CARO part_of NCBITaxon:79327; CL part_of NCBITaxon:79327
1.2
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
editor preferred term
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
example of usage
has curation status
definition
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.
editor note
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
term editor
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
alternative term
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
definition source
An administrative note of use for a curator but of no use for a user
curator note
For external terms/classes, the ontology from which the term was imported
imported from
expand expression to
first order logic expression
An alternative name for a class or property which is unique across the OBO Foundry.
OBO foundry unique label
elucidation
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p
is symmetric relational form of process class
Relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
is direct form of
Relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
is indirect form of
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
has_broad_synonym
database_cross_reference
has_exact_synonym
has_obo_format_version
has_obo_namespace
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
part_of
BFO:0000050
uberon
BFO:0000050
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
has_part
BFO:0000051
BFO:0000051
has part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
BFO:0000054
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realized in
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
BFO:0000055
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
participates_in
BFO:0000056
uberon
BFO:0000056
participates in
BFO:0000060
accidentally included in BFO 1.2 proposal
- should have been BFO_0000062
obsolete preceded by
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
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
BFO:0000062
is preceded by
takes place after
uberon
BFO:0000062
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
BFO:0000063
uberon
BFO:0000063
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
BFO:0000066
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
contains_process
BFO:0000067
uberon
BFO:0000067
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 bisects an organism from head end to opposite end of body or tail: bearer
anterior_to
cjm
2009-07-31T02:15:46Z
BSPO:0000096
uberon
BSPO:0000096
anterior_to
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
distal_to
BSPO:0000097
uberon
BSPO:0000097
distal_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 bisects an organism from back (e.g. spinal column) to front (e.g. belly).
dorsal_to
BSPO:0000098
uberon
BSPO:0000098
dorsal_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 bisects an organism from head end to opposite end of body or tail.
caudal_to
posterior_to
BSPO:0000099
uberon
BSPO:0000099
posterior_to
x proximal_to y iff x is closer to the point of attachment with the body than y.
proximal_to
BSPO:0000100
uberon
BSPO:0000100
proximal_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 bisects an organism from back (e.g. spinal column) to front (e.g. belly).
ventral_to
BSPO:0000102
uberon
BSPO:0000102
ventral_to
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
deep_to
BSPO:0000107
uberon
BSPO:0000107
deep_to
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
superficial_to
BSPO:0000108
uberon
BSPO:0000108
superficial_to
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
in_posterior_side_of
BSPO:0000122
uberon
BSPO:0000122
in_posterior_side_of
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
in_anterior_side_of
BSPO:0000123
uberon
BSPO:0000123
in_anterior_side_of
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
in_proximal_side_of
BSPO:0000124
uberon
BSPO:0000124
in_proximal_side_of
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
in_distal_side_of
BSPO:0000125
uberon
BSPO:0000125
in_distal_side_of
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
in_lateral_side_of
BSPO:0000126
uberon
BSPO:0000126
in_lateral_side_of
X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the superficial portion.
in_superficial_part_of
BSPO:0001100
uberon
BSPO:0001100
in_superficial_part_of
X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion.
in_deep_part_of
BSPO:0001101
uberon
BSPO:0001101
in_deep_part_of
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
proximalmost_part_of
BSPO:0001106
uberon
BSPO:0001106
proximalmost_part_of
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
immediately_deep_to
BSPO:0001107
uberon
BSPO:0001107
immediately_deep_to
X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y
distalmost_part_of
BSPO:0001108
uberon
BSPO:0001108
distalmost_part_of
x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side.
posterior_to (developmentally)
postaxial_to
BSPO:0001114
uberon
BSPO:0001114
postaxial_to
X intersects_median_plane of iff X crosses the midine plane of Y.
intersects_midsagittal_plane_of
BSPO:0005001
uberon
BSPO:0005001
intersects_midsagittal_plane_of
immediately_anterior_to
BSPO:0015009
uberon
BSPO:0015009
immediately_anterior_to
immediately_posterior_to
BSPO:0015012
uberon
BSPO:0015012
immediately_posterior_to
immediately_superficial_to
BSPO:0015014
uberon
BSPO:0015014
immediately_superficial_to
in_dorsal_side_of
BSPO:0015101
uberon
BSPO:0015101
in_dorsal_side_of
in_ventral_side_of
BSPO:0015102
uberon
BSPO:0015102
in_ventral_side_of
nearer to the oral opening of the organism, on the oral-aboral axis.
oral_to
BSPO:0015201
uberon
BSPO:0015201
oral_to
nearer to the aboral opening of the organism, on the oral-aboral axis.
aboral_to
BSPO:0015202
uberon
BSPO:0015202
aboral_to
x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the front.
anterior_to (developmentally)
lateral (radial) to
medial (tibial) to
preaxial_to
BSPO:1000000
uberon
BSPO:1000000
preaxial_to
feature restricted to
Steph Nowotarski
2017-07-24T20:21:09Z
PLANA:0007536
specific_to
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
RO:0000052
inheres in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
bearer_of
RO:0000053
uberon
RO:0000053
bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
RO:0000056
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
RO:0000057
has participant
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
RO:0000079
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
RO:0000080
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
RO:0000081
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
RO:0000085
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has_quality
RO:0000086
uberon
RO:0000086
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
RO:0000087
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
RO:0000091
has disposition
inverse of has disposition
RO:0000092
disposition of
A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.
David Osumi-Sutherland
(forall (?x ?y)
(iff
(neural_circuit_path ?x ?y)
(and
("neuron ; CL_0000540" ?x)
("neuron ; CL_0000540" ?y)
(or
(synapsed_by ?x ?y)
(synapsed_to ?x ?y)))))
(forall (...s ?x ?y ?z)
(iff
(neural_circuit_path ...s ?x ?y ?z)
(and
(neural_circuit_path ...s ?x ?y)
("neuron ; CL_0000540" ?z)
(or
(synapsed_by ?y ?z)
(synapsed_to ?y ?z)))))
(forall (?x ?y)
(iff
(in_neural_circuit_with ?x ?y)
(exists (...s)
(neural_circuit_path ?x ...s ?y))))
RO:0000300
in neural circuit with
A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next.
David Osumi-Sutherland
(forall (?x ?y)
(iff
(upstream_neural_circuit_path ?x ?y)
(and
("neuron ; CL_0000540" ?x)
("neuron ; CL_0000540" ?y)
(synapsed_to ?x ?y))))
(forall (...s ?x ?y ?z)
(iff
(upstream_neural_circuit_path ...s ?x ?y ?z )
(and
(upstream_neural_circuit_path ...s ?x ?y)
("neuron ; CL_0000540" ?z)
(synapsed_to ?y ?z))))
(forall (?x ?y)
(iff
(upstream_in_neural_circuit_with ?x ?y)
(exists (...s)
(upstream_neural_circuit_path ?x ...s ?y))))
RO:0000301
upstream in neural circuit with
A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next.
David Osumi-Sutherland
(forall (?x ?y)
(iff
(downstream_neural_circuit_path ?x ?y)
(and
("neuron ; CL_0000540" ?x)
("neuron ; CL_0000540" ?y)
(synapsed_by ?x ?y))))
(forall (...s ?x ?y ?z)
(iff
(downstream_neural_circuit_path ...s ?x ?y ?z )
(and
(downstream_neural_circuit_path ...s ?x ?y)
("neuron ; CL_0000540" ?z)
(synapsed_by ?y ?z))))
(forall (?x ?y)
(iff
(downstream_in_neural_circuit_with ?x ?y)
(exists (...s)
(downstream_neural_circuit_path ?x ...s ?y))))
RO:0000302
downstream in neural circuit with
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
RO:0001000
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
RO:0001001
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
location_of
RO:0001015
uberon
RO:0001015
location of
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning:
domain: material entity
range: spatial region or site (immaterial continuant)
contained_in
RO:0001018
contained in
contains
contains
RO:0001019
uberon
RO:0001019
contains
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
located_in
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
RO:0001025
uberon
RO:0001025
located in
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
boundary_of
RO:0002000
uberon
RO:0002000
2D boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
David Osumi-Sutherland
has boundary
has_2D_boundary
has_boundary
RO:0002002
uberon
RO:0002002
has 2D boundary
A relation that holds between two neurons that are electrically coupled via gap junctions.
David Osumi-Sutherland
RO:0002003
electrically_synapsed_to
The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).
David Osumi-Sutherland
RO:0002004
tracheates
David Osumi-Sutherland
innervated_by
http://www.ncbi.nlm.nih.gov/pubmed/22402613
RO:0002005
nerve supply
uberon
RO:0002005
http://code.google.com/p/obo-relations/issues/detail?id=6
innervated_by
David Osumi-Sutherland
RO:0002006
has synaptic terminal of
X outer_layer_of Y iff:
. X :continuant that bearer_of some PATO:laminar
. X part_of Y
. exists Z :surface
. X has_boundary Z
. Z boundary_of Y
has_boundary: http://purl.obolibrary.org/obo/RO_0002002
boundary_of: http://purl.obolibrary.org/obo/RO_0002000
David Osumi-Sutherland
bounding_layer_of
RO:0002007
uberon
RO:0002007
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
bounding layer of
A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
Note from NCEAS meeting: consider changing primary label
David Osumi-Sutherland
RO:0002008
Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
coincident with
A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g.
David Osumi-Sutherland
x 'cell expresses' y iff:
cell(x)
AND gene(y)
AND exists some 'transcription, DNA templated (GO_0006351)'(t)
AND t occurs_in x
AND t has_input y
RO:0002009
cell expresses
x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
David Osumi-Sutherland
RO:0002010
regulates in other organism
A relationship that holds between a process that regulates a transport process and the entity transported by that process.
David Osumi-Sutherland
RO:0002011
regulates transport of
A part of relation that applies only between occurents.
RO:0002012
occurent part of
David Osumi-Sutherland
<=
RO:0002081
Primitive instance level timing relation between events
before or simultaneous with
Relation between occurrents, shares start and end boundaries.
David Osumi-Sutherland
simultaneous_with
RO:0002082
coincides_with
is_equal_to
uberon
RO:0002082
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
David Osumi-Sutherland
RO:0002083
t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
before
David Osumi-Sutherland
RO:0002084
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which ends
David Osumi-Sutherland
di
RO:0002085
Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
encompasses
David Osumi-Sutherland
RO:0002086
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
David Osumi-Sutherland
starts_at_end_of
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
immediately_preceded_by
RO:0002087
directly preceded by
is directly preceded by
is immediately preceded by
starts_at_end_of
uberon
RO:0002087
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
David Osumi-Sutherland
RO:0002088
Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which starts
David Osumi-Sutherland
RO:0002089
starts before
David Osumi-Sutherland
ends_at_start_of
meets
RO:0002090
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
David Osumi-Sutherland
io
RO:0002091
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
David Osumi-Sutherland
d
during
RO:0002092
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
David Osumi-Sutherland
o
overlaps
RO:0002093
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
Relation between a neuron and an anatomical structure that its soma is part of.
David Osumi-Sutherland
BFO_0000051 some (
GO_0043025 and BFO_0000050 some ?Y)
RO:0002100
has soma location
relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
David Osumi-Sutherland
fasciculates with
(forall (?x ?y)
(iff
(fasciculates_with ?x ?y)
(exists (?nps ?npbs)
(and
("neuron ; CL_0000540" ?x)
("neuron projection bundle ; CARO_0001001" ?y)
("neuron projection segment ; CARO_0001502" ?nps)
("neuron projection bundle segment ; CARO_0001500' " ?npbs)
(part_of ?npbs ?y)
(part_of ?nps ?x)
(part_of ?nps ?npbs)
(forall (?npbss)
(if
(and
("neuron projection bundle subsegment ; CARO_0001501" ?npbss)
(part_of ?npbss ?npbs)
)
(overlaps ?nps ?npbss)
))))))
RO:0002101
fasciculates with
Relation between a neuron and some structure its axon forms (chemical) synapses in.
Chris Mungall
David Osumi-Sutherland
BFO_0000051 some (
GO_0030424 and BFO_0000051 some (
GO_0042734 and BFO_0000050 some (
GO_0045202 and BFO_0000050 some ?Y)))
RO:0002102
axon synapses in
Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
Chris Mungall
David Osumi-Sutherland
BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))
synapsed_by
RO:0002103
uberon
RO:0002103
synapsed by
Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
Alexander Diehl
Chris Mungall
Lindsay Cowell
BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)
RO:0002104
has plasma membrane part
A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.
David Osumi-Sutherland
Marta Costa
BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
RO:0002105
Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
synapsed_via_type_Ib_bouton_to
A relation between a motor neuron and a muscle that it synapses to via a type Is bouton.
David Osumi-Sutherland
Marta Costa
BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
RO:0002106
Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
synapsed_via_type_Is_bouton_to
A relation between a motor neuron and a muscle that it synapses to via a type II bouton.
David Osumi-Sutherland
Marta Costa
BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
RO:0002107
Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
synapsed_via_type_II_bouton_to
Relation between a muscle and a motor neuron that synapses to it via a type II bouton.
David Osumi-Sutherland
Marta Costa
BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
RO:0002108
Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
synapsed_by_via_type_II_bouton
Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.
David Osumi-Sutherland
Marta Costa
BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
RO:0002109
Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
synapsed_by_via_type_Ib_bouton
Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
Chris Mungall
David Osumi-Sutherland
synapsed in
http://purl.obolibrary.org/obo/BFO_0000051 some (
http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (
http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
RO:0002110
has postsynaptic terminal in
has neurotransmitter
RO:0002111
releases neurotransmitter
Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.
David Osumi-Sutherland
Marta Costa
BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
RO:0002112
Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
synapsed_by_via_type_Is_bouton
Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
synapses in
BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)
RO:0002113
has presynaptic terminal in
A relation between a motor neuron and a muscle that it synapses to via a type III bouton.
BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
RO:0002114
Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
synapsed_via_type_III_bouton_to
Relation between a muscle and a motor neuron that synapses to it via a type III bouton.
BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
RO:0002115
Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
synapsed_by_via_type_III_bouton
Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
Chris Mungall
David Osumi-Sutherland
BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))
RO:0002120
N1 synapsed_to some N2
Expands to:
N1 SubclassOf (
has_part some (
‘pre-synaptic membrane ; GO:0042734’ that part_of some (
‘synapse ; GO:0045202’ that has_part some (
‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))
synapsed to
Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
Chris Mungall
David Osumi-Sutherland
BFO_0000051 some (
GO_0030425 and BFO_0000051 some (
http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (
GO_0045202 and BFO_0000050 some ?Y)))
RO:0002121
dendrite synapsed in
A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
David Osumi-Sutherland
has synapse in
RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)
RO:0002130
has synaptic terminal in
x overlaps y if and only if there exists some z such that x has part z and z part of y
BFO_0000051 some (BFO_0000050 some ?Y)
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
RO:0002131
uberon
RO:0002131
overlaps
The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
David Osumi-Sutherland
has fasciculating component
(forall (?x ?y)
(iff
(has_fasciculating_neuron_projection ?x ?y)
(exists (?nps ?npbs)
(and
("neuron projection bundle ; CARO_0001001" ?x)
("neuron projection ; GO0043005" ?y)
("neuron projection segment ; CARO_0001502" ?nps)
("neuron projection bundle segment ; CARO_0001500" ?npbs)
(part_of ?nps ?y)
(part_of ?npbs ?x)
(part_of ?nps ?npbs)
(forall (?npbss)
(if
(and
("neuron projection bundle subsegment ; CARO_0001501" ?npbss)
(part_of ?npbss ?npbs)
)
(overlaps ?nps ?npbss)
))))))
RO:0002132
has fasciculating neuron projection
Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.
T innervates some R
Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
David Osumi-Sutherland
RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))
innervates
RO:0002134
uberon
RO:0002134
http://code.google.com/p/obo-relations/issues/detail?id=6
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
David Osumi-Sutherland
connected to
The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
continuous_with
RO:0002150
uberon
RO:0002150
continuous with
x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom
proper overlaps
(forall (?x ?y)
(iff
(proper_overlaps ?x ?y)
(and
(overlaps ?x ?y)
(not (part_of ?x ?y))
(not (part_of ?y ?x)))))
RO:0002151
partially overlaps
d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.
ancestral_stucture_of
evolutionarily_descended_from
RO:0002156
derived by descent from
inverse of derived by descent from
RO:0002157
has derived by descendant
two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.
Consider obsoleting and merging with child relation, 'in homology relationship with'
homologous_to
homologous to
RO:0002158
uberon
RO:0002158
VBO calls this homologous_to
shares ancestor with
serially_homologous_to
RO:0002159
uberon
RO:0002159
serially homologous to
lactation SubClassOf 'only in taxon' some 'Mammalia'
X only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.
'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
Chris Mungall
only_in_taxon
RO:0002160
uberon
RO:0002160
only in taxon
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Chris Mungall
Jennifer Deegan
in_taxon
RO:0002162
uberon
RO:0002162
Connects a biological entity to its taxon of origin.
in taxon
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)
RO:0002163
spatially disjoint from
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
A is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
connected_to
RO:0002170
uberon
RO:0002170
Connection does not imply overlaps.
connected to
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
The M8 connects Glasgow and Edinburgh
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
connects
RO:0002176
uberon
RO:0002176
connects
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
attaches_to_part_of
RO:0002177
uberon
RO:0002177
attached to part of
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
supplies
RO:0002178
arterial supply of
uberon
RO:0002178
source: FMA
supplies
drains
RO:0002179
drains blood from
drains from
uberon
RO:0002179
source: Wikipedia
drains
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has_component
RO:0002180
uberon
RO:0002180
has component
A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
Chris Mungall
RO:0002200
has phenotype
inverse of has phenotype
Chris Mungall
RO:0002201
phenotype of
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
develops_from
RO:0002202
uberon
RO:0002202
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
RO:0002203
uberon
RO:0002203
develops into
definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x"
We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g.
Chris Mungall
RO:0002204
gene product of
every HOTAIR lncRNA is the gene product of some HOXC gene
every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
Chris Mungall
RO:0002205
has gene product
'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
Chris Mungall
RO:0002206
expressed in
Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y
Chris Mungall
David Osumi-Sutherland
has developmental precursor
FBbt
directly_develops_from
RO:0002207
uberon
RO:0002207
TODO - add child relations from DOS
directly develops from
inverse of directly develops from
developmental precursor of
RO:0002210
directly develops into
x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y
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
RO:0002211
regulates
x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
Chris Mungall
negatively regulates (process to process)
RO:0002212
negatively regulates
x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y
Chris Mungall
positively regulates (process to process)
RO:0002213
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
RO:0002215
uberon
RO:0002215
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
RO:0002216
uberon
RO:0002216
capable of part of
x actively participates in y if and only if x participates in y and x realizes some active role
Chris Mungall
agent in
RO:0002217
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
RO:0002218
has active participant
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
Chris Mungall
surrounded_by
RO:0002219
uberon
RO:0002219
surrounded by
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
X adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
x adjacent_to y iff: x and y share a boundary
Chris Mungall
adjacent_to
RO:0002220
uberon
RO:0002220
adjacent to
inverse of surrounded by
Chris Mungall
surrounds
RO:0002221
uberon
RO:0002221
surrounds
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
RO:0002222
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
inverse of starts with
Relation between occurrents, shares a start boundary with.
Chris Mungall
Allen
starts
RO:0002223
uberon
RO:0002223
starts
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Chris Mungall
started by
starts_with
RO:0002224
uberon
RO:0002224
starts with
x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
Chris Mungall
develops_from_part_of
RO:0002225
uberon
RO:0002225
develops from part of
x develops_in y if x is located in y whilst x is developing
Chris Mungall
EHDAA2
Jonathan Bard, EHDAA2
develops_in
RO:0002226
uberon
RO:0002226
This relation take from EHDAA2 - precise semantics yet to be defined
develops in
inverse of ends with
Chris Mungall
Relation between occurrents, shares an end boundary with.
ends
RO:0002229
finishes
uberon
RO:0002229
ends
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Chris Mungall
finished by
ends_with
RO:0002230
uberon
RO:0002230
ends with
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
Chris Mungall
starts with process that occurs in
RO:0002231
has start location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
Chris Mungall
ends with process that occurs in
RO:0002232
has end location
p has direct input c iff 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
RO:0002233
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
Chris Mungall
produces
RO:0002234
has output
A broad relationship between an exposure event or process and any entity (e.g., a human, human population, or a human organ) that interacts with an exposure stressor during the exposure event
ExO:0000001
RO:0002240
has exposure receptor
A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.
ExO:0000000
RO:0002241
has exposure stressor
A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor
ExO:0000055
RO:0002242
has exposure route
A broad relationship between an exposure event or process and a the material an agent takes from the source to the target.
RO:0002243
has exposure transport path
g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.
RO:0002245
over-expressed in
g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.
RO:0002246
under-expressed in
b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.
RO:0002252
connecting branch of
inverse of connecting branch of
RO:0002253
has connecting branch
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
RO:0002254
uberon
RO:0002254
has developmental contribution from
inverse of has developmental contribution from
Chris Mungall
developmentally_contributes_to
RO:0002255
uberon
RO:0002255
developmentally contributes to
t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
induced by
Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
GO:0001759
We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
developmentally_induced_by
RO:0002256
uberon
RO:0002256
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
developmentally induced by
Inverse of developmentally induced by
Chris Mungall
RO:0002257
developmentally induces
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
false
Chris Mungall
In general you should not use this relation to make assertions - use one of the more specific relations below this one
developmentally_preceded_by
RO:0002258
uberon
RO:0002258
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
c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)
RO:0002260
has biological role
c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)
RO:0002261
has application role
c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)
RO:0002262
has chemical role
c involved in regulation of p if c enables 'p' and p' causally upstream of p
RO:0002263
acts upstream of
c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p
affects
RO:0002264
acts upstream of or within
x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
Chris Mungall
replaces
developmentally_replaces
RO:0002285
uberon
RO:0002285
developmentally replaces
Inverse of developmentally preceded by
Chris Mungall
RO:0002286
developmentally succeeded by
'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
Chris Mungall
RO:0002287
part of developmental precursor of
x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.
Chris Mungall
RO:0002291
ubiquitously expressed in
Inverse of 'expressed in'
Chris Mungall
RO:0002292
expresses
inverse of ubiquiotously expressed in
Chris Mungall
RO:0002293
ubiquitously expresses
p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
Chris Mungall
results_in_developmental_progression_of
RO:0002295
results in developmental progression of
every flower development (GO:0009908) results in development of some flower (PO:0009046)
p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
Chris Mungall
http://www.geneontology.org/GO.doc.development.shtml
results_in_development_of
RO:0002296
results in development of
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
Chris Mungall
GOC:mtg_berkeley_2013
results_in_formation_of
RO:0002297
results in formation of
an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
Chris Mungall
GOC:mtg_berkeley_2013
results_in_morphogenesis_of
RO:0002298
results in morphogenesis of
an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
Chris Mungall
GOC:mtg_berkeley_2013
results_in_maturation_of
RO:0002299
results in maturation of
foramen ovale closure SubClassOf results in disappearance of foramen ovale
Chris Mungall
May be merged into parent relation
results_in_disappearance_of
RO:0002300
results in disappearance of
every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
Chris Mungall
May be merged into parent relation
RO:0002301
results in developmental regression of
Inverse of 'is substance that treats'
cjm
RO:0002302
is treated by substance
cjm
RO:0002304
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
RO:0002305
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
Chris Mungall
RO:0002312
evolutionary variant of
Holds between p and c when p is a transportation or localization process and the outcome of this process is to regulate the location of c
Chris Mungall
regulates location of
transports
RO:0002313
transports or maintains localization of
q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of inheres in part of
Chris Mungall
RO:0002314
inheres in part of
an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
Chris Mungall
GOC:mtg_berkeley_2013
results_in_acquisition_of_features_of
RO:0002315
results in acquisition of features of
A relationship that holds via some environmental process
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
RO:0002320
evolutionarily related to
An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial.
Chris Mungall
adapted for
adapted_for
confers_advantage_in
RO:0002322
uberon
RO:0002322
confers advantage in
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
RO:0002323
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
RO:0002324
developmentally related to
Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
Chris Mungall
http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with
In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
Gene Ontology Consortium
RO:0002325
colocalizes with
ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
We would like to say
if and only if
exists c', p'
c part_of c' and c' capable_of p
and
c capable_of p' and p' part_of p
then
c contributes_to p
However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
Chris Mungall
http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to
In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
RO:0002326
contributes 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.
RO:0002327
enables
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally_related_to
RO:0002328
uberon
RO:0002328
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
RO:0002329
uberon
RO:0002329
part of structure that is capable of
holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism
RO:0002330
genomically related to
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
RO:0002331
involved in
every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
p regulates levels of c if p regulates some amount (PATO:0000070) of c
Chris Mungall
regulates levels of (process to entity)
RO:0002332
regulates levels of
inverse of enables
Chris Mungall
RO:0002333
enabled by
inverse of regulates
Chris Mungall
regulated by (processual)
RO:0002334
regulated by
inverse of negatively regulates
Chris Mungall
RO:0002335
negatively regulated by
inverse of positively regulates
Chris Mungall
RO:0002336
positively regulated by
A relationship that holds via some process of localization
Chris Mungall
RO:0002337
related via localization to
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
Chris Mungall
RO:0002338
has target start location
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
Chris Mungall
RO:0002339
has target end location
Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.
Chris Mungall
RO:0002340
imports
Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
Chris Mungall
RO:0002341
results in transport along
Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
Chris Mungall
RO:0002342
results in transport across
'pollen tube growth' results_in growth_of some 'pollen tube'
Chris Mungall
RO:0002343
results in growth of
'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
Chris Mungall
RO:0002344
results in transport to from or in
Chris Mungall
RO:0002345
exports
an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron.
p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.
Chris Mungall
http://www.geneontology.org/GO.doc.development.shtml#fate
RO:0002348
results in commitment to
p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.
Chris Mungall
http://www.geneontology.org/GO.doc.development.shtml#fate
RO:0002349
results in determination of
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
is member of
member part of
SIO
member_of
RO:0002350
uberon
RO:0002350
member of
has member is a mereological relation between a collection and an item.
SIO
has_member
RO:0002351
uberon
RO:0002351
has member
inverse of has input
Chris Mungall
input_of
RO:0002352
uberon
RO:0002352
input of
inverse of has output
Chris Mungall
output_of
RO:0002353
uberon
RO:0002353
output of
Chris Mungall
RO:0002354
formed as result of
A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity.
Chris Mungall
RO:0002355
results in structural organization of
The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
Chris Mungall
http://www.geneontology.org/GO.doc.development.shtml#fate
RO:0002356
results in specification of
p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c.
Chris Mungall
RO:0002357
results in developmental induction of
Chris Mungall
http://neurolex.org/wiki/Property:DendriteLocation
RO:0002360
has dendrite location
a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
Chris Mungall
attaches_to
RO:0002371
uberon
RO:0002371
attached to
m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
Chris Mungall
Wikipedia:Insertion_(anatomy)
has_muscle_origin
RO:0002372
uberon
RO:0002372
The origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscles
has muscle origin
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
Chris Mungall
Wikipedia:Insertion_(anatomy)
RO:0002373
has muscle insertion
false
x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat
Chris Mungall
has_fused_element
RO:0002374
uberon
RO:0002374
A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B.
has fused element
A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
RO:0002375
in branching relationship with
https://github.com/obophenotype/uberon/issues/170
drains into
tributary_of
RO:0002376
uberon
RO:0002376
tributary_of
x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
Chris Mungall
anastomoses with
RO:0002378
anabranch of
A lump of clay and a statue
x spatially_coextensive_with y if and inly if x and y have the same location
Chris Mungall
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
RO:0002379
spatially coextensive with
x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve
Chris Mungall
branching_part_of
RO:0002380
uberon
RO:0002380
branching part of
x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
Chris Mungall
RO:0002381
main stem of
x proper_distributary_of y iff x distributary_of y and x does not flow back into y
Chris Mungall
RO:0002382
proper distributary of
x proper_tributary_of y iff x tributary_of y and x does not originate from y
Chris Mungall
RO:0002383
proper tributary 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
RO:0002384
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
RO:0002385
uberon
RO:0002385
has potential to developmentally contribute to
x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
Chris Mungall
RO:0002386
has potential to developmentally induce
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
Chris Mungall
has_potential_to_develop_into
RO:0002387
uberon
RO:0002387
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
RO:0002388
uberon
RO:0002388
has potential to directly develop into
'protein catabolic process' SubClassOf has_direct_input some protein
p has direct input c iff 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
directly consumes
This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
RO:0002400
has direct input
Chris Mungall
RO:0002401
Likely to be obsoleted. See:
https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
obsolete has indirect input
translation SubClassOf has_direct_output some protein
p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
Chris Mungall
directly produces
RO:0002402
obsolete has direct output
Chris Mungall
RO:0002403
Likely to be obsoleted. See:
https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
obsolete has indirect output
inverse of upstream of
Chris Mungall
RO:0002404
causally downstream of
Chris Mungall
RO:0002405
immediately causally downstream of
p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
Chris Mungall
directly positively regulates
directly activates (process to process)
RO:0002406
directly activates
p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
Chris Mungall
indirectly positively regulates
RO:0002407
indirectly activates
Chris Mungall
directly negatively regulates
directly inhibits (process to process)
RO:0002408
directly inhibits
Chris Mungall
indirectly negatively regulates
RO:0002409
indirectly inhibits
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.
RO:0002410
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
RO:0002411
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
RO:0002412
immediately causally upstream of
p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
Chris Mungall
directly provides input for (process to process)
RO:0002413
directly provides input for
transitive form of directly_provides_input_for
Chris Mungall
This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
transitively provides input for (process to process)
RO:0002414
transitively provides input for
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
RO:0002418
causally upstream of or within
false
Chris Mungall
RO:0002424
This is an exploratory relation
differs in
Chris Mungall
RO:0002425
differs in attribute of
Chris Mungall
RO:0002426
differs in attribute
inverse of causally upstream of or within
Chris Mungall
RO:0002427
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
RO:0002428
involved in regulation of
Chris Mungall
RO:0002429
involved in positive regulation of
Chris Mungall
RO:0002430
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
Chris Mungall
involved in or reguates
RO:0002431
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
Chris Mungall
executes activity in
RO:0002432
enables activity in
p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
Chris Mungall
contributes_to_morphology_of
RO:0002433
uberon
RO:0002433
contributes to morphology of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
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
RO:0002434
interacts with
https://github.com/oborel/obo-relations/wiki/InteractionRelations
An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)
Chris Mungall
RO:0002435
genetically interacts with
An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected.
Chris Mungall
binds
molecularly binds with
RO:0002436
molecularly interacts with
An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
Chris Mungall
interacts with on organism level
RO:0002437
biotically interacts with
An interaction relationship in which the partners are related via a feeding relationship.
Chris Mungall
RO:0002438
trophically interacts with
A biotic interaction in which the two organisms live together in more or less intimate association.
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/19278549
We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
RO:0002440
symbiotically interacts with
An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/19278549
RO:0002441
commensually interacts with
An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO).
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/19278549
RO:0002442
mutualistically interacts with
Chris Mungall
has parasite
parasitised by
directly parasitized by
RO:0002445
parasitized by
Porifiera attaches to substrate
A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.
Chris Mungall
semibiotically interacts with
RO:0002446
participates in a abiotic-biotic interaction with
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.
RO:0002447
phosphorylates
Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b
Chris Mungall
RO:0002448
molecularly controls
Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b.
Chris Mungall
inhibits
RO:0002449
molecularly decreases activity of
Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b.
Chris Mungall
activates
RO:0002450
molecularly increases activity of
all dengue disease transmitted by some mosquito
A relationship that holds between a disease and organism
Add domain and range constraints
Chris Mungall
RO:0002451
transmitted by
A relation that holds between a disease or an organism and a phenotype
Chris Mungall
RO:0002452
has symptom
Chris Mungall
RO:0002460
has vector
Chris Mungall
Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target
RO:0002461
partner in
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.
RO:0002464
helper property
Chris Mungall
RO:0002465
is symbiosis
Chris Mungall
RO:0002466
is commensalism
Chris Mungall
RO:0002467
is mutualism
Chris Mungall
RO:0002468
is parasitism
A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and
the a supports either the existence of b, or the truth value of b.
Chris Mungall
RO:0002472
is evidence for
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
Chris Mungall
composed_primarily_of
RO:0002473
uberon
RO:0002473
composed primarily of
ABal nucleus child nucleus of ABa nucleus (in C elegans)
c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d
Chris Mungall
This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage.
RO:0002476
child nucleus of
A child nucleus relationship in which the cells are part of a hermaphroditic organism
Chris Mungall
RO:0002477
child nucleus of in hermaphrodite
A child nucleus relationship in which the cells are part of a male organism
Chris Mungall
RO:0002478
child nucleus of in male
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
RO:0002479
has part that occurs in
An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y
Axiomatization to GO to be added later
Chris Mungall
RO:0002480
ubiquitinates
Chris Mungall
RO:0002481
is kinase activity
Chris Mungall
RO:0002482
is ubiquitination
See notes for inverse relation
Chris Mungall
RO:0002485
receives input from
This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
Chris Mungall
RO:0002486
sends output to
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.
RO:0002487
relation between structure and stage
x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
Chris Mungall
existence_starts_during
RO:0002488
begins_to_exist_during
uberon
RO:0002488
existence starts during
x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
Chris Mungall
existence_starts_with
RO:0002489
uberon
RO:0002489
existence starts with
x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
Chris Mungall
RO:0002490
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 and ends during y if and only if the start of x is part of y and 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) & ω(x) <= ω(y) & ω(x) >= α(y)
Chris Mungall
RO:0002491
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 and ends during
x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
Chris Mungall
existence_ends_during
RO:0002492
ceases_to_exist_during
uberon
RO:0002492
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
x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
Chris Mungall
existence_ends_with
RO:0002493
uberon
RO:0002493
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends with
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
Chris Mungall
transformation_of
RO:0002494
transforms from
uberon
RO:0002494
transformation of
x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
Chris Mungall
immediate_transformation_of
RO:0002495
direct_transformation_of
immediately transforms from
uberon
RO:0002495
immediate transformation of
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
existence_starts_during_or_after
RO:0002496
uberon
RO:0002496
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
existence_ends_during_or_before
RO:0002497
uberon
RO:0002497
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends during or before
A relationship between a material entity and a process where the material entity has some causal role that influences the process
RO:0002500
causal agent in
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.
RO:0002501
causal relation between processes
Chris Mungall
RO:0002502
depends on
q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
Chris Mungall
RO:0002503
towards
'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
Chris Mungall
has intermediate product
RO:0002505
has intermediate
A coral reef environment is determined by a particular coral reef
s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
Chris Mungall
determined by (system to material entity)
Chris Mungall
Pier Buttigieg
RO:0002507
determined by
inverse of determined by
Chris Mungall
determines (material entity to system)
RO:0002508
determines
s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
Chris Mungall
RO:0002509
determined by part of
x is transcribed from y if and only if x is synthesized from template y
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
RO:0002510
transcribed from
inverse of transcribed from
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
RO:0002511
transcribed to
x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
RO:0002512
ribosomal translation of
inverse of ribosomal translation of
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
RO:0002513
ribosomally translates to
A relation that holds between two entities that have the property of being sequences or having sequences.
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene.
RO:0002514
sequentially related to
Every UTR is adjacent to a CDS of the same transcript
Two consecutive DNA residues are sequentially adjacent
Two exons on a processed transcript that were previously connected by an intron are adjacent
x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
RO:0002515
sequentially adjacent to
Every CDS has as a start sequence the start codon for that transcript
x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
Chris Mungall
started by
http://www.ncbi.nlm.nih.gov/pubmed/20226267
RO:0002516
has start sequence
inverse of has start sequence
Chris Mungall
starts
http://www.ncbi.nlm.nih.gov/pubmed/20226267
RO:0002517
is start sequence of
Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)
x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
Chris Mungall
ended by
http://www.ncbi.nlm.nih.gov/pubmed/20226267
RO:0002518
has end sequence
inverse of has end sequence
Chris Mungall
ends
http://www.ncbi.nlm.nih.gov/pubmed/20226267
RO:0002519
is end sequence of
x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.
In the SO paper, this was defined as an instance-type relation
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/20226267
RO:0002520
is consecutive sequence of
Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence.
x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering
Chris Mungall
RO:0002521
is sequentially aligned with
The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y
Chris Mungall
RO:0002522
bounds sequence of
inverse of bounds sequence of
Chris Mungall
RO:0002523
is bound by sequence of
x has subsequence y iff all of the sequence parts of x are sequence parts of y
Chris Mungall
contains
http://www.ncbi.nlm.nih.gov/pubmed/20226267
RO:0002524
has subsequence
inverse of has subsequence
Chris Mungall
contained by
RO:0002525
is subsequence of
x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.
Chris Mungall
RO:0002526
overlaps sequence of
x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
Chris Mungall
disconnected from
RO:0002527
does not overlap sequence of
inverse of downstream of sequence of
Chris Mungall
RO:0002528
is upstream of sequence of
x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.
Chris Mungall
RO:0002529
is downstream of sequence of
A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y
Chris Mungall
RO:0002530
is immediately downstream of sequence of
A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
inverse of immediately downstream of
Chris Mungall
RO:0002531
is immediately upstream of sequence of
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
has sekeletal support
has supporting framework
has_skeleton
RO:0002551
uberon
RO:0002551
has skeleton
p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.
Chris Mungall
RO:0002552
results in ending of
inverse of is evidence for
Chris Mungall
RO:0002558
x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x.
has evidence
Chris Mungall
causally influenced by (material entity to material entity)
RO:0002559
causally influenced by
Chris Mungall
RO:0002563
interaction relation helper property
https://github.com/oborel/obo-relations/wiki/InteractionRelations
Chris Mungall
RO:0002564
molecular interaction relation helper property
Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
Chris Mungall
RO:0002565
results in movement of
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)
RO:0002566
causally influences
A relation that holds between elements of a musculoskeletal system or its analogs.
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
RO:0002567
biomechanically related to
m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
Chris Mungall
Wikipedia:Antagonist_(muscle)
has_muscle_antagonist
RO:0002568
uberon
RO:0002568
has muscle antagonist
inverse of branching part of
Chris Mungall
has_branching_part
RO:0002569
uberon
RO:0002569
has branching part
x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
Chris Mungall
UBERON:cjm
This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
RO:0002570
conduit for
x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
Chris Mungall
GOC:cjm
lumen_of
RO:0002571
uberon
RO:0002571
lumen of
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
Chris Mungall
luminal_space_of
RO:0002572
uberon
RO:0002572
luminal space of
A relation that holds between an attribute or a qualifier and another attribute.
Chris Mungall
This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
RO:0002573
has modifier
Chris Mungall
RO:0002574
participates in a biotic-biotic interaction with
inverse of has skeleton
Chris Mungall
RO:0002576
skeleton of
p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p
Chris Mungall
directly regulates (processual)
RO:0002578
directly regulates
x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends.
RO:0002583
existence starts at point
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
RO:0002584
has part structure that is capable of
p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed.
RO:0002585
results in closure of
p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p
RO:0002586
results in breakdown of
RO:0002587
results in synthesis of
RO:0002588
results in assembly of
p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released.
RO:0002589
results in catabolism of
RO:0002590
results in disassembly of
RO:0002591
results in remodeling of
p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
RO:0002592
results in organization of
x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends.
RO:0002593
existence ends at point
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
RO:0002595
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
RO:0002596
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
RO:0002597
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
RO:0002598
capable of positively regulating
c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
May be ceded to OBI
RO:0002607
is marker for
Inverse of 'causal agent in'
RO:0002608
has causal agent
A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
RO:0002609
related via dependence to
A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
Groups both positive and negative correlation
RO:0002610
correlated with
An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support.
A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.
RO:0002614
In the Gene Ontology association model, this corresponds to the With/From field
is evidence with support from
Inverse of is-model-of
RO:0002615
has model
RO:0002616
related via evidence or inference to
p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p
directly positively regulates (process to process)
RO:0002629
directly positively regulates
p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p
directly negatively regulates (process to process)
RO:0002630
directly negatively regulates
inverse of intracellular endoparasite of
RO:0002641
has intracellular endoparasite
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
produces
RO:0003000
uberon
RO:0003000
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
RO:0003001
uberon
RO:0003001
produced by
Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b.
Logical axioms to be added after the relevant branch of GO is MIREOTed in
RO:0003002
represses expression of
Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.
Logical axioms to be added after the relevant branch of GO is MIREOTed in
RO:0003003
increases expression of
Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.
To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?
Matthew Brush
RO:0003301
The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest.
is model of
The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.
An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition.
Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
RO:0003302
Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.
Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.
causes or contributes to condition
A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition.
RO:0003303
causes condition
A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition.
RO:0003304
contributes to condition
A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual.
contributes to expressivity of condition
RO:0003305
contributes to severity of condition
A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population.
contributes to penetrance of condition
RO:0003306
contributes to frequency of condition
A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.
RO:0003308
correlated with condition
An interaction relationship describing organisms that often occur together at the same time and space or in the same environment.
RO:0008506
co-occurs
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
correspondence
resemblance
ECO:0000041
SO:similar_to
sameness
similar to
RO:HOM0000000
in similarity relationship with
Similarity that results from common evolutionary origin.
homologous to
RO:HOM0000001
This broad definition encompasses all the working definitions proposed so far in the literature.
in homology relationship with
Similarity that results from independent evolution.
analogy
homoplasous to
RO:HOM0000002
in homoplasy relationship with
Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
ECO:0000075
homocracous to
RO:HOM0000003
Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.
in homocracy relationship with
Homoplasy that involves different underlying mechanisms or structures.
analogy
RO:HOM0000004
Convergence usually implies a notion of adaptation.
in convergence relationship with
Homoplasy that involves homologous underlying mechanisms or structures.
parallel evolution
RO:HOM0000005
Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.
in parallelism relationship with
Homology that is defined by similarity with regard to selected structural parameters.
idealistic homology
ECO:0000071
MI:2163
structural homologous to
RO:HOM0000006
in structural homology relationship with
Homology that is defined by common descent.
true homology
homology
ECO:0000080
RO_proposed_relation:homologous_to
SO:0000330
SO:0000853
SO:0000857
SO:homologous_to
TAO:homologous_to
cladistic homology
historical homologous to
phylogenetic homology
taxic homology
RO:HOM0000007
in historical homology relationship with
Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
transformational homology
ECO:0000067
biological homologous to
RO:HOM0000008
Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.
in biological homology relationship with
Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
reversion
atavism
rudiment
RO:HOM0000009
in reversal relationship with
Structural homology that is detected by similarity in content and organization between chromosomes.
synteny
MeSH:Synteny
SO:0000860
SO:0005858
syntenic homologous to
RO:HOM0000010
in syntenic homology relationship with
Historical homology that involves genes that diverged after a duplication event.
SO:0000854
SO:0000859
SO:paralogous_to
paralogous to
RO:HOM0000011
in paralogy relationship with
Paralogy that involves sets of syntenic blocks.
duplicon
paralogon
syntenic paralogous to
RO:HOM0000012
in syntenic paralogy relationship with
Syntenic homology that involves chromosomes of different species.
syntenic orthologous to
RO:HOM0000013
in syntenic orthology relationship with
Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
mixed homology
modular homology
partial correspondence
percent homology
fractional homology
partial homologous to
segmental homology
RO:HOM0000014
in partial homology relationship with
Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
MeSH:Structural_Homology,_Protein
protein structural homologous to
RO:HOM0000015
in protein structural homology relationship with
Structural homology that involves a pseudogenic feature and its functional ancestor.
pseudogene
SO:non_functional_homolog_of
non functional homologous to
RO:HOM0000016
in non functional homology relationship with
Historical homology that involves genes that diverged after a speciation event.
ECO:00000060
SO:0000855
SO:0000858
SO:orthologous_to
orthologous to
RO:HOM0000017
The term is sometimes also used for anatomical structures.
in orthology relationship with
Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
xenologous to
RO:HOM0000018
The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).
in xenology relationship with
Historical homology that involves two members sharing no other homologs in the lineages considered.
1 to 1 homologous to
1:1 homology
one-to-one homology
RO:HOM0000019
in 1 to 1 homology relationship with
Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
1 to 1 orthologous to
1:1 orthology
one-to-one orthology
RO:HOM0000020
in 1 to 1 orthology relationship with
Paralogy that results from a whole genome duplication event.
homoeology
ohnologous to
RO:HOM0000022
in ohnology relationship with
Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
in-paralogous to
inparalogy
symparalogy
RO:HOM0000023
in in-paralogy relationship with
Paralogy that results from a duplication preceding a given speciation event.
alloparalogy
out-paralogous to
outparalogy
RO:HOM0000024
in out-paralogy relationship with
1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
pro-orthologous to
RO:HOM0000025
in pro-orthology relationship with
1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
semi-orthologous to
RO:HOM0000026
The converse of pro-orthologous.
in semi-orthology relationship with
Iterative homology that involves structures arranged along the main body axis.
homonomy
serial homologous to
RO:HOM0000027
in serial homology relationship with
Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
heterochronous homologous to
heterochrony
RO:HOM0000028
in heterochronous homology relationship with
Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
juvenification
pedomorphosis
RO:HOM0000029
in paedomorphorsis relationship with
Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
RO:HOM0000030
in peramorphosis relationship with
Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
RO:HOM0000031
in progenesis relationship with
Paedomorphosis that is produced by a retardation of somatic development.
juvenilization
neotenous to
RO:HOM0000032
in neoteny relationship with
Convergence that results from co-evolution usually involving an evolutionary arms race.
mimicrous to
RO:HOM0000033
in mimicry relationship with
Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
co-orthology
many to 1 orthology
1 to many orthologous to
1:many orthology
one-to-many orthology
RO:HOM0000034
in 1 to many orthology relationship with
Historical homology that involves two members of a larger set of homologs.
many to many homologous to
many-to-many homology
many:many homology
RO:HOM0000036
in many to many homology relationship with
Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
1:many homology
1 to many homologous to
one-to-many homology
RO:HOM0000037
in 1 to many homology relationship with
Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
synapomorphy
apomorphous to
RO:HOM0000042
in apomorphy relationship with
Historical homology that is based on distant shared ancestry.
symplesiomorphy
plesiomorphous to
RO:HOM0000043
This term is usually contrasted to apomorphy.
in plesiomorphy relationship with
Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
generative homology
homoiology
deep genetic homology
deep homologous to
RO:HOM0000044
Used for structures in distantly related taxa.
in deep homology relationship with
Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
hemiplasous to
RO:HOM0000045
in hemiplasy relationship with
Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
gametologous to
RO:HOM0000046
in gametology relationship with
Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
MeSH:Chromosome_Pairing
chromosomal homologous to
RO:HOM0000047
in chromosomal homology relationship with
Orthology that involves two genes that experienced duplications more recent than the species split that created them.
co-orthology
trans-homology
many to many orthologous to
many-to-many orthology
many:many orthology
trans-orthology
RO:HOM0000048
in many to many orthology relationship with
Paralogy that involves genes from the same species.
within-species paralogous to
RO:HOM0000049
in within-species paralogy relationship with
Paralogy that involves genes from different species.
between-species paralogous to
RO:HOM0000050
The genes have diverged before a speciation event.
in between-species paralogy relationship with
Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
post-displacement
RO:HOM0000051
in postdisplacement relationship with
Peramorphosis that is produced by a delay in the offset of development.
RO:HOM0000052
in hypermorphosis relationship with
Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
synologous to
RO:HOM0000053
in synology relationship with
Orthology that involves functional equivalent genes with retention of the ancestral function.
ECO:0000080
isoorthologous to
RO:HOM0000054
in isoorthology relationship with
Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
iterative paralogy
serial paralogy
tandem paralogous to
RO:HOM0000055
in tandem paralogy relationship with
Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
homoiology
homoplastic tendency
re-awakening
apomorphic tendency
cryptic homology
latent homologous to
underlying synapomorphy
RO:HOM0000057
Used for structures in closely related taxa.
in latent homology relationship with
Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
generative homology
syngenous to
RO:HOM0000058
Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.
in syngeny relationship with
Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
1:1 paralogy
apparent 1:1 orthology
apparent orthologous to
pseudoorthology
RO:HOM0000060
The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.
in apparent orthology relationship with
Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
pseudoparalogous to
RO:HOM0000061
These genes may come out as paralogs in a single-genome analysis.
in pseudoparalogy relationship with
Historical homology that involves functional equivalent genes with retention of the ancestral function.
equivalogous to
RO:HOM0000062
This may include examples of orthology, paralogy and xenology.
in equivalogy relationship with
Historical homology that involves orthologous pairs of interacting molecules in different organisms.
interologous to
RO:HOM0000063
in interology relationship with
Similarity that is characterized by interchangeability in function.
functional similarity
RO:HOM0000065
in functional equivalence relationship with
Biological homology that involves parts of the same organism.
iterative homologous to
RO:HOM0000066
in iterative homology relationship with
Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
duplicate xenology
multiple xenology
paraxenologous to
RO:HOM0000068
in paraxenology relationship with
Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
plerologous to
RO:HOM0000069
This phenomenon is usually due to gene conversion process.
in plerology relationship with
Structural homology that involves structures with the same or similar relative positions.
homotopous to
RO:HOM0000071
Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.
in homotopy relationship with
Biological homology that involves an ectopic structure and the normally positioned structure.
heterotopy
RO:HOM0000072
in homeosis relationship with
Synology that results from allopolyploidy.
homoeologous to
RO:HOM0000073
On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.
in homoeology relationship with
Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
axis paramorphism
RO:HOM0000074
in paramorphism relationship with
Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
regulogous to
RO:HOM0000075
in regulogy relationship with
immediate_transformation_of
http://semanticscience.org/resource/SIO_000658
direct_transformation_of
immediately transforms from
SIO:000658
immediate_transformation_of
provenance_notes
UBPROP:0000004
uberon
UBPROP:0000004
obsolete provenance_notes
true
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
uberon
anteriorly_connected_to
anteriorly connected to
carries
uberon
channel_for
channel for
uberon
channels_from
channels_from
uberon
channels_into
channels_into
x is a conduit for y iff y passes through the lumen of x.
uberon
conduit_for
conduit for
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
uberon
distally_connected_to
distally connected to
uberon
existence_starts_and_ends_during
existence starts and ends during
uberon
extends_fibers_into
extends_fibers_into
has_completed
has_completed
A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).
has_high_plasma_membrane_amount
has_high_plasma_membrane_amount
A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).
has_low_plasma_membrane_amount
has_low_plasma_membrane_amount
has_not_completed
has_not_completed
uberon
has_start
has_start
X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.
uberon
in_central_side_of
in_central_side_of
uberon
in_innermost_side_of
in_innermost_side_of
uberon
in_outermost_side_of
in_outermost_side_of
a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s
add to RO
uberon
indirectly_supplies
indirectly_supplies
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y
lacks_part
lacks_part
uberon
layer_part_of
layer part of
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
uberon
posteriorly_connected_to
posteriorly connected to
uberon
protects
protects
x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
uberon
proximally_connected_to
proximally connected to
c site_of p if c is the bearer of a disposition that is realized by a process that has p as part
capable_of_has_part
uberon
site_of
site_of
uberon
subdivision_of
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
subdivision of
.
uberon
transitively_anteriorly_connected_to
transitively anteriorly connected to
uberon
transitively_connected_to
transitively_connected to
.
uberon
transitively_distally_connected_to
transitively distally connected to
.
uberon
transitively_proximally_connected_to
transitively proximally connected to
uberon
trunk_part_of
trunk_part_of
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
Planosphere [https://planosphere.stowers.org/stage1]
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
Stage 2
Planosphere [https://planosphere.stowers.org/stage2]
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
Stage 3
Planosphere [https://planosphere.stowers.org/stage3]
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
Stage 4
Planosphere [https://planosphere.stowers.org/stage4]
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.
Stage 5
Planosphere [https://planosphere.stowers.org/stage5]
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
Stage 6
Planosphere [https://planosphere.stowers.org/stage6]
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
Stage 7
Planosphere [https://planosphere.stowers.org/stage7]
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
Stage 8
Planosphere [https://planosphere.stowers.org/stage8]
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
Planosphere [https://planosphere.stowers.org/sigmaneoblast]
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
Planosphere [https://planosphere.stowers.org/protonephridialprogenitor]
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
Planosphere [https://planosphere.stowers.org/neuralprogenitor]
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
Planosphere [https://planosphere.stowers.org/zetaneoblast]
An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s).
PMID:25017721
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
Planosphere [https://planosphere.stowers.org/definitivepharynx]
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
Planosphere [https://planosphere.stowers.org/photoreceptorneuron]
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
Planosphere [https://planosphere.stowers.org/category4cell]
Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells.
PMID:25017721
PMID:26457503
myoD+ neoblasts and their post-mitotic, differentiating daughters implicated in the maintenance and regeneration of muscles.
Planarian_Anatomy
PLANA:0000019
muscle progenitor
Planosphere [https://planosphere.stowers.org/muscleprogenitor]
myoD+ neoblasts and their post-mitotic, differentiating daughters implicated in the maintenance and regeneration of muscles.
PMID:25017721
Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct.
Planarian_Anatomy
PLANA:0000020
protonephridia
Planosphere [https://planosphere.stowers.org/protonephridia]
Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct.
OCLC:16809160
PMID:21828097
PMID:26057828
Post-mitotic, ciliated epidermal cells.
Planarian_Anatomy
PLANA:0000022
Category 5 cell
Planosphere [https://planosphere.stowers.org/category5cell]
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 with anatomical feature noted with black indicators.
temporary embryonic pharynx
Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynx]
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
Planosphere [https://planosphere.stowers.org/nervoussystem]
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.
Planarian_Anatomy
PLANA:0000026
definitive gut
Planosphere [https://planosphere.stowers.org/definitivegut]
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:3490491
Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts.
Planarian_Anatomy
PLANA:0000028
Category 2 cell
Planosphere [https://planosphere.stowers.org/category2cell]
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
Planosphere [https://planosphere.stowers.org/primitiveectoderm]
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
Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup.
Planarian_Anatomy
PLANA:0000031
pigment cup cell
Planosphere [https://planosphere.stowers.org/pigmentcupcell]
Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup.
PMID:21852957
PMID:22884275
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
epidermal progenitor
Planosphere [https://planosphere.stowers.org/epidermalprogenitor]
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
A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal.
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
Planosphere [https://planosphere.stowers.org/definitiveepidermis]
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
Planosphere [https://planosphere.stowers.org/category3cell]
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
eye
Planosphere [https://planosphere.stowers.org/eye]
Adult tissues built during organogenesis that are present in juveniles at birth.
Planarian_Anatomy
PLANA:0000037
definitive tissue
Planosphere [https://planosphere.stowers.org/definitivetissue]
Adult tissues built during organogenesis that are present in juveniles at birth.
PMID:28072387
PMID:2888018
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
Planosphere [https://planosphere.stowers.org/gammaneoblast]
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
Planosphere [https://planosphere.stowers.org/schmidteamediterraneadevelopmentalstage]
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
Planosphere [https://planosphere.stowers.org/aboralhemisphere]
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
anterior primary gut branch
Planosphere [https://planosphere.stowers.org/anteriorprimarygutbranch]
The single, central gut branch of the triclad gut anterior to the definitive pharynx.
PMID:3490491
The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head.
brain
Planarian_Anatomy
PLANA:0000044
cephalic ganglia
Planosphere [https://planosphere.stowers.org/cephalicganglia]
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
Planosphere [https://planosphere.stowers.org/circularmusclefiber]
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
Planosphere [https://planosphere.stowers.org/clonogenicneoblast]
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.
Planarian_Anatomy
PLANA:0000047
collecting duct
Planosphere [https://planosphere.stowers.org/collectingduct]
Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis.
PMID:26057828
Body wall muscle fibers arrayed diagonally along the anteroposterior axis.
Planarian_Anatomy
PLANA:0000048
diagonal muscle fiber
Planosphere [https://planosphere.stowers.org/diagonalmusclefiber]
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
Planosphere [https://planosphere.stowers.org/digestivesystem]
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
UBERON:0013765
Planarian_Anatomy
PLANA:0000050
digestive system element
Planosphere [https://planosphere.stowers.org/digestivesystemelement]
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
Planosphere [https://planosphere.stowers.org/directdevelopment]
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
Planosphere [https://planosphere.stowers.org/dispersedcleavage]
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
distal tubule
Planosphere [https://planosphere.stowers.org/distaltubule]
Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells.
PMID:21828097
Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe.
Planarian_Anatomy
PLANA:0000054
dorsal epidermis
Planosphere [https://planosphere.stowers.org/dorsalepidermis]
Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe.
OCLC:16809160
Ciliated epithelial cells along the dorsal midline.
Planarian_Anatomy
PLANA:0000055
dorsal stripe
Planosphere [https://planosphere.stowers.org/dorsalstripe]
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
Planosphere [https://planosphere.stowers.org/ectolecithalembryo]
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
Planosphere [https://planosphere.stowers.org/embryoniccleavage]
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
Planosphere [https://planosphere.stowers.org/embryonicdigestivesystem]
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
Planosphere [https://planosphere.stowers.org/embryonicgutcell]
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
Planosphere [https://planosphere.stowers.org/embryonicwall]
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 muscle
Planosphere [https://planosphere.stowers.org/entericmuscle]
Attachment between the triclad gut and the proximal end of the definitive pharynx.
Planarian_Anatomy
PLANA:0000062
esophagus
Planosphere [https://planosphere.stowers.org/esophagus]
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
UBERON:0000478
Planarian_Anatomy
PLANA:0000063
extraembryonic structure
Planosphere [https://planosphere.stowers.org/extraembryonicstructure]
Terminal structure of protonephridia unit; consists of flame cells.
Planarian_Anatomy
PLANA:0000064
flame bulb
Planosphere [https://planosphere.stowers.org/flamebulb]
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.
Planarian_Anatomy
PLANA:0000065
flame cell
Planosphere [https://planosphere.stowers.org/flamecell]
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
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
Planosphere [https://planosphere.stowers.org/gastrodermis]
The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle.
PMID:3490491
Secretory cells that release digestive enzymes into the lumen of the intestine.
Planarian_Anatomy
PLANA:0000067
goblet cell
Planosphere [https://planosphere.stowers.org/gobletcell]
Secretory cells that release digestive enzymes into the lumen of the intestine.
PMID:3490491
Lumen of embryonic digestive tract, prior to formation of the branched defintive gut.
Planarian_Anatomy
PLANA:0000068
embryonic gut cavity
Planosphere [https://planosphere.stowers.org/embryonicgutcavity]
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
Planosphere [https://planosphere.stowers.org/innerlongitudinalmusclefiber]
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
Planosphere [https://planosphere.stowers.org/intestinalphagocyte]
Absorptive digestive cells that engulf food particles for intracellular digestion.
PMID:3490491
Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers.
Planarian_Anatomy
PLANA:0000071
longitudinal muscle fiber
Planosphere [https://planosphere.stowers.org/longitudinalmusclefiber]
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
Planosphere [https://planosphere.stowers.org/mouth]
The sole point of entry and exit for the Triclad planarian flatworm gut. The mouth is connected to the pharyngeal pouch to allow for exit and re-entry of the 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
Planosphere [https://planosphere.stowers.org/oocyte]
A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons.
Planarian_Anatomy
PLANA:0000075
optic cup
Planosphere [https://planosphere.stowers.org/opticcup]
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
Planosphere [https://planosphere.stowers.org/oralhemisphere]
Stage 3-5 embryo hemisphere centered around the temporary embryonic pharynx.
PMID:28072387
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
UBERON:0000111
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000077
organogenesis
Planosphere [https://planosphere.stowers.org/organogenesis]
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
Planosphere [https://planosphere.stowers.org/outerlongitudinalmusclefiber]
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
parenchymal musculature
Planosphere [https://planosphere.stowers.org/parenchymalmusculature]
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
Planosphere [https://planosphere.stowers.org/peripheralnervoussystem]
An epithelial structure housing the definitive pharynx, connected to the esophagus and mouth.
Planarian_Anatomy
PLANA:0000081
pharyngeal pouch
Planosphere [https://planosphere.stowers.org/pharyngealpouch]
An epithelial structure housing the definitive pharynx, connected to the esophagus and mouth.
OCLC:16809160
The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch.
Planarian_Anatomy
PLANA:0000084
posterior primary gut branch
Planosphere [https://planosphere.stowers.org/posteriorprimarygutbranch]
The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch.
PMID:3490491
Four large phagocytic cells associated with the temporary embryonic pharynx.
Planarian_Anatomy
PLANA:0000085
primitive gut cell
Planosphere [https://planosphere.stowers.org/primitivegutcell]
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
Planosphere [https://planosphere.stowers.org/protosphere]
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
proximal tubule
Planosphere [https://planosphere.stowers.org/proximaltubule]
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
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
Planosphere [https://planosphere.stowers.org/renalsystem]
Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge.
Planarian_Anatomy
PLANA:0000089
secondary gut branch
Planosphere [https://planosphere.stowers.org/secondarygutbranch]
Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge.
PMID:3490491
A mature male germ cell that develops from a spermatid.
CL:0000019
spermatozoa
Planarian_Anatomy
PLANA:0000090
sperm
Planosphere [https://planosphere.stowers.org/sperm]
Generation of a multilayered spherical embryo comprised of temporary extraembryonic tissues and undifferentiated blastomeres.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000091
sphere formation
Planosphere [https://planosphere.stowers.org/sphereformation]
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
Planosphere [https://planosphere.stowers.org/syncytialyolkcell]
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
tertiary gut branch
Planosphere [https://planosphere.stowers.org/tertiarygutbranch]
Gut branches originating from and connected to the secondary gut branches.
PMID:3490491
The process in which the anatomical structures of a tissue are generated and organized.
GO:0048729
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000094
tissue morphogenesis
Planosphere [https://planosphere.stowers.org/tissuemorphogenesis]
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
Planosphere [https://planosphere.stowers.org/trailcell]
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
Planarian_Anatomy
PLANA:0000096
ventral epidermis
Planosphere [https://planosphere.stowers.org/ventralepidermis]
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
Planosphere [https://planosphere.stowers.org/ventralnervecord]
Diploid cell produced by the fusion of sperm cell nucleus and egg cell.
CL:0000365
Planarian_Anatomy
PLANA:0000098
zygote
Planosphere [https://planosphere.stowers.org/zygote]
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
CL:0000540
Planarian_Anatomy
PLANA:0000099
neuron
Planosphere [https://planosphere.stowers.org/neuron]
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
Planosphere [https://planosphere.stowers.org/epithelialcell]
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
Planosphere [https://planosphere.stowers.org/musclecell]
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
Planosphere [https://planosphere.stowers.org/centralnervoussystem]
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
Planosphere [https://planosphere.stowers.org/rhabdite]
A cell that specializes in controlled release of one or more substances.
CL:0000151
Planarian_Anatomy
PLANA:0000105
secretory cell
Planosphere [https://planosphere.stowers.org/secretorycell]
An epithelial cell that has a cillia.
CL:0000067
Planarian_Anatomy
PLANA:0000106
ciliated epithelial cell
Planosphere [https://planosphere.stowers.org/cilaitedepithelialcell]
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
Planosphere [https://planosphere.stowers.org/yolkcell]
An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo.
PMID:27149082
foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the definitive pharynx.
Planarian_Anatomy
PLANA:0000110
definitive pharynx progenitor cell
Planosphere [https://planosphere.stowers.org/definitivepharynxprogenitorcell]
foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the definitive pharynx.
PMID:24737865
PMID:25254346
A term used to describe a developmental process during Schmidtea mediterranea embryogenesis.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000112
Schmidtea mediterranea developmental term
Planosphere [https://planosphere.stowers.org/schmidteamediterraneadevelomentalterm]
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
Planosphere [https://planosphere.stowers.org/tissue]
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
UBERON:0000479
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
Planosphere [https://planosphere.stowers.org/anatomicalsystem]
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
Planosphere [https://planosphere.stowers.org/embryo]
Anatomical structure that is part of an embryo.
UBERON:0002050
Planarian_Anatomy
PLANA:0000117
embryonic structure
Planosphere [https://planosphere.stowers.org/embryonicstructure]
A post-mitotic, terminally differentiated cell type found in planarian embryos, juveniles and/or adult animals.
Planarian_Anatomy
PLANA:0000119
terminally differentiated cell
Planosphere [https://planosphere.stowers.org/terminallydifferentiatedcell]
A cycling neoblast and/or post-mitotic cell that is primed or irreversibly committed to a tissue-specific differentation program
Planarian_Anatomy
PLANA:0000120
progenitor cell
Planosphere [https://planosphere.stowers.org/progenitorcell]
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
Planosphere [https://planosphere.stowers.org/stemcell]
A mature sexual reproductive cell having a single set of unpaired chromosomes.
CL:0000300
Planarian_Anatomy
PLANA:0000122
gamete
Planosphere [https://planosphere.stowers.org/gamete]
A cell of the embryo.
CL:0002321
Planarian_Anatomy
PLANA:0000123
embryonic cell
Planosphere [https://planosphere.stowers.org/embryoniccell]
The sensory system subserving the sense of vision.
UBERON:0002104
Planarian_Anatomy
PLANA:0000124
visual system
Planosphere [https://planosphere.stowers.org/visualsystem]
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
UBERON:0001032
Planarian_Anatomy
PLANA:0000125
sensory system
Planosphere [https://planosphere.stowers.org/sensorysystem]
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
Planosphere [https://planosphere.stowers.org/reproductivesystem]
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CL:0000000
Planarian_Anatomy
PLANA:0000127
definitive cell type
Planosphere [https://planosphere.stowers.org/celltype]
A cell that, by division or terminal differentiation, can give rise to other cell types.
CL:0011115
Planarian_Anatomy
PLANA:0000128
precursor cell
Planosphere [https://planosphere.stowers.org/precursorcell]
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
anatomical structure
Planosphere [https://planosphere.stowers.org/anatomicalstructure]
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
Planosphere [https://planosphere.stowers.org/primordium]
The production of haploid germ cells from diploid precursor cells through meiosis.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000132
gametogenesis
Planosphere [https://planosphere.stowers.org/gametogenesis]
A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
mechanoreceptor
Planarian_Anatomy
PLANA:0000133
mechanoreceptor cell
Planosphere [https://planosphere.stowers.org/mechanoreceptorcell]
Somatic male and female accessory organs and structures of the hermaphroditic reproductive system. Somatic reproductive elements are only made in the Smed sexual biotype and form during juvenile development.
Planarian_Anatomy
PLANA:0000200
somatic reproductive system element
Planosphere [https://planosphere.stowers.org/somaticreproductivesystemelement]
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
Planosphere [https://planosphere.stowers.org/bursalcanal]
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
Planosphere [https://planosphere.stowers.org/gonopore]
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
Planosphere [https://planosphere.stowers.org/ovary]
A gonad containing female germline stem cells which fuel oocyte production. Two ovaries are located ventally, underneath the body wall musculature, immediately posterior to the cephalic ganglia (brain) and adjacent to the ventral nerve cords. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuel formation of the ovaries during juvenile development.
PMID:17376870
Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium.
Planarian_Anatomy
PLANA:0000205
oviduct
Planosphere [https://planosphere.stowers.org/oviduct]
Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium.
PMID:22074376
A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal.
Planarian_Anatomy
PLANA:0000206
penis papilla
Planosphere [https://planosphere.stowers.org/penispapilla]
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
Planosphere [https://planosphere.stowers.org/spermduct]
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
Planosphere [https://planosphere.stowers.org/testis]
A gonad containing male germline stem cells which fuel sperm production. Testes are located dorsolaterally, and are excluded from the head. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuels formation of testes during juvenile development and regeneration.
PMID:19022767
Anatomical structure that is present during embryonic development.
UBERON:0005423
Planarian_Anatomy
PLANA:0000209
developing anatomical structure
Planosphere [https://planosphere.stowers.org/developinganatomicalstructure]
Any of the cell types, tissues, organs or elements that are part of the embryonic digestive system. Examples include the temporary embryonic pharynx, primitive gut cells, embryonic gut cells and the central gut cavity.
Planarian_Anatomy
PLANA:0000210
embryonic digestive system element
Planosphere [https://planosphere.stowers.org/embryonicdigestivesystemelement]
Any of the cell types, tissues, organs or elements that are part of the embryonic digestive system. Examples include the temporary embryonic pharynx, primitive gut cells, embryonic gut cells and the central gut cavity.
PMID:28072387
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
Planosphere [https://planosphere.stowers.org/primitiveectodermcell]
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
Planosphere [https://planosphere.stowers.org/blastomerecompartment]
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
Planosphere [https://planosphere.stowers.org/juvenile]
Products of the reproductive system include gametes, zygotes, yolk cells and egg capsules.
Planarian_Anatomy
PLANA:0000215
reproductive system product
Planosphere [https://planosphere.stowers.org/reproductivesystemproduct]
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
egg capsule
Planosphere [https://planosphere.stowers.org/eggcapsule]
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
Planosphere [https://planosphere.stowers.org/gonad]
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
primordial germ cell
Planosphere [https://planosphere.stowers.org/primordialgermcell]
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
Planosphere [https://planosphere.stowers.org/malegermlinestemcell]
gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm.
PMID:20844018, PMID:19022767, 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
Planosphere [https://planosphere.stowers.org/spermatogonium]
An euploid male germ cell of an early stage of spermatogenesis. In planaria, the gh4+ stem cell daughter exiting the niche undergoes three rounds of transit amplifying division with incomplete cytokinesis prior to transitioning to terminal differentiation.
PMID:27163480, PMID:27330085
A tektin-1+ male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids.
CL:0000017
Planarian_Anatomy
PLANA:0000221
spermatocyte
Planosphere [https://planosphere.stowers.org/spermatocyte]
A tektin-1+ male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids.
PMID:27330085
A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa.
CL:0000018
Planarian_Anatomy
PLANA:0000222
spermatid
Planosphere [https://planosphere.stowers.org/spermatid]
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
Planosphere [https://planosphere.stowers.org/femalegermlinestemcell]
A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes.
PMID:20844018, PMID:19022767
Glands surrounding the copulatory bursa that are required for production of the proteinaceous egg capsule shell and stalk.
Planarian_Anatomy
PLANA:0000224
cement gland
Planosphere [https://planosphere.stowers.org/cementgland]
Glands surrounding the copulatory bursa that are required for production of the proteinaceous egg capsule shell and stalk.
PMID:18942102, PMID:27149082, ASIN:B000M4NK9M, PMID:22074376
A reproductive strategy in which eggs are laid, with most embryonic development occurring outside of the parent.
Schmidtea_mediterranea_Developmental_Terms
PLANA:0000225
oviparity
Planosphere [https://planosphere.stowers.org/oviparity]
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
Planosphere [https://planosphere.stowers.org/cross-fertilization]
Fertilization of an oocyte by sperm from a different individual. Reciprocal exchange of sperm occurs during Schmidtea mediterranea copulation.
PMID:19022767
doi:10.1038/s41559-016-0019
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
Planosphere [https://planosphere.stowers.org/germcell]
A male germ cell is a germ cell that supports male gamete production.
CL:0000015
Planarian_Anatomy
PLANA:0000228
male germ cell
Planosphere [https://planosphere.stowers.org/malegermcell]
Female germ cell is a germ cell that supports female gamete production.
CL:0000021
Planarian_Anatomy
PLANA:0000229
female germ cell
Planosphere [https://planosphere.stowers.org/femalegermcell]
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
Planosphere [https://planosphere.stowers.org/tuba]
A sperm storage organ located immediately posterior to the ovary, at the anterior end of the oviduct. Oocytes exiting the ovary are fertilized in the tuba as they enter the oviduct.
PMID:19022767
PMID:20844018
PMID:22074376
PMID:27149082
Glands surrounding the oviducts which produce yolk cells. Yolk cells deposited into the oviducts travel to the genital atrium where they are packaged, along with one or more zygotes, into developing egg capsules.
Planarian_Anatomy
PLANA:0000231
vitelline gland
Planosphere [https://planosphere.stowers.org/vitellinegland]
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
Planosphere [https://planosphere.stowers.org/copulatoryapparatus]
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.
genital atrium
Planarian_Anatomy
PLANA:0000233
copulatory bursa
Planosphere [https://planosphere.stowers.org/copulatorybursa]
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
Planosphere [https://planosphere.stowers.org/seminalvesicle]
Glandular pouches adjoining the sperm ducts which produce seminal fluid.
PMID:22074376, PMID:19022767
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
Planosphere [https://planosphere.stowers.org/roundspermatid]
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
Planosphere [https://planosphere.stowers.org/elongatespermatid]
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
Planosphere [https://planosphere.stowers.org/oogonialcell]
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
body wall musculature
Planarian_Anatomy
PLANA:0000240
musculature of body wall
Planosphere [https://planosphere.stowers.org/musculatureofbodywall]
Pharynx muscle fibers running anteroposterior (proximal to distal).
Planarian_Anatomy
PLANA:0000241
pharyngeal longitudinal muscle fiber
Planosphere [https://planosphere.stowers.org/pharyngeallongitudinalmusclefiber]
Pharynx muscle fibers running anteroposterior (proximal to distal).
ASIN:B000M4NK9M
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
PLANA:0000242
anatomical cavity
Planosphere [https://planosphere.stowers.org/anatomicalcavity]
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
anatomical entity
Planosphere [https://planosphere.stowers.org/anatomicalentity]
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
UBERON:0000466
VHOG:0001727
immaterial physical anatomical entity
Planarian_Anatomy
PLANA:0000401
immaterial anatomical entity
Planosphere [https://planosphere.stowers.org/immaterialanatomicalentity]
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
anatomical point
Planosphere [https://planosphere.stowers.org/anatomicalpoint]
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
anatomical space
Planosphere [https://planosphere.stowers.org/anatomicalspace]
A anatomical space that is enclosed by a pharynx.
UBERON:0001731
Planarian_Anatomy
PLANA:0000404
cavity of pharynx
Planosphere [https://planosphere.stowers.org/cavityofpharynx]
An anatomical space that is surrounded by a digestive tract.
UBERON:0006909
Planarian_Anatomy
PLANA:0000405
lumen of digestive tract
Planosphere [https://planosphere.stowers.org/lumenofdigestivetract]
The orifice that connects the mouth to the exterior of the body.
UBERON:0000166
Planarian_Anatomy
PLANA:0000406
oral opening
Planosphere [https://planosphere.stowers.org/oralopening]
The space within the parapharyngeal pouch not occupied by the pharynx proper.
Planarian_Anatomy
PLANA:0000407
parapharnygeal pouch cavity
Planosphere [https://planosphere.stowers.org/parapharyngealpouch]
A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.
UBERON:0006984
Planarian_Anatomy
PLANA:0000408
anatomical surface
Planosphere [https://planosphere.stowers.org/anatomicalsurface]
The apical surface of the single layered epithelium epidermis that is in contact with the environment.
Planarian_Anatomy
PLANA:0000409
apical epidermis surface
Planosphere [https://planosphere.stowers.org/apicalepidermissurface]
The basal surface of the epidermial epithelium in contact with the basal lamina.
Planarian_Anatomy
PLANA:0000410
basal epidermis surface
Planosphere [https://planosphere.stowers.org/basalepidermissurface]
The surface of the gut lumen in contact with ingested food.
Planarian_Anatomy
PLANA:0000411
lumen gut surface
Planosphere [https://planosphere.stowers.org/lumengutsurface]
The epithelial surface lining the interior of the pharynx, facing the lumen.
Planarian_Anatomy
PLANA:0000412
pharynx lumen epithelial surface
Planosphere [https://planosphere.stowers.org/pharynxlumenepithelialsurface]
Epithelial surface covering the outside of the pharynx.
Planarian_Anatomy
PLANA:0000413
pharynx outer epithelial surface
Planosphere [https://planosphere.stowers.org/pharynxouterepithelialsurface]
The surface of the parapharyngeal pouch facing the pharynx.
Planarian_Anatomy
PLANA:0000414
parapharyngeal pouch surface
Planosphere [https://planosphere.stowers.org/parapharyngealpouchsurface]
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
UBERON:0000015
Planarian_Anatomy
PLANA:0000415
non-material anatomical boundary
Planosphere [https://planosphere.stowers.org/non-materialanatomicalboundary]
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
organism subdivision
Planosphere [https://planosphere.stowers.org/organismsubdivision]
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
Planosphere [https://planosphere.stowers.org/definitiveorganismsubdivision]
The head is the anterior-most division of the body [GO].
UBERON:0000033
Planarian_Anatomy
PLANA:0000418
head
Planosphere [https://planosphere.stowers.org/head]
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
neck
Planosphere [https://planosphere.stowers.org/neck]
Region of the animal lateral to and surrounding the pharyngeal pouch.
Planarian_Anatomy
PLANA:0000420
parapharyngeal region
Planosphere [https://planosphere.stowers.org/parapharyngealregion]
Caudal region, beginning at the mouth and ending at posterior pole.
Planarian_Anatomy
PLANA:0000421
tail
Planosphere [https://planosphere.stowers.org/tail]
Medial region of the tail; the parenchymal space between the posterior primary gut branches.
Planarian_Anatomy
PLANA:0000422
tail stripe
Planosphere [https://planosphere.stowers.org/tailstripe]
Anatomical structure which is a subdivision of a whole developing/ embryonic organism, consisting of components of multiple anatomical systems.
Planarian_Anatomy
PLANA:0000423
embryonic organism subdivision
Planosphere [https://planosphere.stowers.org/embryonicorganismsubdivision]
Anatomical entity that has mass.
UBERON:0000465
Planarian_Anatomy
PLANA:0000424
material anatomical entity
Planosphere [https://planosphere.stowers.org/materialanatomicalentity]
Anatomical structure present in juvenile and adult planaria.
Planarian_Anatomy
PLANA:0000425
definitive anatomical structure
Planosphere [https://planosphere.stowers.org/definitiveanatomicalstructure]
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
acellular anatomical structure
Planosphere [https://planosphere.stowers.org/acellularanatomicalstructure]
An anatomical structure that has more than one cell as a part.
UBERON:0010000
Planarian_Anatomy
PLANA:0000427
multicellular anatomical structure
Planosphere [https://planosphere.stowers.org/multicellularanatomicalstructure]
Total musculature of the planarian body.
Planarian_Anatomy
PLANA:0000428
musculature system
Planosphere [https://planosphere.stowers.org/musculaturesystem]
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
Planosphere [https://planosphere.stowers.org/neoblastcompartment]
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
Planosphere [https://planosphere.stowers.org/epithelialcellcomponent]
Anatomical structure that performs a specific function or group of functions.
UBERON:0000062
Planarian_Anatomy
PLANA:0000431
organ
Planosphere [https://planosphere.stowers.org/organ]
An anatomical structure that is undergoing regeneration.
UBERON:0007567
Planarian_Anatomy
PLANA:0000432
regenerating anatomical structure
Planosphere [https://planosphere.stowers.org/regeneratinganatomicalstructure]
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
Planosphere [https://planosphere.stowers.org/cellularcomponent]
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
Planosphere [https://planosphere.stowers.org/opticchiasma]
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
Planosphere [https://planosphere.stowers.org/anteriorcommissure]
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
Planosphere [https://planosphere.stowers.org/lateralbranches]
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:9493832, PMID:4452894, PMID:18466009, PMID:27612384
A cell that performs a sensory function.
Planarian_Anatomy
PLANA:0000462
sensory cell
Planosphere [https://planosphere.stowers.org/sensorycell]
Neurons that express choline acetyltransferase.
Planarian_Anatomy
PLANA:0000463
cholinergic neuron
Planosphere [https://planosphere.stowers.org/cholinergricneuron]
Neurons that express choline acetyltransferase.
PMID:20338223
Neurons that express glutamine decarboxylase.
Planarian_Anatomy
PLANA:0000464
GABAergic neuron
Planosphere [https://planosphere.stowers.org/gabaergicneuron]
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
Planosphere [https://planosphere.stowers.org/pharynxnerveplexus]
Plexus of nerves located just between the definitive epidermis and the body wall musculature.
Planarian_Anatomy
PLANA:0000466
subepidermal nerve plexus
Planosphere [https://planosphere.stowers.org/subepidermalnerveplexus]
Plexus of nerves that innervate the body wall muscles.
Planarian_Anatomy
PLANA:0000467
submuscular nerve plexus
Planosphere [https://planosphere.stowers.org/submuscularplexus]
A thin net of single nerve fibers located around the gut.
Planarian_Anatomy
PLANA:0000468
gastrodermal plexus
Planosphere [https://planosphere.stowers.org/gastrodermalplexus]
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
Planosphere [https://planosphere.stowers.org/neuropil]
A cluster of neurites that is part of a nervous system and forms a network of dendrites and axons where synapses are present and in which neuronal somata do not occur.
PMID:27612384
Heavily ciliated epidermal cells covering the outer surface of the pharynx shaft. These are "insunk" epidermal cells in which the nuclei reside behind the layers of longitudinal and circumferential muscles and the epithelial cell body sends out a ciliated projection to the surface to cover and encase the shaft.
Planarian_Anatomy
PLANA:0000472
outer pharyngeal epithelium
Planosphere [https://planosphere.stowers.org/outerpharyngealepithelium]
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
Planosphere [https://planosphere.stowers.org/outerpharyngealcircularmusclefiber]
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
Planosphere [https://planosphere.stowers.org/innerpharyngealcircularmusclefiber]
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
Planosphere [https://planosphere.stowers.org/innerpharyngeallongitudinalmusclefiber]
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
Planosphere [https://planosphere.stowers.org/outerpharyngeallongitudinalmusclefiber]
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
Planosphere [https://planosphere.stowers.org/pharyngealradialmusclefiber]
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
Planosphere [https://planosphere.stowers.org/musculatureofpharynx]
Ring of the pharynx nerve plexus that is proximal to the lumen.
Planarian_Anatomy
PLANA:0000479
inner pharynx nerve plexus
Planosphere [https://planosphere.stowers.org/innerpharynxnerveplexus]
Ring of the pharynx nerve plexus that is proximal to the exterior surface.
Planarian_Anatomy
PLANA:0000480
outer pharynx nerve plexus
Planosphere [https://planosphere.stowers.org/outerpharynxnerveplexus]
Neurons that express the neurotransmitter serotonin.
Planarian_Anatomy
PLANA:0000481
serotonergic neuron
Planosphere [https://planosphere.stowers.org/serotonergicneuron]
Neurons that express the neurotransmitter serotonin.
PMID:17624455
A neuron that expresses the neurotransmitter dopamine.
Planarian_Anatomy
PLANA:0000482
dopaminergic neuron
Planosphere [https://planosphere.stowers.org/dopaminergicneuron]
A neuron that expresses the neurotransmitter dopamine.
PMID:17565705
Neurons that express the biogenic amine octopamine.
Planarian_Anatomy
PLANA:0000483
octopaminergic neuron
Planosphere [https://planosphere.stowers.org/octopaminergicneuron]
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
Planosphere [https://planosphere.stowers.org/secretorysystem]
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
Planosphere [https://planosphere.stowers.org/glandcell]
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
Planosphere [https://planosphere.stowers.org/secretorypore]
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 dorsal/ ventral border of the animal. May also be referred to as eosinophilic gland cells.
Planarian_Anatomy
PLANA:0000487
acidophilic gland cell
Planosphere [https://planosphere.stowers.org/acidophilicglandcell]
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 dorsal/ ventral border of the animal. May also be referred to as eosinophilic gland cells.
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
Planosphere [https://planosphere.stowers.org/basophilicglandcell]
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
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
anatomical line
Planosphere [https://planosphere.stowers.org/anatomicalline]
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.
anatomical plane
Planosphere [https://planosphere.stowers.org/anatomicalplane]
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
Planosphere [https://planosphere.stowers.org/planeofautotomy]
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
Planosphere [https://planosphere.stowers.org/nerveplexus]
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
Planosphere [https://planosphere.stowers.org/nervoussystemcommissure]
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
Planosphere [https://planosphere.stowers.org/braincommissure]
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
Planosphere [https://planosphere.stowers.org/blastema]
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
UBERON:0000015
Planarian_Anatomy
PLANA:0000496
anatomical boundary
Planosphere [https://planosphere.stowers.org/anatomicalboundary]
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
anatomical junction
Planosphere [https://planosphere.stowers.org/anatomicaljunction]
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
UBERON:0013701
Planarian_Anatomy
PLANA:0000498
main body axis
Planosphere [https://planosphere.stowers.org/mainbodyaxis]
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
Planosphere [https://planosphere.stowers.org/cell]
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
Planosphere [https://planosphere.stowers.org/cellpart]
A prolongation or process extending from a cell.
GO_0042995
Planarian_Anatomy
PLANA:0000501
cell projection
Planosphere [https://planosphere.stowers.org/cellprojection]
A cell projection supported by an assembly of actin filaments.
GO_0098858
Planarian_Anatomy
PLANA:0000502
actin-based cell projection
Planosphere [https://planosphere.stowers.org/actin-basedcellprojection]
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
Planosphere [https://planosphere.stowers.org/cilium]
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
Planosphere [https://planosphere.stowers.org/microvillus]
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
Planosphere [https://planosphere.stowers.org/cell-cellcontactzone]
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
Planosphere [https://planosphere.stowers.org/celljunction]
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
Planosphere [https://planosphere.stowers.org/cell-celljunction]
The attachment of one cell to another cell via adhesion molecules.
GO:0098609
Planarian_Anatomy
PLANA:0000508
cell-cell adhesion
Planosphere [https://planosphere.stowers.org/cell-celladhesion]
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
Planosphere [https://planosphere.stowers.org/intracellularpart]
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
Planosphere [https://planosphere.stowers.org/cytoplasm]
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
Planosphere [https://planosphere.stowers.org/acidophiliccytoplasm]
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
Planosphere [https://planosphere.stowers.org/basophiliccytoplasm]
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
Planosphere [https://planosphere.stowers.org/cytoplasmicpart]
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
Planosphere [https://planosphere.stowers.org/cytoplasmicvesiclepart]
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
Planosphere [https://planosphere.stowers.org/vacuole]
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
Planosphere [https://planosphere.stowers.org/cytoskeletonorganization]
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
Planosphere [https://planosphere.stowers.org/intracellularorganelle]
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
Planosphere [https://planosphere.stowers.org/intracellularnon-membrane-boundedorganelle]
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
Planosphere [https://planosphere.stowers.org/membrane]
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
Planosphere [https://planosphere.stowers.org/boundingmembraneoforganelle]
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
Planosphere [https://planosphere.stowers.org/membranepart]
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
Planosphere [https://planosphere.stowers.org/plasmamembranepart]
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
Planosphere [https://planosphere.stowers.org/organellemembrane]
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
Planosphere [https://planosphere.stowers.org/organelle]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
GO:0043227
Planarian_Anatomy
PLANA:0000526
membrane-bounded organelle
Planosphere [https://planosphere.stowers.org/membrane-boundedorganelle]
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
Planosphere [https://planosphere.stowers.org/intracellularmembrane-boundedorganelle]
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
Planosphere [https://planosphere.stowers.org/golgiapparatus]
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
Planosphere [https://planosphere.stowers.org/nucleus]
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
Planosphere [https://planosphere.stowers.org/secretoryvesicle]
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
Planosphere [https://planosphere.stowers.org/non-membrane-boundedorganelle]
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
Planosphere [https://planosphere.stowers.org/nuclearpart]
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
Planosphere [https://planosphere.stowers.org/nucleolus]
The ordered and organized complex of DNA, protein (histones), and sometimes RNA, that forms the chromosome.
GO_0000785
Planarian_Anatomy
PLANA:0000534
chromatin
Planosphere [https://planosphere.stowers.org/chromatin]
A compact and highly condensed form of chromatin.
GO_0000792
Planarian_Anatomy
PLANA:0000535
heterochromatin
Planosphere [https://planosphere.stowers.org/heterochromatin]
A dispersed and relatively uncompacted form of chromatin.
GO_0000791
Planarian_Anatomy
PLANA:0000536
euchromatin
Planosphere [https://planosphere.stowers.org/euchromatin]
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
Planosphere [https://planosphere.stowers.org/ribosome]
A group of axons linking two or more neuropils and having a common origin, termination
UBERON:0001018
Planarian_Anatomy
PLANA:0000538
axon tract
Planosphere [https://planosphere.stowers.org/axontract]
A cell whose function is determined by its response to an electric signal.
CL:0000393
Planarian_Anatomy
PLANA:0000539
electrically responsive cell
Planosphere [https://planosphere.stowers.org/electricallyresponsivecell]
A cell that initiates an electrical signal and passes that signal to another cell.
CL:0000404
Planarian_Anatomy
PLANA:0000540
electrically signaling cell
Planosphere [https://planosphere.stowers.org/electricallysignalingcell]
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
Planosphere [https://planosphere.stowers.org/nerve]
A cell that is part of the nervous system.
tmeehan
2010-09-15T01:34:57Z
CALOHA:TS-2040
CL:0002319
FMA:70333
Planarian_Anatomy
PLANA:0000542
neural cell
Planosphere [https://planosphere.stowers.org/neuralcell]
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
CARO:0001001
Planarian_Anatomy
PLANA:0000543
neuron projection bundle
Planosphere [https://planosphere.stowers.org/neuronprojectionbundle]
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
UBERON_0000073
part of nervous system
Planarian_Anatomy
PLANA:0000544
regional part of nervous system
Planosphere [https://planosphere.stowers.org/regionalpartofnervoussystem]
A neuron which conveys sensory information centrally from the periphery.
CL:0000526
FMA:87653
input neuron
Planarian_Anatomy
PLANA:0000545
afferent neuron
Planosphere [https://planosphere.stowers.org/afferentneuron]
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
Planosphere [https://planosphere.stowers.org/bipolarneuron]
A neuron that has an axon which crosses the midline.
CL:0000678
Planarian_Anatomy
PLANA:0000547
commissural neuron
Planosphere [https://planosphere.stowers.org/commissuralneuron]
A neuron which sends impulses peripherally to activate muscles or secretory cells.
CL:0000527
output neuron
Planarian_Anatomy
PLANA:0000548
efferent neuron
Planosphere [https://planosphere.stowers.org/efferentneuron]
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
Planosphere [https://planosphere.stowers.org/excitatorymotorneuron]
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
Planosphere [https://planosphere.stowers.org/interneuron]
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
Planosphere [https://planosphere.stowers.org/sensoryneuron]
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
Planosphere [https://planosphere.stowers.org/motorneuron]
Neuronal cells which synthesize, store and release neurohormones.
CL:0000381
FBbt:00005130
Planarian_Anatomy
PLANA:0000556
neurosecretory neuron
Planosphere [https://planosphere.stowers.org/neurosecretoryneuron]
A neuron that is part of nerve found outside the central nervous system.
CL:0000111
FMA:84664
Planarian_Anatomy
PLANA:0000557
peripheral neuron
Planosphere [https://planosphere.stowers.org/peripheralneuron]
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
Planosphere [https://planosphere.stowers.org/sympatheticneuron]
Neuron with one neurite that extends from the cell body.
CL:0000106
FMA:67278
Planarian_Anatomy
PLANA:0000559
unipolar neuron
Planosphere [https://planosphere.stowers.org/unipolarneuron]
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
Planosphere [https://planosphere.stowers.org/multipolarneuron]
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)
Planosphere [https://planosphere.stowers.org/neuronassociatedcell]
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
Planosphere [https://planosphere.stowers.org/centralnervoussystemneuron]
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
Planosphere [https://planosphere.stowers.org/peripheralnervoussystemneuron]
A neruon whose cell body is within an autonomic ganglion.
CL:0000107
FMA:80121
Planarian_Anatomy
PLANA:0000565
autonomic neuron
Planosphere [https://planosphere.stowers.org/autonomicneuron]
Neuron that is part of the enteric nervous system.
haendel
2012-06-28T08:20:31Z
CL:0007011
Planarian_Anatomy
PLANA:0000566
enteric neuron
Planosphere [https://planosphere.stowers.org/entericneuron]
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
basal lamina of epithelium
Planosphere [https://planosphere.stowers.org/basallaminaofepithelium]
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
sexually mature adult
Planosphere [https://planosphere.stowers.org/sexuallymatureadult]
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
asexual adult
Planosphere [https://planosphere.stowers.org/asexualadult]
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
PLANA:0004506
testis somatic gonadal cell
Planosphere [https://planosphere.stowers.org/testissomaticgonadalcell]
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
PLANA:0004507
ovarian somatic gonadal cell
Planosphere [https://planosphere.stowers.org/ovariansomaticgonadalcell]
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 between the oral and aboral poles 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.
Erin Davies
2017-07-27T14:55:23Z
oral-aboral axis
Planosphere [https://planosphere.stowers.org/oral-aboralaxis]
Axis that runs between the oral and aboral poles 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
The apical surface of the single layered primitive ectoderm that is in contact with the environment.
Erin Davies
2017-07-27T16:25:14Z
primitive ectoderm surface
Planosphere [https://planosphere.stowers.org/primitiveectodermsurface]
The apical surface of the single layered primitive ectoderm that is in contact with the environment.
OCLC:20423827
OCLC:464776945
OCLC:82522822
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
primtive gut surface
Planosphere [https://planosphere.stowers.org/primitivegutsurface]
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
embryonic gut cell surface
Planosphere [https://planosphere.stowers.org/embryonicgutcellsurface]
The surface of phagocytic embryonic gut cells in contact with ingested yolk cells.
PMID:28072387
The epithelial surface lining the interior of the temporary embryonic pharynx, facing the lumen.
Erin Davies
2017-07-27T16:26:16Z
temporary embryonic pharynx lumen epithelial surface
Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxlumenepithelialsurface]
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
blastomere
Planosphere [https://planosphere.stowers.org/blastomere]
An undifferentiated, cycling embryonic cell in Stage 1-5 embryos that expresses piwi-1, numerous adult asexual neoblast enriched genes, and early embryo enriched genes.
PMID:28072387
Erin Davies
2017-07-27T20:00:04Z
extraembryonic cell
Planosphere [https://planosphere.stowers.org/extraembryoniccell]
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
temporary embryonic pharynx neuronal cell
Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxneuronalcell]
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
temporary embryonic pharynx radial muscle cell
Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxradialmusclecell]
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
temporary embryonic pharynx epithelial cell
Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxepithelialcell]
foxA1+ epithelial cell contained in the temporary embryonic pharynx.
PMID:28072387, PMID:20100474
A muscle fiber that connects and runs perpendicular to a circular muscle fiber surrounding the luminal opening of the temporary embryonic pharynx.
Erin Davies
2017-07-27T20:11:31Z
temporary embryonic pharynx radial muscle fiber
Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxradialmusclefiber]
A muscle fiber that connects and runs perpendicular to a circular muscle fiber surrounding the luminal opening of the temporary embryonic pharynx.
PMID:16932928
A muscle fiber that encircles the luminal opening of the temporary embryonic pharynx.
Erin Davies
2017-07-27T20:43:07Z
temporary embryonic pharynx circular muscle fiber
Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxcircularmusclefiber]
A muscle fiber that encircles the luminal opening of the temporary embryonic pharynx.
PMID:16932928
Differentiated muscle cell present in a circular muscle fiber of the temporary embryonic pharynx.
Erin Davies
2017-07-27T20:43:26Z
temporary embryonic pharynx circular muscle cell
Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxcircularmusclecell]
Differentiated muscle cell present in a circular muscle fiber of the temporary embryonic pharynx.
PMID:16932928
Erin Davies
2017-08-28T18:16:26Z
sexual tail
Planosphere [https://planosphere.stowers.org/sexualtail]
Erin Davies
2017-08-28T18:16:47Z
asexual tail
Planosphere [https://planosphere.stowers.org/asexualtail]
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
copulatory region
Planosphere [https://planosphere.stowers.org/copulatoryregion]
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
pharyngeal epithelium
Planosphere [https://planosphere.stowers.org/pharyngealepithelium]
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
integumental system
Planosphere [https://planosphere.stowers.org/integumentalsystem]
Anatomical space enclosed by the oviduct epithelium.
Erin Davies
2017-09-01T17:52:16Z
Planarian_Anatomy
oviduct lumen
Planosphere [https://planosphere.stowers.org/oviductlumen]
Anatomical space enclosed by the sperm duct epithelium.
Erin Davies
2017-09-02T22:26:19Z
Planarian_Anatomy
sperm duct lumen
Planosphere [https://planosphere.stowers.org/spermductlumen]
Ciliated epithelium lining the oviduct.
Erin Davies
2017-09-02T22:35:10Z
Planarian_Anatomy
oviduct epithelium
Planosphere [https://planosphere.stowers.org/oviductepithelium]
Ciliated epithelium lining the sperm duct.
Erin Davies
2017-09-02T22:43:04Z
Planarian_Anatomy
sperm duct epithelium
Planosphere [https://planosphere.stowers.org/spermductepithelium]
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
tuba lumen
Planosphere [https://planosphere.stowers.org/tubalumen]
Anatomical plane which divides the body into superior and inferior parts. It always contains the midline and is perpendicular to the coronal and sagittal planes. It is also known as the horizontal plane, axial plane, or transaxial plane.
Steph Nowotarski
2017-04-26T19:31:44Z
Planarian_Anatomy
PLANA:0007501
transverse plane
Planosphere [https://planosphere.stowers.org/transverseplane]
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
coronal plane
Planosphere [https://planosphere.stowers.org/coronalplane]
Anatomical plane which divides the body into right and left parts. This plane passes through the midline.
Steph Nowotarski
2017-04-26T19:32:33Z
Planarian_Anatomy
PLANA:0007503
sagittal plane
Planosphere [https://planosphere.stowers.org/sagittalplane]
Position along the dorsoventral axis that is above the anteroposterior axis, or closer to the back.
Steph Nowotarski
2017-04-27T16:38:48Z
Planarian_Anatomy
PLANA:0007504
dorsal
Planosphere [https://planosphere.stowers.org/dorsal]
Position along the dorsoventral axis that is below the anteroposterior axis, or closer to the belly.
Steph Nowotarski
2017-04-27T16:38:59Z
Planarian_Anatomy
PLANA:0007505
ventral
Planosphere [https://planosphere.stowers.org/ventral]
Position along the anteroposterior axis closer to the head rather than the tail.
Steph Nowotarski
2017-04-27T16:39:34Z
Planarian_Anatomy
PLANA:0007506
anterior
Planosphere [https://planosphere.stowers.org/anterior]
Position along the anteroposterior axis that is closer to the tail rather than the head.
Steph Nowotarski
2017-04-27T16:39:59Z
Planarian_Anatomy
PLANA:0007507
posterior
Planosphere [https://planosphere.stowers.org/posterior]
Anatomical structures that exist outside of cells; non-cellular.
Steph Nowotarski
2017-05-03T13:48:26Z
WBbt:0005732
Planarian_Anatomy
PLANA:0007508
extracellular component
Planosphere [https://planosphere.stowers.org/extracellularcomponent]
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
Planosphere [https://planosphere.stowers.org/plasmamembrane]
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
Planosphere [https://planosphere.stowers.org/extracellularorganelle]
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
Planosphere [https://planosphere.stowers.org/mitochondrion]
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
Planosphere [https://planosphere.stowers.org/endoplasmicreticulum]
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
Planosphere [https://planosphere.stowers.org/roughendoplasmicreticulum]
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
Planosphere [https://planosphere.stowers.org/smoothendoplasmicreticulum]
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
Planosphere [https://planosphere.stowers.org/nuclearpore]
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
Planosphere [https://planosphere.stowers.org/lysosome]
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.
Steph Nowotarski
2017-05-04T17:59:38Z
Planarian_Anatomy
PLANA:0007519
anteroposterior axis
Planosphere [https://planosphere.stowers.org/anteroposterioraxis]
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.
Steph Nowotarski
2017-05-04T18:00:07Z
Planarian_Anatomy
PLANA:0007520
dorsoventral axis
Planosphere [https://planosphere.stowers.org/dorsoventralaxis]
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.
Steph Nowotarski
2017-05-04T18:00:51Z
Planarian_Anatomy
PLANA:0007521
dextro-sinister axis
Planosphere [https://planosphere.stowers.org/dextro-sinisteraxis]
Axis that runs from the center of the body, starting at the anteroposterior axis and out the the lateral (left, right, dorsal or ventral) surface of the animal.
Steph Nowotarski
2017-05-04T18:01:37Z
Planarian_Anatomy
PLANA:0007522
mediolateral axis
Planosphere [https://planosphere.stowers.org/mediolateralaxis]
Axis that starts at the distal (close to the body) part of an appendage and runs to the proximal (farthest from the body) part of an appendage.
Steph Nowotarski
2017-05-04T18:02:04Z
Planarian_Anatomy
PLANA:0007523
proximodistal axis
Planosphere [https://planosphere.stowers.org/proximodistralaxis]
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
Planosphere [https://planosphere.stowers.org/anteriorpole]
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
Planosphere [https://planosphere.stowers.org/posteriorpole]
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
Planosphere [https://planosphere.stowers.org/glialcell]
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
Planosphere [https://planosphere.stowers.org/ganglion]
Region of the sexual biotype animal lateral to and surrounding the pharyngeal pouch.
Steph Nowotarski
2017-07-24T18:38:16Z
Planarian_Anatomy
PLANA:0007530
sexual parapharyngeal region
Planosphere [https://planosphere.stowers.org/sexualparapharyngealregion]
Region of the asexual biotype animal lateral to and surrounding the pharyngeal pouch.
Steph Nowotarski
2017-07-24T18:38:28Z
Planarian_Anatomy
PLANA:0007531
asexual parapharyngeal region
Planosphere [https://planosphere.stowers.org/asexualparapharyngealregion]
Region of the asexual biotype animal between the posterior end of the cephalic ganglia and the anterior end of the definitive pharynx.
Steph Nowotarski
2017-07-24T18:41:25Z
Planarian_Anatomy
PLANA:0007532
asexual neck
Planosphere [https://planosphere.stowers.org/asexualneck]
Region of the juvenile or adult sexual biotype animal between the posterior end of the cephalic ganglia and the anterior end of the definitive pharynx.
Steph Nowotarski
2017-07-24T18:41:33Z
Planarian_Anatomy
PLANA:0007533
sexual neck
Planosphere [https://planosphere.stowers.org/sexualneck]
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
Planosphere [https://planosphere.stowers.org/innerpharyngealepithelium]
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
Planosphere [https://planosphere.stowers.org/pharyngealcircularmusclefiber]
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
brain
Planosphere [https://planosphere.stowers.org/brain]
Specialized epithelial cells located along the body margin lining the dorsoventral margin. Adhesion glands are comprised of three cell types, the viscid and relasing gland cells which penetrate through an epithelial anchor cell and terminate at the epithelial surface.
Steph Nowotarski
2017-09-05T14:32:51Z
Planarian_Anatomy
adhesion glands
Planosphere [https://planosphere.stowers.org/adhesionglands]
Specialized epithelial cells located along the body margin lining the dorsoventral margin. Adhesion glands are comprised of three cell types, the viscid and relasing 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
anchor cell
Planosphere [https://planosphere.stowers.org/anchorcell]
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
viscid gland cell
Planosphere [https://planosphere.stowers.org/viscidglandcell]
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
releasing gland cell
Planosphere [https://planosphere.stowers.org/releasingglandcell]
Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance.
OCLC:16809160
PMID: 20865784