Planarian_Anatomy
1.2
CARO part_of NCBITaxon:79327; CL part_of NCBITaxon:79327
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
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.obfoundry.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
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
Chris Mungall
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
IAO:0100001
namespace-id-rule
IAO:0100001
synonym_type_property
has_alternative_id
has_broad_synonym
IAO:0100001
database_cross_reference
IAO:0100001
has_exact_synonym
IAO:0100001
has_narrow_synonym
IAO:0100001
has_obo_format_version
IAO:0100001
has_obo_namespace
IAO:0100001
has_related_synonym
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
Sofia Robb
2017-09-11T16:38:22Z
depiction
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
BFO:0000050
external
spatial
uberon
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
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
spatial
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
On the same side as. For example, the left arm is ipsilateral to the left leg.
BSPO:0000105
spatial
ipsilateral_to
ipsilateral_to
ipsilateral to
On the same side as. For example, the left arm is ipsilateral to the left leg.
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 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
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
x immediately deep to y iff x deep_to y and x is contiguous with y.
BSPO:0001107
spatial
uberon
immediately_deep_to
immediately_deep_to
immediately deep to
immediately_deep_to
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
x immediately deep to y iff x deep_to y and x is contiguous with y.
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
uberon
immediately_superficial_to
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
is_about is 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
feature restricted to
Steph Nowotarski
2017-07-24T20:21:09Z
Planarian_Relationship
specific_to
specific to
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
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
A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
dos
2017-07-19T17:30:36Z
has ligand
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
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
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
Terry Meehan
This is the transitive form of the develops from relation
develops from
inverse of develops from
Chris Mungall
David Osumi-Sutherland
Terry Meehan
develops into
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
negatively regulates (process to process)
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
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)".
RO_0000053 some (RO_0000054 only ?Y)
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
RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
capable of part of
true
x actively participates in y if and only if x participates in y and x realizes some active role
Chris Mungall
agent in
actively participates in
'heart development' has active participant some Shh protein
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
Chris Mungall
has agent
obsolete has active participant
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.
x adjacent_to y iff: x and y share a boundary
This relation acts as a join point with BSPO
Chris Mungall
RO:0002220
spatial
uberon
adjacent_to
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
Chris Mungall
has developmental contribution from
inverse of has developmental contribution from
Chris Mungall
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
Chris Mungall
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
Chris Mungall
developmentally succeeded by
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
cjm
holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
causally upstream of, negative effect
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)
Chris Mungall
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
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.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
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).
Chris Mungall
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
Chris Mungall
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
Chris Mungall
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
Chris Mungall
has potential to directly develop into
inverse of upstream of
Chris Mungall
causally downstream of
Chris Mungall
immediately causally downstream of
This relation groups causal relations between material entities and causal relations between processes
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
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
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
Chris Mungall
immediately causally upstream of
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
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.
Chris Mungall
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.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
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/MI_0914
https://github.com/oborel/obo-relations/wiki/InteractionRelations
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
Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
Chris Mungall
molecularly controls
activity directly regulates activity of
Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
Chris Mungall
inhibits
molecularly decreases activity of
activity directly negatively regulates activity of
Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
Chris Mungall
activates
molecularly increases activity of
activity 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.
Chris Mungall
has part that occurs in
true
Chris Mungall
is kinase activity
Chris Mungall
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 structure and 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))
Chris Mungall
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).
Chris Mungall
RO:0002496
uberon
existence_starts_during_or_after
existence_starts_during_or_after
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence starts during or after
x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
Chris Mungall
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 of direct activation or direct inhibition. 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
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 material entities
Chris Mungall
causally influenced by (material entity to material entity)
causally influenced by
Chris Mungall
interaction relation helper property
https://github.com/oborel/obo-relations/wiki/InteractionRelations
Chris Mungall
molecular interaction relation helper property
Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b
Chris Mungall
causally influences (material entity to material entity)
causally influences
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
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
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
directly positively regulates (process to process)
directly positively regulates
Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
directly negatively regulates (process to process)
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.
Melissa Haendel
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.
Melissa Haendel
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
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
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]
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
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.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
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]
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
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
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
spatial
CARO:0000000
anatomical entity
anatomical entity
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
CARO:MAH
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
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
A developmental process in which a progressive change in the state of some part of an organism 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 specifically contributes to its ability to form offspring.
GOC:dph
GOC:isa_complete
puberty
GOC:dph
reproductive developmental process
GOC:dph
GOC:tb
molecular process
molecular_function
catalytic activity
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
MIPS_funcat:41
biological_process
GO:0007275
Note that this term was 'developmental process'.
multicellular organism development
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
GOC:dph
GOC:ems
GOC:isa_complete
GOC:tb
The union of male and female gametes to form a zygote.
MIPS_funcat:41.05.01
biological_process
zygote biosynthesis
zygote formation
GO:0007338
single fertilization
The union of male and female gametes to form a zygote.
GOC:ems
GOC:mtg_sensu
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.
janelomax
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 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
The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
Wikipedia:Fertilisation
syngamy
biological_process
GO:0009566
fertilization
The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
GOC:tb
ISBN:0198506732
The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
embryogenesis and morphogenesis
Wikipedia:Morphogenesis
anatomical structure organization
morphogenesis
biological_process
GO:0009653
anatomical structure morphogenesis
The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
GOC:go_curators
ISBN:0521436125
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
GO:0009795
embryogenesis and morphogenesis
Wikipedia:Embryogenesis
embryogenesis
embryonal development
biological_process
GO:0009790
embryo development
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
GOC:go_curators
GOC:isa_complete
GOC:mtg_sensu
The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
histogenesis and organogenesis
Wikipedia:Histogenesis
histogenesis
biological_process
GO:0009888
tissue development
The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
ISBN:0471245208
Any process that 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.
janelomax
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
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
true
kinase activity
transferase activity
transferase activity, transferring phosphorus-containing groups
A reproduction process that creates a new organism by combining the genetic material of two gametes, which may come from two organisms or from a single organism, in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two gametes join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny.
Wikipedia:Sexual_reproduction
biological_process
GO:0019953
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 reproduction process that creates a new organism by combining the genetic material of two gametes, which may come from two organisms or from a single organism, in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two gametes join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny.
GOC:jl
GOC:kmv
GOC:krc
GOC:tb
ISBN:0387520546
http://en.wikipedia.org/wiki/Sexual_reproduction
A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism.
reproductive cellular process in multicellular organism
biological_process
GO:0022412
cellular process involved in reproduction in multicellular organism
A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism.
GOC:isa_complete
reproductive cellular process in multicellular organism
GOC:curators
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.
janelomax
2012-09-19T15:56:06Z
GO:0044702
biological_process
single organism reproductive process
GO:0022414
reproductive process
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
GOC:dph
GOC:isa_complete
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
janelomax
2012-09-19T16:07:47Z
GO:0044707
GO:0050874
organismal physiological process
biological_process
single-multicellular organism process
GO:0032501
multicellular organismal process
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
GOC:curators
GOC:dph
GOC:isa_complete
GOC:tb
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
janelomax
2012-12-19T12:21:31Z
GO:0044767
development
biological_process
single-organism developmental process
GO:0032502
developmental process
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
GOC:isa_complete
The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
biological_process
GO:0032504
multicellular organism reproduction
The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
GOC:isa_complete
GOC:jid
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 biological process that directly contributes to the process of producing new individuals, involving another organism.
janelomax
2012-09-19T15:56:30Z
biological_process
GO:0044703
multi-organism reproductive process
A biological process that directly contributes to the process of producing new individuals, involving another organism.
GOC:jl
The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.
organismal reproductive process
reproductive process in a multicellular organism
biological_process
GO:0048609
multicellular organismal reproductive process
The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.
GOC:dph
GOC:jid
GOC:tb
organismal reproductive process
GOC:curators
reproductive process in a multicellular organism
GOC:curators
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
This term was added by GO_REF:0000021.
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.
GOC:mtg_15jun06
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
A biological process which involves another organism of the same or different species.
GO:0051706
interaction between organisms
physiological interaction between organisms
physiological interaction with other organism
biological_process
GO:0051704
multi-organism process
A biological process which involves another organism of the same or different species.
GOC:jl
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
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 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
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
D0-D2. Zygote and dispersed blastomere cleavage in a yolk syncytium. Days 0-2 post-egg capsule deposition at 20˚C.
Schmidtea_mediterranea_Developmental_Stages
PLANA:0000001
Stage 1
https://planosphere.stowers.org/ontology/PLANA_0000001
D0-D2. Zygote and dispersed blastomere cleavage in a yolk syncytium. Days 0-2 post-egg capsule deposition at 20˚C.
PMID:28072387
D2-D3. 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. Days 2-3 post-egg capsule deposition at 20˚C.
Schmidtea_mediterranea_Developmental_Stages
PLANA:0000002
Depicted by field contains hematoxylin and eosin staining section of a stage 2 embryo. Scale bar = 100um
Stage 2
https://planosphere.stowers.org/ontology/PLANA_0000002
D2-D3. 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. Days 2-3 post-egg capsule deposition at 20˚C.
PMID:28072387
D2-D4. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity. Days 2-4 post-egg capsule deposition at 20˚C.
Schmidtea_mediterranea_Developmental_Stages
PLANA:0000003
Depicted by field contains hematoxylin and eosin staining section of a stage 3 embryo. Scale bar = 100um
Stage 3
https://planosphere.stowers.org/ontology/PLANA_0000003
D2-D4. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity. Days 2-4 post-egg capsule deposition at 20˚C.
PMID:28072387
D3-D5. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation. Days 3-5 post-egg capsule deposition at 20˚C.
Schmidtea_mediterranea_Developmental_Stages
PLANA:0000004
Depicted by field contains hematoxylin and eosin staining section of a stage 4 embryo. Scale bar = 100um
Stage 4
https://planosphere.stowers.org/ontology/PLANA_0000004
D3-D5. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation. Days 3-5 post-egg capsule deposition at 20˚C.
PMID:28072387
D5-D7. 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. Days 5-7 post-egg capsule deposition at 20˚C.
Schmidtea_mediterranea_Developmental_Stages
PLANA:0000005
Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo. Scale bar = 100um
Stage 5
https://planosphere.stowers.org/ontology/PLANA_0000005
D5-D7. 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. Days 5-7 post-egg capsule deposition at 20˚C.
PMID:28072387
D7-D9. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation. Days 7-9 post-egg capsule deposition at 20˚C.
Schmidtea_mediterranea_Developmental_Stages
PLANA:0000006
Depicted by field contains hematoxylin and eosin staining section of a stage 6 embryo. Scale bar = 100um
Stage 6
https://planosphere.stowers.org/ontology/PLANA_0000006
D7-D9. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation. Days 7-9 post-egg capsule deposition at 20˚C.
PMID:28072387
D9-D11. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility. Days 9-11 post-egg capsule deposition at 20˚C.
Schmidtea_mediterranea_Developmental_Stages
PLANA:0000007
Depicted by field contains hematoxylin and eosin staining section of a stage 7 embryo. Scale bar = 100um
Stage 7
https://planosphere.stowers.org/ontology/PLANA_0000007
D9-D11. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility. Days 9-11 post-egg capsule deposition at 20˚C.
PMID:28072387
D13-D15. Organogenesis and organ maturation continues. Hatching. Days 13-15 post-egg capsule deposition at 20˚C.
Schmidtea_mediterranea_Developmental_Stages
PLANA:0000008
Depicted by field contains hematoxylin and eosin staining section of a stage 8 embryo. Scale bar = 100um
Stage 8
https://planosphere.stowers.org/ontology/PLANA_0000008
D13-D15. Organogenesis and organ maturation continues. Hatching. Days 13-15 post-egg capsule deposition at 20˚C.
PMID:28072387
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.
Planarian_Anatomy
PLANA:0000009
sigma neoblast
https://planosphere.stowers.org/ontology/PLANA_0000009
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
https://planosphere.stowers.org/ontology/PLANA_0000011
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:21937596
Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system.
Planarian_Anatomy
PLANA:0000012
neural progenitor
https://planosphere.stowers.org/ontology/PLANA_0000012
Musculature surrounding internal organs of the body.
Erin Davies
Planarian_Anatomy
PLANA:0000013
visceral musculature
https://planosphere.stowers.org/ontology/PLANA_0000013
Musculature surrounding internal organs of the body.
PMID:26904543
An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s).
Planarian_Anatomy
PLANA:0000014
zeta neoblast
https://planosphere.stowers.org/ontology/PLANA_0000014
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.
Planarian_Anatomy
PLANA:0000015
non ciliated epithelial cell
https://planosphere.stowers.org/ontology/PLANA_0000015
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.
Planarian_Anatomy
PLANA:0000016
definitive pharynx
https://planosphere.stowers.org/ontology/PLANA_0000016
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.
Planarian_Anatomy
PLANA:0000017
photoreceptor neuron
https://planosphere.stowers.org/ontology/PLANA_0000017
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.
Planarian_Anatomy
PLANA:0000018
Category 4 cell
https://planosphere.stowers.org/ontology/PLANA_0000018
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.
Planarian_Anatomy
PLANA:0000019
muscle progenitor
https://planosphere.stowers.org/ontology/PLANA_0000019
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.
Planarian_Anatomy
PLANA:0000020
Depicted by field contains a whole-mount acetylated tubulin (AcTub) staining. Scale bars: 500 μm. Inset to right shows depth-coded projection of AcTub staining. Superficial structures are in blue and deeper structures are in red. Scale bars: 50 μm
protonephridia
https://planosphere.stowers.org/ontology/PLANA_0000020
Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct.
OCLC:16809160
PMID:21828097
PMID:26057828
PMID:26057828
Organisms sharing a specified genotype or karyotype.
Planarian_Anatomy
PLANA:0000021
biotype
https://planosphere.stowers.org/ontology/PLANA_0000021
Post-mitotic, ciliated epidermal cells.
Planarian_Anatomy
PLANA:0000022
Category 5 cell
https://planosphere.stowers.org/ontology/PLANA_0000022
Post-mitotic, ciliated epidermal cells.
PMID:25017721
An innervated, muscular pump that ingests yolk cells into the gut cavity. The temporary embryonic pharynx is an extraembryonic tissue that forms during Stage 2, functions during Stages 3-5, and degenerates during Stages 6-7.
PMID:28072387
Planarian_Anatomy
PLANA:0000023
Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo that zooms into the temporary embryonic pharynx.
temporary embryonic pharynx
https://planosphere.stowers.org/ontology/PLANA_0000023
Obligate asexual animals 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.
Planarian_Anatomy
PLANA:0000024
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.
Smed asexual biotype
https://planosphere.stowers.org/ontology/PLANA_0000024
Obligate asexual animals 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:23136835
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
Planarian_Anatomy
PLANA:0000025
nervous system
https://planosphere.stowers.org/ontology/PLANA_0000025
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 definitive 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 definitive gut through the defintive pharynx.
gut
Planarian_Anatomy
PLANA:0000026
definitive gut
https://planosphere.stowers.org/ontology/PLANA_0000026
The planarian triclad gut contains a central anterior gut branch connected to two posterior gut branches arranged around the definitive 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 definitive gut through the defintive pharynx.
PMID:21664348
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.
Planarian_Anatomy
PLANA:0000027
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.
Smed sexual biotype
https://planosphere.stowers.org/ontology/PLANA_0000027
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:23136835
Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts.
Planarian_Anatomy
PLANA:0000028
Category 2 cell
https://planosphere.stowers.org/ontology/PLANA_0000028
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.
Planarian_Anatomy
PLANA:0000029
primitive ectoderm
https://planosphere.stowers.org/ontology/PLANA_0000029
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.
Planarian_Anatomy
PLANA:0000030
midline
https://planosphere.stowers.org/ontology/PLANA_0000030
Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup.
Planarian_Anatomy
PLANA:0000031
pigment cup cell
https://planosphere.stowers.org/ontology/PLANA_0000031
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.
midline of dorsal region
dorsal midline
The median line/plane of bilateral symmetry along the anteroposterior axis on the dorsal surface of the animal.
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.
Planarian_Anatomy
PLANA:0000033
Depicted by shows multiple epithelia progenitor cell markers via in situ as progenitors mature towards the epidermis in a transverse plane.
epidermal progenitor
https://planosphere.stowers.org/ontology/PLANA_0000033
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:18786419
PMID:20040488
PMID:22385657
PMID:25017721
PMID:26114597
PMID:26457503
PMID:26457503
A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal.
epidermis
Planarian_Anatomy
PLANA:0000034
At present, this definition does not apply to epithelial structures other than the dorsal and ventral epidermis (i.e., the pharyngeal epithelium).
definitive epidermis
https://planosphere.stowers.org/ontology/PLANA_0000034
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.
Planarian_Anatomy
PLANA:0000035
Category 3 cell
https://planosphere.stowers.org/ontology/PLANA_0000035
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.
UBERON:0000970
Planarian_Anatomy
PLANA:0000036
Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The eyes are indicated by arrows. Scale bar = 250um
eye
https://planosphere.stowers.org/ontology/PLANA_0000036
Adult tissues built during organogenesis that are present in juveniles at birth.
Planarian_Anatomy
PLANA:0000037
definitive tissue
https://planosphere.stowers.org/ontology/PLANA_0000037
Adult tissues built during organogenesis that are present in juveniles at birth.
PMID:28072387
PMID:2888018
The median line/ plane of bilateral symmetry along the anteroposterior axis on the ventral surface of the animal.
midline of ventral region
ventral midline
The median line/ plane of bilateral symmetry along the anteroposterior axis on the ventral surface of the animal.
An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut.
Planarian_Anatomy
PLANA:0000039
gamma neoblast
https://planosphere.stowers.org/ontology/PLANA_0000039
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
A stage of embryonic development defined by a unique gene expression signature, morphology and chronological time post-egg capsule deposition for hermaphrodites reared at 20˚C.
Schmidtea_mediterranea_Developmental_Stages
PLANA:0000040
Schmidtea mediterranea developmental stage
https://planosphere.stowers.org/ontology/PLANA_0000040
A stage of embryonic development defined by a unique gene expression signature, morphology and chronological time post-egg capsule deposition for hermaphrodites reared at 20˚C.
PMID:28072387
Stage 3-5 embryo hemisphere centered around the pole opposite the temporary embryonic pharynx.
Planarian_Anatomy
PLANA:0000041
aboral hemisphere
https://planosphere.stowers.org/ontology/PLANA_0000041
Stage 3-5 embryo hemisphere centered around the pole opposite the temporary embryonic pharynx.
PMID:28072387
The single, central gut branch of the triclad gut anterior to the definitive pharynx.
Planarian_Anatomy
PLANA:0000042
Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. Anterior primary gut branch indicated by arrows. Scale bar = 250um
anterior primary gut branch
https://planosphere.stowers.org/ontology/PLANA_0000042
The single, central gut branch of the triclad gut anterior to the definitive pharynx.
PMID:21664348
Region along the edge of the animal where the dorsal and ventral surfaces meet.
edge
whole organism of dorsal/ventral compartment boundary
Planarian_Anatomy
PLANA:0000043
dorsal ventral margin
dorsoventral margin
https://planosphere.stowers.org/ontology/PLANA_0000043
Region along the edge of the animal where the dorsal and ventral surfaces meet.
The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head.
brain
Planarian_Anatomy
PLANA:0000044
cephalic ganglia
https://planosphere.stowers.org/ontology/PLANA_0000044
The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head.
OCLC:16809160
PMID:17999079
Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema.
Planarian_Anatomy
PLANA:0000045
circular muscle fiber
https://planosphere.stowers.org/ontology/PLANA_0000045
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
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.
Planarian_Anatomy
PLANA:0000046
clonogenic neoblast
https://planosphere.stowers.org/ontology/PLANA_0000046
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.
collection duct
Planarian_Anatomy
PLANA:0000047
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 the collecting 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.
collecting duct
https://planosphere.stowers.org/ontology/PLANA_0000047
Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis.
PMID:26057828
PMID:26057828
Body wall muscle fibers arrayed diagonally along the anteroposterior axis.
Planarian_Anatomy
PLANA:0000048
diagonal muscle fiber
https://planosphere.stowers.org/ontology/PLANA_0000048
Body wall muscle fibers arrayed diagonally along the anteroposterior axis.
PMID:26904543
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
Planarian_Anatomy
PLANA:0000049
digestive system
https://planosphere.stowers.org/ontology/PLANA_0000049
Embryonic development producing juvenile animals with body plans and feeding behavior similar to adults. Juveniles grow and mature into adults without undergoing metamorphosis.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000051
direct development
https://planosphere.stowers.org/ontology/PLANA_0000051
Embryonic development producing juvenile animals with body plans and feeding behavior similar to adults. Juveniles grow and mature into adults without undergoing metamorphosis.
PMID:12888018
A derived form of early embryonic cleavage present in ectolecithal embryos. Blastomeres divide asynchronously within a yolk syncytium, and division progeny do not remain in direct contact with one another.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000052
dispersed cleavage
https://planosphere.stowers.org/ontology/PLANA_0000052
A derived form of early embryonic cleavage present in ectolecithal embryos. Blastomeres divide asynchronously within a yolk syncytium, and division progeny do not remain in direct contact with one another.
OCLC:20423827
OCLC:42792751
OCLC:464776945
OCLC:82522822
PMID:15599763
PMID:19197510
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md
Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells.
Planarian_Anatomy
PLANA:0000053
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 the collecting 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.
distal tubule
https://planosphere.stowers.org/ontology/PLANA_0000053
Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells.
PMID:21828097
PMID:26057828
Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe.
definitive epidermis of dorsal region
Planarian_Anatomy
PLANA:0000054
dorsal epidermis
https://planosphere.stowers.org/ontology/PLANA_0000054
Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe.
Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe.
OCLC:16809160
Ciliated epithelial cells along the dorsal midline.
racing stripe
Planarian_Anatomy
PLANA:0000055
dorsal stripe
https://planosphere.stowers.org/ontology/PLANA_0000055
Ciliated epithelial cells along the dorsal midline.
PMID:17553481
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.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000056
ectolecithal embryo
https://planosphere.stowers.org/ontology/PLANA_0000056
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
The first few specialized divisions of an activated animal egg.
GO:0040016
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000057
embryonic cleavage
https://planosphere.stowers.org/ontology/PLANA_0000057
A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the temporary 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.
Planarian_Anatomy
PLANA:0000058
embryonic digestive system
https://planosphere.stowers.org/ontology/PLANA_0000058
A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the temporary 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.
Planarian_Anatomy
PLANA:0000059
embryonic gut cell
https://planosphere.stowers.org/ontology/PLANA_0000059
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.
Planarian_Anatomy
PLANA:0000060
Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo with anatomical feature noted with black indicators.
embryonic wall
https://planosphere.stowers.org/ontology/PLANA_0000060
The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos.
OCLC:16809160
PMID:12888018
Visceral muscle surrounding the definitive gut.
Planarian_Anatomy
PLANA:0000061
enteric musculature
https://planosphere.stowers.org/ontology/PLANA_0000061
Visceral muscle surrounding the definitive gut.
PMID:26904543
Attachment between the triclad gut and the proximal end of the definitive pharynx.
Planarian_Anatomy
PLANA:0000062
esophagus
https://planosphere.stowers.org/ontology/PLANA_0000062
Attachment between the triclad gut and the proximal end of the definitive pharynx.
PMID:24737865
OCLC:16809160
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
Planarian_Anatomy
PLANA:0000063
extraembryonic structure
https://planosphere.stowers.org/ontology/PLANA_0000063
Terminal structure of protonephridia unit; consists of flame cells.
Planarian_Anatomy
PLANA:0000064
Depicted by field contains a diagram representing the protonephrida unit (top) as well as a 3D rendering of confocal data depicting the same (bottom). In the diagram, terminal flame cells and their corresponding cilia (flame bulb) are in blues, the proximal tubule is in reds, the distal tubule is in greens while the collecting 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.
flame bulb
https://planosphere.stowers.org/ontology/PLANA_0000064
Terminal structure of protonephridia unit; consists of flame cells.
PMID:21828097
PMID:26057828
PMID:26057828
Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the ‘filtration weir’, 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.
Has functional homology with vertebrate podocytes.
Planarian_Anatomy
PLANA:0000065
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 the collecting 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.
flame cell
https://planosphere.stowers.org/ontology/PLANA_0000065
Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the ‘filtration weir’, 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
Has functional homology with vertebrate podocytes.
PMID:26057828
PMID:26057828
The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle.
Planarian_Anatomy
PLANA:0000066
gastrodermis
https://planosphere.stowers.org/ontology/PLANA_0000066
The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle.
PMID:21664348
Secretory cells that release digestive enzymes into the lumen of the intestine.
Planarian_Anatomy
PLANA:0000067
goblet cell
https://planosphere.stowers.org/ontology/PLANA_0000067
Secretory cells that release digestive enzymes into the lumen of the intestine.
PMID:21664348
Lumen of embryonic digestive tract, prior to formation of the branched defintive gut.
Planarian_Anatomy
PLANA:0000068
embryonic gut cavity
https://planosphere.stowers.org/ontology/PLANA_0000068
Lumen of 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.
Planarian_Anatomy
PLANA:0000069
inner longitudinal muscle fiber
https://planosphere.stowers.org/ontology/PLANA_0000069
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.
Planarian_Anatomy
PLANA:0000070
intestinal phagocyte
https://planosphere.stowers.org/ontology/PLANA_0000070
Absorptive digestive cells that engulf food particles for intracellular digestion.
PMID:21664348
Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers.
Planarian_Anatomy
PLANA:0000071
longitudinal muscle fiber
https://planosphere.stowers.org/ontology/PLANA_0000071
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
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 definitive pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells.
Manus
Planarian_Anatomy
PLANA:0000072
mouth
https://planosphere.stowers.org/ontology/PLANA_0000072
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 definitive pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells.
OCLC:16809160
Manus
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000006.md
A female germ cell that has entered meiosis.
CL:0000023
Planarian_Anatomy
PLANA:0000074
oocyte
https://planosphere.stowers.org/ontology/PLANA_0000074
A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons.
Planarian_Anatomy
PLANA:0000075
optic cup
https://planosphere.stowers.org/ontology/PLANA_0000075
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 temporary embryonic pharynx.
Planarian_Anatomy
PLANA:0000076
oral hemisphere
https://planosphere.stowers.org/ontology/PLANA_0000076
Stage 3-5 embryo hemisphere centered around the temporary embryonic pharynx.
PMID:28072387
UBERON:0000111
organogenesis
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000077
organogenesis stage
https://planosphere.stowers.org/ontology/PLANA_0000077
Outer most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thinner than the inner longitudinal muscle fibers.
Planarian_Anatomy
PLANA:0000078
outer longitudinal muscle fiber
https://planosphere.stowers.org/ontology/PLANA_0000078
Outer most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thinner than the inner longitudinal muscle fibers.
PMID:26904543
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md
Dorsal-ventral muscle fibers present through the mesenchyme.
dorsoventral muscle fibers
Planarian_Anatomy
PLANA:0000079
The depicted by field is a hemotoxylin and eosin stained sagittal section with the dorsal side up and anterior to the right. The parenchymal musculature, or dorsal ventral muscle fibers are the periodic vertical strands apparent in the middle of the image. Scale bar is 200um.
parenchymal musculature
https://planosphere.stowers.org/ontology/PLANA_0000079
Dorsal-ventral muscle fibers present through the mesenchyme.
OCLC:16809160
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
Planarian_Anatomy
PLANA:0000080
peripheral nervous system
https://planosphere.stowers.org/ontology/PLANA_0000080
An epithelial structure housing the definitive pharynx, connected to the esophagus and mouth.
Planarian_Anatomy
PLANA:0000081
pharyngeal pouch
https://planosphere.stowers.org/ontology/PLANA_0000081
An epithelial structure housing the definitive pharynx, connected to the esophagus and mouth.
OCLC:16809160
Ciliated epidermal cells located along the dorsal midline.
Planarian_Anatomy
PLANA:0000082
racing stripe
https://planosphere.stowers.org/ontology/PLANA_0000082
Ciliated epidermal cells located along the dorsal midline.
PMID:17553481
The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch.
Planarian_Anatomy
PLANA:0000084
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
posterior primary gut branch
https://planosphere.stowers.org/ontology/PLANA_0000084
The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch.
PMID:21664348
Four large phagocytic cells associated with the temporary embryonic pharynx.
Planarian_Anatomy
PLANA:0000085
primitive gut cell
https://planosphere.stowers.org/ontology/PLANA_0000085
Four large phagocytic cells associated with the temporary embryonic pharynx.
PMID:28072387
Stage 2 embryo undergoing the process of sphere formation.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000086
protosphere
https://planosphere.stowers.org/ontology/PLANA_0000086
Stage 2 embryo undergoing the process of sphere formation.
PMID:28072387
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.
Planarian_Anatomy
PLANA:0000087
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 the collecting 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.
proximal tubule
https://planosphere.stowers.org/ontology/PLANA_0000087
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
PMID:26057828
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
Planarian_Anatomy
PLANA:0000088
renal system
https://planosphere.stowers.org/ontology/PLANA_0000088
Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge.
Planarian_Anatomy
PLANA:0000089
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
secondary gut branch
https://planosphere.stowers.org/ontology/PLANA_0000089
Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge.
PMID:21664348
A mature male germ cell that develops from a spermatid.
CL:0000019
spermatozoa
Planarian_Anatomy
PLANA:0000090
sperm
https://planosphere.stowers.org/ontology/PLANA_0000090
Generation of a multilayered spherical embryo comprised of temporary extraembryonic tissues and undifferentiated blastomeres.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000091
sphere formation
https://planosphere.stowers.org/ontology/PLANA_0000091
Generation of a multilayered spherical embryo comprised of temporary extraembryonic tissues and undifferentiated blastomeres.
OCLC:20423827
OCLC:464776945
PMID:12888018
PMID:15599763
PMID:28072387
Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000092
syncytial yolk cell
https://planosphere.stowers.org/ontology/PLANA_0000092
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.
Planarian_Anatomy
PLANA:0000093
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
tertiary gut branch
https://planosphere.stowers.org/ontology/PLANA_0000093
Gut branches originating from and connected to the secondary gut branches.
PMID:21664348
The process in which the anatomical structures of a tissue are generated and organized.
GO:0048729
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000094
tissue morphogenesis
https://planosphere.stowers.org/ontology/PLANA_0000094
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.
Planarian_Anatomy
PLANA:0000095
trail cell
https://planosphere.stowers.org/ontology/PLANA_0000095
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
definitive epidermis of ventral region
Planarian_Anatomy
PLANA:0000096
ventral epidermis
ventral region of the epidermal compartment
https://planosphere.stowers.org/ontology/PLANA_0000096
Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells
The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO].
A cluster of neurons that extends posteriorly from the embryonic and larval brain and is surrounded by a connective tissue sheath.
The ventral nerve cords make up the nervous system of some phyla of the invertebrates, particularly within the nematodes, annelids and the arthropods. It usually consists of cerebral ganglia anteriorly with the nerve cords running down the ventral ('belly', as opposed to back) plane of the organism. This characteristic is important in qualifying the difference compared to the chordates, which have a dorsal nerve cord. Ventral nerve cords from anterior to posterior (the thoracic and abdominal tagma in the arthropods) are made up of segmented ganglia that are connected by a tract of nerve fibers passing from one side to the other of the nerve cord called commissures. The complete system bears some likeness to a rope ladder. In some animals the bilateral ganglia are fused into a single large ganglion per segment. This characteristic is found mostly in the insects.
BTO:0002328
EFO:0000896
FBbt:00001102
MAT:0000339
MIAA:0000339
UBERON:0000934
WBbt:0005829
http://en.wikipedia.org/wiki/Ventral_nerve_cord
nlx:146329
ventral cord
Planarian_Anatomy
PLANA:0000097
ventral nerve cord
https://planosphere.stowers.org/ontology/PLANA_0000097
Diploid cell resulting from the fusion of male and female gametes at fertilization. [ The_Dictionary_of_Cell_and_Molecular_Biology:Third_Edition ]
Diploid cell produced by the fusion of sperm cell nucleus and egg cell.
BTO:0000854
Planarian_Anatomy
PLANA:0000098
zygote
https://planosphere.stowers.org/ontology/PLANA_0000098
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.
neural cell
CL:0000540
Planarian_Anatomy
PLANA:0000099
neuron
https://planosphere.stowers.org/ontology/PLANA_0000099
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
Planarian_Anatomy
PLANA:0000100
epithelial cell
https://planosphere.stowers.org/ontology/PLANA_0000100
A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
CL:0000187
Planarian_Anatomy
PLANA:0000101
muscle cell
https://planosphere.stowers.org/ontology/PLANA_0000101
A subdivision of an anatomical compartment.
Planarian_Anatomy
PLANA:0000102
anatomical compartment subdivision
https://planosphere.stowers.org/ontology/PLANA_0000102
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
Planarian_Anatomy
PLANA:0000103
central nervous system
https://planosphere.stowers.org/ontology/PLANA_0000103
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.
Planarian_Anatomy
PLANA:0000104
rhabdite
https://planosphere.stowers.org/ontology/PLANA_0000104
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
A cell that specializes in controlled release of one or more substances.
CL:0000151
Planarian_Anatomy
PLANA:0000105
secretory cell
https://planosphere.stowers.org/ontology/PLANA_0000105
An epithelial cell that has cilia.
CL:0000067
Planarian_Anatomy
PLANA:0000106
ciliated epithelial cell
https://planosphere.stowers.org/ontology/PLANA_0000106
An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo.
CL:0000428
Planarian_Anatomy
PLANA:0000107
yolk cell
https://planosphere.stowers.org/ontology/PLANA_0000107
An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo.
PMID:27149082
Feature of an organism that is a subdivision of a local region. For example, the anterior pole is a subdivision of the head.
Planarian_Anatomy
PLANA:0000109
anatomical compartment subdivision feature
https://planosphere.stowers.org/ontology/PLANA_0000109
foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the definitive pharynx.
pharynx progenitor
Planarian_Anatomy
PLANA:0000110
definitive pharynx progenitor
https://planosphere.stowers.org/ontology/PLANA_0000110
foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the definitive pharynx.
PMID:24737865
PMID:25254346
Ciliated epithelial cells that assemble into proximal tubules.
Planarian_Anatomy
PLANA:0000111
proximal tubule epithelial cell
https://planosphere.stowers.org/ontology/PLANA_0000111
Ciliated epithelial cells that assemble into proximal tubules.
PMID:21828097
A term used to describe a developmental process during Schmidtea mediterranea embryogenesis.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000112
Schmidtea mediterranea developmental term
https://planosphere.stowers.org/ontology/PLANA_0000112
A term used to describe a developmental process during Schmidtea mediterranea embryogenesis.
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000000.md
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.
Planarian_Anatomy
PLANA:0000113
tissue
https://planosphere.stowers.org/ontology/PLANA_0000113
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
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000000.md
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
UBERON:0000467
Planarian_Anatomy
PLANA:0000114
anatomical system
https://planosphere.stowers.org/ontology/PLANA_0000114
Nonciliated epithelial cells that assemble into protonephridial proximal tubules.
Planarian_Anatomy
PLANA:0000115
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 the collecting 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.
distal tubule epithelial cell
https://planosphere.stowers.org/ontology/PLANA_0000115
Nonciliated epithelial cells that assemble into protonephridial proximal tubules.
PMID:21828097
PMID:26057828
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
Planarian_Anatomy
PLANA:0000116
embryo
https://planosphere.stowers.org/ontology/PLANA_0000116
Anatomical structure that is part of an embryo.
UBERON:0002050
Planarian_Anatomy
PLANA:0000117
embryonic structure
https://planosphere.stowers.org/ontology/PLANA_0000117
Nonciliated epithelial cells that assemble into collecting ducts.
Planarian_Anatomy
PLANA:0000118
collecting duct epithelial cell
https://planosphere.stowers.org/ontology/PLANA_0000118
Nonciliated epithelial cells that assemble into collecting ducts.
PMID:26057828
A post-mitotic, terminally differentiated cell type found in planarian embryos, juveniles and/or adult animals.
Planarian_Anatomy
PLANA:0000119
terminally differentiated cell
https://planosphere.stowers.org/ontology/PLANA_0000119
A cycling neoblast and/or post-mitotic cell that is primed or irreversibly committed to a tissue-specific differentation program
precursor cell
Planarian_Anatomy
PLANA:0000120
progenitor cell
https://planosphere.stowers.org/ontology/PLANA_0000120
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
Planarian_Anatomy
PLANA:0000121
stem cell
https://planosphere.stowers.org/ontology/PLANA_0000121
A mature sexual reproductive cell having a single set of unpaired chromosomes.
CL:0000300
Planarian_Anatomy
PLANA:0000122
gamete
https://planosphere.stowers.org/ontology/PLANA_0000122
A cell of the embryo.
CL:0002321
Planarian_Anatomy
PLANA:0000123
embryonic cell
https://planosphere.stowers.org/ontology/PLANA_0000123
The sensory system subserving the sense of vision.
UBERON:0002104
Planarian_Anatomy
PLANA:0000124
visual system
https://planosphere.stowers.org/ontology/PLANA_0000124
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
UBERON:0001032
Planarian_Anatomy
PLANA:0000125
sensory system
https://planosphere.stowers.org/ontology/PLANA_0000125
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.
UBERON:0000990
Planarian_Anatomy
PLANA:0000126
reproductive system
https://planosphere.stowers.org/ontology/PLANA_0000126
Ciliated epithelial cells that assemble into the oviduct.
Planarian_Anatomy
PLANA:0000127
oviduct epithelial cell
https://planosphere.stowers.org/ontology/PLANA_0000127
Ciliated epithelial cells that assemble into the oviduct.
PMID:22074376
Ciliated epithelial cells comprising the sperm ducts.
Planarian_Anatomy
PLANA:0000128
sperm duct epithelial cell
https://planosphere.stowers.org/ontology/PLANA_0000128
Ciliated epithelial cells comprising the sperm ducts.
PMID:19022767
PMID:22074376
OBSOLETE 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
Planarian_Anatomy
PLANA:0000129
replacing with UBERON term
obsolete anatomical structure
https://planosphere.stowers.org/ontology/PLANA_0000129
true
piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers.
Planarian_Anatomy
PLANA:0000130
circular muscle progenitor cell
https://planosphere.stowers.org/ontology/PLANA_0000130
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.
UBERON:0001048
Planarian_Anatomy
PLANA:0000131
primordium
https://planosphere.stowers.org/ontology/PLANA_0000131
The production of haploid germ cells from diploid precursor cells through meiosis.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000132
gametogenesis
https://planosphere.stowers.org/ontology/PLANA_0000132
The production of haploid germ cells from diploid precursor cells through meiosis.
PMID:19022767
A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
mechanoreceptor
Planarian_Anatomy
PLANA:0000133
mechanoreceptor cell
https://planosphere.stowers.org/ontology/PLANA_0000133
A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
PMID:7466176
PMID:18202849
piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers.
Planarian_Anatomy
PLANA:0000134
longitudinal muscle progenitor cell
https://planosphere.stowers.org/ontology/PLANA_0000134
piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers.
PMID:29168507
Definition forthcoming
Planarian_Anatomy
PLANA:0000135
female primordial germ cell
https://planosphere.stowers.org/ontology/PLANA_0000135
Anatomical structure that is an individual member of of Schmidtea mediterranea or any other flatworm of the class Turbellaria.
UBERON:0000468
whole animal
whole body
Planarian_Anatomy
PLANA:0000136
whole organism
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
Wikipedia:Regeneration_(biology)
regernative development
biological_process
PLANA:0000137
regeneration
The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass).
GOC:mah
GOC:pr
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.
Steph Nowotarski
2018-08-03T19:14:32Z
Planarian_Anatomy
Depcited by is an immuno electron microscopy image of a mesenchymal cell labeled with anti-PROG-2-5 immuno-gold. Large rhod-shaped granules resembling rhabdites are found in the same cell labeled with PROG-2-5+ oval-shaped granules (pseudo-colored in blue). Higher magnification of the boxed region is shown in the panel below. e, endoplasmic reticulum; m, mitochondria; n, nucleus; rh, rhabdite. Scale bar, 1 μm.
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
PMID:29100657
Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus.
whole organism of anterior region
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.
OCLC:16809160
Three dimensional compartment along the dorsoventral axis that is above the anteroposterior axis, containing the eyes.
whole organism of dorsal region
dorsal region of the whole animal
Three dimensional compartment along the dorsoventral axis that is above the anteroposterior axis, containing the eyes.
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.
whole organism of posterior region
posterior compartment of the whole animal
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.
Compartment along the dorsoventral axis that is below the anteroposterior axis.
whole organism of ventral region
ventral compartment of the whole animal
Compartment along the dorsoventral axis that is below the anteroposterior axis.
The passageway connecting the gonopore to the bursa (genital atrium). Part of the copulatory apparatus. During mating, sperm from a partner is deposited into the bursal canal, where it collects in the bursa before travelling up the oviducts to the bursa. Egg capsules pass through the bursal canal as they are laid through the gonopore.
Planarian_Anatomy
PLANA:0000201
bursal canal
https://planosphere.stowers.org/ontology/PLANA_0000201
The passageway connecting the gonopore to the bursa (genital atrium). Part of the copulatory apparatus. During mating, sperm from a partner is deposited into the bursal canal, where it collects in the bursa before travelling up the oviducts to the bursa. Egg capsules pass through the bursal canal as they are laid through the gonopore.
PMID:22074376
The gonopore, a component of the copulatory apparatus, is an opening located on the ventral side of the animal posterior to the definitive 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.
genital pore
Planarian_Anatomy
PLANA:0000203
gonopore
https://planosphere.stowers.org/ontology/PLANA_0000203
The gonopore, a component of the copulatory apparatus, is an opening located on the ventral side of the animal posterior to the definitive 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.
Planarian_Anatomy
PLANA:0000204
ovary
https://planosphere.stowers.org/ontology/PLANA_0000204
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.
Planarian_Anatomy
PLANA:0000205
oviduct
https://planosphere.stowers.org/ontology/PLANA_0000205
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.
Planarian_Anatomy
PLANA:0000206
penis papilla
https://planosphere.stowers.org/ontology/PLANA_0000206
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.
Planarian_Anatomy
PLANA:0000207
sperm duct
https://planosphere.stowers.org/ontology/PLANA_0000207
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.
Planarian_Anatomy
PLANA:0000208
testis
https://planosphere.stowers.org/ontology/PLANA_0000208
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
OBSOLETE Anatomical structure that is present during embryonic development.
UBERON:0005423
Planarian_Anatomy
PLANA:0000209
replacing with UBERON term
obsolete developing anatomical structure
https://planosphere.stowers.org/ontology/PLANA_0000209
true
Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2.
Planarian_Anatomy
PLANA:0000211
primitive ectoderm cell
https://planosphere.stowers.org/ontology/PLANA_0000211
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
https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md
Undifferentiated, zygote-derived cleavage progeny that 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.
Planarian_Anatomy
PLANA:0000212
blastomere compartment
https://planosphere.stowers.org/ontology/PLANA_0000212
Undifferentiated, zygote-derived cleavage progeny that 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
A sexually immature member of the Schmidtea mediterranea sexuallly reproducing biotype.
Schmidtea_mediterranea_Developmental_Stages
PLANA:0000214
juvenile
https://planosphere.stowers.org/ontology/PLANA_0000214
Products of the reproductive system include gametes, zygotes, yolk cells and egg capsules.
Planarian_Anatomy
PLANA:0000215
reproductive system product
https://planosphere.stowers.org/ontology/PLANA_0000215
A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos. Egg capsules are anchored to a substrate via a stalk.
Planarian_Anatomy
PLANA:0000216
Depicted by field shows a light microscopy image of egg capsules with a scale bar of 3mm
egg capsule
https://planosphere.stowers.org/ontology/PLANA_0000216
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).
UBERON:0000991
Planarian_Anatomy
PLANA:0000217
gonad
https://planosphere.stowers.org/ontology/PLANA_0000217
Neoblasts coexpressing piwi-1 and nanos that are required for male and female gonad formation. Primordial germ cells are present in both asexual and sexual adults.
Planarian_Anatomy
PLANA:0000218
male primordial germ cell
https://planosphere.stowers.org/ontology/PLANA_0000218
Neoblasts coexpressing piwi-1 and nanos that are required for male and female gonad formation. Primordial germ cells are present in both asexual and sexual adults.
PMID:17376870
gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm.
spermatogonial stem cell (SSC)
Planarian_Anatomy
PLANA:0000219
male germline stem cell
https://planosphere.stowers.org/ontology/PLANA_0000219
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.
CL:0000020
Planarian_Anatomy
PLANA:0000220
spermatogonium
https://planosphere.stowers.org/ontology/PLANA_0000220
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.
CL:0000017
Planarian_Anatomy
PLANA:0000221
spermatocyte
https://planosphere.stowers.org/ontology/PLANA_0000221
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.
CL:0000018
Planarian_Anatomy
PLANA:0000222
spermatid
https://planosphere.stowers.org/ontology/PLANA_0000222
A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes.
Planarian_Anatomy
PLANA:0000223
female germline stem cell
https://planosphere.stowers.org/ontology/PLANA_0000223
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 copulatory bursa that are required for production of the proteinaceous egg capsule shell and stalk.
Planarian_Anatomy
PLANA:0000224
cement gland
https://planosphere.stowers.org/ontology/PLANA_0000224
Glands surrounding the copulatory bursa that are required for production of the proteinaceous egg capsule shell and stalk.
ASIN:B000M4NK9M
PMID:18942102
PMID:22074376
PMID:27149082
A reproductive strategy in which eggs are laid, with most embryonic development occurring outside of the parent.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000225
oviparity
https://planosphere.stowers.org/ontology/PLANA_0000225
A reproductive strategy in which eggs are laid, with most embryonic development occurring outside of the parent.
PMID:19022767
Fertilization of an oocyte by sperm from a different individual. Reciprocal exchange of sperm occurs during Schmidtea mediterranea copulation.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000226
cross-fertilization
https://planosphere.stowers.org/ontology/PLANA_0000226
Fertilization of an oocyte by sperm from a different individual. Reciprocal exchange of sperm occurs during Schmidtea mediterranea copulation.
PMID:19022767
PMID:28812561
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
Planarian_Anatomy
PLANA:0000227
germ cell
https://planosphere.stowers.org/ontology/PLANA_0000227
A male germ cell is a germ cell that supports male gamete production.
CL:0000015
Planarian_Anatomy
PLANA:0000228
male germ cell
https://planosphere.stowers.org/ontology/PLANA_0000228
Female germ cell is a germ cell that supports female gamete production.
CL:0000021
Planarian_Anatomy
PLANA:0000229
female germ cell
https://planosphere.stowers.org/ontology/PLANA_0000229
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.
Planarian_Anatomy
PLANA:0000230
tuba
https://planosphere.stowers.org/ontology/PLANA_0000230
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.
Planarian_Anatomy
PLANA:0000231
vitelline gland
https://planosphere.stowers.org/ontology/PLANA_0000231
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.
Planarian_Anatomy
PLANA:0000232
copulatory apparatus
https://planosphere.stowers.org/ontology/PLANA_0000232
Accessory reproductive structures involved in copulation, egg capsule development and laying.
PMID:22074376
A chamber where egg capsules are formed. One or more zygotes and yolk cells produced by the vitelline glands collect in the copulatory bursa; glands surrounding the copulatory bursa produce the egg capsule shell.
Nascent egg capsules exit the body by passing through the bursal canal and gonopore. The copulatory bursa is synonymous with the term genital atrium.
bursa
genital atrium
Planarian_Anatomy
PLANA:0000233
copulatory bursa
https://planosphere.stowers.org/ontology/PLANA_0000233
A chamber where egg capsules are formed. One or more zygotes and yolk cells produced by the vitelline glands collect in the copulatory bursa; glands surrounding the copulatory bursa produce the egg capsule shell.
Nascent egg capsules exit the body by passing through the bursal canal and gonopore. The copulatory bursa is synonymous with the term genital atrium.
PMID:22074376
Glandular pouches adjoining the sperm ducts which produce seminal fluid.
Planarian_Anatomy
PLANA:0000234
seminal vesicle
https://planosphere.stowers.org/ontology/PLANA_0000234
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, and undergo morphogenesis to produce mature sperm.
Planarian_Anatomy
PLANA:0000237
round spermatid
https://planosphere.stowers.org/ontology/PLANA_0000237
A cyst of 8 interconnected spermatocytes undergoes meiosis, producing 32 haploid round spermatids. Round spermatids express protein kinase A, and undergo morphogenesis to produce mature sperm.
PMID:27163480
PMID:27330085
Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm.
Planarian_Anatomy
PLANA:0000238
elongate spermatid
https://planosphere.stowers.org/ontology/PLANA_0000238
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.
FMA:83673
Planarian_Anatomy
PLANA:0000239
oogonial cell
https://planosphere.stowers.org/ontology/PLANA_0000239
Any collection of muscles that is part of a body wall [Automatically generated definition].
define generically to encompass both vertebrates and invertebrates
body wall muscles
BSA:0000058
BTO:0001863
FMA:86931
UBERON:0004462
WBbt:0005813
Planarian_Anatomy
PLANA:0000240
body wall musculature
https://planosphere.stowers.org/ontology/PLANA_0000240
Pharynx muscle fibers running anteroposterior (proximal to distal).
Planarian_Anatomy
PLANA:0000241
pharyngeal longitudinal muscle fiber
https://planosphere.stowers.org/ontology/PLANA_0000241
Pharynx muscle fibers running anteroposterior (proximal to distal).
ASIN:B000M4NK9M
OBSOLETE 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.
UBERON:0002553
Planarian_Anatomy
PLANA:0000242
replacing with UBERON term
obsolete anatomical cavity
https://planosphere.stowers.org/ontology/PLANA_0000242
true
OBSOLETE Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
UBERON:0001062
Planarian_Anatomy
PLANA:0000400
replacing with UBERON term
obsolete anatomical entity
https://planosphere.stowers.org/ontology/PLANA_0000400
true
OBSOLETE Anatomical entity that has no mass.
AAO:0010265
AEO:0000007
BILA:0000007
EHDAA2:0003007
FBbt:00007015
FMA:67112
HAO:0000007
PLANA:0000401
TAO:0001835
TGMA:0001827
UBERON:0000466
VHOG:0001727
immaterial physical anatomical entity
Planarian_Anatomy
replacing with UBERON term
obsolete immaterial anatomical entity
https://planosphere.stowers.org/ontology/PLANA_0000401
true
OBSOLETE Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface.
AAO:0010266
AEO:0000009
BILA:0000009
CARO:0000009
EHDAA2:0003009
FMA:9658
TAO:0001839
UBERON:0006983
Planarian_Anatomy
PLANA:0000402
replacing with UBERON term
obsolete anatomical point
https://planosphere.stowers.org/ontology/PLANA_0000402
true
OBSOLETE Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
anatomical spaces
lumen
space
AAO:0010110
AEO:0000005
BILA:0000005
C94478
CARO:0000005
EHDAA2:0003005
FBbt:00007017
FMA:5897
HAO:0000005
TAO:0001668
TGMA:0001825
UBERON:0000464
UMLS:C0524461
VHOG:0001728
XAO:0003190
ZFA:0001643
http://linkedlifedata.com/resource/umls/id/C0524461
lumen space
Planarian_Anatomy
PLANA:0000403
replacing with UBERON term
obsolete anatomical space
https://planosphere.stowers.org/ontology/PLANA_0000403
true
A anatomical space that is enclosed by a pharynx.
UBERON:0001731
Planarian_Anatomy
PLANA:0000404
Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. Cavity of pharynx is indicated by arrows. Scale bar = 250um
cavity of pharynx
https://planosphere.stowers.org/ontology/PLANA_0000404
An anatomical space that is surrounded by a digestive tract.
UBERON:0006909
Planarian_Anatomy
PLANA:0000405
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
lumen of digestive tract
https://planosphere.stowers.org/ontology/PLANA_0000405
An anatomical space that is surrounded by a digestive tract.
PMID:21664348
The orifice that connects the mouth to the exterior of the body.
UBERON:0000166
Planarian_Anatomy
PLANA:0000406
oral opening
https://planosphere.stowers.org/ontology/PLANA_0000406
Anatomical space between the definitive pharynx and the epithelial cells comprising parapharyngeal pouch.
Planarian_Anatomy
PLANA:0000407
Depicted by field contains hematoxylin and eosin staining coronal section section of a asexual adult animal. Parapharyngeal pouch cavity is indicated by arrows. Scale bar = 250um
pharnygeal pouch cavity
https://planosphere.stowers.org/ontology/PLANA_0000407
Anatomical space between the definitive pharynx and the epithelial cells comprising parapharyngeal pouch.
OCLC:16809160
The apical surface of the single layered epidermis that is in contact with the environment.
definitive epidermis of apical surface
apical surface of the epidermal compartment
The apical surface of the single layered epidermis that is in contact with the environment.
Depicted by field is an 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 epidermal epithelium in direct contact with the basal lamina.
definitive epidermis of basal surface
basal surface of the epidermal compartment
The basal surface of the epidermal epithelium in direct contact with the basal lamina.
The depicted by field is an 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 gut lumen in contact with ingested food.
Planarian_Anatomy
PLANA:0000411
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.
lumen gut surface
https://planosphere.stowers.org/ontology/PLANA_0000411
The surface of the gut lumen in contact with ingested food.
PMID:21664348
The epithelial surface lining the interior of the pharynx, facing the lumen.
Planarian_Anatomy
PLANA:0000412
The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the pharynx and surrounding tissues. The pharynx lumen epithelial surface is marked by black arrows. Scale bar is 200um.
pharynx lumen epithelial surface
https://planosphere.stowers.org/ontology/PLANA_0000412
The epithelial surface lining the interior of the pharynx, facing the lumen.
UBERON:0001731
Epithelial surface covering the outside of the pharynx.
Planarian_Anatomy
PLANA:0000413
The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the pharynx and surrounding tissues. The pharynx outer epithelial surface is marked by black arrows. Scale bar is 200um.
pharynx outer epithelial surface
https://planosphere.stowers.org/ontology/PLANA_0000413
Epithelial surface covering the outside of the pharynx.
doi:10.1002/jmor.1052060308
PMID:29865769
The surface of the parapharyngeal pouch facing the pharynx.
Planarian_Anatomy
PLANA:0000414
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.
pharyngeal pouch surface
https://planosphere.stowers.org/ontology/PLANA_0000414
The surface of the parapharyngeal pouch facing the pharynx.
OCLC:16809160
OBSOLETE 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.
UBERON:0000475
Planarian_Anatomy
PLANA:0000416
replacing with UBERON term
obsolete organism subdivision
https://planosphere.stowers.org/ontology/PLANA_0000416
true
Anatomical structure which is a subdivision of a whole adult or juvenile organism, consisting of components of multiple anatomical systems.
Planarian_Anatomy
PLANA:0000417
definitive organism subdivision
https://planosphere.stowers.org/ontology/PLANA_0000417
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).
UBERON:0000033
Planarian_Anatomy
PLANA:0000418
Depicted by field contains diagram representation of body region.
head
https://planosphere.stowers.org/ontology/PLANA_0000418
Region of the juvenile or adult animal between the posterior end of the cephalic ganglia and the anterior end of the definitive pharynx.
Planarian_Anatomy
PLANA:0000419
prepharyngeal region
https://planosphere.stowers.org/ontology/PLANA_0000419
Region of the animal lateral to and surrounding the definitive pharynx.
Trunk is a synonym here because the parapharyngeal region is always contained in a trunk fragment. However, a trunk fragment may also contain some neck and some tail.
trunk
Planarian_Anatomy
PLANA:0000420
parapharyngeal region
https://planosphere.stowers.org/ontology/PLANA_0000420
Caudal region, beginning at the mouth and ending at posterior pole.
Planarian_Anatomy
PLANA:0000421
Depicted by field contains diagram representation of body region.
tail
https://planosphere.stowers.org/ontology/PLANA_0000421
Medial region of the tail; the parenchymal space between the posterior primary gut branches.
Planarian_Anatomy
PLANA:0000422
tail stripe
https://planosphere.stowers.org/ontology/PLANA_0000422
Anatomical structure which is a subdivision of a whole developing/ embryonic organism, consisting of components of multiple anatomical systems.
Planarian_Anatomy
PLANA:0000423
embryonic subdivision
https://planosphere.stowers.org/ontology/PLANA_0000423
OBSOLETE Anatomical entity that has mass.
UBERON:0000465
Planarian_Anatomy
PLANA:0000424
replacing with UBERON term
obsolete material anatomical entity
https://planosphere.stowers.org/ontology/PLANA_0000424
true
Anatomical structure present in juvenile and adult planaria.
Planarian_Anatomy
PLANA:0000425
definitive anatomical structure
https://planosphere.stowers.org/ontology/PLANA_0000425
OBSOLETE Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
acellular anatomical structures
AAO:0010268
AEO:0000040
BILA:0000040
CARO:0000040
EHDAA2:0003040
FBbt:00007013
FMA:63863
HAO:0000040
TAO:0000382
TGMA:0001841
XAO:0003162
ZFA:0000382
Planarian_Anatomy
PLANA:0000426
replacing with UBERON term
obsolete acellular anatomical structure
https://planosphere.stowers.org/ontology/PLANA_0000426
true
An anatomical structure that has more than one cell as a part.
UBERON:0010000
Planarian_Anatomy
PLANA:0000427
multicellular anatomical structure
https://planosphere.stowers.org/ontology/PLANA_0000427
Total musculature of the planarian body.
http://purl.obolibrary.org/obo/UBERON_0001015
Planarian_Anatomy
PLANA:0000428
musculature system
https://planosphere.stowers.org/ontology/PLANA_0000428
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.
Planarian_Anatomy
PLANA:0000429
neoblast compartment
https://planosphere.stowers.org/ontology/PLANA_0000429
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
A part of an epithelial cell.
Planarian_Anatomy
PLANA:0000430
epithelial cell component
https://planosphere.stowers.org/ontology/PLANA_0000430
Anatomical structure that performs a specific function or group of functions.
UBERON:0000062
Planarian_Anatomy
PLANA:0000431
organ
https://planosphere.stowers.org/ontology/PLANA_0000431
OBSOLETE An anatomical structure that is undergoing regeneration.
UBERON:0007567
Planarian_Anatomy
PLANA:0000432
replacing with UBERON term
obsolete regenerating anatomical structure
https://planosphere.stowers.org/ontology/PLANA_0000432
true
The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. Source: NIF_Subcellular:sao-1337158144, GOC:go_curators
GO:0005575
Planarian_Anatomy
PLANA:0000433
cellular component
https://planosphere.stowers.org/ontology/PLANA_0000433
A decussation of the diencephalon where the fibers of the optic nerve cross
The point at which fibers of the optic nerves cross.[AAO]
The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG]
chiasma
chiasma nervorum opticorum
optic chiasm (Rufus of Ephesus)
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
Optic:chiasm
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
chiasma opticum
decussation of optic nerve fibers
optic chiasm
Planarian_Anatomy
PLANA:0000459
optic chiasma
https://planosphere.stowers.org/ontology/PLANA_0000459
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.
UBERON:0000935
Planarian_Anatomy
PLANA:0000460
anterior commissure
https://planosphere.stowers.org/ontology/PLANA_0000460
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.
Planarian_Anatomy
PLANA:0000461
lateral branches
https://planosphere.stowers.org/ontology/PLANA_0000461
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.
Planarian_Anatomy
PLANA:0000462
sensory cell
https://planosphere.stowers.org/ontology/PLANA_0000462
Neurons that express choline acetyltransferase.
Planarian_Anatomy
PLANA:0000463
cholinergic neuron
https://planosphere.stowers.org/ontology/PLANA_0000463
Neurons that express choline acetyltransferase.
PMID:20338223
Neurons that express glutamine decarboxylase.
Planarian_Anatomy
PLANA:0000464
GABAergic neuron
https://planosphere.stowers.org/ontology/PLANA_0000464
Neurons that express glutamine decarboxylase.
PMID:18440152
Plexus of nerves located in the definitive pharynx comprised of inner and outer wall rings.
Planarian_Anatomy
PLANA:0000465
pharynx nerve plexus
https://planosphere.stowers.org/ontology/PLANA_0000465
Plexus of nerves located just between the definitive epidermis and the body wall musculature.
Planarian_Anatomy
PLANA:0000466
subepidermal nerve plexus
https://planosphere.stowers.org/ontology/PLANA_0000466
Plexus of nerves located just between the definitive epidermis and the body wall musculature.
PMID:27612384
doi:10.1002/jmor.1051550208
Plexus of nerves that innervate the body wall muscles.
Planarian_Anatomy
PLANA:0000467
submuscular nerve plexus
https://planosphere.stowers.org/ontology/PLANA_0000467
A thin net of single nerve fibers located around the gut.
Planarian_Anatomy
PLANA:0000468
gastrodermal plexus
https://planosphere.stowers.org/ontology/PLANA_0000468
A thin net of single nerve fibers located around the gut.
PMID:17999079
doi.org/10.1002/jmor.1051550208
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.
Multi-cell component structure of the central nervous system consisting largely of neuron projections (tracts and synaptic neuropil domains) and associated glial cells. This corresponds to the part of the CNS that is enclosed by the cortex.
neuropilus
BTO:0005268
C12617
CALOHA:TS-2403
FBbt:00005139
FMA:261269
GAID:740
MESH:D019581
NIF_Subcellular:sao205380252
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
Planarian_Anatomy
PLANA:0000470
neuropil
https://planosphere.stowers.org/ontology/PLANA_0000470
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.
Planarian_Anatomy
PLANA:0000472
outer pharyngeal epithelium
https://planosphere.stowers.org/ontology/PLANA_0000472
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.
Planarian_Anatomy
PLANA:0000473
outer pharyngeal circular muscle fiber
https://planosphere.stowers.org/ontology/PLANA_0000473
Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles.
ASIN:B000M4NK9M
Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers.
Planarian_Anatomy
PLANA:0000474
inner pharyngeal circular muscle fiber
https://planosphere.stowers.org/ontology/PLANA_0000474
Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers.
ASIN:B000M4NK9M
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.
Planarian_Anatomy
PLANA:0000475
inner pharyngeal longitudinal muscle fiber
https://planosphere.stowers.org/ontology/PLANA_0000475
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
Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium.
Planarian_Anatomy
PLANA:0000476
outer pharyngeal longitudinal muscle fiber
https://planosphere.stowers.org/ontology/PLANA_0000476
Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium.
ASIN:B000M4NK9M
Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts.
Planarian_Anatomy
PLANA:0000477
pharyngeal radial muscle fiber
https://planosphere.stowers.org/ontology/PLANA_0000477
Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts.
ASIN:B000M4NK9M
The total musculature within the pharynx.
UBERON:0004467
Planarian_Anatomy
PLANA:0000478
musculature of pharynx
https://planosphere.stowers.org/ontology/PLANA_0000478
The total musculature within the pharynx.
PMID:26904543
Ring of the pharynx nerve plexus that is proximal to the lumen.
Planarian_Anatomy
PLANA:0000479
inner pharynx nerve plexus
https://planosphere.stowers.org/ontology/PLANA_0000479
Ring of the pharynx nerve plexus that is proximal to the exterior surface.
Planarian_Anatomy
PLANA:0000480
outer pharynx nerve plexus
https://planosphere.stowers.org/ontology/PLANA_0000480
Ring of the pharynx nerve plexus that is proximal to the exterior surface.
doi:10.1002/jmor.1051550208
PMID:27612384
Neurons that express the neurotransmitter serotonin.
Planarian_Anatomy
PLANA:0000481
serotonergic neuron
https://planosphere.stowers.org/ontology/PLANA_0000481
Neurons that express the neurotransmitter serotonin.
PMID:17624455
A neuron that expresses the neurotransmitter dopamine.
Planarian_Anatomy
PLANA:0000482
dopaminergic neuron
https://planosphere.stowers.org/ontology/PLANA_0000482
A neuron that expresses the neurotransmitter dopamine.
PMID:17565705
Neurons that express the biogenic amine octopamine.
Planarian_Anatomy
PLANA:0000483
octopaminergic neuron
https://planosphere.stowers.org/ontology/PLANA_0000483
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.
Planarian_Anatomy
PLANA:0000484
secretory system
https://planosphere.stowers.org/ontology/PLANA_0000484
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 through epithelial cells and form a secretory pore at the surface.
Planarian_Anatomy
PLANA:0000485
gland cell
https://planosphere.stowers.org/ontology/PLANA_0000485
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 through epithelial cells and form a secretory pore at the surface.
PMID:20865784
The opening by which the gland cells secrete mucus to the exterior of the animal.
Planarian_Anatomy
PLANA:0000486
secretory pore
https://planosphere.stowers.org/ontology/PLANA_0000486
The opening by which the gland cells secrete mucus to the exterior of the animal.
PMID:20865784
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 dorsalventral border of the animal.
eosinophilic gland cell
Planarian_Anatomy
PLANA:0000487
acidophilic gland cell
https://planosphere.stowers.org/ontology/PLANA_0000487
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 dorsalventral 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.
Planarian_Anatomy
PLANA:0000488
basophilic gland cell
https://planosphere.stowers.org/ontology/PLANA_0000488
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
OBSOLETE Non-material anatomical entity of one dimension, which forms a boundary of an anatomical surface or is a modulation of an anatomical surface.
AAO:0010267
AEO:0000008
BILA:0000008
CARO:0000008
EHDAA2:0003008
FMA:9657
HAO:0000008
TAO:0001837
TGMA:0001828
UBERON:0006800
XAO:0004003
ZFA:0001689
Planarian_Anatomy
PLANA:0000489
reolacing with CARO term
obsolete anatomical line
https://planosphere.stowers.org/ontology/PLANA_0000489
true
OBSOLETE A flat anatomical 2D surface that bisects an anatomical structure or an anatomical space.
fiat anatomical surface
CARO:0001013
FMA:242982
UBERON:0035085
Planarian_Anatomy
PLANA:0000490
All anatomical planes are fiat anatomical boundaries - no morphological boundary could ever be a perfect plane.
replacing with BSPO term
obsolete anatomical plane
https://planosphere.stowers.org/ontology/PLANA_0000490
true
An anatomical plane that bisects a zone of weakness in an appendage. When autotomy occurs, the appendage divides along this plane.
this class is intended for autotomy that bisects an appendage. Other forms of autotomy are possible: for example, a sea cucumber and autotomitize internal organs
UBERON:0035086
Planarian_Anatomy
PLANA:0000491
plane of autotomy
https://planosphere.stowers.org/ontology/PLANA_0000491
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].
in FMA this is a subtype of junction rather than tissue
plexus
AEO:0000138
BTO:0000205
C12929
EHDAA2:0003138
EHDAA:3780
FMA:5901
MA:0002407
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
Planarian_Anatomy
PLANA:0000492
nerve plexus
https://planosphere.stowers.org/ontology/PLANA_0000492
Axon tract that crosses the midline of the central nervous system[NIF, modified]. In the context of Drosophila refers to a broad band of axons connecting equivalent neuropils each side of the brain[FBbt].
White matter fiber bundle that crosses the midline of the brain or spinal cord, that connects similar structures on both sides. (CUMBO; Heimer, L. The Human Brain, 2nd ed., 1995, pg 6)
commissural
white matter commissure
commissure
C32349
FBbt:00005103
FMA:83906
OpenCyc:Mx4rdBrmE6gOEdudWQACs5b6Bw
TADS:0000201
UBERON:0001020
UMLS:C1185742
http://en.wikipedia.org/wiki/Commissure
http://linkedlifedata.com/resource/umls/id/C1185742
nlx:110
nlx_anat:20090513
commissure of neuraxis
neuraxis commissure
Planarian_Anatomy
PLANA:0000493
*not* the same as FMA:76741 Commissure
nervous system commissure
https://planosphere.stowers.org/ontology/PLANA_0000493
any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain
any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain[MP]
UBERON:0005970
Planarian_Anatomy
PLANA:0000494
brain commissure
https://planosphere.stowers.org/ontology/PLANA_0000494
A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise
AEO:0000192
BTO:0001638
CARO:0000010
EFO:0003658
FMA:50705
TAO:0001270
UBERON:0005306
XAO:0004060
ncithesaurus:Blastemal_Cell
blastema cell
Planarian_Anatomy
PLANA:0000495
blastema
https://planosphere.stowers.org/ontology/PLANA_0000495
OBSOLETE A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
UBERON:0000015
Planarian_Anatomy
PLANA:0000496
non-material anatomical boundary
obsolete anatomical boundary
https://planosphere.stowers.org/ontology/PLANA_0000496
true
OBSOLETE An anatomical structure that connects two structures
junction
FMA:5898
UBERON:0007651
http://www.snomedbrowser.com/Codes/Details/91833003
anatomical junction
Planarian_Anatomy
PLANA:0000497
replacing with UBERON term
obsolete anatomical junction
https://planosphere.stowers.org/ontology/PLANA_0000497
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.
CALOHA:TS-2035
FMA:68646
GO:0005623
KUPO:0000002
VHOG:0001533
WBbt:0004017
XAO:0003012
Planarian_Anatomy
PLANA:0000499
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
https://planosphere.stowers.org/ontology/PLANA_0000499
Anatomical structure that is a direct part of the cell.
TODO - move metadata to GO and obsolete this class once homes have been found for existing children. Note the inconsistency between the usage of the label 'cell component' in GO and CARO
cell component
AAO:0010271
BILA:0000014
C34070
CARO:0000014
FBbt:00007012
FMA:86454
GO:0044464
HAO:0000014
NIF_Subcellular:sao-1337158144
OpenCyc:Mx4rwQwkcZwpEbGdrcN5Y29ycA
TGMA:0001834
UBERON:0000470
UMLS:C1178969
http://linkedlifedata.com/resource/umls/id/C1178969
Planarian_Anatomy
PLANA:0000500
cell part
https://planosphere.stowers.org/ontology/PLANA_0000500
A prolongation or process extending from a cell.
GO_0042995
Planarian_Anatomy
PLANA:0000501
cell projection
https://planosphere.stowers.org/ontology/PLANA_0000501
A cell projection supported by an assembly of actin filaments.
GO_0098858
Planarian_Anatomy
PLANA:0000502
actin-based cell projection
https://planosphere.stowers.org/ontology/PLANA_0000502
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.
GO_0005929
Planarian_Anatomy
PLANA:0000503
cilium
https://planosphere.stowers.org/ontology/PLANA_0000503
Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments.
GO:0005902
Planarian_Anatomy
PLANA:0000504
microvillus
https://planosphere.stowers.org/ontology/PLANA_0000504
Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions.
GO_0044291
Planarian_Anatomy
PLANA:0000505
cell-cell contact zone
https://planosphere.stowers.org/ontology/PLANA_0000505
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
Planarian_Anatomy
PLANA:0000506
cell junction
https://planosphere.stowers.org/ontology/PLANA_0000506
A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
GO:0005911
Planarian_Anatomy
PLANA:0000507
cell-cell junction
https://planosphere.stowers.org/ontology/PLANA_0000507
The attachment of one cell to another cell via adhesion molecules.
GO:0098609
Planarian_Anatomy
PLANA:0000508
cell-cell adhesion
https://planosphere.stowers.org/ontology/PLANA_0000508
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
Planarian_Anatomy
PLANA:0000509
intracellular part
https://planosphere.stowers.org/ontology/PLANA_0000509
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures
GO:0005737
Planarian_Anatomy
PLANA:0000510
cytoplasm
https://planosphere.stowers.org/ontology/PLANA_0000510
Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions.
eosinophilic
tmeehan
2009-12-22T04:23:25Z
CP_0000027
Planarian_Anatomy
PLANA:0000511
acidophilic cytoplasm
https://planosphere.stowers.org/ontology/PLANA_0000511
Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions.
tmeehan
2009-12-22T04:24:54Z
CP_0000028
Planarian_Anatomy
PLANA:0000512
basophilic cytoplasm
https://planosphere.stowers.org/ontology/PLANA_0000512
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
Planarian_Anatomy
PLANA:0000513
cytoplasmic part
https://planosphere.stowers.org/ontology/PLANA_0000513
Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell.
GO:0044433
Planarian_Anatomy
PLANA:0000514
cytoplasmic vesicle part
https://planosphere.stowers.org/ontology/PLANA_0000514
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
Planarian_Anatomy
PLANA:0000515
vacuole
https://planosphere.stowers.org/ontology/PLANA_0000515
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
GO_0007010
Planarian_Anatomy
PLANA:0000516
cytoskeleton organization
https://planosphere.stowers.org/ontology/PLANA_0000516
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
Planarian_Anatomy
PLANA:0000518
intracellular organelle
https://planosphere.stowers.org/ontology/PLANA_0000518
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
Planarian_Anatomy
PLANA:0000519
intracellular non-membrane-bounded organelle
https://planosphere.stowers.org/ontology/PLANA_0000519
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
GO_0016020
Planarian_Anatomy
PLANA:0000520
membrane
https://planosphere.stowers.org/ontology/PLANA_0000520
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
Planarian_Anatomy
PLANA:0000521
bounding membrane of organelle
https://planosphere.stowers.org/ontology/PLANA_0000521
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
Planarian_Anatomy
PLANA:0000522
membrane part
https://planosphere.stowers.org/ontology/PLANA_0000522
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
Planarian_Anatomy
PLANA:0000523
plasma membrane part
https://planosphere.stowers.org/ontology/PLANA_0000523
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
Planarian_Anatomy
PLANA:0000524
organelle membrane
https://planosphere.stowers.org/ontology/PLANA_0000524
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
Planarian_Anatomy
PLANA:0000525
organelle
https://planosphere.stowers.org/ontology/PLANA_0000525
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
Planarian_Anatomy
PLANA:0000526
membrane-bounded organelle
https://planosphere.stowers.org/ontology/PLANA_0000526
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
Planarian_Anatomy
PLANA:0000527
intracellular membrane-bounded organelle
https://planosphere.stowers.org/ontology/PLANA_0000527
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
Planarian_Anatomy
PLANA:0000528
Golgi apparatus
https://planosphere.stowers.org/ontology/PLANA_0000528
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
Planarian_Anatomy
PLANA:0000529
nucleus
https://planosphere.stowers.org/ontology/PLANA_0000529
A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space.
GO_0099503
Planarian_Anatomy
PLANA:0000530
secretory vesicle
https://planosphere.stowers.org/ontology/PLANA_0000530
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.
GO_0043228
Planarian_Anatomy
PLANA:0000531
non-membrane-bounded organelle
https://planosphere.stowers.org/ontology/PLANA_0000531
Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.
GO_0044428
Planarian_Anatomy
PLANA:0000532
nuclear part
https://planosphere.stowers.org/ontology/PLANA_0000532
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_0005730
Planarian_Anatomy
PLANA:0000533
nucleolus
https://planosphere.stowers.org/ontology/PLANA_0000533
The ordered and organized complex of DNA, protein (histones), and sometimes RNA, that forms the chromosome.
GO_0000785
Planarian_Anatomy
PLANA:0000534
chromatin
https://planosphere.stowers.org/ontology/PLANA_0000534
A compact and highly condensed form of chromatin.
GO_0000792
Planarian_Anatomy
PLANA:0000535
heterochromatin
https://planosphere.stowers.org/ontology/PLANA_0000535
A dispersed and relatively uncompacted form of chromatin.
GO_0000791
Planarian_Anatomy
PLANA:0000536
euchromatin
https://planosphere.stowers.org/ontology/PLANA_0000536
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.
GO_0005840
Planarian_Anatomy
PLANA:0000537
ribosome
https://planosphere.stowers.org/ontology/PLANA_0000537
A group of axons linking two or more neuropils and having a common origin, termination
UBERON:0001018
Planarian_Anatomy
PLANA:0000538
axon tract
https://planosphere.stowers.org/ontology/PLANA_0000538
A cell whose function is determined by its response to an electric signal.
CL:0000393
Planarian_Anatomy
PLANA:0000539
electrically responsive cell
https://planosphere.stowers.org/ontology/PLANA_0000539
A cell that initiates an electrical signal and passes that signal to another cell.
CL:0000404
Planarian_Anatomy
PLANA:0000540
electrically signaling cell
https://planosphere.stowers.org/ontology/PLANA_0000540
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.
neural subtree
UBERON:0001021
nerves
peripheral nerve
Planarian_Anatomy
PLANA:0000541
nerve
https://planosphere.stowers.org/ontology/PLANA_0000541
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
CARO:0001001
Planarian_Anatomy
PLANA:0000543
neuron projection bundle
https://planosphere.stowers.org/ontology/PLANA_0000543
A neuron which conveys sensory information centrally from the periphery.
CL:0000526
FMA:87653
input neuron
Planarian_Anatomy
PLANA:0000545
afferent neuron
https://planosphere.stowers.org/ontology/PLANA_0000545
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
FMA:67282
Planarian_Anatomy
PLANA:0000546
bipolar neuron
https://planosphere.stowers.org/ontology/PLANA_0000546
A neuron that has an axon which crosses the midline.
CL:0000678
Planarian_Anatomy
PLANA:0000547
commissural neuron
https://planosphere.stowers.org/ontology/PLANA_0000547
A neuron which sends impulses peripherally to activate muscles or secretory cells.
CL:0000527
output neuron
Planarian_Anatomy
PLANA:0000548
efferent neuron
https://planosphere.stowers.org/ontology/PLANA_0000548
A motor neuron that is capable of directly inducing muscle contraction.
CL:0008014
Planarian_Anatomy
PLANA:0000549
In vertebrates, all motor neurons are excitatory, but various types of inhibitory motor neurons exist in invertebrates.
excitatory motor neuron
https://planosphere.stowers.org/ontology/PLANA_0000549
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.
BTO:0003811
CL:0000099
FBbt:00005125
FMA:67313
WBbt:0005113
Planarian_Anatomy
PLANA:0000550
interneuron
https://planosphere.stowers.org/ontology/PLANA_0000550
Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
BTO:0001037
CL:0000101
FBbt:00005124
FMA:84649
WBbt:0005759
Planarian_Anatomy
PLANA:0000552
sensory neuron
https://planosphere.stowers.org/ontology/PLANA_0000552
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.
BTO:0000312
CL:0000100
FMA:83617
WBbt:0005409
motoneuron
Planarian_Anatomy
PLANA:0000553
motor neuron
https://planosphere.stowers.org/ontology/PLANA_0000553
Neuronal cells which synthesize, store and release neurohormones.
CL:0000381
FBbt:00005130
Planarian_Anatomy
PLANA:0000556
neurosecretory neuron
https://planosphere.stowers.org/ontology/PLANA_0000556
Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides.
CL:0011103
Planarian_Anatomy
PLANA:0000558
sympathetic neuron
https://planosphere.stowers.org/ontology/PLANA_0000558
Neuron with one neurite that extends from the cell body.
CL:0000106
FMA:67278
Planarian_Anatomy
PLANA:0000559
unipolar neuron
https://planosphere.stowers.org/ontology/PLANA_0000559
Neuron with one neurite that extends from the cell body.
PMID:18499291
Neuron with an axon and two or more dendrites.
CL:0000104
FMA:67287
Planarian_Anatomy
PLANA:0000560
multipolar neuron
https://planosphere.stowers.org/ontology/PLANA_0000560
Neuron with an axon and two or more dendrites.
PMID:18499291
Cells that are in close proximity to neurons.
CL:0000130
Planarian_Anatomy
PLANA:0000561
neuron associated cell (sensu Nematoda and Protostomia)
https://planosphere.stowers.org/ontology/PLANA_0000561
Any neuron that is part of a central nervous system.
TermGenie
2014-06-25T01:17:43Z
CL:2000029
Planarian_Anatomy
PLANA:0000562
central nervous system neuron
https://planosphere.stowers.org/ontology/PLANA_0000562
Any neuron that is part of a peripheral nervous system.
TermGenie
2014-06-25T02:28:17Z
CL:2000032
Planarian_Anatomy
PLANA:0000564
peripheral nervous system neuron
https://planosphere.stowers.org/ontology/PLANA_0000564
A neruon whose cell body is within an autonomic ganglion.
CL:0000107
FMA:80121
Planarian_Anatomy
PLANA:0000565
autonomic neuron
https://planosphere.stowers.org/ontology/PLANA_0000565
Neuron that is part of the enteric nervous system.
haendel
2012-06-28T08:20:31Z
CL:0007011
Planarian_Anatomy
PLANA:0000566
enteric neuron
https://planosphere.stowers.org/ontology/PLANA_0000566
Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue.
this class represents a continuous sheet of basal lamina which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal lamina' represents a portion of substance on the scale of a single cell.
A basal lamina is certainly present in Bilateria and was evaluated as an autapomorphy of this taxon.[well established][VHOG]
basal lamina
basal laminae
lamina basalis
AAO:0010269
AEO:0000065
BILA:0000065
Basal:lamina
C32186
CARO:0000065
EHDAA2:0003065
FMA:62918
HAO:0000065
MESH:D001485
NIF_Subcellular:sao1397492660
TAO:0001485
TGMA:0001850
UMLS:C0085872
VHOG:0001592
WBbt:0005756
XAO:0003163
ZFA:0001485
http://linkedlifedata.com/resource/umls/id/C0085872
basal lamina of connective tissue
Planarian_Anatomy
PLANA:0001005
Depicted by field is an electron micrograph of the dorsal epidermis in a transverse plane from an asexual adult animal. The basal lamina is noted with a magenta bracket. Scale bar is 5um.
basal lamina of epithelium
https://planosphere.stowers.org/ontology/PLANA_0001005
A fully formed, sexually mature organism. The sexually reproducing Schmidtea mediterranea biotype exists as an obligate cross-fertilizing hermaphrodite.
Erin Davies
2017-04-24T02:52:06Z
Schmidtea_mediterranea_Developmental_Stages
PLANA:0004503
Depcited by field shows a light microscopy image of a sexually mature adult with a scale bar of 2 mm.
sexually mature adult
https://planosphere.stowers.org/ontology/PLANA_0004503
A fully formed, sexually mature organism. The sexually reproducing Schmidtea mediterranea biotype exists as an obligate cross-fertilizing hermaphrodite.
PMID:19022767
PMID:11972158
The asexually reproducing Schmidtea mediterranea biotype exists as a constitutive adult, undergoing successive cycles of fission and whole animal regeneration. Asexual Schmidtea mediterranea contain primordial germ cells, but do not possess a reproductive system.
Erin Davies
2017-04-24T02:59:06Z
Schmidtea_mediterranea_Developmental_Stages
PLANA:0004504
Depicted by field shows an asexual adult with a scale bar of 500um
asexual adult
https://planosphere.stowers.org/ontology/PLANA_0004504
The asexually reproducing Schmidtea mediterranea biotype exists as a constitutive adult, 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
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.
Erin Davies
2017-07-19T21:05:52Z
Planarian_Anatomy
PLANA:0004506
testis somatic gonadal cell
https://planosphere.stowers.org/ontology/PLANA_0004506
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.
Erin Davies
2017-07-19T21:35:08Z
Planarian_Anatomy
PLANA:0004507
ovarian somatic gonadal cell
https://planosphere.stowers.org/ontology/PLANA_0004507
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 temporary embryonic pharynx; the aboral pole is located opposite the temporary embryonic pharynx.
embryo of oral-aboral axis
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 temporary embryonic pharynx; the aboral pole is located opposite the temporary embryonic pharynx.
PMID:28072387
Depicted by is an illustration noting the oral-aboral axis in cyan double headed arrow. Note it starts at the temporary embryonic pharynx and extends to opposite.
The apical surface of the single layered primitive ectoderm that is in contact with the environment.
Erin Davies
2017-07-27T16:25:14Z
Planarian_Anatomy
PLANA:0004512
primitive ectoderm surface
https://planosphere.stowers.org/ontology/PLANA_0004512
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.
Erin Davies
2017-07-27T16:25:35Z
Planarian_Anatomy
PLANA:0004513
primtive gut cell surface
https://planosphere.stowers.org/ontology/PLANA_0004513
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.
Erin Davies
2017-07-27T16:25:45Z
Planarian_Anatomy
PLANA:0004514
embryonic gut cell surface
https://planosphere.stowers.org/ontology/PLANA_0004514
The surface of phagocytic embryonic gut cells in contact with ingested yolk cells.
PMID:28072387
The epithelial cell surface lining the temporary embryonic pharynx lumen.
Erin Davies
2017-07-27T16:26:16Z
Planarian_Anatomy
PLANA:0004516
temporary embryonic pharynx lumen epithelial surface
https://planosphere.stowers.org/ontology/PLANA_0004516
The epithelial cell surface lining the temporary embryonic pharynx lumen.
PMID:20100474
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.
Erin Davies
2017-07-27T19:54:22Z
Planarian_Anatomy
PLANA:0004517
blastomere
https://planosphere.stowers.org/ontology/PLANA_0004517
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.
PMID:28072387
Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues.
Erin Davies
2017-07-27T20:00:04Z
Planarian_Anatomy
PLANA:0004518
extraembryonic cell
https://planosphere.stowers.org/ontology/PLANA_0004518
Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues.
PMID:28072387
A neuronal cell innervating the temporary embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening.
Erin Davies
2017-07-27T20:01:15Z
Planarian_Anatomy
PLANA:0004519
temporary embryonic pharynx neuron
https://planosphere.stowers.org/ontology/PLANA_0004519
A neuronal cell innervating the temporary embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening.
PMID:28072387
Differentiated radial muscle cell present in the temporary embryonic pharynx.
Erin Davies
2017-07-27T20:01:39Z
Planarian_Anatomy
PLANA:0004520
temporary embryonic pharynx radial muscle cell
https://planosphere.stowers.org/ontology/PLANA_0004520
Differentiated radial muscle cell present in the temporary embryonic pharynx.
PMID:16932928
foxA1+ epithelial cell contained in the temporary embryonic pharynx.
Erin Davies
2017-07-27T20:02:04Z
Planarian_Anatomy
PLANA:0004521
temporary embryonic pharynx epithelial cell
https://planosphere.stowers.org/ontology/PLANA_0004521
foxA1+ epithelial cell contained in the temporary embryonic pharynx.
PMID:20100474
PMID:28072387
Differentiated muscle cell present in a circular muscle fiber of the temporary embryonic pharynx.
Erin Davies
2017-07-27T20:43:26Z
Planarian_Anatomy
PLANA:0004524
temporary embryonic pharynx circular muscle fiber
https://planosphere.stowers.org/ontology/PLANA_0004524
Differentiated muscle cell present in a circular muscle fiber of the temporary 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.
Erin Davies
2017-08-28T18:20:43Z
Planarian_Anatomy
PLANA:0004527
Depicted by field contains diagram representation of body region.
copulatory region
https://planosphere.stowers.org/ontology/PLANA_0004527
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
Epithelia associated with the pharynx organ.
Erin Davies
2017-08-31T14:53:38Z
Planarian_Anatomy
PLANA:0004528
pharyngeal epithelium
https://planosphere.stowers.org/ontology/PLANA_0004528
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.
Erin Davies
2017-08-31T19:21:09Z
UBERON:0002416
Planarian_Anatomy
PLANA:0004529
integumental system
https://planosphere.stowers.org/ontology/PLANA_0004529
Anatomical space enclosed by the oviduct epithelium.
Erin Davies
2017-09-01T17:52:16Z
Planarian_Anatomy
PLANA:0004530
oviduct lumen
https://planosphere.stowers.org/ontology/PLANA_0004530
Anatomical space enclosed by the oviduct epithelium.
PMID:22074376
Anatomical space enclosed by the sperm duct epithelium.
Erin Davies
2017-09-02T22:26:19Z
Planarian_Anatomy
PLANA:0004531
sperm duct lumen
https://planosphere.stowers.org/ontology/PLANA_0004531
Anatomical space enclosed by the sperm duct epithelium.
PMID:19022767
PMID:22074376
Ciliated epithelium lining the oviduct.
Erin Davies
2017-09-02T22:35:10Z
Planarian_Anatomy
PLANA:0004532
oviduct epithelium
https://planosphere.stowers.org/ontology/PLANA_0004532
Ciliated epithelium lining the oviduct.
PMID:22074376
Ciliated epithelium lining the sperm duct.
Erin Davies
2017-09-02T22:43:04Z
Planarian_Anatomy
PLANA:0004533
sperm duct epithelium
https://planosphere.stowers.org/ontology/PLANA_0004533
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.
Erin Davies
2017-09-02T22:55:44Z
Planarian_Anatomy
PLANA:0004534
tuba lumen
https://planosphere.stowers.org/ontology/PLANA_0004534
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
Anatomial plane which divides the body into ventral and dorsal regions. This plane always includes the midline and is also known as the frontal plane.
Steph Nowotarski
2017-04-26T19:32:04Z
Planarian_Anatomy
PLANA:0007502
Depicted by field contains hematoxylin and eosin staining of a coronal plane section of a asexual adult animal. Scale bar = 250um
coronal plane
https://planosphere.stowers.org/ontology/PLANA_0007502
Anatomical plane which divides the body into right and left parts. This plane passes through the midline.
whole organism of sagittal plane
sagittal plane of the whole animal
Anatomical plane which divides the body into right and left parts. This plane passes through the midline.
Three dimensional compartment along the dorsoventral axis that is above the anteroposterior axis, containing the eyes.
Steph Nowotarski
2017-04-27T16:38:48Z
BSPO:0000089
FBcv:0000035
FBql:00005876
Planarian_Anatomy
PLANA:0007504
dorsal compartment
https://planosphere.stowers.org/ontology/PLANA_0007504
Compartment along the dorsoventral axis that is below the anteroposterior axis.
Steph Nowotarski
2017-04-27T16:38:59Z
BSPO:0000091
FBql:00005877
Planarian_Anatomy
PLANA:0007505
ventral compartment
https://planosphere.stowers.org/ontology/PLANA_0007505
Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus.
Steph Nowotarski
2017-04-27T16:39:34Z
BSPO:0000087
FBql:00005874
Planarian_Anatomy
PLANA:0007506
anterior compartment
https://planosphere.stowers.org/ontology/PLANA_0007506
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.
Steph Nowotarski
2017-04-27T16:39:59Z
BSPO:0000090
FBcv:0000036
FBql:00005875
Planarian_Anatomy
PLANA:0007507
posterior compartment
https://planosphere.stowers.org/ontology/PLANA_0007507
Anatomical structures that exist outside of cells; non-cellular.
Steph Nowotarski
2017-05-03T13:48:26Z
WBbt:0005732
Planarian_Anatomy
PLANA:0007508
extracellular component
https://planosphere.stowers.org/ontology/PLANA_0007508
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
Steph Nowotarski
2017-05-03T13:48:41Z
GO:0005886
Planarian_Anatomy
PLANA:0007509
plasma membrane
https://planosphere.stowers.org/ontology/PLANA_0007509
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.
Steph Nowotarski
2017-05-03T18:08:16Z
GO:0043230
Planarian_Anatomy
PLANA:0007511
extracellular organelle
https://planosphere.stowers.org/ontology/PLANA_0007511
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.
Steph Nowotarski
2017-05-03T18:19:46Z
Planarian_Anatomy
PLANA:0007512
mitochondrion
https://planosphere.stowers.org/ontology/PLANA_0007512
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.
Steph Nowotarski
2017-05-04T14:46:22Z
Planarian_Anatomy
PLANA:0007513
endoplasmic reticulum
https://planosphere.stowers.org/ontology/PLANA_0007513
Endoplasmic reticululum that is studded with ribosomes, leading to a "rough" or "granular" appearance.
Steph Nowotarski
2017-05-04T14:47:41Z
Planarian_Anatomy
PLANA:0007514
rough endoplasmic reticulum
https://planosphere.stowers.org/ontology/PLANA_0007514
Endoplamic reticulum that does not contain ribosomes, which synthesizes lipids, phospholipids, and steroids.
Steph Nowotarski
2017-05-04T14:48:11Z
Planarian_Anatomy
PLANA:0007515
smooth endoplasmic reticulum
https://planosphere.stowers.org/ontology/PLANA_0007515
Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
Steph Nowotarski
2017-05-04T14:49:17Z
GO:0005643
Planarian_Anatomy
PLANA:0007516
nuclear pore
https://planosphere.stowers.org/ontology/PLANA_0007516
The digestive component of the cell. They are homogenous, dense, membrane bound organelles filled with acid hydrolases which break down polymers.
Steph Nowotarski
2017-05-04T15:35:23Z
Planarian_Anatomy
PLANA:0007518
lysosome
https://planosphere.stowers.org/ontology/PLANA_0007518
The digestive component of the cell. They are homogenous, dense, membrane bound organelles filled with acid hydrolases which break down polymers.
ISBN:0-71677033-4
PMID:4853064
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.
whole organism of anterior-posterior axis
anterior-posterior axis of the whole animal
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.
Depiction shows an asexual with the term annoated 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.
whole organism of dorsal-ventral axis
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.
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.
whole organism of left-right axis
dextro-sinister axis of the whole animal
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.
Depiction shows an asexual with the term annoated 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.
whole organism of medial-lateral axis
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.
Depiction shows an asexual with the term annoated 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.
whole organism of proximal-distal axis
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.
Depicted by shows a planarian pharynx 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.
Steph Nowotarski
2017-05-15T18:28:35Z
Planarian_Anatomy
PLANA:0007524
anterior pole
https://planosphere.stowers.org/ontology/PLANA_0007524
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
Distinct posterior cluster of muscle cells located at the midline which express wnt1.
Steph Nowotarski
2017-05-15T18:28:47Z
Planarian_Anatomy
PLANA:0007525
posterior pole
https://planosphere.stowers.org/ontology/PLANA_0007525
Distinct posterior cluster of muscle cells located at the midline which express wnt1.
PMID:18063755
PMID:21680047
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.
Steph Nowotarski
2017-06-22T17:12:28Z
CL:0000125
Planarian_Anatomy
PLANA:0007528
glial cell
https://planosphere.stowers.org/ontology/PLANA_0007528
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
A biological tissue mass of nerve cell bodies.
Steph Nowotarski
2017-06-22T18:29:52Z
UBERON:0000045
Planarian_Anatomy
PLANA:0007529
ganglion
https://planosphere.stowers.org/ontology/PLANA_0007529
Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft.
Steph Nowotarski
2017-07-24T19:28:03Z
Planarian_Anatomy
PLANA:0007534
inner pharyngeal epithelium
https://planosphere.stowers.org/ontology/PLANA_0007534
Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft.
doi:10.1002/jmor.1051550208
OCLC:16809160
Pharynx muscle fibers running parallel to the diameter of the pharynx.
Steph Nowotarski
2017-07-24T19:39:14Z
Planarian_Anatomy
PLANA:0007535
pharyngeal circular muscle fiber
https://planosphere.stowers.org/ontology/PLANA_0007535
Pharynx muscle fibers running parallel to the diameter of the pharynx.
ASIN:B000M4NK9M
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell.
Steph Nowotarski
2017-09-05T14:18:21Z
UBERON:0000955
Planarian_Anatomy
PLANA:0007537
brain
https://planosphere.stowers.org/ontology/PLANA_0007537
Specialized epithelial cells located along the dorsoventral 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 epithelial surface.
Steph Nowotarski
2017-09-05T14:32:51Z
Planarian_Anatomy
PLANA:0007538
adhesion gland
https://planosphere.stowers.org/ontology/PLANA_0007538
Specialized epithelial cells located along the dorsoventral 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 epithelial surface.
OCLC:16809160
PMID:20865784
Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells.
Steph Nowotarski
2017-09-05T15:08:27Z
Planarian_Anatomy
PLANA:0007539
anchor cell
https://planosphere.stowers.org/ontology/PLANA_0007539
Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells.
OCLC:16809160
PMID:20865784
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.
Steph Nowotarski
2017-09-05T15:08:38Z
Planarian_Anatomy
PLANA:0007540
viscid gland cell
https://planosphere.stowers.org/ontology/PLANA_0007540
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
Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance.
Steph Nowotarski
2017-09-05T15:08:48Z
Planarian_Anatomy
PLANA:0007541
releasing gland cell
https://planosphere.stowers.org/ontology/PLANA_0007541
Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance.
OCLC:16809160
PMID:20865784
A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2.
Planarian_Anatomy
PLANA:0007543
TrpA+ central nervous system neuron
https://planosphere.stowers.org/ontology/PLANA_0007543
A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2.
PMID:22549959
A subset of sensory neurons located along the dorsal head margin.
Planarian_Anatomy
PLANA:0007544
cintillo+ sensory neuron
https://planosphere.stowers.org/ontology/PLANA_0007544
A subset of sensory neurons located along the dorsal head margin.
PMID:12557210
The outermost region of the deep-superficial axis. This anatomical compartment contains definitive epidermis, basal lamina and subepidermal nerve plexus.
epidermal surface
epidermis surface
Planarian_Anatomy
PLANA:0007545
epidermal compartment
https://planosphere.stowers.org/ontology/PLANA_0007545
piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons.
Planarian_Anatomy
PLANA:0007546
TrpA+ neural progenitor cell
https://planosphere.stowers.org/ontology/PLANA_0007546
piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons.
PMID:25254346
PMID:22549959
piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole.
Planarian_Anatomy
PLANA:0007547
anterior pole progenitor cell
https://planosphere.stowers.org/ontology/PLANA_0007547
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.
Planarian_Anatomy
PLANA:0007548
transverse commissure
https://planosphere.stowers.org/ontology/PLANA_0007548
Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords.
PMID:17999079
An anatomical compartment of the deep-superficial axis containing the body wall musculature and underlying submuscular nerve plexus.
Planarian_Anatomy
PLANA:0007549
body wall musculature compartment
https://planosphere.stowers.org/ontology/PLANA_0007549
piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons.
Planarian_Anatomy
PLANA:0007550
serotonergic neural progenitor cell
https://planosphere.stowers.org/ontology/PLANA_0007550
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.
Planarian_Anatomy
PLANA:0007551
klf+ sensory neuron progenitor cell
https://planosphere.stowers.org/ontology/PLANA_0007551
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.
Planarian_Anatomy
PLANA:0007552
nu neoblast
https://planosphere.stowers.org/ontology/PLANA_0007552
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.
Planarian_Anatomy
PLANA:0007553
lateral nerve
https://planosphere.stowers.org/ontology/PLANA_0007553
A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus.
PMID:17999079
An anatomical compartment of the deep-superficial axis between the gastrodermal nerve plexus and submuscular nerve plexus.
mesenchyme
Planarian_Anatomy
PLANA:0007554
parenchymal compartment
https://planosphere.stowers.org/ontology/PLANA_0007554
piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons.
Planarian_Anatomy
PLANA:0007555
pax3/7+ neural progenitor cell
https://planosphere.stowers.org/ontology/PLANA_0007555
piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons.
PMID: 25254346
Anatomical space enclosed by the temporary embryonic pharynx epithelial cells. Lumen through which yolk cells are transported into the embryonic gut cavity.
Erin Davies
Planarian_Anatomy
PLANA:0007556
temporary embryonic pharynx cavity
https://planosphere.stowers.org/ontology/PLANA_0007556
Anatomical space enclosed by the temporary embryonic pharynx epithelial cells. Lumen through which yolk cells are transported into the embryonic gut cavity.
PMID:28072387
Nerve plexus surrounding the testis.
Planarian_Anatomy
PLANA:0007557
testis nerve plexus
https://planosphere.stowers.org/ontology/PLANA_0007557
Nerve plexus surrounding the testis.
PMID:7833618
PMID:17999079
Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs.
Erin Davies
Planarian_Anatomy
PLANA:0007558
fission plane
https://planosphere.stowers.org/ontology/PLANA_0007558
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.
Planarian_Anatomy
PLANA:0007559
ovary nerve plexus
https://planosphere.stowers.org/ontology/PLANA_0007559
Nerve plexus surrounding the ovary.
PMID:7833618
PMID:17999079
The innermost anatomical compartment of the deep-superficial axis, extending from the definitive gut lumen to the gastrodermal nerve plexus.
Planarian_Anatomy
PLANA:0007560
gastrovascular compartment
https://planosphere.stowers.org/ontology/PLANA_0007560
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
TAO:0000037
TGMA:0001823
VHOG:0001759
XAO:0003000
ZFA:0000037
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
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.
stage succeeding embryo, including mature structure
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
BilaDO:0000003
OGES:000010
OGES:000014
OGES:000024
WBls:0000022
WBls:0000093
WBls:0000103
postembryonic stage
post-hatching stage
uberon
postembryonic
UBERON:0000092
post-embryonic stage
stage succeeding embryo, including mature structure
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
FBdv:00000000
HsapDv:0000001
MmusDv:0000001
OGES:000011
ncithesaurus:Life
entire life cycle
entire lifespan
life
lifespan
uberon
UBERON:0000104
life cycle
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
BILS:0000105
EFO:0000399
FBdv:00007012
FMA:24120
HsapDv:0000000
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.
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
BILS:0000106
BilaDO:0000005
EFO:0001322
EHDAA:27
FBdv:00005288
NCIT:C12601
PdumDv:0000100
VHOG:0000745
XAO:1000001
ZFS:0000001
1-cell stage
fertilized egg stage
one cell stage
uberon
fertilized egg stage
one-cell stage
zygote
zygotum
UBERON:0000106
zygote stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
2012-09-17
VHOG:0000745
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107
fertilized egg stage
BTO:0000854
one-cell stage
VHOG:0000745
zygote
VHOG:0000745
zygotum
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
BILS:0000111
BilaDO:0000010
HsapDv:0000015
MmusDv:0000018
OGES:000005
OGES:000032
uberon
segmentation stage
UBERON:0000111
organogenesis stage
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
lumen
space
AAO:0010110
AEO:0000005
BILA:0000005
CARO:0000005
EHDAA2:0003005
FBbt:00007017
FMA:5897
HAO:0000005
NCIT:C94478
TAO:0001668
TGMA:0001825
UMLS:C0524461
VHOG:0001728
XAO:0003190
ZFA:0001643
lumen space
uberon
anatomical spaces
UBERON:0000464
anatomical space
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
UMLS:C0524461
ncithesaurus:Lumen_Space
anatomical spaces
ZFA:0001643
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.
Anatomical entity that has no mass.
AAO:0010265
AEO:0000007
BILA:0000007
CARO:0000007
EHDAA2:0003007
FBbt:00007015
FMA:67112
HAO:0000007
TAO:0001835
TGMA:0001827
VHOG:0001727
immaterial physical anatomical entity
uberon
UBERON:0000466
immaterial anatomical entity
Anatomical entity that has no mass.
immaterial physical anatomical entity
FMA:67112
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
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
OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA
TAO:0001308
TGMA:0001840
UMLS:C0229962
VHOG:0001758
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
UMLS:C0229962
ncithesaurus:Body_Part
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.
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
CARO:0000000
EHDAA2:0002229
FBbt:10000000
FBbt_root:00000000
FMA:62955
HAO:0000000
MA:0000001
NCIT:C12219
TAO:0100000
TGMA:0001822
UMLS:C1515976
WBbt:0000100
XAO:0000000
ZFA:0100000
uberon
UBERON:0001062
anatomical entity
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
FMA:62955
UMLS:C1515976
ncithesaurus:Anatomic_Structure_System_or_Substance
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
EMAPA:37442
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
EMAPA:37442
MA:th
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.
A portion of tissue that is regrowing after damage or amputation.[TAO]
EHDAA2:0003233
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.
A portion of tissue that is regrowing after damage or amputation.[TAO]
2012-08-14
TAO:0005147
TAO
ZFIN:curator
regenerating tissue
ZFA:0005147
regenerating tissues
ZFA:0005147
example to be eventually removed
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
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
term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
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
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
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
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
core
placeholder removed
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
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
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
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.
other
true
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
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
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
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
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
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
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
From ligand activity to has_ligand
This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps"
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
From has_ligand to ligand activity