
X1 cell
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.
PMID:16872450
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:21566185
Planarian_Anatomy
X1(FS) cell
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.
PMID:21566185
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:16872450
PMID:18786419
PMID:19048075
PMID:20215344
PMID:20223763
PMID:22427692
PMID:22543868
PMID:23629965
PMID:24367277
PMID:25017721
PMID:27013241
PMID:27150006
PMID:27502555
PMID:27606067
PMID:27864883
PMID:28137894
PMID:29674432
Planarian_Anatomy
X2 cell
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.
PMID:16872450
A sorted cell population of irradiation-insensitive cells that contains a variety of post-mitotic, differentiated cell types.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:16872450
PMID:17670787
PMID:18456843
PMID:18786419
PMID:19048075
PMID:20215344
PMID:20223763
PMID:22427692
PMID:22479207
PMID:22543868
PMID:23629965
PMID:24367277
PMID:24992682
PMID:25558068
PMID:25956527
PMID:26114597
PMID:26457503
PMID:26711341
PMID:27013241
PMID:27502555
PMID:29100657
PMID:29674432
PMID:29906446
PMID:30194301
Xins
Xins cell population
Xins cells
Planarian_Anatomy
Xins cell
A sorted cell population of irradiation-insensitive cells that contains a variety of post-mitotic, differentiated cell types.
PMID:16872450
Posterior to the pharynx.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
post pharyngeal
post-pharyngeal
post-pharyngeal region
postpharyngeal region
Planarian_Anatomy
postpharyngeal region
Adjacent to blastema, or proximal to blastema.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
post-blastema
postblastema
postblastema region
Planarian_Anatomy
post-blastema region
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
fission fragment
term is not needed.
obsolete oblique
true
The avascular cellular layers that cover body surfaces and cavities and may form glands.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
NCIT:C12710
UBERON:0000483
Planarian_Anatomy
epithelium
The avascular cellular layers that cover body surfaces and cavities and may form glands.
NCIT:C12710
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
gut 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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
extraembryonic organ
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
SO:0000830
Planarian_Anatomy
chromosome part
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.
SO:0000830
An event or occurrence that causes damage to a tissue or organ.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
insult
Planarian_Anatomy
perturbation
structural element of a chromosome, for example, a telomere and a centromere
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
SO:0000628
chromosomal structural element
Planarian_Anatomy
chromosomal_structural_element
structural element of a chromosome, for example, a telomere and a centromere
SO:0000628
A longitudinal fragment containing the preexisting midline and medial structures.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
thick fragment
Illustration of a thick fragment (in green).
A longitudinal fragment lacking a midline and medial structures.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
thin fragment
Illustration of a thin fragment (in green).
A piece of tissue isolated from the body.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
piece
Planarian_Anatomy
fragment
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
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
longitudinal region
Illustration of a longitudinal region (green).
An intentional wound produced by non-autonomous chemical means.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
chemical wound
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
plug wound
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
wedge wound
Illustration of a wedge wound.
A fragment that has undergone wound healing and is undergoing tissue replacement and morphallaxis.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
regenerating fragment
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
longitudinal orientation
Planarian_Anatomy
sagittal orientation
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PATO:0005023
Planarian_Anatomy
parasagittal orientation
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.
PATO:0005023
An anatomical entity consisting of a single or a few multinucleated structures
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
AEO:0000203
BTO:0005784
PMID:27330085
Planarian_Anatomy
syncytium
An anatomical entity consisting of a single or a few multinucleated structures
AEO:0000203
Cytoplasmic part which forms a distinctive granular particle, which may or may not be visible using light microscopy.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
MICRO:0000215
Planarian_Anatomy
intracellular granule
Cytoplasmic part which forms a distinctive granular particle, which may or may not be visible using light microscopy.
MICRO:0000215
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
FACS sorted cell population
Cells isolated from dissociated planarian tissue.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
derived cell population
An epithelial monolayer lining the pharynx pouch cavity.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:16809160
Planarian_Anatomy
pharynx pouch epithelium
An epithelial monolayer lining the pharynx pouch cavity.
OCLC:16809160
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:19022767
PMID:22074376
Planarian_Anatomy
sperm duct epithelial surface
Epithelial surface lining the sperm duct.
PMID:19022767
PMID:22074376
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:16809160
mesenchyme
Planarian_Anatomy
parenchyma
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.
OCLC:16809160
The dorsal region of the tail.
dorsal region of tail region
Planarian_Anatomy
PLANA:0003000
dorsal region of tail
Illustration of the dorsal region of the tail (in green).
The lateral region of the medio-lateral axis of the whole animal.
lateral region of whole organism
Planarian_Anatomy
PLANA:0003001
lateral region of the whole animal
The anterior region of the eye.
anterior region of eye
Planarian_Anatomy
PLANA:0003002
anterior region of the eye
The posterior region of the eye.
posterior region of eye
Planarian_Anatomy
PLANA:0003003
posterior region of the eye
The center-most region just anterior to the pharynx
prepharyngeal region of midline
Planarian_Anatomy
PLANA:0003004
prepharyngeal midline
cell which is part of the testis
Planarian_Anatomy
PLANA:0003100
testis cell
cell which is part of the testis
PMID:29674431
cell which is part of the ventral epidermis
ventral ciliated cell
ventral epithelial cell
ventral motile ciliated cell
ventral multiciliated cell
Planarian_Anatomy
PLANA:0003101
ventral epidermis cell
cell which is part of the ventral epidermis
PMID:22479207
PMID:23144623
cell which is part of the visual system
visual cell
Planarian_Anatomy
PLANA:0003102
visual system cell
cell which is part of the visual system
PMID:17905225
PMID:24922054
cell which is part of the eye
photoreceptor cell
photosensitive cell
Planarian_Anatomy
PLANA:0003103
eye cell
cell which is part of the eye
PMID:29357350
cell which is part of the enteric musculature
gut muscle cell
intestinal muscle cell
Planarian_Anatomy
PLANA:0003104
enteric muscle cell
cell which is part of the enteric musculature
PMID:23954785
PMID:25558068
cell which is part of the dorsal region of the epidermis
dorsal epithelial cell
Planarian_Anatomy
PLANA:0003105
dorsal epidermis cell
cell which is part of the dorsal region of the epidermis
PMID:22479207
cell which is part of the adhesion gland
Planarian_Anatomy
PLANA:0003106
adhesion gland cell
cell which is part of the adhesion gland
PMID:16890156
PMID:28976975
cell which is part of the body wall musculature
body wall muscle fiber
body-wall muscle cell
Planarian_Anatomy
PLANA:0003107
body wall muscle cell
cell which is part of the body wall musculature
PMID:23954785
PMID:24992682
PMID:25254346
PMID:25725068
PMID:26525673
cell which is part of the gastrodermis
gut cell
intestinal cell
Planarian_Anatomy
PLANA:0003108
gastrodermal cell
cell which is part of the gastrodermis
PMID:19174194
PMID:22479207
PMID:27122174
cell which is part of the anterior pole
Planarian_Anatomy
PLANA:0003109
anterior pole cell
cell which is part of the anterior pole
PMID:24992682
PMID:29674431
PMID:30471994
neuron which is part of the pharynx
pharyngeal neuron
Planarian_Anatomy
PLANA:0003110
pharynx neuron
neuron which is part of the pharynx
PMID:18202849
PMID:29674431
PMID:30485821
epithelial cell which is part of the pharynx
pharynx epithelial cell
Planarian_Anatomy
PLANA:0003111
pharynx epithelial cell
epithelial cell which is part of the pharynx
PMID:20511647
muscle cell which is part of the pharynx
pharynx muscle fiber
Planarian_Anatomy
PLANA:0003112
pharynx muscle cell
muscle cell which is part of the pharynx
PMID:27068018
epithelial cell which is part of the pharynx pouch
pharyngeal cavity epithelial cell
pharynx cavity epithelial cell
Planarian_Anatomy
PLANA:0003113
pharynx pouch epithelial cell
pigment granule which is part of the eumelanin
melanin
melanosome
photoreceptor pigment
Planarian_Anatomy
PLANA:0003114
melanin pigment granule
pigment granule which is part of the eumelanin
PMID:25356635
PMID:26017970
PMID:27551436
pigment granule which is part of the ommochrome pigment cell
Planarian_Anatomy
PLANA:0003115
ommochrome pigment granule
cell which is part of the parenchyma
Planarian_Anatomy
PLANA:0003116
parenchymal cell
cell which is part of the parenchyma
PMID:19247960
PMID:29674431
cell which is part of the parapharyngeal region
Planarian_Anatomy
PLANA:0003117
parapharyngeal cell
cell which is part of the prepharyngeal region
Planarian_Anatomy
PLANA:0003118
prepharyngeal cell
neoblast undergoing mitotic G1 phase
Planarian_Anatomy
PLANA:0003200
G1 phase neoblast
neoblast undergoing mitotic S phase
Planarian_Anatomy
PLANA:0003201
S phase neoblast
neoblast undergoing mitotic G2 phase
Planarian_Anatomy
PLANA:0003202
G2 phase neoblast
neoblast undergoing mitotic prophase
Planarian_Anatomy
PLANA:0003203
prophase neoblast
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.
neoblast undergoing mitotic metaphase
M phase neoblast
Planarian_Anatomy
PLANA:0003204
metaphase neoblast
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.
neoblast undergoing mitotic anaphase
Planarian_Anatomy
PLANA:0003205
anaphase neoblast
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.
neoblast undergoing mitotic telophase
Planarian_Anatomy
PLANA:0003206
telophase neoblast
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
Planarian_Anatomy
PLANA:0003207
G1 phase spermatogonial stem cell
spermatogonial stem cell undergoing mitotic S phase
Planarian_Anatomy
PLANA:0003208
S phase spermatogonial stem cell
spermatogonial stem cell undergoing mitotic G2 phase
Planarian_Anatomy
PLANA:0003209
G2 phase spermatogonial stem cell
spermatogonial stem cell undergoing mitotic prophase
Planarian_Anatomy
PLANA:0003210
prophase spermatogonial stem cell
spermatogonial stem cell undergoing mitotic metaphase
Planarian_Anatomy
PLANA:0003211
metaphase spermatogonial stem cell
spermatogonial stem cell undergoing mitotic anaphase
Planarian_Anatomy
PLANA:0003212
anaphase spermatogonial stem cell
spermatogonial stem cell undergoing mitotic telophase
Planarian_Anatomy
PLANA:0003213
telophase spermatogonial stem cell
oogonial stem cell undergoing mitotic G1 phase
Planarian_Anatomy
PLANA:0003214
G1 phase oogonial stem cell
oogonial stem cell undergoing mitotic S phase
Planarian_Anatomy
PLANA:0003215
S phase oogonial stem cell
oogonial stem cell undergoing mitotic G2 phase
Planarian_Anatomy
PLANA:0003216
G2 phase oogonial stem cell
oogonial stem cell undergoing mitotic prophase
Planarian_Anatomy
PLANA:0003217
prophase oogonial stem cell
oogonial stem cell undergoing mitotic metaphase
Planarian_Anatomy
PLANA:0003218
metaphase oogonial stem cell
oogonial stem cell undergoing mitotic anaphase
Planarian_Anatomy
PLANA:0003219
anaphase oogonial stem cell
oogonial stem cell undergoing mitotic telophase
Planarian_Anatomy
PLANA:0003220
telophase oogonial stem cell
spermatogonium undergoing mitotic G1 phase
Planarian_Anatomy
PLANA:0003221
G1 phase spermatogonium
spermatogonium undergoing mitotic S phase
Planarian_Anatomy
PLANA:0003222
S phase spermatogonium
spermatogonium undergoing mitotic G2 phase
Planarian_Anatomy
PLANA:0003223
G2 phase spermatogonium
spermatogonium undergoing mitotic prophase
Planarian_Anatomy
PLANA:0003224
prophase spermatogonium
spermatogonium undergoing mitotic metaphase
Planarian_Anatomy
PLANA:0003225
metaphase spermatogonia
spermatogonium undergoing mitotic anaphase
Planarian_Anatomy
PLANA:0003226
anaphase spermatogonia
spermatogonium undergoing mitotic telophase
Planarian_Anatomy
PLANA:0003227
telophase spermatogonium
oogonial cell undergoing mitotic G1 phase
Planarian_Anatomy
PLANA:0003228
G1 phase oogonial cell
oogonial cell undergoing mitotic S phase
Planarian_Anatomy
PLANA:0003229
S phase oogonial cell
oogonial cell undergoing mitotic G2 phase
Planarian_Anatomy
PLANA:0003230
G2 phase oogonial cell
oogonial cell undergoing mitotic prophase
Planarian_Anatomy
PLANA:0003231
prophase oogonial cell
oogonial cell undergoing mitotic metaphase
Planarian_Anatomy
PLANA:0003232
metaphase oogonial cell
oogonial cell undergoing mitotic anaphase
Planarian_Anatomy
PLANA:0003233
anaphase oogonial cell
oogonial cell undergoing mitotic telophase
Planarian_Anatomy
PLANA:0003234
telophase oogonial cell
germ cell cyst undergoing mitotic G1 phase
Planarian_Anatomy
PLANA:0003235
G1 phase germ cell cyst
germ cell cyst undergoing mitotic S phase
Planarian_Anatomy
PLANA:0003236
S phase germ cell cyst
germ cell cyst undergoing mitotic G2 phase
Planarian_Anatomy
PLANA:0003237
G2 phase germ cell cyst
germ cell cyst undergoing mitotic prophase
Planarian_Anatomy
PLANA:0003238
prophase germ cell cyst
germ cell cyst undergoing mitotic metaphase
Planarian_Anatomy
PLANA:0003239
metaphase germ cell cyst
germ cell cyst undergoing mitotic anaphase
Planarian_Anatomy
PLANA:0003240
anaphase germ cell cyst
germ cell cyst undergoing mitotic telophase
Planarian_Anatomy
PLANA:0003241
telophase germ cell cyst
spermatocyte undergoing meiotic S phase
Planarian_Anatomy
PLANA:0003242
meiotic S phase spermatocyte
spermatocyte undergoing meiotic G1 phase
Planarian_Anatomy
PLANA:0003243
meiotic G1 phase spermatocyte
spermatocyte undergoing meiotic G2 phase
Planarian_Anatomy
PLANA:0003244
meiotic G2 phase spermatocyte
spermatocyte undergoing meiotic prophase I
Planarian_Anatomy
PLANA:0003245
meiotic prophase I spermatocyte
spermatocyte undergoing leptotene
Planarian_Anatomy
PLANA:0003246
leptotene stage spermatocyte
spermatocyte undergoing zygotene
Planarian_Anatomy
PLANA:0003247
zygotene stage spermatocyte
spermatocyte undergoing zygotene
https://doi.org/10.1101/279364
spermatocyte undergoing pachytene
Planarian_Anatomy
PLANA:0003248
pachytene stage spermatocyte
spermatocyte undergoing pachytene
https://doi.org/10.1101/279364
spermatocyte undergoing diplotene
Planarian_Anatomy
PLANA:0003249
diplotene stage spermatocyte
spermatocyte undergoing diakinesis
Planarian_Anatomy
PLANA:0003250
diakinesis stage spermatocyte
spermatocyte undergoing meiotic metaphase I
Planarian_Anatomy
PLANA:0003251
meiotic metaphase 1 stage spermatocyte
spermatocyte undergoing meiotic anaphase I
Planarian_Anatomy
PLANA:0003252
meiotic anaphase I stage spermatocyte
spermatocyte undergoing meiotic telophase I
Planarian_Anatomy
PLANA:0003253
meiotic telophase I spermatocyte
spermatocyte undergoing meiosis II cell cycle phase
Planarian_Anatomy
PLANA:0003254
meiosis II stage spermatocyte
spermatocyte undergoing meiotic prophase II
Planarian_Anatomy
PLANA:0003255
meiotic prophase II spermatocyte
spermatocyte undergoing meiotic metaphase II
Planarian_Anatomy
PLANA:0003256
meiotic metaphase 2 spermatocyte
spermatocyte undergoing meiotic anaphase II
Planarian_Anatomy
PLANA:0003257
meiotic anaphase II spermatocyte
spermatocyte undergoing meiotic telophase II
Planarian_Anatomy
PLANA:0003258
meiotic telophase II spermatocyte
This primordium develops into cephalic ganglia
PMID:16033796
PMID:17553481
PMID:17905225
PMID:19174194
PMID:21806978
PMID:22339734
PMID:23318635
PMID:25772472
PMID:26525673
brain primordia
brain primordium
brain primoridia
brain rudiment
cephalic ganglia primordia
cephalic ganglia primordium
Planarian_Anatomy
PLANA:0003300
cephalic ganglia primordium
This primordium develops into eye
PMID:22884275
eye aggregate
Planarian_Anatomy
PLANA:0003301
eye primordium
This primordium develops into pharynx
PMID:18202849
PMID:21282632
PMID:25254346
PMID:26556349
PMID:27074666
Planarian_Anatomy
PLANA:0003302
pharynx primordium
This primordium develops into optic cup
PMID:21852957
optic cup primordium
Planarian_Anatomy
PLANA:0003303
pigment cup primordium
This primordium develops into testis
PMID:23652002
Planarian_Anatomy
PLANA:0003304
testis primordium
This primordium develops into gonad
Planarian_Anatomy
PLANA:0003305
gonad primoridium
This primordium develops into ovary
Planarian_Anatomy
PLANA:0003306
ovary primordium
lumen which is part of the protonephridia
Planarian_Anatomy
PLANA:0003400
protonephridial lumen
lumen which is part of the protonephridia
PMID:26057828
lumen which is part of the testis
Planarian_Anatomy
PLANA:0003401
testis lumen
lumen which is part of the testis
PMID:17390146
lumen which is part of the ovary
Planarian_Anatomy
PLANA:0003402
ovary lumen
lumen which is part of the ovary
PMID:19247960
lumen which is part of the flame cell
flame cell barrel lumen
Planarian_Anatomy
PLANA:0003403
flame cell lumen
lumen which is part of the flame cell
PMID:21828097
A progenitor cell that gives rise to one or more of the cell type(s) in the nervous system.
brain progenitor
brain progentitor cell
Planarian_Anatomy
cephalic ganglia progenitor cell
A progenitor cell that gives rise to one or more of the cell type(s) in the nervous system.
PMID:26525673
A progenitor cell that gives rise to one or more of the cell type(s) in the dorsal epidermis.
Planarian_Anatomy
dorsal epidermis progenitor cell
A progenitor cell that gives rise to one or more of the cell type(s) in the dorsal epidermis.
PMID:28292427
A progenitor cell that gives rise to optic cup cells of the eye.
optic cup trail cell
Planarian_Anatomy
optic cup progenitor cell
A progenitor cell that gives rise to optic cup cells of the eye.
PMID:21852957
A progenitor cell that gives rise to one or more of the cell type(s) in the epidermis.
Planarian_Anatomy
PLANA:0003503
ventral epidermis progenitor cell
A progenitor cell that gives rise to one or more of the cell type(s) in the epidermis.
PMID:28292427
This progenitor cell develops into testis somatic gonadal cell
Planarian_Anatomy
PLANA:0003504
testis somatic gonadal cell progenitor cell
This progenitor cell develops into testis somatic gonadal cell
PMID: 23652002
A fragment derived from a prepharyngeal amputation encompassing the head.
head piece
Planarian_Anatomy
PLANA:0003600
head fragment
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.
trunk piece
Planarian_Anatomy
PLANA:0003601
trunk fragment
Illustration of a trunk fragment (in green).
A fragment derived from a postpharyngeal amputation encompassing the tail.
tail piece
Planarian_Anatomy
PLANA:0003602
tail fragment
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.
neck fragment
neck piece
Planarian_Anatomy
PLANA:0003603
prepharyngeal fragment
Illustration of a prepharyngeal fragment (in green).
A fragment derived from two postpharyngeal amputations, removing the anterior region and the tail tip.
post-pharyngeal fragment
post-pharyngeal piece
postpharyngeal piece
Planarian_Anatomy
PLANA:0003604
postpharyngeal fragment
Illustration of a postpharyngeal fragment (in green).
A fragment encompassing all or part of the anterior region of the animal.
Planarian_Anatomy
PLANA:0003605
anterior fragment
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.
Planarian_Anatomy
PLANA:0003606
posterior fragment
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]
edge fragment
longitudinal fragment
sagittal fragment
side fragment
Planarian_Anatomy
PLANA:0003607
lateral fragment
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.
Planarian_Anatomy
PLANA:0003608
longitudinal fragment
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.
Planarian_Anatomy
PLANA:0003609
plug fragment
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.
Planarian_Anatomy
PLANA:0003610
wedge fragment
Illustration of an example wedge fragment in green.
The dorsal region of a fragment derived from a prepharyngeal amputation encompassing the head.
dorsal region of head fragment
Planarian_Anatomy
dorsal region of head fragment
Illustration of the dorsal region of a head fragment (green).
The ventral region of a fragment derived from a prepharyngeal amputation encompassing the head.
ventral region of head fragment
Planarian_Anatomy
ventral region of head fragment
Illustration of the ventral region of a head fragment (green).
The anterior region of a fragment derived from a prepharyngeal amputation encompassing the head.
anterior region of head fragment
Planarian_Anatomy
anterior region of head fragment
Illustration of the anterior region of a head fragment (green).
The posterior region of a fragment derived from a prepharyngeal amputation encompassing the head.
posterior region of head fragment
Planarian_Anatomy
posterior region of head fragment
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.
dorsal region of trunk fragment
Planarian_Anatomy
dorsal region of trunk fragment
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.
ventral region of trunk fragment
Planarian_Anatomy
ventral region of trunk fragment
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.
anterior region of trunk fragment
Planarian_Anatomy
anterior region of trunk fragment
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.
posterior region of trunk fragment
Planarian_Anatomy
posterior region of trunk fragment
Illustration of the posterior region of a trunk fragment (green).
The dorsal region of a fragment derived from a postpharyngeal amputation encompassing the tail.
dorsal region of tail fragment
Planarian_Anatomy
dorsal region of tail fragment
Illustration of the dorsal region of a tail fragment (green).
The ventral region of a fragment derived from a postpharyngeal amputation encompassing the tail.
ventral region of tail fragment
Planarian_Anatomy
ventral region of tail fragment
Illustration of the ventral region of a tail fragment (green).
The anterior region of a fragment derived from a postpharyngeal amputation encompassing the tail.
anterior region of tail fragment
Planarian_Anatomy
anterior region of tail fragment
Illustration of the anterior region of a tail fragment (green).
The posterior region of a fragment derived from a postpharyngeal amputation encompassing the tail.
posterior region of tail fragment
Planarian_Anatomy
posterior region of tail fragment
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.
dorsal region of prepharyngeal fragment
Planarian_Anatomy
dorsal region of prepharyngeal fragment
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
Planarian_Anatomy
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
Planarian_Anatomy
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
Planarian_Anatomy
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
Planarian_Anatomy
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
Planarian_Anatomy
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
Planarian_Anatomy
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
Planarian_Anatomy
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.
dorsal region of anterior fragment
Planarian_Anatomy
dorsal region of anterior fragment
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.
ventral region of anterior fragment
Planarian_Anatomy
ventral region of anterior fragment
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.
anterior region of anterior fragment
Planarian_Anatomy
anterior region of anterior fragment
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.
posterior region of anterior fragment
Planarian_Anatomy
posterior region of anterior fragment
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.
dorsal region of posterior fragment
Planarian_Anatomy
dorsal region of posterior fragment
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.
ventral region of posterior fragment
Planarian_Anatomy
ventral region of posterior fragment
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.
anterior region of posterior fragment
Planarian_Anatomy
anterior region of posterior fragment
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.
posterior region of posterior fragment
Planarian_Anatomy
posterior region of posterior fragment
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.
dorsal region of lateral fragment
Planarian_Anatomy
dorsal region of lateral fragment
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.
ventral region of lateral fragment
Planarian_Anatomy
ventral region of lateral fragment
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.
anterior region of lateral fragment
Planarian_Anatomy
anterior region of lateral fragment
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.
posterior region of lateral fragment
Planarian_Anatomy
posterior region of lateral fragment
Illustration of the posterior region of a lateral fragment (green).
The dorsal region of a fragment derived from an amputation parallel to the midline.
dorsal region of longitudinal fragment
Planarian_Anatomy
dorsal region of longitudinal fragment
Illustration of the dorsal region of a longitudinal fragment (green).
The ventral region of a fragment derived from an amputation parallel to the midline.
ventral region of longitudinal fragment
Planarian_Anatomy
ventral region of longitudinal fragment
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
Planarian_Anatomy
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
Planarian_Anatomy
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.
dorsal region of plug fragment
Planarian_Anatomy
dorsal region of plug fragment
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.
ventral region of plug fragment
Planarian_Anatomy
ventral region of plug fragment
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.
anterior region of plug fragment
Planarian_Anatomy
anterior region of plug fragment
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.
posterior region of plug fragment
Planarian_Anatomy
posterior region of plug fragment
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.
dorsal region of wedge fragment
Planarian_Anatomy
dorsal region of wedge fragment
Illustration of the dorsal region of a plug fragment (green).
The ventral region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
ventral region of wedge fragment
Planarian_Anatomy
ventral region of wedge fragment
Illustration of the ventral region of a plug fragment (green).
The anterior region of a piece of tissue removed from the lateral margin at any given point that extendes interiorly to more medial structures.
anterior region of wedge fragment
Planarian_Anatomy
anterior region of wedge fragment
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.
posterior region of wedge fragment
Planarian_Anatomy
posterior region of wedge fragment
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
Planarian_Anatomy
anterior photoreceptor neuron
photoreceptor neuron is contained in the anterior region of the eye
PMID: 20967238
photoreceptor neuron is contained in the posterior region of the eye
photoreceptor neuron contained in posterior region of the eye
Planarian_Anatomy
posterior photoreceptor neuron
photoreceptor neuron is contained in the posterior region of the eye
PMID: 20967238
muscle cell is contained in the lateral region
muscle cell contained in lateral region
Planarian_Anatomy
lateral muscle cell
muscle cell is contained in the lateral region
PMID: 29674431
muscle cell is contained in the anterior region
muscle cell contained in anterior region
Planarian_Anatomy
anterior muscle cell
muscle cell is contained in the anterior region
PMID: 29674432
muscle cell is contained in the posterior region
muscle cell contained in posterior region
Planarian_Anatomy
posterior muscle cell
muscle cell is contained in the posterior region
PMID: 29674433
blastema which develops into head region
Planarian_Anatomy
PLANA:0003900
head blastema
blastema which develops into tail region
Planarian_Anatomy
PLANA:0003901
tail blastema
a head fragment that is regenerating
Planarian_Anatomy
regenerating head fragment
a trunk fragment that is regenerating
Planarian_Anatomy
regenerating trunk fragment
a tail fragment that is regenerating
Planarian_Anatomy
regenerating tail fragment
a prepharyngeal fragment that is regenerating
Planarian_Anatomy
regenerating prepharyngeal fragment
a postpharyngeal fragment that is regenerating
Planarian_Anatomy
regenerating postpharyngeal fragment
a anterior fragment that is regenerating
Planarian_Anatomy
regenerating anterior fragment
a posterior fragment that is regenerating
Planarian_Anatomy
regenerating posterior fragment
a lateral fragment that is regenerating
Planarian_Anatomy
regenerating lateral fragment
a longitudinal fragment that is regenerating
Planarian_Anatomy
regenerating longitudinal fragment
a plug fragment that is regenerating
Planarian_Anatomy
regenerating plug fragment
a wedge fragment that is regenerating
Planarian_Anatomy
regenerating wedge fragment
A fully formed, sexually mature organism that reproduces through cross-fertilization.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:11972158
PMID:19022767
sexual adult
sexually mature adult
Planarian_Anatomy
adult hermaphrodite
A fully formed, sexually mature organism that reproduces through cross-fertilization.
PMID:11972158
PMID:19022767
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:11972158
PMID:17376870
Planarian_Anatomy
asexual adult
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.
PMID:11972158
PMID:17376870
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:23652002
PMID:27163480
somatic gonadal cell of the testis
somatic niche cell of the testis
somatic testis cell
Planarian_Anatomy
testis somatic gonadal cell
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.
PMID:23652002
PMID:27163480
ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:27163480
somatic follicular cell of the ovary
somatic ovarian cell
Planarian_Anatomy
ovarian somatic gonadal cell
ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia.
PMID:27163480
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.
oral-aboral axis of embryo
Planarian_Anatomy
PLANA:0004511
oral-aboral axis of the embryo
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.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:20423827
OCLC:464776945
OCLC:82522822
PMID:28072387
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md
Planarian_Anatomy
primitive ectoderm surface
The apical surface of the single layered primitive ectoderm that is in contact with the environment.
OCLC:20423827
OCLC:464776945
OCLC:82522822
PMID:28072387
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md
The surface of the primitive gut cells in contact with the embryonic wall.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Planarian_Anatomy
primtive gut cell surface
The surface of the primitive gut cells in contact with the embryonic wall.
PMID:28072387
The surface of phagocytic embryonic gut cells in contact with ingested yolk cells.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Planarian_Anatomy
embryonic gut cell surface
The surface of phagocytic embryonic gut cells in contact with ingested yolk cells.
PMID:28072387
The epithelial cell surface lining the embryonic pharynx lumen.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:20100474
PMID:28072387
Planarian_Anatomy
embryonic pharynx lumen epithelial surface
The epithelial cell surface lining the embryonic pharynx lumen.
PMID:28072387
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000353
PMID:28072387
Planarian_Anatomy
blastomere
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.
PMID:28072387
Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000349
PMID:28072387
Planarian_Anatomy
extraembryonic cell
Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues.
PMID:28072387
A neuronal cell innervating the embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Planarian_Anatomy
embryonic pharynx neuron
A neuronal cell innervating the embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening.
PMID:28072387
Differentiated radial muscle cell present in the embryonic pharynx.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:16932928
embryonic pharynx radial muscle fiber
Planarian_Anatomy
embryonic pharynx radial muscle cell
Differentiated radial muscle cell present in the embryonic pharynx.
PMID:16932928
foxA1+ epithelial cell contained in the embryonic pharynx.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:20100474
PMID:28072387
Planarian_Anatomy
embryonic pharynx epithelial cell
foxA1+ epithelial cell contained in the embryonic pharynx.
PMID:28072387
Differentiated muscle cell present in a circular muscle fiber of the embryonic pharynx.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:16932928
embryonic pharynx circular muscle fiber
Planarian_Anatomy
embryonic pharynx circular muscle cell
Differentiated muscle cell present in a circular muscle fiber of the embryonic pharynx.
PMID:16932928
Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:22074376
Planarian_Anatomy
copulatory region
Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus.
PMID:22074376
Depicted by field contains diagram representation of body region.
Epithelia associated with the pharynx organ.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0003351
pharnyx epidermis
pharyngeal epidermis
pharyngeal epithelium
Planarian_Anatomy
pharynx epithelium
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0002416
Planarian_Anatomy
integumental system
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.
UBERON:0002416
Anatomical space enclosed by the oviduct epithelium.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:22074376
TADS:0000435
Planarian_Anatomy
oviduct lumen
Anatomical space enclosed by the oviduct epithelium.
PMID:22074376
Anatomical space enclosed by the sperm duct epithelium.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:19022767
PMID:22074376
Planarian_Anatomy
sperm duct lumen
Anatomical space enclosed by the sperm duct epithelium.
PMID:19022767
PMID:22074376
Ciliated epithelium lining the oviduct.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:2000064
PMID:22074376
UBERON:0004804
Planarian_Anatomy
oviduct epithelium
Ciliated epithelium lining the oviduct.
PMID:22074376
Ciliated epithelium lining the sperm duct.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:19022767
PMID:22074376
Planarian_Anatomy
sperm duct epithelium
Ciliated epithelium lining the sperm duct.
PMID:19022767
PMID:22074376
Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:19022767
PMID:20844018
PMID:22074376
PMID:27149082
Planarian_Anatomy
tuba lumen
Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct.
PMID:19022767
PMID:20844018
PMID:22074376
PMID:27149082
let odk import from BSPO if needed
obsolete coronal plane
true
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.
sagittal plane of whole organism
Planarian_Anatomy
PLANA:0007503
sagittal plane of the whole animal
Illustration of a sagittal plane of the whole animal (in green).
replaced by dorsal region PLANA:0000141
obsolete dorsal compartment
true
now using patterned term ventral region PLANA:0000143
obsolete ventral compartment
true
now using patterned term anterior region
obsolete anterior compartment
true
replaced
replacing duplicate PLANA term
obsolete posterior compartment
true
choosing to use UBERON:0000476, acellular anatomical structure instead
obsolete extracellular component
true
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005886
PMID:20511647
PMID:27523733
cell membrane
cytoplasmic membrane
Planarian_Anatomy
plasma membrane
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0005886
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0043230
Planarian_Anatomy
extracellular organelle
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.
GO:0043230
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005739
PMID:21828097
PMID:22318224
PMID:26516985
PMID:29100657
mitochondria
Planarian_Anatomy
mitochondrion
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005783
PMID:30143032
Planarian_Anatomy
endoplasmic reticulum
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005791
PMID:30143032
Planarian_Anatomy
rough endoplasmic reticulum
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005790
Planarian_Anatomy
smooth endoplasmic reticulum
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005643
Planarian_Anatomy
nuclear pore
Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
GO:0005643
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
GO:0005764
ISBN:0-71677033-4
PMID:4853064
Planarian_Anatomy
lysosome
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
anterior-posterior axis of whole organism
body axis
longitudinal axis
main body axis
Planarian_Anatomy
PLANA:0007519
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.
D/V axis
DV axis
dorsal-ventral axis
dorsal-ventral axis of whole organism
Planarian_Anatomy
PLANA:0007520
dorsal-ventral axis of the whole animal
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.
PMID:18287199
PMID:18786419
PMID:19174194
PMID:21295481
PMID:21295483
PMID:21664348
PMID:21806978
PMID:22445864
PMID:23318641
PMID:23954785
PMID:24415944
PMID:24523458
PMID:25017721
PMID:27063937
PMID:27523733
PMID:27612382
PMID:28137894
PMID:28292427
PMID:28686611
PMID:29100657
PMID:29547123
PMID:29674431
PMID:30471994
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.
dextro-sinister axis
left-right axis
left-right axis of whole organism
Planarian_Anatomy
PLANA:0007521
left-right axis of the whole animal
Depiction shows an asexual adult with the term annotated in yellow. Scale bar =500um
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.
medial-lateral axis
medial-lateral axis of whole organism
mediolateral
mediolateral axis
Planarian_Anatomy
PLANA:0007522
medial-lateral axis of the whole animal
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.
PMID:20707997
PMID:21282632
PMID:21295483
PMID:21664348
PMID:21806978
PMID:23250205
PMID:23318641
PMID:23903188
PMID:23954785
PMID:25017721
PMID:26062938
PMID:26525673
PMID:27523733
PMID:28287248
PMID:29291981
PMID:29547123
PMID:30471994
PMID:30962434
Depiction shows an asexual adult with the term annotated in yellow. Scale bar =500um
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
proximal-distal axis of whole organism
Planarian_Anatomy
PLANA:0007523
proximal-distal axis of the whole 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.
PMID:21828097
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:18063755
PMID:21566195
PMID:23297191
PMID:23318641
PMID:23903188
PMID:23954785
PMID:24040508
PMID:24415944
PMID:24523458
PMID:24704339
PMID:24992682
PMID:25254346
PMID:25725068
PMID:26062938
PMID:26525673
PMID:27074666
PMID:27800171
PMID:28216315
PMID:28292427
PMID:28893948
PMID:29547123
PMID:29906446
PMID:30485821
anterior signaling center
Planarian_Anatomy
anterior pole
Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD.
PMID:21566195
PMID:23297191
PMID:24040508
PMID:24415944
PMID:24704339
PMID:24992682
Illustration of the anterior pole (green).
Distinct posterior cluster of muscle cells located at the midline which express wnt1.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:18063755
PMID:19805089
PMID:21566195
PMID:23318641
PMID:23903188
PMID:24415944
PMID:25725068
PMID:26062938
PMID:27074666
PMID:30485821
posterior regeneration pole
Planarian_Anatomy
posterior pole
Distinct posterior cluster of muscle cells located at the midline which express wnt1.
PMID:18063755
PMID:21680047
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000125
PMID:27612382
PMID:27612384
PMID:28137894
PMID:29674431
PMID:29674432
PMID:30471994
glia
glia cell
Planarian_Anatomy
glial cell
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.
PMID:27612384
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
UBERON:0000045
ganglia
Planarian_Anatomy
ganglion
A biological tissue mass of nerve cell bodies.
UBERON:0000045
Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:16809160
PMID:24120894
doi:10.1002/jmor.1051550208
epithelial pharynx lining
epithelium lining the lumen of the pharynx
inner epithelium
inner pharyngeal epidermis
inner pharyngeal epithelium
inner pharynx epidermis
inner pharynx epithelium
Planarian_Anatomy
pharynx inner epithelium
Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft.
OCLC:16809160
doi:10.1002/jmor.1051550208
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.
Pharynx muscle fibers running circumferentially about the pharynx.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ASIN:B000M4NK9M
pharyngeal circular muscle cell
pharynx circular muscle cell
pharynx circular muscle fiber
Planarian_Anatomy
pharynx circular muscle cell
Pharynx muscle fibers running circumferentially about the pharynx.
ASIN:B000M4NK9M
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.
using part of instead
obsolete specific_to
true
replacing duplicate PLANA term
obsolete brain
true
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
ISBN:9780070316607
OCLC:16809160
PMID:20865784
marginal adhesive gland
Planarian_Anatomy
adhesion gland
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.
OCLC:16809160
PMID:20865784
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:16809160
PMID:20865784
Planarian_Anatomy
anchor cell
Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells.
OCLC:16809160
PMID:20865784
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:16809160
PMID:20865784
Planarian_Anatomy
viscid gland cell
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.
OCLC:16809160
PMID:20865784
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:16809160
PMID:20865784
Planarian_Anatomy
releasing gland cell
Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance.
OCLC:16809160
PMID:20865784
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:25254346
TrpA+ neuron
Planarian_Anatomy
TrpA+ central nervous system neuron
A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2.
PMID:25254346
A subset of sensory neurons located along the dorsal head margin.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:12557210
PMID:25254346
PMID:29674431
cintillo+ neuron
Planarian_Anatomy
cintillo+ sensory neuron
A subset of sensory neurons located along the dorsal head margin.
PMID:12557210
PMID:25254346
PMID:29674431
no longer designating mediolateral regions using the contained_in object property
obsolete epidermal compartment
true
piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:25254346
Planarian_Anatomy
TrpA+ neural progenitor cell
piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons.
PMID:25254346
piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:24415944
Planarian_Anatomy
anterior pole progenitor cell
piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole.
PMID:24415944
Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17999079
Planarian_Anatomy
transverse commissure
Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords.
PMID:17999079
no longer designating mediolateral regions using the contained_in object property
obsolete body wall musculature compartment
true
piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:23903188
PMID:24131630
PMID:25254346
Planarian_Anatomy
serotonergic neural progenitor cell
piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons.
PMID:23903188
PMID:24131630
PMID:25254346
piwi-1+, klf+ progenitor neoblasts required for production of cintillo+ sensory neurons.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:25254346
Planarian_Anatomy
klf+ sensory neuron progenitor cell
piwi-1+, klf+ progenitor neoblasts required for production of cintillo+ sensory neurons.
PMID:25254346
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:27150006
vNeoblast
Planarian_Anatomy
nu neoblast
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.
PMID:27150006
A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17999079
Planarian_Anatomy
lateral nerve
A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus.
PMID:17999079
no longer designating mediolateral regions using the contained_in object property
obsolete parenchymal compartment
true
piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:25254346
Planarian_Anatomy
pax3/7+ neural progenitor cell
piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons.
PMID:25254346
A lumen enclosed by the embryonic pharynx epithelial cells through which yolk cells are transported into the embryonic gut cavity.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:28072387
Planarian_Anatomy
embryonic pharynx lumen
A lumen enclosed by the embryonic pharynx epithelial cells through which yolk cells are transported into the embryonic gut cavity.
PMID:28072387
Nerve plexus surrounding the testis.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17999079
PMID:7833618
Planarian_Anatomy
testis nerve plexus
Nerve plexus surrounding the testis.
PMID:17999079
PMID:7833618
Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
OCLC:16809160
PMID:11972158
Planarian_Anatomy
fission plane
Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs.
OCLC:16809160
PMID:11972158
Nerve plexus surrounding the ovary.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
PMID:17999079
PMID:7833618
Planarian_Anatomy
ovary nerve plexus
Nerve plexus surrounding the ovary.
PMID:17999079
PMID:7833618
no longer designating mediolateral regions using the contained_in object property
obsolete gastrovascular compartment
true
Peripheral region of the head.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
head margin
Neurons that express the biogenic amine glutamate.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CL:0000679
PMID:24131630
Planarian_Anatomy
glutamatergic neuron
Neurons that express the biogenic amine glutamate.
PMID:24131630
An individual member of the sexual biotype of Schmidtea mediterranea.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
sexual organism
An individual member of the asexual biotype of Schmidtea mediterranea.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
CARO:0000030
Planarian_Anatomy
asexual organism
A neuron cell that does not have cilia.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
non cilated neuron
uncilated neuon
Planarian_Anatomy
non-ciliated neuron
A neuron cell that does not have cilia.
PMID:29674431
A neuron that has cilia.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
WBbt:0006816
Planarian_Anatomy
cilated neuron
A neuron that has cilia.
PMID:29674431
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
guidepost cell
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.
PMID:32586989
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
NME cell
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.
PMID:32586989
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
NMC cell
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.
PMID:32586989
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.
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
Planarian_Anatomy
NBC cell
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.
PMID:32586989
A sexually immature member of the Schmidtea mediterranea sexuallly reproducing biotype
https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407
juvenile
Planarian_Anatomy
juvenile organism
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
EMAPA:0
FBbt:00007001
FMA:305751
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:D000825
SCTID:362889002
TAO:0000037
TGMA:0001823
VHOG:0001759
XAO:0003000
ZFA:0000037
http://dbpedia.org/ontology/AnatomicalStructure
biological structure
connected biological structure
uberon
UBERON:0000061
anatomical structure
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
CARO:0000003
connected biological structure
CARO:0000003
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
BilaDO:0000002
EV:0300001
FBdv:00005289
FMA:72652
HsapDv:0000002
MmusDv:0000002
OGES:000000
OGES:000022
SCTID:296280003
WBls:0000003
WBls:0000092
WBls:0000102
XAO:1000012
embryonic stage
uberon
embryogenesis
UBERON:0000068
embryo stage
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
http://orcid.org/0000-0002-6601-2165
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
BILS:0000105
EFO:0000399
FBdv:00007012
FMA:24120
HsapDv:0000000
MESH:D008018
MmusDv:0000000
OlatDv:0000010
PdumDv:0000090
WBls:0000002
XAO:1000000
ZFS:0000000
ZFS:0100000
ncithesaurus:Developmental_Stage
developmental stage
stage
uberon
UBERON:0000105
life cycle stage
A spatiotemporal region encompassing some part of the life cycle of an organism.
https://orcid.org/0000-0002-6601-2165
Anatomical entity that has mass.
AAO:0010264
AEO:0000006
BILA:0000006
CARO:0000006
EHDAA2:0003006
FBbt:00007016
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
VHOG:0001721
uberon
UBERON:0000465
material anatomical entity
Anatomical entity that has mass.
http://orcid.org/0000-0001-9114-8737
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
AAO:0010053
AEO:0000032
BILA:0000032
BIRNLEX:7
CALOHA:TS-2084
CARO:0000032
EFO:0000808
EHDAA2:0003032
EMAPA:36031
FBbt:00007009
FMA:7153
HAO:0000032
MA:0002433
MAT:0000293
MESH:D001829
MIAA:0000293
NCIT:C32221
TAO:0001308
TGMA:0001840
VHOG:0001758
Wikipedia:Body_part
XAO:0003013
ZFA:0001308
galen:BodyPart
anatomic region
uberon
body part
body region
cardinal body part
UBERON:0000475
organism subdivision
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.
CARO:0000032
CARO:DOS
http://orcid.org/0000-0001-9114-8737
anatomic region
MA:0002433
body region
FMA:7153
cardinal body part
FMA:7153
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
AAO:0010268
AEO:0000040
BILA:0000040
CARO:0000040
EHDAA2:0003040
FBbt:00007013
FMA:63863
HAO:0000040
TAO:0000382
TGMA:0001841
XAO:0003162
ZFA:0000382
uberon
acellular anatomical structures
UBERON:0000476
acellular anatomical structure
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
http://orcid.org/0000-0001-9114-8737
acellular anatomical structures
ZFA:0000382
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
AAO:0010841
AEO:0000000
BILA:0000000
BIRNLEX:6
CARO:0000000
EHDAA2:0002229
FBbt:10000000
FMA:62955
HAO:0000000
MA:0000001
NCIT:C12219
TAO:0100000
TGMA:0001822
WBbt:0000100
XAO:0000000
ZFA:0100000
uberon
UBERON:0001062
anatomical entity
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
FMA:62955
http://orcid.org/0000-0001-9114-8737
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.
cavity
BIRNLEX:1011
FMA:67552
MA:0002447
NCIT:C34007
galen:Cavity
uberon
UBERON:0002553
anatomical cavity
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.
FMA:67552
AEO:0000125
CALOHA:TS-2122
EHDAA2:0003125
FBbt:00007006
FMA:292313
MIAA:0000019
uberon
developing structure
developmental structure
developmental tissue
UBERON:0005423
developing anatomical structure
developmental tissue
MIAA:0000019
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.
AEO:0000200
EHDAA2:0003233
TAO:0005147
XAO:0004059
ZFA:0005147
uberon
regenerating tissue
regenerating tissues
regenerative tissue
UBERON:0007567
regenerating anatomical structure
An anatomical structure that is undergoing regeneration.
http://orcid.org/0000-0002-6601-2165
regenerating tissue
ZFA:0005147
regenerating tissues
ZFA:0005147
example to be eventually removed
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
Person:Alan Ruttenberg
failed exploratory term
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
ready for release
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
pending final vetting
placeholder removed
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term imported
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
term split
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
Alan Ruttenberg
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
universal
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
Alan Ruttenberg
defined class
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
Alan Ruttenberg
named class expression
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI
requires discussion
The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
https://github.com/information-artifact-ontology/ontology-metadata/issues/77
https://orcid.org/0000-0001-5208-3432
out of scope
true
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
infer input from direct reg
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
enabling an MF enables its parts
true
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
involved in BP
This can't be added as a property chain because it causes a circularity violation for 'part of'.
This can't be added as a property chain because it causes a circularity violation for 'part of'.
This can't be added as a property chain because it causes a circularity violation for 'part of'.
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X