Planarian_Anatomy 1.2 CARO part_of NCBITaxon:79327; CL part_of NCBITaxon:79327 definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> editor note curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from term replaced by Relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y Chris Mungall is indirect form of If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. external_definition Notes on the homology status of this class. homology_notes has_relational_adjective Notes on the how instances of this class vary across species. taxon_notes Notes on how similar or equivalent classes are represented in other ontologies. external_ontology_notes IAO:0100001 synonym typically used in the context of human anatomy IAO:0100001 synonym typically used in the context of vertebrate anatomy IAO:0100001 namespace-id-rule IAO:0100001 synonym_type_property has_alternative_id has_broad_synonym IAO:0100001 database_cross_reference IAO:0100001 has_exact_synonym IAO:0100001 has_narrow_synonym IAO:0100001 has_obo_format_version IAO:0100001 has_obo_namespace IAO:0100001 has_related_synonym IAO:0100001 has_scope IAO:0100001 has_synonym_type in_subset IAO:0100001 shorthand Sofia Robb 2017-07-26T18:19:59Z treat-xrefs-as-genus-differentia Sofia Robb 2017-09-11T16:38:22Z depiction is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 external spatial uberon part_of part_of part of part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 external spatial has_part has_part has part has part preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:0000096 rostral_to spatial anterior_to anterior_to anterior to x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 spatial dorsal_to dorsal_to dorsal to x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:0000099 caudal to spatial posterior_to posterior_to posterior to x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm caudal to x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 spatial ventral_to ventral_to ventral to x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole. BSPO:0000104 spatial approximately_perpendicular_to approximately_perpendicular_to approximately perpendicular to Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole. BSPO:cjm On the same side as. For example, the left arm is ipsilateral to the left leg. BSPO:0000105 spatial ipsilateral_to ipsilateral_to ipsilateral to On the same side as. For example, the left arm is ipsilateral to the left leg. BSPO:cjm Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 spatial deep_to deep_to deep to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:cjm Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 spatial superficial_to superficial_to superficial to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:cjm Direcly opposite to. i.e. on the opposite side through the axis. BSPO:0000113 spatial opposite_to opposite_to opposite to Direcly opposite to. i.e. on the opposite side through the axis. BSPO:cjm X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure BSPO:0000126 spatial in_lateral_side_of in_lateral_side_of in lateral side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure UBERON:cjm This relation holds when both the deep_to and ajdacent_to relationship similarly hold. x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:0001107 spatial uberon immediately_deep_to immediately_deep_to immediately deep to immediately_deep_to This relation holds when both the deep_to and ajdacent_to relationship similarly hold. x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:curators BSPO:0015001 spatial finishes_axis finishes_axis A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. If s finishes axis x, and x has end point p, then x overlaps p finishes axis crossing at right angles BSPO:0015005 spatial orthogonal_to orthogonal_to orthogonal to crossing at right angles BSPO:cjm Intersects at two points. BSPO:0015006 spatial passes_through passes_through passes through Intersects at two points. BSPO:cjm BSPO:0015007 spatial starts_axis starts_axis A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. . If s starts axis x, and x has start point p, then x overlaps p starts axis BSPO:0015008 spatial surface_of surface_of placeholder. used for relation between anatomical surface and an anatomical side. surface of x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:0015014 spatial uberon immediately_superficial_to immediately_superficial_to immediately superficial to immediately_superficial_to x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:curators This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about feature restricted to Steph Nowotarski 2017-07-24T20:21:09Z Planarian_Relationship specific_to specific to participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains contains A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. dos 2017-07-19T17:30:36Z has ligand dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y x overlaps y iff they have some part in common. http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 spatial overlaps overlaps "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF [] overlaps overlaps true x overlaps y iff they have some part in common. BSPO:cjm A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan This is the transitive form of the develops from relation develops from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan develops into process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of true x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in actively participates in 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent obsolete has active participant true A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. x adjacent_to y iff: x and y share a boundary This relation acts as a join point with BSPO Chris Mungall RO:0002220 spatial uberon adjacent_to adjacent_to adjacent to adjacent to adjacent_to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall has developmental contribution from inverse of has developmental contribution from Chris Mungall developmentally contributes to Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within Inverse of developmentally preceded by Chris Mungall developmentally succeeded by cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of involved in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by inverse of has input Chris Mungall input of x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y Chris Mungall has potential to developmentally contribute to x has the potential to develop into y iff x develops into y or if x is capable of developing into y Chris Mungall has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y Chris Mungall has potential to directly develop into inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. Chris Mungall molecularly controls activity directly regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall inhibits molecularly decreases activity of activity directly negatively regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall activates molecularly increases activity of activity directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true Chris Mungall is kinase activity Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between structure and stage x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). Chris Mungall RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entities Chris Mungall causally influenced by (material entity to material entity) causally influenced by Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall causally influences (material entity to material entity) causally influences Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel produced by Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. spatial parallel_to parallel to x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. BSPO:curators entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] An entity that has temporal parts and that happens, unfolds or develops through time. occurrent A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity immaterial entity A 2D surface of an anatomical continuant. FMA:24137 surface spatial BSPO:0000005 to be merged into CARO anatomical surface A 2D surface of an anatomical continuant. BSPO:cjm A straight line through space, intersecting an anatomical entity. http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG spatial BSPO:0000010 Axis directions are defined in terms of axes. anatomical axis A straight line through space, intersecting an anatomical entity. BSPO:cjm An axis that extends through an organism from head end to opposite end of body or tail. A-P axis AP axis anteroposterior axis cephalocaudal axis craniocaudal axis rostral/caudal rostrocaudal axis spatial longitudinal axis BSPO:0000013 In sponges, AP is used to indicate the direction of movement [in larval stage] (as it is in other metazoans that move, e.g., the basal bilaterians). [PM] anterior-posterior axis An axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm cephalocaudal axis http://en.wikipedia.org/wiki/Anatomical_terms_of_location craniocaudal axis rostral/caudal rostrocaudal axis An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure. apical/basal spatial longitudinal axis BSPO:0000014 apical-basal axis relative to substrate An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure. BSPO:mah An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal). proximal/distal proximodistal spatial BSPO:0000015 In some communities, proximal and distal are used when specifying the position of parts of elements that are contained within the body, such as gill arches or vertebral spines. In these cases, use of the classes medial-lateral axis or medial-external axis are more appropriate. proximal-distal axis An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal). BSPO:curators http://en.wikipedia.org/wiki/Anatomical_terms_of_location An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body. D-V axis DV axis dorsoventral axis anterior-posterior axis spatial BSPO:0000016 dorsal-ventral axis An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body. BSPO:curators anterior-posterior axis An axis that bisects an organism from left to right sides of body, through a sagittal plane. L-R axis LR axis R-L axis RL axis dextro-sinister axis left to right axis right to left axis right-left axis spatial BSPO:0000017 left-right axis An axis that bisects an organism from left to right sides of body, through a sagittal plane. BSPO:cjm Anatomical plane that divides body into anterior and posterior parts. FMA:12247 axial plane axial section transverse section spatial cross-section BSPO:0000018 transverse plane Anatomical plane that divides body into anterior and posterior parts. BSPO:mah Anatomical plane that divides bilateral body into dorsal and ventral parts. FMA:52810 frontal plane horizontal anatomical plane horizontal section spatial coronal section frontal section BSPO:0000019 horizontal plane Anatomical plane that divides bilateral body into dorsal and ventral parts. BSPO:mah horizontal anatomical plane FMA:52810 Anatomical region that overlaps the anterior and dorsal regions of a body or body part. Melissa Haendel 2009-06-15T01:01:38Z anterodorsal region spatial BSPO:0000026 antero-dorsal region Anatomical region that overlaps the anterior and dorsal regions of a body or body part. BSPO:wd Anatomical region that overlaps the anterior and ventral regions of a body or body part. Melissa Haendel 2009-06-15T01:04:59Z anteroventral region spatial BSPO:0000027 antero-ventral region Anatomical region that overlaps the anterior and ventral regions of a body or body part. BSPO:wd Anatomical region that overlaps the posterior and lateral regions of the body or body part. Melissa Haendel 2009-06-15T01:06:01Z posterolateral region spatial BSPO:0000028 postero-lateral region Anatomical region that overlaps the posterior and lateral regions of the body or body part. BSPO:wd Anatomical region that overlaps the anterior and lateral regions of a body or body part. Melissa Haendel 2009-06-15T01:07:18Z anterolateral region spatial BSPO:0000029 antero-lateral region Anatomical region that overlaps the anterior and lateral regions of a body or body part. BSPO:wd Anatomical region that overlaps the posterior and dorsal regions of the body or body part. Melissa Haendel 2009-06-15T01:08:13Z posterodorsal region spatial BSPO:0000030 postero-dorsal region Anatomical region that overlaps the posterior and dorsal regions of the body or body part. BSPO:wd Anatomical region that overlaps the posterior and ventral regions of a body or body part. Melissa Haendel 2009-06-15T01:08:38Z posteroventral region spatial BSPO:0000035 postero-ventral region Anatomical region that overlaps the posterior and ventral regions of a body or body part. BSPO:wd An anatomical region bounded by a plane perpendicular to an axis through the middle. FBql:00005841 spatial BSPO:0000054 anatomical side An anatomical region bounded by a plane perpendicular to an axis through the middle. BSPO:cjm An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane. FBcv:0000053 FBql:00005848 anterior rostral spatial BSPO:0000055 anterior side An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:RW An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane. FBcv:0000065 FBql:00005849 posterior caudal spatial BSPO:0000056 posterior side An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:RW BSPO:wd caudal Anatomical side that is located on the apical end of an organism or structure. FBcv:0000054 FBql:00005854 apical spatial BSPO:0000057 apical side Anatomical side that is located on the apical end of an organism or structure. BSPO:wd Anatomical side that is located on the basal end of an organism or structure. FBcv:0000055 FBql:00005855 basal spatial BSPO:0000058 The part of the organism attached to a substrate. Axis of symmetry. basal side Anatomical side that is located on the basal end of an organism or structure. BSPO:wd An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane. FBcv:0000059 FBql:00005842 dorsal spatial BSPO:0000063 dorsal side An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane. BSPO:wd FBcv:0000063 FBql:00005844 lateral spatial BSPO:0000066 lateral side An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. FBcv:0000070 FBql:00005843 ventral spatial BSPO:0000068 ventral side An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. BSPO:RW BSPO:wd A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. FBql:00005841 spatial BSPO:0000070 to be merged into CARO anatomical region A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. BSPO:cjm Anatomical region anteriorly located on the body or body part. FBql:00005848 spatial BSPO:0000071 anterior region Anatomical region anteriorly located on the body or body part. BSPO:wd Anatomical region posteriorly located on the body or body part. FBql:00005849 spatial BSPO:0000072 posterior region Anatomical region posteriorly located on the body or body part. BSPO:wd Anatomical region located on the apical end on the body or body part. FBql:00005854 spatial BSPO:0000073 apical region Anatomical region located on the apical end on the body or body part. BSPO:wd Anatomical region located basally on the body or body part. FBql:00005855 spatial BSPO:0000074 basal region Anatomical region located basally on the body or body part. BSPO:wd Anatomical region dorsally located on the body or body part. FBql:00005842 spatial BSPO:0000079 dorsal region Anatomical region dorsally located on the body or body part. BSPO:wd Anatomical region that overlaps the dorsal and lateral regions of a body or body part. FBql:00005845 dorsolateral region spatial BSPO:0000080 dorso-lateral region Anatomical region that overlaps the dorsal and lateral regions of a body or body part. BSPO:wd Anatomical region laterally located on the body or body part. FBql:00005844 spatial BSPO:0000082 lateral region Anatomical region laterally located on the body or body part. BSPO:wd Anatomical region ventrally located on the body or body part. FBql:00005843 spatial BSPO:0000084 ventral region Anatomical region ventrally located on the body or body part. BSPO:wd Anatomical region that overlaps the ventral and lateral regions of a body or body part. FBql:00005846 ventrolateral region spatial BSPO:0000085 This is an example of a composition of two axis positions. ventro-lateral region Anatomical region that overlaps the ventral and lateral regions of a body or body part. BSPO:wd FBql:00005873 FMA:9647 spatial BSPO:0000086 to be merged into CARO anatomical compartment FBql:00005881 spatial BSPO:0000092 to be merged into CARO anatomical compartment boundary FBcv:0000034 FBql:00005879 spatial BSPO:0000094 dorsal/ventral compartment boundary An anatomical axis that extends from the center of the body outwards or externally. wasila.dahdul 2013-07-02T11:21:42Z spatial proximal-distal axis BSPO:0000196 The medial-external axis could apply to a sphere-shaped body. medial-external axis An anatomical axis that extends from the center of the body outwards or externally. BSPO:curators An axis that extends from the oral opening to the furthest point in an organism that is directly opposite. wasila.dahdul 2013-07-02T11:29:33Z spatial BSPO:0000198 oral-aboral axis An axis that extends from the oral opening to the furthest point in an organism that is directly opposite. BSPO:PM Anatomical surface that is located on the anterior side of the body or body part. FBql:00005848 spatial BSPO:0000371 anterior surface Anatomical surface that is located on the anterior side of the body or body part. BSPO:wd Anatomical surface that is located on the posterior side of the body or body part. FBql:00005849 spatial BSPO:0000372 posterior surface Anatomical surface that is located on the posterior side of the body or body part. BSPO:wd Anatomical surface that is located on the apical side of the body or body part. FBql:00005854 spatial BSPO:0000373 apical surface Anatomical surface that is located on the apical side of the body or body part. BSPO:wd Anatomical surface that is located on the basal side of the body or body part. FBql:00005855 spatial BSPO:0000374 basal surface Anatomical surface that is located on the basal side of the body or body part. BSPO:wd Anatomical surface that located on the dorsal side of the body or body part. FBql:00005842 spatial BSPO:0000379 dorsal surface Anatomical surface that located on the dorsal side of the body or body part. BSPO:wd Anatomical surface that located on the lateral side of the body or body part. FBql:00005844 spatial BSPO:0000382 lateral surface Anatomical surface that located on the lateral side of the body or body part. BSPO:wd Anatomical surface that is located on the ventral side of the body or body part. FBql:00005843 spatial BSPO:0000384 ventral surface Anatomical surface that is located on the ventral side of the body or body part. BSPO:wd A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions. FMA:242982 anatomical cross-section anatomical section plane section spatial cross-section BSPO:0000400 These anatomical sections are applicable to most bilaterally symmetrical animals, but bipedal animals such as humans have more complex usage of these terms. For example, in post-embryonic humans a coronal plane is vertical and a transverse plane is horizontal, but for embryos and quadrupeds a coronal plane is horizontal and a transverse plane is vertical. anatomical plane A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions. BSPO:cjm Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size. FMA:11361 left/right plane median plane sagittal section spatial BSPO:0000417 sagittal plane Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size. BSPO:DOS BSPO:cjm BSPO:mah An axis that extends from the center of organism to one or other side. http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG M-L axis ML axis medio-lateral axis mediolateral axis spatial proximal-distal axis BSPO:0001001 Properly, the ML axis is a half axis; practically, its usage is less clumsy and less linguistically biased than "left-right". The terms may still be used relatively to describe locations along the LR axis. The gills are medial to the operculum, but lateral to the heart. medial-lateral axis An axis that extends from the center of organism to one or other side. BSPO:cjm Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. spatial CARO:0000000 anatomical entity anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. CARO:MAH Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. spatial CARO:0000003 anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CC:DOS An anatomical entity that has mass. spatial CARO:0000006 material anatomical entity material anatomical entity An anatomical entity that has mass. CC:DOS An anatomical entity that has no mass. spatial CARO:0000007 immaterial anatomical entity An anatomical entity that has no mass. CC:DOS A one dimensional, immaterial anatomical entity. spatial CARO:0000008 anatomical line A one dimensional, immaterial anatomical entity. CC:DOS A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. spatial CARO:0000010 anatomical boundary A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. CC:DOS biological entity The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GO:0019952 GO:0050876 Wikipedia:Reproduction reproductive physiological process biological_process GO:0000003 reproduction The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GOC:go_curators GOC:isa_complete GOC:jl ISBN:0198506732 A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring. puberty biological_process reproductive developmental process GO:0003006 developmental process involved in reproduction A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring. GOC:dph GOC:isa_complete puberty GOC:dph reproductive developmental process GOC:dph GOC:tb molecular process molecular_function catalytic activity The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). MIPS_funcat:41 biological_process GO:0007275 Note that this term was 'developmental process'. multicellular organism development The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:dph GOC:ems GOC:isa_complete GOC:tb The union of male and female gametes to form a zygote. MIPS_funcat:41.05.01 biological_process zygote biosynthesis zygote formation GO:0007338 single fertilization The union of male and female gametes to form a zygote. GOC:ems GOC:mtg_sensu A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. janelomax 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). Wikipedia:Fertilisation syngamy biological_process GO:0009566 fertilization The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). GOC:tb ISBN:0198506732 The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. embryogenesis and morphogenesis Wikipedia:Morphogenesis anatomical structure organization morphogenesis biological_process GO:0009653 anatomical structure morphogenesis The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. GOC:go_curators ISBN:0521436125 The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis embryonal development biological_process GO:0009790 embryo development The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. GOC:go_curators GOC:isa_complete GOC:mtg_sensu The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure. histogenesis and organogenesis Wikipedia:Histogenesis histogenesis biological_process GO:0009888 tissue development The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure. ISBN:0471245208 Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. janelomax 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete true kinase activity transferase activity transferase activity, transferring phosphorus-containing groups A reproduction process that creates a new organism by combining the genetic material of two gametes, which may come from two organisms or from a single organism, in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two gametes join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny. Wikipedia:Sexual_reproduction biological_process GO:0019953 Sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times. sexual reproduction A reproduction process that creates a new organism by combining the genetic material of two gametes, which may come from two organisms or from a single organism, in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two gametes join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny. GOC:jl GOC:kmv GOC:krc GOC:tb ISBN:0387520546 http://en.wikipedia.org/wiki/Sexual_reproduction A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism. reproductive cellular process in multicellular organism biological_process GO:0022412 cellular process involved in reproduction in multicellular organism A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism. GOC:isa_complete reproductive cellular process in multicellular organism GOC:curators A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. janelomax 2012-09-19T15:56:06Z GO:0044702 biological_process single organism reproductive process GO:0022414 reproductive process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:dph GOC:isa_complete Any biological process, occurring at the level of a multicellular organism, pertinent to its function. janelomax 2012-09-19T16:07:47Z GO:0044707 GO:0050874 organismal physiological process biological_process single-multicellular organism process GO:0032501 multicellular organismal process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. GOC:curators GOC:dph GOC:isa_complete GOC:tb A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. janelomax 2012-12-19T12:21:31Z GO:0044767 development biological_process single-organism developmental process GO:0032502 developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. GOC:isa_complete The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. biological_process GO:0032504 multicellular organism reproduction The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:isa_complete GOC:jid The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. biological_process GO:0043473 pigmentation The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. GOC:jl A biological process that directly contributes to the process of producing new individuals, involving another organism. janelomax 2012-09-19T15:56:30Z biological_process GO:0044703 multi-organism reproductive process A biological process that directly contributes to the process of producing new individuals, involving another organism. GOC:jl The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. organismal reproductive process reproductive process in a multicellular organism biological_process GO:0048609 multicellular organismal reproductive process The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. GOC:dph GOC:jid GOC:tb organismal reproductive process GOC:curators reproductive process in a multicellular organism GOC:curators The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. development of an anatomical structure biological_process GO:0048856 This term was added by GO_REF:0000021. anatomical structure development The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GOC:mtg_15jun06 GO_REF:0000021 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. Wikipedia:Cell_division biological_process GO:0051301 Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. cell division The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. GOC:di GOC:go_curators GOC:pr A biological process which involves another organism of the same or different species. GO:0051706 interaction between organisms physiological interaction between organisms physiological interaction with other organism biological_process GO:0051704 multi-organism process A biological process which involves another organism of the same or different species. GOC:jl data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type D0-D2. Zygote and dispersed blastomere cleavage in a yolk syncytium. Days 0-2 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000001 Stage 1 https://planosphere.stowers.org/ontology/PLANA_0000001 D0-D2. Zygote and dispersed blastomere cleavage in a yolk syncytium. Days 0-2 post-egg capsule deposition at 20˚C. PMID:28072387 D2-D3. Sphere formation. A fraction of the blastomeres differentiate into temporary embryonic tissues that provide form and function to the embryo. Undifferentiated blastomeres remain in the embryonic wall. Days 2-3 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000002 Depicted by field contains hematoxylin and eosin staining section of a stage 2 embryo. Scale bar = 100um Stage 2 https://planosphere.stowers.org/ontology/PLANA_0000002 D2-D3. Sphere formation. A fraction of the blastomeres differentiate into temporary embryonic tissues that provide form and function to the embryo. Undifferentiated blastomeres remain in the embryonic wall. Days 2-3 post-egg capsule deposition at 20˚C. PMID:28072387 D2-D4. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity. Days 2-4 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000003 Depicted by field contains hematoxylin and eosin staining section of a stage 3 embryo. Scale bar = 100um Stage 3 https://planosphere.stowers.org/ontology/PLANA_0000003 D2-D4. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity. Days 2-4 post-egg capsule deposition at 20˚C. PMID:28072387 D3-D5. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation. Days 3-5 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000004 Depicted by field contains hematoxylin and eosin staining section of a stage 4 embryo. Scale bar = 100um Stage 4 https://planosphere.stowers.org/ontology/PLANA_0000004 D3-D5. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation. Days 3-5 post-egg capsule deposition at 20˚C. PMID:28072387 D5-D7. Organogenesis onset. Downregulation of early embryo enriched transcripts and birth of adult lineages within the blastomere population. Early embryonic gut formation continues. Yolk ingestion into the gut cavity. Days 5-7 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000005 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo. Scale bar = 100um Stage 5 https://planosphere.stowers.org/ontology/PLANA_0000005 D5-D7. Organogenesis onset. Downregulation of early embryo enriched transcripts and birth of adult lineages within the blastomere population. Early embryonic gut formation continues. Yolk ingestion into the gut cavity. Days 5-7 post-egg capsule deposition at 20˚C. PMID:28072387 D7-D9. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation. Days 7-9 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000006 Depicted by field contains hematoxylin and eosin staining section of a stage 6 embryo. Scale bar = 100um Stage 6 https://planosphere.stowers.org/ontology/PLANA_0000006 D7-D9. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation. Days 7-9 post-egg capsule deposition at 20˚C. PMID:28072387 D9-D11. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility. Days 9-11 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000007 Depicted by field contains hematoxylin and eosin staining section of a stage 7 embryo. Scale bar = 100um Stage 7 https://planosphere.stowers.org/ontology/PLANA_0000007 D9-D11. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility. Days 9-11 post-egg capsule deposition at 20˚C. PMID:28072387 D13-D15. Organogenesis and organ maturation continues. Hatching. Days 13-15 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000008 Depicted by field contains hematoxylin and eosin staining section of a stage 8 embryo. Scale bar = 100um Stage 8 https://planosphere.stowers.org/ontology/PLANA_0000008 D13-D15. Organogenesis and organ maturation continues. Hatching. Days 13-15 post-egg capsule deposition at 20˚C. PMID:28072387 A heterogeneous subpopulation of neoblasts with enriched expression of SoxP-1 and SoxP-2 thought to contain both pluripotent stem cells and tissue-specific progenitors. Planarian_Anatomy PLANA:0000009 sigma neoblast https://planosphere.stowers.org/ontology/PLANA_0000009 A heterogeneous subpopulation of neoblasts with enriched expression of SoxP-1 and SoxP-2 thought to contain both pluripotent stem cells and tissue-specific progenitors. PMID:25017721 Neoblasts and post-mitotic, differentiating daughters coexpressing POU2-3, six1/2-2, Sal1, Eya and Osr, required for maintenance and regeneration of protonephridial cell types. Planarian_Anatomy PLANA:0000011 protonephridial progenitor https://planosphere.stowers.org/ontology/PLANA_0000011 Neoblasts and post-mitotic, differentiating daughters coexpressing POU2-3, six1/2-2, Sal1, Eya and Osr, required for maintenance and regeneration of protonephridial cell types. PMID:21937596 Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system. Planarian_Anatomy PLANA:0000012 neural progenitor https://planosphere.stowers.org/ontology/PLANA_0000012 Musculature surrounding internal organs of the body. Erin Davies Planarian_Anatomy PLANA:0000013 visceral musculature https://planosphere.stowers.org/ontology/PLANA_0000013 Musculature surrounding internal organs of the body. PMID:26904543 An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s). Planarian_Anatomy PLANA:0000014 zeta neoblast https://planosphere.stowers.org/ontology/PLANA_0000014 An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s). PMID:25017721 An epithelial cell lacking cilia. Planarian_Anatomy PLANA:0000015 non ciliated epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000015 A plicate and protrusible organ that is the sole point of entry and exit for the Triclad gut. It contains epithelial, muscular, secretory and neuronal cell types. Planarian_Anatomy PLANA:0000016 definitive pharynx https://planosphere.stowers.org/ontology/PLANA_0000016 A plicate and protrusible organ that is the sole point of entry and exit for the Triclad gut. It contains epithelial, muscular, secretory and neuronal cell types. OCLC:16809160 Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain. Planarian_Anatomy PLANA:0000017 photoreceptor neuron https://planosphere.stowers.org/ontology/PLANA_0000017 Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain. PMID:21852957 PMID:22884275 Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells. Planarian_Anatomy PLANA:0000018 Category 4 cell https://planosphere.stowers.org/ontology/PLANA_0000018 Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells. PMID:25017721 PMID:26457503 Progenitor neoblasts implicated in the maintenance and regeneration of muscle fibers. Planarian_Anatomy PLANA:0000019 muscle progenitor https://planosphere.stowers.org/ontology/PLANA_0000019 Progenitor neoblasts implicated in the maintenance and regeneration of muscle fibers. PMID:25017721 Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct. Planarian_Anatomy PLANA:0000020 Depicted by field contains a whole-mount acetylated tubulin (AcTub) staining. Scale bars: 500 μm. Inset to right shows depth-coded projection of AcTub staining. Superficial structures are in blue and deeper structures are in red. Scale bars: 50 μm protonephridia https://planosphere.stowers.org/ontology/PLANA_0000020 Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct. OCLC:16809160 PMID:21828097 PMID:26057828 PMID:26057828 Organisms sharing a specified genotype or karyotype. Planarian_Anatomy PLANA:0000021 biotype https://planosphere.stowers.org/ontology/PLANA_0000021 Post-mitotic, ciliated epidermal cells. Planarian_Anatomy PLANA:0000022 Category 5 cell https://planosphere.stowers.org/ontology/PLANA_0000022 Post-mitotic, ciliated epidermal cells. PMID:25017721 An innervated, muscular pump that ingests yolk cells into the gut cavity. The temporary embryonic pharynx is an extraembryonic tissue that forms during Stage 2, functions during Stages 3-5, and degenerates during Stages 6-7. PMID:28072387 Planarian_Anatomy PLANA:0000023 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo that zooms into the temporary embryonic pharynx. temporary embryonic pharynx https://planosphere.stowers.org/ontology/PLANA_0000023 Obligate asexual animals that reproduce solely through fission followed by whole body regeneration. Asexual Smed are stable diploids that harbor a chromosome translocation, making them karyotypically distinct from sexual Smed. Planarian_Anatomy PLANA:0000024 Depicted by field contains light micrscope image of asexual and sexual biotypes of Schmidtea meditteranea with their respective karyotypes. Note that the asexual bioptype has a chromosome inversion compared to the sexual. Smed asexual biotype https://planosphere.stowers.org/ontology/PLANA_0000024 Obligate asexual animals that reproduce solely through fission followed by whole body regeneration. Asexual Smed are stable diploids that harbor a chromosome translocation, making them karyotypically distinct from sexual Smed. PMID:11972158 PMID:23136835 The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organisms, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. UBERON:0001016 Planarian_Anatomy PLANA:0000025 nervous system https://planosphere.stowers.org/ontology/PLANA_0000025 The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organisms, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. UBERON:0001016 The planarian triclad gut contains a central anterior gut branch connected to two posterior gut branches arranged around the definitive pharynx. Secondary gut branches extend laterally from the primary gut branches, while tertiary gut branches extend from the secondary branches. Food and waste enter and exit the definitive gut through the defintive pharynx. gut Planarian_Anatomy PLANA:0000026 definitive gut https://planosphere.stowers.org/ontology/PLANA_0000026 The planarian triclad gut contains a central anterior gut branch connected to two posterior gut branches arranged around the definitive pharynx. Secondary gut branches extend laterally from the primary gut branches, while tertiary gut branches extend from the secondary branches. Food and waste enter and exit the definitive gut through the defintive pharynx. PMID:21664348 Cross-fertilizing hemaphrodites that reproduce sexually and do not undergo fission. After mating, each parent lays an egg capsule containing one or more embryos. Sexual Smed are stable diploids. Planarian_Anatomy PLANA:0000027 Depicted by field contains light micrscope image of asexual and sexual biotypes of Schmidtea meditteranea with their respective karyotypes. Note that the asexual bioptype has a chromosome inversion compared to the sexual. Smed sexual biotype https://planosphere.stowers.org/ontology/PLANA_0000027 Cross-fertilizing hemaphrodites that reproduce sexually and do not undergo fission. After mating, each parent lays an egg capsule containing one or more embryos. Sexual Smed are stable diploids. PMID:11972158 PMID:23136835 Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts. Planarian_Anatomy PLANA:0000028 Category 2 cell https://planosphere.stowers.org/ontology/PLANA_0000028 Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts. PMID:18786419 PMID:20040488 PMID:22385657 PMID:25017721 PMID:26114597 A single cell layer of extraembryonic, post-mitotic ectodermal cells bounding the embryo. The primitive ectoderm forms during Stage 2 and is thought to degenerate as the definitive epidermis forms during Stages 5-7. Planarian_Anatomy PLANA:0000029 primitive ectoderm https://planosphere.stowers.org/ontology/PLANA_0000029 A single cell layer of extraembryonic, post-mitotic ectodermal cells bounding the embryo. The primitive ectoderm forms during Stage 2 and is thought to degenerate as the definitive epidermis forms during Stages 5-7. OCLC:20423827 OCLC:464776945 OCLC:82522822 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md The median line/ plane of bilateral symmetry along the anteroposterior axis. Planarian_Anatomy PLANA:0000030 midline https://planosphere.stowers.org/ontology/PLANA_0000030 Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup. Planarian_Anatomy PLANA:0000031 pigment cup cell https://planosphere.stowers.org/ontology/PLANA_0000031 Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup. PMID:21852957 PMID:22884275 The median line/plane of bilateral symmetry along the anteroposterior axis on the dorsal surface of the animal. midline of dorsal region dorsal midline The median line/plane of bilateral symmetry along the anteroposterior axis on the dorsal surface of the animal. Mitotically active zeta neoblasts and their post-mitotic descendants which undergo progressive differentiation and outward directed movement through the mesenchyme prior to incorporation into the epidermis, where terminal differentiation occurs. Planarian_Anatomy PLANA:0000033 Depicted by shows multiple epithelia progenitor cell markers via in situ as progenitors mature towards the epidermis in a transverse plane. epidermal progenitor https://planosphere.stowers.org/ontology/PLANA_0000033 Mitotically active zeta neoblasts and their post-mitotic descendants which undergo progressive differentiation and outward directed movement through the mesenchyme prior to incorporation into the epidermis, where terminal differentiation occurs. PMID:18786419 PMID:20040488 PMID:22385657 PMID:25017721 PMID:26114597 PMID:26457503 PMID:26457503 A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal. epidermis Planarian_Anatomy PLANA:0000034 At present, this definition does not apply to epithelial structures other than the dorsal and ventral epidermis (i.e., the pharyngeal epithelium). definitive epidermis https://planosphere.stowers.org/ontology/PLANA_0000034 A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal. OCLC:16809160 Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells. Planarian_Anatomy PLANA:0000035 Category 3 cell https://planosphere.stowers.org/ontology/PLANA_0000035 Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells. PMID:18786419 PMID:20040488 PMID:26114597 PMID:26457503 An organ that detects light. UBERON:0000970 Planarian_Anatomy PLANA:0000036 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The eyes are indicated by arrows. Scale bar = 250um eye https://planosphere.stowers.org/ontology/PLANA_0000036 Adult tissues built during organogenesis that are present in juveniles at birth. Planarian_Anatomy PLANA:0000037 definitive tissue https://planosphere.stowers.org/ontology/PLANA_0000037 Adult tissues built during organogenesis that are present in juveniles at birth. PMID:28072387 PMID:2888018 The median line/ plane of bilateral symmetry along the anteroposterior axis on the ventral surface of the animal. midline of ventral region ventral midline The median line/ plane of bilateral symmetry along the anteroposterior axis on the ventral surface of the animal. An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut. Planarian_Anatomy PLANA:0000039 gamma neoblast https://planosphere.stowers.org/ontology/PLANA_0000039 An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut. PMID:25017721 A stage of embryonic development defined by a unique gene expression signature, morphology and chronological time post-egg capsule deposition for hermaphrodites reared at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000040 Schmidtea mediterranea developmental stage https://planosphere.stowers.org/ontology/PLANA_0000040 A stage of embryonic development defined by a unique gene expression signature, morphology and chronological time post-egg capsule deposition for hermaphrodites reared at 20˚C. PMID:28072387 Stage 3-5 embryo hemisphere centered around the pole opposite the temporary embryonic pharynx. Planarian_Anatomy PLANA:0000041 aboral hemisphere https://planosphere.stowers.org/ontology/PLANA_0000041 Stage 3-5 embryo hemisphere centered around the pole opposite the temporary embryonic pharynx. PMID:28072387 The single, central gut branch of the triclad gut anterior to the definitive pharynx. Planarian_Anatomy PLANA:0000042 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. Anterior primary gut branch indicated by arrows. Scale bar = 250um anterior primary gut branch https://planosphere.stowers.org/ontology/PLANA_0000042 The single, central gut branch of the triclad gut anterior to the definitive pharynx. PMID:21664348 Region along the edge of the animal where the dorsal and ventral surfaces meet. edge whole organism of dorsal/ventral compartment boundary Planarian_Anatomy PLANA:0000043 dorsal ventral margin dorsoventral margin https://planosphere.stowers.org/ontology/PLANA_0000043 Region along the edge of the animal where the dorsal and ventral surfaces meet. The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head. brain Planarian_Anatomy PLANA:0000044 cephalic ganglia https://planosphere.stowers.org/ontology/PLANA_0000044 The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head. OCLC:16809160 PMID:17999079 Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema. Planarian_Anatomy PLANA:0000045 circular muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000045 Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md Pluripotent piwi-1+ stem cells that self-renew, form expanding colonies and produce differentiating daughters that contribute to multiple organ systems. cNeoblasts are predicted to be broadly distributed across the anteroposterior axis of the adult worm. Planarian_Anatomy PLANA:0000046 clonogenic neoblast https://planosphere.stowers.org/ontology/PLANA_0000046 Pluripotent piwi-1+ stem cells that self-renew, form expanding colonies and produce differentiating daughters that contribute to multiple organ systems. cNeoblasts are predicted to be broadly distributed across the anteroposterior axis of the adult worm. PMID:21566185 Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis. collection duct Planarian_Anatomy PLANA:0000047 Depicted by field contains a diagram representing the protonephrida unit (top) as well as a 3D rendering of confocal data depicting the same. In the diagram, terminal flame cells and their corresponding cilia are in blues, the proximal tubule is in reds, the distal tubule is in greens while the collecting duct is in purple. In the 3D rendering below the cilia (AcTub) are in blue, portions of the proximal tubule (slc6a-13) are in red while the distal tubule (slc6a-12) is in green. collecting duct https://planosphere.stowers.org/ontology/PLANA_0000047 Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis. PMID:26057828 PMID:26057828 Body wall muscle fibers arrayed diagonally along the anteroposterior axis. Planarian_Anatomy PLANA:0000048 diagonal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000048 Body wall muscle fibers arrayed diagonally along the anteroposterior axis. PMID:26904543 Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. UBERON:0001007 Planarian_Anatomy PLANA:0000049 digestive system https://planosphere.stowers.org/ontology/PLANA_0000049 Embryonic development producing juvenile animals with body plans and feeding behavior similar to adults. Juveniles grow and mature into adults without undergoing metamorphosis. Schmidtea_mediterranea_Developmental_Terms PLANA:0000051 direct development https://planosphere.stowers.org/ontology/PLANA_0000051 Embryonic development producing juvenile animals with body plans and feeding behavior similar to adults. Juveniles grow and mature into adults without undergoing metamorphosis. PMID:12888018 A derived form of early embryonic cleavage present in ectolecithal embryos. Blastomeres divide asynchronously within a yolk syncytium, and division progeny do not remain in direct contact with one another. Schmidtea_mediterranea_Developmental_Terms PLANA:0000052 dispersed cleavage https://planosphere.stowers.org/ontology/PLANA_0000052 A derived form of early embryonic cleavage present in ectolecithal embryos. Blastomeres divide asynchronously within a yolk syncytium, and division progeny do not remain in direct contact with one another. OCLC:20423827 OCLC:42792751 OCLC:464776945 OCLC:82522822 PMID:15599763 PMID:19197510 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells. Planarian_Anatomy PLANA:0000053 Depicted by field contains a diagram representing the protonephrida unit (top) as well as a 3D rendering of confocal data depicting the same. In the diagram, terminal flame cells and their corresponding cilia are in blues, the proximal tubule is in reds, the distal tubule is in greens while the collecting duct is in purple. In the 3D rendering below the cilia (AcTub) are in blue, portions of the proximal tubule (slc6a-13) are in red while the distal tubule (slc6a-12) is in green. distal tubule https://planosphere.stowers.org/ontology/PLANA_0000053 Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells. PMID:21828097 PMID:26057828 Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe. definitive epidermis of dorsal region Planarian_Anatomy PLANA:0000054 dorsal epidermis https://planosphere.stowers.org/ontology/PLANA_0000054 Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe. Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe. OCLC:16809160 Ciliated epithelial cells along the dorsal midline. racing stripe Planarian_Anatomy PLANA:0000055 dorsal stripe https://planosphere.stowers.org/ontology/PLANA_0000055 Ciliated epithelial cells along the dorsal midline. PMID:17553481 Turbellarian (freshwater flatworm) embryos that undergo a modified form of cleavage due to separation of oocyte and yolk. Yolk is not contained within oocytes, and is produced by somatic vitellogenic gland cells. Schmidtea_mediterranea_Developmental_Terms PLANA:0000056 ectolecithal embryo https://planosphere.stowers.org/ontology/PLANA_0000056 Turbellarian (freshwater flatworm) embryos that undergo a modified form of cleavage due to separation of oocyte and yolk. Yolk is not contained within oocytes, and is produced by somatic vitellogenic gland cells. PMID:22074376 PMID:27149082 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000002.md The first few specialized divisions of an activated animal egg. GO:0040016 Schmidtea_mediterranea_Developmental_Terms PLANA:0000057 embryonic cleavage https://planosphere.stowers.org/ontology/PLANA_0000057 A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the temporary embryonic pharynx and primitive gut cells. Embryonic gut cells, likely produced from blastomeres, form a phagocytic tissue layer surrounding the inner gut cavity during Stages 4-6. It is not known whether the embryonic gut is temporary embryonic tissue or a definitive tissue. For convenience, the embryonic gut is currently designated as an extraembryonic structure because cell type specific markers for the embryonic gut do not stain the definitive gut in hatchlings or adult animals. Planarian_Anatomy PLANA:0000058 embryonic digestive system https://planosphere.stowers.org/ontology/PLANA_0000058 A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the temporary embryonic pharynx and primitive gut cells. Embryonic gut cells, likely produced from blastomeres, form a phagocytic tissue layer surrounding the inner gut cavity during Stages 4-6. It is not known whether the embryonic gut is temporary embryonic tissue or a definitive tissue. For convenience, the embryonic gut is currently designated as an extraembryonic structure because cell type specific markers for the embryonic gut do not stain the definitive gut in hatchlings or adult animals. PMID:28072387 Dispersed, phagocytic gut cells that appear during Stage 4 and ultimately generate a honeycomb-like lattice surrounding the central gut cavity in Stage 5 embryos. Early embryonic gut cell specific transcripts are expressed from Stage 4-6, and are downregulated during Stage 7. Planarian_Anatomy PLANA:0000059 embryonic gut cell https://planosphere.stowers.org/ontology/PLANA_0000059 Dispersed, phagocytic gut cells that appear during Stage 4 and ultimately generate a honeycomb-like lattice surrounding the central gut cavity in Stage 5 embryos. Early embryonic gut cell specific transcripts are expressed from Stage 4-6, and are downregulated during Stage 7. PMID:28072387 The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos. Planarian_Anatomy PLANA:0000060 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo with anatomical feature noted with black indicators. embryonic wall https://planosphere.stowers.org/ontology/PLANA_0000060 The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos. OCLC:16809160 PMID:12888018 Visceral muscle surrounding the definitive gut. Planarian_Anatomy PLANA:0000061 enteric musculature https://planosphere.stowers.org/ontology/PLANA_0000061 Visceral muscle surrounding the definitive gut. PMID:26904543 Attachment between the triclad gut and the proximal end of the definitive pharynx. Planarian_Anatomy PLANA:0000062 esophagus https://planosphere.stowers.org/ontology/PLANA_0000062 Attachment between the triclad gut and the proximal end of the definitive pharynx. PMID:24737865 OCLC:16809160 A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. UBERON:0000478 Planarian_Anatomy PLANA:0000063 extraembryonic structure https://planosphere.stowers.org/ontology/PLANA_0000063 Terminal structure of protonephridia unit; consists of flame cells. Planarian_Anatomy PLANA:0000064 Depicted by field contains a diagram representing the protonephrida unit (top) as well as a 3D rendering of confocal data depicting the same (bottom). In the diagram, terminal flame cells and their corresponding cilia (flame bulb) are in blues, the proximal tubule is in reds, the distal tubule is in greens while the collecting duct is in purple. In the 3D rendering below the cilia (AcTub) are in blue, portions of the proximal tubule (slc6a-13) are in red while the distal tubule (slc6a-12) is in green. flame bulb https://planosphere.stowers.org/ontology/PLANA_0000064 Terminal structure of protonephridia unit; consists of flame cells. PMID:21828097 PMID:26057828 PMID:26057828 Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the ‘filtration weir’, which consists of closely apposed strands of cytoplasm surrounding a central cilia bundle, and by numerous microvilli between weir and cilia. Positive for acetyated tubulin. Has functional homology with vertebrate podocytes. Planarian_Anatomy PLANA:0000065 Depicted by field contains a diagram representing the protonephrida unit (top) as well as a 3D rendering of confocal data depicting the same. In the diagram, terminal flame cells and their corresponding cilia are in blues, the proximal tubule is in reds, the distal tubule is in greens while the collecting duct is in purple. In the 3D rendering below the cilia (AcTub) are in blue, portions of the proximal tubule (slc6a-13) are in red while the distal tubule (slc6a-12) is in green. flame cell https://planosphere.stowers.org/ontology/PLANA_0000065 Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the ‘filtration weir’, which consists of closely apposed strands of cytoplasm surrounding a central cilia bundle, and by numerous microvilli between weir and cilia. Positive for acetyated tubulin. OCLC:16809160 PMID:21828097 PMID:26057828 Has functional homology with vertebrate podocytes. PMID:26057828 PMID:26057828 The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle. Planarian_Anatomy PLANA:0000066 gastrodermis https://planosphere.stowers.org/ontology/PLANA_0000066 The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle. PMID:21664348 Secretory cells that release digestive enzymes into the lumen of the intestine. Planarian_Anatomy PLANA:0000067 goblet cell https://planosphere.stowers.org/ontology/PLANA_0000067 Secretory cells that release digestive enzymes into the lumen of the intestine. PMID:21664348 Lumen of embryonic digestive tract, prior to formation of the branched defintive gut. Planarian_Anatomy PLANA:0000068 embryonic gut cavity https://planosphere.stowers.org/ontology/PLANA_0000068 Lumen of embryonic digestive tract, prior to formation of the branched defintive gut. PMID:28072387 Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole. Planarian_Anatomy PLANA:0000069 inner longitudinal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000069 Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md Absorptive digestive cells that engulf food particles for intracellular digestion. Planarian_Anatomy PLANA:0000070 intestinal phagocyte https://planosphere.stowers.org/ontology/PLANA_0000070 Absorptive digestive cells that engulf food particles for intracellular digestion. PMID:21664348 Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers. Planarian_Anatomy PLANA:0000071 longitudinal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000071 Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md The sole point of entry and exit for the Triclad planarian flatworm gut. The mouth is connected to the pharyngeal pouch to allow for exit and re-entry of the definitive pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells. Manus Planarian_Anatomy PLANA:0000072 mouth https://planosphere.stowers.org/ontology/PLANA_0000072 The sole point of entry and exit for the Triclad planarian flatworm gut. The mouth is connected to the pharyngeal pouch to allow for exit and re-entry of the definitive pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells. OCLC:16809160 Manus https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000006.md A female germ cell that has entered meiosis. CL:0000023 Planarian_Anatomy PLANA:0000074 oocyte https://planosphere.stowers.org/ontology/PLANA_0000074 A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons. Planarian_Anatomy PLANA:0000075 optic cup https://planosphere.stowers.org/ontology/PLANA_0000075 A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons. PMID:21852957 PMID:22884275 Stage 3-5 embryo hemisphere centered around the temporary embryonic pharynx. Planarian_Anatomy PLANA:0000076 oral hemisphere https://planosphere.stowers.org/ontology/PLANA_0000076 Stage 3-5 embryo hemisphere centered around the temporary embryonic pharynx. PMID:28072387 UBERON:0000111 organogenesis Schmidtea_mediterranea_Developmental_Terms PLANA:0000077 organogenesis stage https://planosphere.stowers.org/ontology/PLANA_0000077 Outer most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thinner than the inner longitudinal muscle fibers. Planarian_Anatomy PLANA:0000078 outer longitudinal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000078 Outer most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thinner than the inner longitudinal muscle fibers. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md Dorsal-ventral muscle fibers present through the mesenchyme. dorsoventral muscle fibers Planarian_Anatomy PLANA:0000079 The depicted by field is a hemotoxylin and eosin stained sagittal section with the dorsal side up and anterior to the right. The parenchymal musculature, or dorsal ventral muscle fibers are the periodic vertical strands apparent in the middle of the image. Scale bar is 200um. parenchymal musculature https://planosphere.stowers.org/ontology/PLANA_0000079 Dorsal-ventral muscle fibers present through the mesenchyme. OCLC:16809160 A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. UBERON:0000010 Planarian_Anatomy PLANA:0000080 peripheral nervous system https://planosphere.stowers.org/ontology/PLANA_0000080 An epithelial structure housing the definitive pharynx, connected to the esophagus and mouth. Planarian_Anatomy PLANA:0000081 pharyngeal pouch https://planosphere.stowers.org/ontology/PLANA_0000081 An epithelial structure housing the definitive pharynx, connected to the esophagus and mouth. OCLC:16809160 Ciliated epidermal cells located along the dorsal midline. Planarian_Anatomy PLANA:0000082 racing stripe https://planosphere.stowers.org/ontology/PLANA_0000082 Ciliated epidermal cells located along the dorsal midline. PMID:17553481 The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch. Planarian_Anatomy PLANA:0000084 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The posterior primary gut branch is indicated by arrows. Scale bar = 250um posterior primary gut branch https://planosphere.stowers.org/ontology/PLANA_0000084 The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch. PMID:21664348 Four large phagocytic cells associated with the temporary embryonic pharynx. Planarian_Anatomy PLANA:0000085 primitive gut cell https://planosphere.stowers.org/ontology/PLANA_0000085 Four large phagocytic cells associated with the temporary embryonic pharynx. PMID:28072387 Stage 2 embryo undergoing the process of sphere formation. Schmidtea_mediterranea_Developmental_Terms PLANA:0000086 protosphere https://planosphere.stowers.org/ontology/PLANA_0000086 Stage 2 embryo undergoing the process of sphere formation. PMID:28072387 Ciliated epithelial cells form tubules, generating coiled, branching units terminating in flame bulbs. Tubules are formed via intercellular junctions between two epithelial cells. Proximal tubules are connected to non-ciliated distal tubules within the parenchyma. Planarian_Anatomy PLANA:0000087 Depicted by field contains a diagram representing the protonephrida unit (top) as well as a 3D rendering of confocal data depicting the same. In the diagram, terminal flame cells and their corresponding cilia are in blues, the proximal tubule is in reds, the distal tubule is in greens while the collecting duct is in purple. In the 3D rendering below the cilia (AcTub) are in blue, portions of the proximal tubule (slc6a-13) are in red while the distal tubule (slc6a-12) is in green. proximal tubule https://planosphere.stowers.org/ontology/PLANA_0000087 Ciliated epithelial cells form tubules, generating coiled, branching units terminating in flame bulbs. Tubules are formed via intercellular junctions between two epithelial cells. Proximal tubules are connected to non-ciliated distal tubules within the parenchyma. PMID:21828097 PMID:26057828 The renal system is an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. UBERON:0001008 Planarian_Anatomy PLANA:0000088 renal system https://planosphere.stowers.org/ontology/PLANA_0000088 Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge. Planarian_Anatomy PLANA:0000089 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The secondary gut branch is indicated by arrows. Scale bar = 250um secondary gut branch https://planosphere.stowers.org/ontology/PLANA_0000089 Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge. PMID:21664348 A mature male germ cell that develops from a spermatid. CL:0000019 spermatozoa Planarian_Anatomy PLANA:0000090 sperm https://planosphere.stowers.org/ontology/PLANA_0000090 Generation of a multilayered spherical embryo comprised of temporary extraembryonic tissues and undifferentiated blastomeres. Schmidtea_mediterranea_Developmental_Terms PLANA:0000091 sphere formation https://planosphere.stowers.org/ontology/PLANA_0000091 Generation of a multilayered spherical embryo comprised of temporary extraembryonic tissues and undifferentiated blastomeres. OCLC:20423827 OCLC:464776945 PMID:12888018 PMID:15599763 PMID:28072387 Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2. Schmidtea_mediterranea_Developmental_Terms PLANA:0000092 syncytial yolk cell https://planosphere.stowers.org/ontology/PLANA_0000092 Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2. PMID:15599763 Gut branches originating from and connected to the secondary gut branches. Planarian_Anatomy PLANA:0000093 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The tertiary gut branch indicated is by arrows. Scale bar = 250um tertiary gut branch https://planosphere.stowers.org/ontology/PLANA_0000093 Gut branches originating from and connected to the secondary gut branches. PMID:21664348 The process in which the anatomical structures of a tissue are generated and organized. GO:0048729 Schmidtea_mediterranea_Developmental_Terms PLANA:0000094 tissue morphogenesis https://planosphere.stowers.org/ontology/PLANA_0000094 Ovo+ neoblasts and post-mitotic eye progenitors that simultaneously migrate and differentiate into photoreceptor neurons and non-neuronal pigment cup cells comprising the optic cup. Planarian_Anatomy PLANA:0000095 trail cell https://planosphere.stowers.org/ontology/PLANA_0000095 Ovo+ neoblasts and post-mitotic eye progenitors that simultaneously migrate and differentiate into photoreceptor neurons and non-neuronal pigment cup cells comprising the optic cup. PMID:22884275 Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells definitive epidermis of ventral region Planarian_Anatomy PLANA:0000096 ventral epidermis ventral region of the epidermal compartment https://planosphere.stowers.org/ontology/PLANA_0000096 Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO]. A cluster of neurons that extends posteriorly from the embryonic and larval brain and is surrounded by a connective tissue sheath. The ventral nerve cords make up the nervous system of some phyla of the invertebrates, particularly within the nematodes, annelids and the arthropods. It usually consists of cerebral ganglia anteriorly with the nerve cords running down the ventral ('belly', as opposed to back) plane of the organism. This characteristic is important in qualifying the difference compared to the chordates, which have a dorsal nerve cord. Ventral nerve cords from anterior to posterior (the thoracic and abdominal tagma in the arthropods) are made up of segmented ganglia that are connected by a tract of nerve fibers passing from one side to the other of the nerve cord called commissures. The complete system bears some likeness to a rope ladder. In some animals the bilateral ganglia are fused into a single large ganglion per segment. This characteristic is found mostly in the insects. BTO:0002328 EFO:0000896 FBbt:00001102 MAT:0000339 MIAA:0000339 UBERON:0000934 WBbt:0005829 http://en.wikipedia.org/wiki/Ventral_nerve_cord nlx:146329 ventral cord Planarian_Anatomy PLANA:0000097 ventral nerve cord https://planosphere.stowers.org/ontology/PLANA_0000097 Diploid cell resulting from the fusion of male and female gametes at fertilization. [ The_Dictionary_of_Cell_and_Molecular_Biology:Third_Edition ] Diploid cell produced by the fusion of sperm cell nucleus and egg cell. BTO:0000854 Planarian_Anatomy PLANA:0000098 zygote https://planosphere.stowers.org/ontology/PLANA_0000098 The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. neural cell CL:0000540 Planarian_Anatomy PLANA:0000099 neuron https://planosphere.stowers.org/ontology/PLANA_0000099 A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where the apical part is directed towards the lumen and the basal part to the basal lamina. CL:0000066 Planarian_Anatomy PLANA:0000100 epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000100 A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. CL:0000187 Planarian_Anatomy PLANA:0000101 muscle cell https://planosphere.stowers.org/ontology/PLANA_0000101 A subdivision of an anatomical compartment. Planarian_Anatomy PLANA:0000102 anatomical compartment subdivision https://planosphere.stowers.org/ontology/PLANA_0000102 The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. UBERON:0001017 Planarian_Anatomy PLANA:0000103 central nervous system https://planosphere.stowers.org/ontology/PLANA_0000103 Straight or curved rod-like structures within the epidermal cells, oriented with long axis at right angles to the epidermal surface, that are discharged into mucous secretions. Planarian_Anatomy PLANA:0000104 rhabdite https://planosphere.stowers.org/ontology/PLANA_0000104 Straight or curved rod-like structures within the epidermal cells, oriented with long axis at right angles to the epidermal surface, that are discharged into mucous secretions. OCLC:16809160 A cell that specializes in controlled release of one or more substances. CL:0000151 Planarian_Anatomy PLANA:0000105 secretory cell https://planosphere.stowers.org/ontology/PLANA_0000105 An epithelial cell that has cilia. CL:0000067 Planarian_Anatomy PLANA:0000106 ciliated epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000106 An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo. CL:0000428 Planarian_Anatomy PLANA:0000107 yolk cell https://planosphere.stowers.org/ontology/PLANA_0000107 An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo. PMID:27149082 Feature of an organism that is a subdivision of a local region. For example, the anterior pole is a subdivision of the head. Planarian_Anatomy PLANA:0000109 anatomical compartment subdivision feature https://planosphere.stowers.org/ontology/PLANA_0000109 foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the definitive pharynx. pharynx progenitor Planarian_Anatomy PLANA:0000110 definitive pharynx progenitor https://planosphere.stowers.org/ontology/PLANA_0000110 foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the definitive pharynx. PMID:24737865 PMID:25254346 Ciliated epithelial cells that assemble into proximal tubules. Planarian_Anatomy PLANA:0000111 proximal tubule epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000111 Ciliated epithelial cells that assemble into proximal tubules. PMID:21828097 A term used to describe a developmental process during Schmidtea mediterranea embryogenesis. Schmidtea_mediterranea_Developmental_Terms PLANA:0000112 Schmidtea mediterranea developmental term https://planosphere.stowers.org/ontology/PLANA_0000112 A term used to describe a developmental process during Schmidtea mediterranea embryogenesis. https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000000.md Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. Planarian_Anatomy PLANA:0000113 tissue https://planosphere.stowers.org/ontology/PLANA_0000113 Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. UBERON:0000479 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000000.md Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. UBERON:0000467 Planarian_Anatomy PLANA:0000114 anatomical system https://planosphere.stowers.org/ontology/PLANA_0000114 Nonciliated epithelial cells that assemble into protonephridial proximal tubules. Planarian_Anatomy PLANA:0000115 Depicted by field contains a diagram representing the protonephrida unit (top) as well as a 3D rendering of confocal data depicting the same. In the diagram, terminal flame cells and their corresponding cilia are in blues, the proximal tubule is in reds, the distal tubule is in greens while the collecting duct is in purple. In the 3D rendering below the cilia (AcTub) are in blue, portions of the proximal tubule (slc6a-13) are in red while the distal tubule (slc6a-12) is in green. distal tubule epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000115 Nonciliated epithelial cells that assemble into protonephridial proximal tubules. PMID:21828097 PMID:26057828 Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. UBERON:0000922 Planarian_Anatomy PLANA:0000116 embryo https://planosphere.stowers.org/ontology/PLANA_0000116 Anatomical structure that is part of an embryo. UBERON:0002050 Planarian_Anatomy PLANA:0000117 embryonic structure https://planosphere.stowers.org/ontology/PLANA_0000117 Nonciliated epithelial cells that assemble into collecting ducts. Planarian_Anatomy PLANA:0000118 collecting duct epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000118 Nonciliated epithelial cells that assemble into collecting ducts. PMID:26057828 A post-mitotic, terminally differentiated cell type found in planarian embryos, juveniles and/or adult animals. Planarian_Anatomy PLANA:0000119 terminally differentiated cell https://planosphere.stowers.org/ontology/PLANA_0000119 A cycling neoblast and/or post-mitotic cell that is primed or irreversibly committed to a tissue-specific differentation program precursor cell Planarian_Anatomy PLANA:0000120 progenitor cell https://planosphere.stowers.org/ontology/PLANA_0000120 A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. CL:0000034 Planarian_Anatomy PLANA:0000121 stem cell https://planosphere.stowers.org/ontology/PLANA_0000121 A mature sexual reproductive cell having a single set of unpaired chromosomes. CL:0000300 Planarian_Anatomy PLANA:0000122 gamete https://planosphere.stowers.org/ontology/PLANA_0000122 A cell of the embryo. CL:0002321 Planarian_Anatomy PLANA:0000123 embryonic cell https://planosphere.stowers.org/ontology/PLANA_0000123 The sensory system subserving the sense of vision. UBERON:0002104 Planarian_Anatomy PLANA:0000124 visual system https://planosphere.stowers.org/ontology/PLANA_0000124 Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. UBERON:0001032 Planarian_Anatomy PLANA:0000125 sensory system https://planosphere.stowers.org/ontology/PLANA_0000125 Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. UBERON:0001032 Anatomical system that has as its parts the organs concerned with reproduction. UBERON:0000990 Planarian_Anatomy PLANA:0000126 reproductive system https://planosphere.stowers.org/ontology/PLANA_0000126 Ciliated epithelial cells that assemble into the oviduct. Planarian_Anatomy PLANA:0000127 oviduct epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000127 Ciliated epithelial cells that assemble into the oviduct. PMID:22074376 Ciliated epithelial cells comprising the sperm ducts. Planarian_Anatomy PLANA:0000128 sperm duct epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000128 Ciliated epithelial cells comprising the sperm ducts. PMID:19022767 PMID:22074376 OBSOLETE Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 Planarian_Anatomy PLANA:0000129 replacing with UBERON term obsolete anatomical structure https://planosphere.stowers.org/ontology/PLANA_0000129 true piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers. Planarian_Anatomy PLANA:0000130 circular muscle progenitor cell https://planosphere.stowers.org/ontology/PLANA_0000130 piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers. PMID:29168507 Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue. UBERON:0001048 Planarian_Anatomy PLANA:0000131 primordium https://planosphere.stowers.org/ontology/PLANA_0000131 The production of haploid germ cells from diploid precursor cells through meiosis. Schmidtea_mediterranea_Developmental_Terms PLANA:0000132 gametogenesis https://planosphere.stowers.org/ontology/PLANA_0000132 The production of haploid germ cells from diploid precursor cells through meiosis. PMID:19022767 A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. mechanoreceptor Planarian_Anatomy PLANA:0000133 mechanoreceptor cell https://planosphere.stowers.org/ontology/PLANA_0000133 A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. PMID:7466176 PMID:18202849 piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers. Planarian_Anatomy PLANA:0000134 longitudinal muscle progenitor cell https://planosphere.stowers.org/ontology/PLANA_0000134 piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers. PMID:29168507 Definition forthcoming Planarian_Anatomy PLANA:0000135 female primordial germ cell https://planosphere.stowers.org/ontology/PLANA_0000135 Anatomical structure that is an individual member of of Schmidtea mediterranea or any other flatworm of the class Turbellaria. UBERON:0000468 whole animal whole body Planarian_Anatomy PLANA:0000136 whole organism The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass). GO:0031099 Wikipedia:Regeneration_(biology) regernative development biological_process PLANA:0000137 regeneration The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass). GOC:mah GOC:pr PROG-2-5 positive granules that range in size from 0.5um to 1um present in epithelia and epithelia progenitor cells. These are distinct from rhabdites. Steph Nowotarski 2018-08-03T19:14:32Z Planarian_Anatomy Depcited by is an immuno electron microscopy image of a mesenchymal cell labeled with anti-PROG-2-5 immuno-gold. Large rhod-shaped granules resembling rhabdites are found in the same cell labeled with PROG-2-5+ oval-shaped granules (pseudo-colored in blue). Higher magnification of the boxed region is shown in the panel below. e, endoplasmic reticulum; m, mitochondria; n, nucleus; rh, rhabdite. Scale bar, 1 μm. hyman vesicle PROG-2-5 positive granules that range in size from 0.5um to 1um present in epithelia and epithelia progenitor cells. These are distinct from rhabdites. PMID:29100657 PMID:29100657 Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus. whole organism of anterior region anterior region of the whole animal Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus. OCLC:16809160 Three dimensional compartment along the dorsoventral axis that is above the anteroposterior axis, containing the eyes. whole organism of dorsal region dorsal region of the whole animal Three dimensional compartment along the dorsoventral axis that is above the anteroposterior axis, containing the eyes. Three dimensional compartment along the anteroposterior axis that is closer to the tail rather than the head, from the anterior boundary of the pharyngeal pouch to the tip of the tail. whole organism of posterior region posterior compartment of the whole animal Three dimensional compartment along the anteroposterior axis that is closer to the tail rather than the head, from the anterior boundary of the pharyngeal pouch to the tip of the tail. Compartment along the dorsoventral axis that is below the anteroposterior axis. whole organism of ventral region ventral compartment of the whole animal Compartment along the dorsoventral axis that is below the anteroposterior axis. The passageway connecting the gonopore to the bursa (genital atrium). Part of the copulatory apparatus. During mating, sperm from a partner is deposited into the bursal canal, where it collects in the bursa before travelling up the oviducts to the bursa. Egg capsules pass through the bursal canal as they are laid through the gonopore. Planarian_Anatomy PLANA:0000201 bursal canal https://planosphere.stowers.org/ontology/PLANA_0000201 The passageway connecting the gonopore to the bursa (genital atrium). Part of the copulatory apparatus. During mating, sperm from a partner is deposited into the bursal canal, where it collects in the bursa before travelling up the oviducts to the bursa. Egg capsules pass through the bursal canal as they are laid through the gonopore. PMID:22074376 The gonopore, a component of the copulatory apparatus, is an opening located on the ventral side of the animal posterior to the definitive pharynx. The gonopore is the sole point of exit and entry for the reproductive system, allowing from reciprocal exchange of sperm during copulation and egg capsule laying. genital pore Planarian_Anatomy PLANA:0000203 gonopore https://planosphere.stowers.org/ontology/PLANA_0000203 The gonopore, a component of the copulatory apparatus, is an opening located on the ventral side of the animal posterior to the definitive pharynx. The gonopore is the sole point of exit and entry for the reproductive system, allowing from reciprocal exchange of sperm during copulation and egg capsule laying. PMID:22074376 A gonad containing female germline stem cells which fuel oocyte production. Two ovaries are located ventally, underneath the body wall musculature, immediately posterior to the cephalic ganglia (brain) and adjacent to the ventral nerve cords. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuel formation of the ovaries during juvenile development. Planarian_Anatomy PLANA:0000204 ovary https://planosphere.stowers.org/ontology/PLANA_0000204 A gonad containing female germline stem cells which fuel oocyte production. Two ovaries are located ventally, underneath the body wall musculature, immediately posterior to the cephalic ganglia (brain) and adjacent to the ventral nerve cords. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuel formation of the ovaries during juvenile development. PMID:17376870 Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium. Planarian_Anatomy PLANA:0000205 oviduct https://planosphere.stowers.org/ontology/PLANA_0000205 Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium. PMID:22074376 A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal. Planarian_Anatomy PLANA:0000206 penis papilla https://planosphere.stowers.org/ontology/PLANA_0000206 A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal. PMID:22074376 A network of tubes that transport sperm from the testes to the seminal vesicles. Tubes connect each testis to ducts that run along the ventral nerve cords. The ducts bifurcate immediately posterior to the pharynx, where they connect to the seminal vesicles. Planarian_Anatomy PLANA:0000207 sperm duct https://planosphere.stowers.org/ontology/PLANA_0000207 A network of tubes that transport sperm from the testes to the seminal vesicles. Tubes connect each testis to ducts that run along the ventral nerve cords. The ducts bifurcate immediately posterior to the pharynx, where they connect to the seminal vesicles. PMID:19022767 PMID:22074376 A gonad containing male germline stem cells which fuel sperm production. Testes are located dorsolaterally, and are excluded from the head. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuels formation of testes during juvenile development and regeneration. Planarian_Anatomy PLANA:0000208 testis https://planosphere.stowers.org/ontology/PLANA_0000208 A gonad containing male germline stem cells which fuel sperm production. Testes are located dorsolaterally, and are excluded from the head. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuels formation of testes during juvenile development and regeneration. PMID:19022767 OBSOLETE Anatomical structure that is present during embryonic development. UBERON:0005423 Planarian_Anatomy PLANA:0000209 replacing with UBERON term obsolete developing anatomical structure https://planosphere.stowers.org/ontology/PLANA_0000209 true Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2. Planarian_Anatomy PLANA:0000211 primitive ectoderm cell https://planosphere.stowers.org/ontology/PLANA_0000211 Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2. OCLC:20423827 OCLC:464776945 OCLC:82522822 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md Undifferentiated, zygote-derived cleavage progeny that give rise to temporary embryonic tissues during Stage 2, continue dividing asynchronously in the embryonic wall, and ultimately give rise to neoblasts and adult lineage progenitors beginning in Stage 5. Planarian_Anatomy PLANA:0000212 blastomere compartment https://planosphere.stowers.org/ontology/PLANA_0000212 Undifferentiated, zygote-derived cleavage progeny that give rise to temporary embryonic tissues during Stage 2, continue dividing asynchronously in the embryonic wall, and ultimately give rise to neoblasts and adult lineage progenitors beginning in Stage 5. PMID:28072387 A sexually immature member of the Schmidtea mediterranea sexuallly reproducing biotype. Schmidtea_mediterranea_Developmental_Stages PLANA:0000214 juvenile https://planosphere.stowers.org/ontology/PLANA_0000214 Products of the reproductive system include gametes, zygotes, yolk cells and egg capsules. Planarian_Anatomy PLANA:0000215 reproductive system product https://planosphere.stowers.org/ontology/PLANA_0000215 A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos. Egg capsules are anchored to a substrate via a stalk. Planarian_Anatomy PLANA:0000216 Depicted by field shows a light microscopy image of egg capsules with a scale bar of 3mm egg capsule https://planosphere.stowers.org/ontology/PLANA_0000216 A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos. Egg capsules are anchored to a substrate via a stalk. PMID:18942102 Reproductive organ that produces and releases eggs (ovary) or sperm (testis). UBERON:0000991 Planarian_Anatomy PLANA:0000217 gonad https://planosphere.stowers.org/ontology/PLANA_0000217 Neoblasts coexpressing piwi-1 and nanos that are required for male and female gonad formation. Primordial germ cells are present in both asexual and sexual adults. Planarian_Anatomy PLANA:0000218 male primordial germ cell https://planosphere.stowers.org/ontology/PLANA_0000218 Neoblasts coexpressing piwi-1 and nanos that are required for male and female gonad formation. Primordial germ cells are present in both asexual and sexual adults. PMID:17376870 gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm. spermatogonial stem cell (SSC) Planarian_Anatomy PLANA:0000219 male germline stem cell https://planosphere.stowers.org/ontology/PLANA_0000219 gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm. PMID:19022767 PMID:20844018 PMID:27163480 PMID:27330085 An euploid male germ cell of an early stage of spermatogenesis. In planaria, the gh4+ stem cell daughter exiting the niche undergoes three rounds of transit amplifying division with incomplete cytokinesis prior to transitioning to terminal differentiation. CL:0000020 Planarian_Anatomy PLANA:0000220 spermatogonium https://planosphere.stowers.org/ontology/PLANA_0000220 An euploid male germ cell of an early stage of spermatogenesis. In planaria, the gh4+ stem cell daughter exiting the niche undergoes three rounds of transit amplifying division with incomplete cytokinesis prior to transitioning to terminal differentiation. PMID:27163480 PMID:27330085 A tektin-1+ male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. CL:0000017 Planarian_Anatomy PLANA:0000221 spermatocyte https://planosphere.stowers.org/ontology/PLANA_0000221 A tektin-1+ male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. PMID:27330085 A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa. CL:0000018 Planarian_Anatomy PLANA:0000222 spermatid https://planosphere.stowers.org/ontology/PLANA_0000222 A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes. Planarian_Anatomy PLANA:0000223 female germline stem cell https://planosphere.stowers.org/ontology/PLANA_0000223 A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes. PMID:19022767 PMID:20844018 Glands surrounding the copulatory bursa that are required for production of the proteinaceous egg capsule shell and stalk. Planarian_Anatomy PLANA:0000224 cement gland https://planosphere.stowers.org/ontology/PLANA_0000224 Glands surrounding the copulatory bursa that are required for production of the proteinaceous egg capsule shell and stalk. ASIN:B000M4NK9M PMID:18942102 PMID:22074376 PMID:27149082 A reproductive strategy in which eggs are laid, with most embryonic development occurring outside of the parent. Schmidtea_mediterranea_Developmental_Terms PLANA:0000225 oviparity https://planosphere.stowers.org/ontology/PLANA_0000225 A reproductive strategy in which eggs are laid, with most embryonic development occurring outside of the parent. PMID:19022767 Fertilization of an oocyte by sperm from a different individual. Reciprocal exchange of sperm occurs during Schmidtea mediterranea copulation. Schmidtea_mediterranea_Developmental_Terms PLANA:0000226 cross-fertilization https://planosphere.stowers.org/ontology/PLANA_0000226 Fertilization of an oocyte by sperm from a different individual. Reciprocal exchange of sperm occurs during Schmidtea mediterranea copulation. PMID:19022767 PMID:28812561 1. A gamete (as an egg or sperm cell) or one of its antecedent cells. 2. A mature male or female germ cell usually possessing a haploid chromosome set and capable of initiating formation of a new diploid individual by fusion with a gamete of the opposite sex. BTO:0000535 Planarian_Anatomy PLANA:0000227 germ cell https://planosphere.stowers.org/ontology/PLANA_0000227 A male germ cell is a germ cell that supports male gamete production. CL:0000015 Planarian_Anatomy PLANA:0000228 male germ cell https://planosphere.stowers.org/ontology/PLANA_0000228 Female germ cell is a germ cell that supports female gamete production. CL:0000021 Planarian_Anatomy PLANA:0000229 female germ cell https://planosphere.stowers.org/ontology/PLANA_0000229 A sperm storage organ located immediately posterior to the ovary, at the anterior end of the oviduct. Oocytes exiting the ovary are fertilized in the tuba as they enter the oviduct. Planarian_Anatomy PLANA:0000230 tuba https://planosphere.stowers.org/ontology/PLANA_0000230 A sperm storage organ located immediately posterior to the ovary, at the anterior end of the oviduct. Oocytes exiting the ovary are fertilized in the tuba as they enter the oviduct. PMID:19022767 PMID:20844018 PMID:22074376 PMID:27149082 Glands surrounding the oviducts which produce yolk cells. Yolk cells deposited into the oviducts travel to the genital atrium where they are packaged, along with one or more zygotes, into developing egg capsules. Planarian_Anatomy PLANA:0000231 vitelline gland https://planosphere.stowers.org/ontology/PLANA_0000231 Glands surrounding the oviducts which produce yolk cells. Yolk cells deposited into the oviducts travel to the genital atrium where they are packaged, along with one or more zygotes, into developing egg capsules. PMID:16932928 PMID:18942102 PMID:27149082 Accessory reproductive structures involved in copulation, egg capsule development and laying. Planarian_Anatomy PLANA:0000232 copulatory apparatus https://planosphere.stowers.org/ontology/PLANA_0000232 Accessory reproductive structures involved in copulation, egg capsule development and laying. PMID:22074376 A chamber where egg capsules are formed. One or more zygotes and yolk cells produced by the vitelline glands collect in the copulatory bursa; glands surrounding the copulatory bursa produce the egg capsule shell. Nascent egg capsules exit the body by passing through the bursal canal and gonopore. The copulatory bursa is synonymous with the term genital atrium. bursa genital atrium Planarian_Anatomy PLANA:0000233 copulatory bursa https://planosphere.stowers.org/ontology/PLANA_0000233 A chamber where egg capsules are formed. One or more zygotes and yolk cells produced by the vitelline glands collect in the copulatory bursa; glands surrounding the copulatory bursa produce the egg capsule shell. Nascent egg capsules exit the body by passing through the bursal canal and gonopore. The copulatory bursa is synonymous with the term genital atrium. PMID:22074376 Glandular pouches adjoining the sperm ducts which produce seminal fluid. Planarian_Anatomy PLANA:0000234 seminal vesicle https://planosphere.stowers.org/ontology/PLANA_0000234 Glandular pouches adjoining the sperm ducts which produce seminal fluid. PMID:19022767 PMID:22074376 A cyst of 8 interconnected spermatocytes undergoes meiosis, producing 32 haploid round spermatids. Round spermatids express protein kinase A, and undergo morphogenesis to produce mature sperm. Planarian_Anatomy PLANA:0000237 round spermatid https://planosphere.stowers.org/ontology/PLANA_0000237 A cyst of 8 interconnected spermatocytes undergoes meiosis, producing 32 haploid round spermatids. Round spermatids express protein kinase A, and undergo morphogenesis to produce mature sperm. PMID:27163480 PMID:27330085 Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm. Planarian_Anatomy PLANA:0000238 elongate spermatid https://planosphere.stowers.org/ontology/PLANA_0000238 Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm. PMID:27163480 PMID:27330085 An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes. FMA:83673 Planarian_Anatomy PLANA:0000239 oogonial cell https://planosphere.stowers.org/ontology/PLANA_0000239 Any collection of muscles that is part of a body wall [Automatically generated definition]. define generically to encompass both vertebrates and invertebrates body wall muscles BSA:0000058 BTO:0001863 FMA:86931 UBERON:0004462 WBbt:0005813 Planarian_Anatomy PLANA:0000240 body wall musculature https://planosphere.stowers.org/ontology/PLANA_0000240 Pharynx muscle fibers running anteroposterior (proximal to distal). Planarian_Anatomy PLANA:0000241 pharyngeal longitudinal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000241 Pharynx muscle fibers running anteroposterior (proximal to distal). ASIN:B000M4NK9M OBSOLETE Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. UBERON:0002553 Planarian_Anatomy PLANA:0000242 replacing with UBERON term obsolete anatomical cavity https://planosphere.stowers.org/ontology/PLANA_0000242 true OBSOLETE Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. UBERON:0001062 Planarian_Anatomy PLANA:0000400 replacing with UBERON term obsolete anatomical entity https://planosphere.stowers.org/ontology/PLANA_0000400 true OBSOLETE Anatomical entity that has no mass. AAO:0010265 AEO:0000007 BILA:0000007 EHDAA2:0003007 FBbt:00007015 FMA:67112 HAO:0000007 PLANA:0000401 TAO:0001835 TGMA:0001827 UBERON:0000466 VHOG:0001727 immaterial physical anatomical entity Planarian_Anatomy replacing with UBERON term obsolete immaterial anatomical entity https://planosphere.stowers.org/ontology/PLANA_0000401 true OBSOLETE Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface. AAO:0010266 AEO:0000009 BILA:0000009 CARO:0000009 EHDAA2:0003009 FMA:9658 TAO:0001839 UBERON:0006983 Planarian_Anatomy PLANA:0000402 replacing with UBERON term obsolete anatomical point https://planosphere.stowers.org/ontology/PLANA_0000402 true OBSOLETE Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. anatomical spaces lumen space AAO:0010110 AEO:0000005 BILA:0000005 C94478 CARO:0000005 EHDAA2:0003005 FBbt:00007017 FMA:5897 HAO:0000005 TAO:0001668 TGMA:0001825 UBERON:0000464 UMLS:C0524461 VHOG:0001728 XAO:0003190 ZFA:0001643 http://linkedlifedata.com/resource/umls/id/C0524461 lumen space Planarian_Anatomy PLANA:0000403 replacing with UBERON term obsolete anatomical space https://planosphere.stowers.org/ontology/PLANA_0000403 true A anatomical space that is enclosed by a pharynx. UBERON:0001731 Planarian_Anatomy PLANA:0000404 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. Cavity of pharynx is indicated by arrows. Scale bar = 250um cavity of pharynx https://planosphere.stowers.org/ontology/PLANA_0000404 An anatomical space that is surrounded by a digestive tract. UBERON:0006909 Planarian_Anatomy PLANA:0000405 Depicted by field contains hematoxylin and eosin staining on a coronal section of a asexual adult animal. The lumen of the digestive tract is indicated by arrows. Scale bar = 250um lumen of digestive tract https://planosphere.stowers.org/ontology/PLANA_0000405 An anatomical space that is surrounded by a digestive tract. PMID:21664348 The orifice that connects the mouth to the exterior of the body. UBERON:0000166 Planarian_Anatomy PLANA:0000406 oral opening https://planosphere.stowers.org/ontology/PLANA_0000406 Anatomical space between the definitive pharynx and the epithelial cells comprising parapharyngeal pouch. Planarian_Anatomy PLANA:0000407 Depicted by field contains hematoxylin and eosin staining coronal section section of a asexual adult animal. Parapharyngeal pouch cavity is indicated by arrows. Scale bar = 250um pharnygeal pouch cavity https://planosphere.stowers.org/ontology/PLANA_0000407 Anatomical space between the definitive pharynx and the epithelial cells comprising parapharyngeal pouch. OCLC:16809160 The apical surface of the single layered epidermis that is in contact with the environment. definitive epidermis of apical surface apical surface of the epidermal compartment The apical surface of the single layered epidermis that is in contact with the environment. Depicted by field is an electron micrograph of the dorsal epidermis in a transverse plane from an asexual adult animal. The apical epidermis surface is noted with magenta arrows. Scale bar is 5um. The basal surface of the epidermal epithelium in direct contact with the basal lamina. definitive epidermis of basal surface basal surface of the epidermal compartment The basal surface of the epidermal epithelium in direct contact with the basal lamina. The depicted by field is an electron micrograph of the dorsal epidermis in a transverse plane. The basal epidermis surface is noted with magenta arrows. Scale bar is 5um. The surface of the gut lumen in contact with ingested food. Planarian_Anatomy PLANA:0000411 The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the anterior primary gut branch. The lumen gut surface is marked by black arrows. Scale bar is 200um. lumen gut surface https://planosphere.stowers.org/ontology/PLANA_0000411 The surface of the gut lumen in contact with ingested food. PMID:21664348 The epithelial surface lining the interior of the pharynx, facing the lumen. Planarian_Anatomy PLANA:0000412 The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the pharynx and surrounding tissues. The pharynx lumen epithelial surface is marked by black arrows. Scale bar is 200um. pharynx lumen epithelial surface https://planosphere.stowers.org/ontology/PLANA_0000412 The epithelial surface lining the interior of the pharynx, facing the lumen. UBERON:0001731 Epithelial surface covering the outside of the pharynx. Planarian_Anatomy PLANA:0000413 The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the pharynx and surrounding tissues. The pharynx outer epithelial surface is marked by black arrows. Scale bar is 200um. pharynx outer epithelial surface https://planosphere.stowers.org/ontology/PLANA_0000413 Epithelial surface covering the outside of the pharynx. doi:10.1002/jmor.1052060308 PMID:29865769 The surface of the parapharyngeal pouch facing the pharynx. Planarian_Anatomy PLANA:0000414 The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the pharynx and surrounding tissues. Anterior is up. The parapharyngeal pouch surface is marked by black arrows. Scale bar is 200um. pharyngeal pouch surface https://planosphere.stowers.org/ontology/PLANA_0000414 The surface of the parapharyngeal pouch facing the pharynx. OCLC:16809160 OBSOLETE Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. UBERON:0000475 Planarian_Anatomy PLANA:0000416 replacing with UBERON term obsolete organism subdivision https://planosphere.stowers.org/ontology/PLANA_0000416 true Anatomical structure which is a subdivision of a whole adult or juvenile organism, consisting of components of multiple anatomical systems. Planarian_Anatomy PLANA:0000417 definitive organism subdivision https://planosphere.stowers.org/ontology/PLANA_0000417 The head is the anterior-most division of the body [GO]. A three dimensional compartment bounded by the anterior margin or the head and the posterior boundary of the cephalic ganglia (brain). UBERON:0000033 Planarian_Anatomy PLANA:0000418 Depicted by field contains diagram representation of body region. head https://planosphere.stowers.org/ontology/PLANA_0000418 Region of the juvenile or adult animal between the posterior end of the cephalic ganglia and the anterior end of the definitive pharynx. Planarian_Anatomy PLANA:0000419 prepharyngeal region https://planosphere.stowers.org/ontology/PLANA_0000419 Region of the animal lateral to and surrounding the definitive pharynx. Trunk is a synonym here because the parapharyngeal region is always contained in a trunk fragment. However, a trunk fragment may also contain some neck and some tail. trunk Planarian_Anatomy PLANA:0000420 parapharyngeal region https://planosphere.stowers.org/ontology/PLANA_0000420 Caudal region, beginning at the mouth and ending at posterior pole. Planarian_Anatomy PLANA:0000421 Depicted by field contains diagram representation of body region. tail https://planosphere.stowers.org/ontology/PLANA_0000421 Medial region of the tail; the parenchymal space between the posterior primary gut branches. Planarian_Anatomy PLANA:0000422 tail stripe https://planosphere.stowers.org/ontology/PLANA_0000422 Anatomical structure which is a subdivision of a whole developing/ embryonic organism, consisting of components of multiple anatomical systems. Planarian_Anatomy PLANA:0000423 embryonic subdivision https://planosphere.stowers.org/ontology/PLANA_0000423 OBSOLETE Anatomical entity that has mass. UBERON:0000465 Planarian_Anatomy PLANA:0000424 replacing with UBERON term obsolete material anatomical entity https://planosphere.stowers.org/ontology/PLANA_0000424 true Anatomical structure present in juvenile and adult planaria. Planarian_Anatomy PLANA:0000425 definitive anatomical structure https://planosphere.stowers.org/ontology/PLANA_0000425 OBSOLETE Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. acellular anatomical structures AAO:0010268 AEO:0000040 BILA:0000040 CARO:0000040 EHDAA2:0003040 FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 TGMA:0001841 XAO:0003162 ZFA:0000382 Planarian_Anatomy PLANA:0000426 replacing with UBERON term obsolete acellular anatomical structure https://planosphere.stowers.org/ontology/PLANA_0000426 true An anatomical structure that has more than one cell as a part. UBERON:0010000 Planarian_Anatomy PLANA:0000427 multicellular anatomical structure https://planosphere.stowers.org/ontology/PLANA_0000427 Total musculature of the planarian body. http://purl.obolibrary.org/obo/UBERON_0001015 Planarian_Anatomy PLANA:0000428 musculature system https://planosphere.stowers.org/ontology/PLANA_0000428 A heterogeneous population of pluripotent, somatic adult stem cells and lineage primed progenitors that are required for maintenance and regeneration of all cell types in planaria, including the germline. Planarian_Anatomy PLANA:0000429 neoblast compartment https://planosphere.stowers.org/ontology/PLANA_0000429 A heterogeneous population of pluripotent, somatic adult stem cells and lineage primed progenitors that are required for maintenance and regeneration of all cell types in planaria, including the germline. PMID:16311336 PMID:21566185 PMID:22899852 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md A part of an epithelial cell. Planarian_Anatomy PLANA:0000430 epithelial cell component https://planosphere.stowers.org/ontology/PLANA_0000430 Anatomical structure that performs a specific function or group of functions. UBERON:0000062 Planarian_Anatomy PLANA:0000431 organ https://planosphere.stowers.org/ontology/PLANA_0000431 OBSOLETE An anatomical structure that is undergoing regeneration. UBERON:0007567 Planarian_Anatomy PLANA:0000432 replacing with UBERON term obsolete regenerating anatomical structure https://planosphere.stowers.org/ontology/PLANA_0000432 true The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. Source: NIF_Subcellular:sao-1337158144, GOC:go_curators GO:0005575 Planarian_Anatomy PLANA:0000433 cellular component https://planosphere.stowers.org/ontology/PLANA_0000433 A decussation of the diencephalon where the fibers of the optic nerve cross The point at which fibers of the optic nerves cross.[AAO] The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG] chiasma chiasma nervorum opticorum optic chiasm (Rufus of Ephesus) AAO:0010622 BAMS:DC BAMS:OC BAMS:och BAMS:ox BM:Tel-OCX C90609 DHBA:10644 DMBA:17783 EHDAA2:0001302 EHDAA:10227 EMAPA:17603 FMA:62045 GAID:832 HBA:9310 MA:0001098 MBA:117 MESH:D009897 Optic:chiasm TAO:0000556 UBERON:0000959 UMLS:C0029126 VHOG:0000190 XAO:0004071 ZFA:0000556 birnlex:1416 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=459 http://linkedlifedata.com/resource/umls/id/C0029126 http://www.snomedbrowser.com/Codes/Details/244453006 chiasma opticum decussation of optic nerve fibers optic chiasm Planarian_Anatomy PLANA:0000459 optic chiasma https://planosphere.stowers.org/ontology/PLANA_0000459 A decussation of the diencephalon where the fibers of the optic nerve cross PMID:18466009 A bundle of nerve fibers connecting the two cephalic ganglia. UBERON:0000935 Planarian_Anatomy PLANA:0000460 anterior commissure https://planosphere.stowers.org/ontology/PLANA_0000460 Nerve branches that extend from the lateral side of each cephalic ganglia lobe. Each lobe has nine lateral branches which terminate in sensory organs. Evidence suggests they play a role in chemosensation. Planarian_Anatomy PLANA:0000461 lateral branches https://planosphere.stowers.org/ontology/PLANA_0000461 Nerve branches that extend from the lateral side of each cephalic ganglia lobe. Each lobe has nine lateral branches which terminate in sensory organs. Evidence suggests they play a role in chemosensation. PMID:12128224 PMID:18466009 PMID:27612384 PMID:4452894 PMID:9493832 A cell that performs a sensory function. Planarian_Anatomy PLANA:0000462 sensory cell https://planosphere.stowers.org/ontology/PLANA_0000462 Neurons that express choline acetyltransferase. Planarian_Anatomy PLANA:0000463 cholinergic neuron https://planosphere.stowers.org/ontology/PLANA_0000463 Neurons that express choline acetyltransferase. PMID:20338223 Neurons that express glutamine decarboxylase. Planarian_Anatomy PLANA:0000464 GABAergic neuron https://planosphere.stowers.org/ontology/PLANA_0000464 Neurons that express glutamine decarboxylase. PMID:18440152 Plexus of nerves located in the definitive pharynx comprised of inner and outer wall rings. Planarian_Anatomy PLANA:0000465 pharynx nerve plexus https://planosphere.stowers.org/ontology/PLANA_0000465 Plexus of nerves located just between the definitive epidermis and the body wall musculature. Planarian_Anatomy PLANA:0000466 subepidermal nerve plexus https://planosphere.stowers.org/ontology/PLANA_0000466 Plexus of nerves located just between the definitive epidermis and the body wall musculature. PMID:27612384 doi:10.1002/jmor.1051550208 Plexus of nerves that innervate the body wall muscles. Planarian_Anatomy PLANA:0000467 submuscular nerve plexus https://planosphere.stowers.org/ontology/PLANA_0000467 A thin net of single nerve fibers located around the gut. Planarian_Anatomy PLANA:0000468 gastrodermal plexus https://planosphere.stowers.org/ontology/PLANA_0000468 A thin net of single nerve fibers located around the gut. PMID:17999079 doi.org/10.1002/jmor.1051550208 A cluster of neurites that is part of a nervous system and forms a network of dendrites and axons where synapses are present and in which neuronal somata do not occur. Multi-cell component structure of the central nervous system consisting largely of neuron projections (tracts and synaptic neuropil domains) and associated glial cells. This corresponds to the part of the CNS that is enclosed by the cortex. neuropilus BTO:0005268 C12617 CALOHA:TS-2403 FBbt:00005139 FMA:261269 GAID:740 MESH:D019581 NIF_Subcellular:sao205380252 UBERON:0002606 UMLS:C0228081 birnlex:1142 http://en.wikipedia.org/wiki/Neuropil http://linkedlifedata.com/resource/umls/id/C0228081 http://www.snomedbrowser.com/Codes/Details/67146008 Planarian_Anatomy PLANA:0000470 neuropil https://planosphere.stowers.org/ontology/PLANA_0000470 A cluster of neurites that is part of a nervous system and forms a network of dendrites and axons where synapses are present and in which neuronal somata do not occur. PMID:27612384 Heavily ciliated epidermal cells covering the outer surface of the pharynx shaft. These are "insunk" epidermal cells in which the nuclei reside behind the layers of longitudinal and circumferential muscles and the epithelial cell body sends out a ciliated projection to the surface to cover and encase the shaft. Planarian_Anatomy PLANA:0000472 outer pharyngeal epithelium https://planosphere.stowers.org/ontology/PLANA_0000472 Heavily ciliated epidermal cells covering the outer surface of the pharynx shaft. These are "insunk" epidermal cells in which the nuclei reside behind the layers of longitudinal and circumferential muscles and the epithelial cell body sends out a ciliated projection to the surface to cover and encase the shaft. ASIN:B000M4NK9M Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles. Planarian_Anatomy PLANA:0000473 outer pharyngeal circular muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000473 Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles. ASIN:B000M4NK9M Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers. Planarian_Anatomy PLANA:0000474 inner pharyngeal circular muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000474 Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers. ASIN:B000M4NK9M Pharynx muscle fibers running anteroposterior which lie beneath both the inner circular muscle fibers and the apical, ciliated portion of the epithium lining the lumenal surface. Planarian_Anatomy PLANA:0000475 inner pharyngeal longitudinal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000475 Pharynx muscle fibers running anteroposterior which lie beneath both the inner circular muscle fibers and the apical, ciliated portion of the epithium lining the lumenal surface. ASIN:B000M4NK9M Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium. Planarian_Anatomy PLANA:0000476 outer pharyngeal longitudinal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000476 Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium. ASIN:B000M4NK9M Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts. Planarian_Anatomy PLANA:0000477 pharyngeal radial muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000477 Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts. ASIN:B000M4NK9M The total musculature within the pharynx. UBERON:0004467 Planarian_Anatomy PLANA:0000478 musculature of pharynx https://planosphere.stowers.org/ontology/PLANA_0000478 The total musculature within the pharynx. PMID:26904543 Ring of the pharynx nerve plexus that is proximal to the lumen. Planarian_Anatomy PLANA:0000479 inner pharynx nerve plexus https://planosphere.stowers.org/ontology/PLANA_0000479 Ring of the pharynx nerve plexus that is proximal to the exterior surface. Planarian_Anatomy PLANA:0000480 outer pharynx nerve plexus https://planosphere.stowers.org/ontology/PLANA_0000480 Ring of the pharynx nerve plexus that is proximal to the exterior surface. doi:10.1002/jmor.1051550208 PMID:27612384 Neurons that express the neurotransmitter serotonin. Planarian_Anatomy PLANA:0000481 serotonergic neuron https://planosphere.stowers.org/ontology/PLANA_0000481 Neurons that express the neurotransmitter serotonin. PMID:17624455 A neuron that expresses the neurotransmitter dopamine. Planarian_Anatomy PLANA:0000482 dopaminergic neuron https://planosphere.stowers.org/ontology/PLANA_0000482 A neuron that expresses the neurotransmitter dopamine. PMID:17565705 Neurons that express the biogenic amine octopamine. Planarian_Anatomy PLANA:0000483 octopaminergic neuron https://planosphere.stowers.org/ontology/PLANA_0000483 Neurons that express the biogenic amine octopamine. PMID:18926867 Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus. Planarian_Anatomy PLANA:0000484 secretory system https://planosphere.stowers.org/ontology/PLANA_0000484 Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus. PMID:20865784 Specialized insunk epithelial cells located in the mesenchyme that participate in mucus secretion. They are characterized by elongated cell bodies with long cytoplasmic projections that terminate between, or penetrate directly through epithelial cells and form a secretory pore at the surface. Planarian_Anatomy PLANA:0000485 gland cell https://planosphere.stowers.org/ontology/PLANA_0000485 Specialized insunk epithelial cells located in the mesenchyme that participate in mucus secretion. They are characterized by elongated cell bodies with long cytoplasmic projections that terminate between, or penetrate directly through epithelial cells and form a secretory pore at the surface. PMID:20865784 The opening by which the gland cells secrete mucus to the exterior of the animal. Planarian_Anatomy PLANA:0000486 secretory pore https://planosphere.stowers.org/ontology/PLANA_0000486 The opening by which the gland cells secrete mucus to the exterior of the animal. PMID:20865784 One of two distinct histochemical classes of gland cells, these can be found throughout the body but primarily form clusters of subepidermal marginal adhesive glands along the dorsalventral border of the animal. eosinophilic gland cell Planarian_Anatomy PLANA:0000487 acidophilic gland cell https://planosphere.stowers.org/ontology/PLANA_0000487 One of two distinct histochemical classes of gland cells, these can be found throughout the body but primarily form clusters of subepidermal marginal adhesive glands along the dorsalventral border of the animal. PMID:20865784 One of two distinct histochemical classes of gland cells, these are found near the ventral mesenchyme, the pharynx and in the dorsal region of the head. May also be called cyanophilic gland cells. Planarian_Anatomy PLANA:0000488 basophilic gland cell https://planosphere.stowers.org/ontology/PLANA_0000488 One of two distinct histochemical classes of gland cells, these are found near the ventral mesenchyme, the pharynx and in the dorsal region of the head. May also be called cyanophilic gland cells. PMID:20865784 OBSOLETE Non-material anatomical entity of one dimension, which forms a boundary of an anatomical surface or is a modulation of an anatomical surface. AAO:0010267 AEO:0000008 BILA:0000008 CARO:0000008 EHDAA2:0003008 FMA:9657 HAO:0000008 TAO:0001837 TGMA:0001828 UBERON:0006800 XAO:0004003 ZFA:0001689 Planarian_Anatomy PLANA:0000489 reolacing with CARO term obsolete anatomical line https://planosphere.stowers.org/ontology/PLANA_0000489 true OBSOLETE A flat anatomical 2D surface that bisects an anatomical structure or an anatomical space. fiat anatomical surface CARO:0001013 FMA:242982 UBERON:0035085 Planarian_Anatomy PLANA:0000490 All anatomical planes are fiat anatomical boundaries - no morphological boundary could ever be a perfect plane. replacing with BSPO term obsolete anatomical plane https://planosphere.stowers.org/ontology/PLANA_0000490 true An anatomical plane that bisects a zone of weakness in an appendage. When autotomy occurs, the appendage divides along this plane. this class is intended for autotomy that bisects an appendage. Other forms of autotomy are possible: for example, a sea cucumber and autotomitize internal organs UBERON:0035086 Planarian_Anatomy PLANA:0000491 plane of autotomy https://planosphere.stowers.org/ontology/PLANA_0000491 Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA]. in FMA this is a subtype of junction rather than tissue plexus AEO:0000138 BTO:0000205 C12929 EHDAA2:0003138 EHDAA:3780 FMA:5901 MA:0002407 UBERON:0001810 UMLS:C0501403 http://en.wikipedia.org/wiki/Nervous_system_plexus http://linkedlifedata.com/resource/umls/id/C0501403 http://www.snomedbrowser.com/Codes/Details/122455009 Planarian_Anatomy PLANA:0000492 nerve plexus https://planosphere.stowers.org/ontology/PLANA_0000492 Axon tract that crosses the midline of the central nervous system[NIF, modified]. In the context of Drosophila refers to a broad band of axons connecting equivalent neuropils each side of the brain[FBbt]. White matter fiber bundle that crosses the midline of the brain or spinal cord, that connects similar structures on both sides. (CUMBO; Heimer, L. The Human Brain, 2nd ed., 1995, pg 6) commissural white matter commissure commissure C32349 FBbt:00005103 FMA:83906 OpenCyc:Mx4rdBrmE6gOEdudWQACs5b6Bw TADS:0000201 UBERON:0001020 UMLS:C1185742 http://en.wikipedia.org/wiki/Commissure http://linkedlifedata.com/resource/umls/id/C1185742 nlx:110 nlx_anat:20090513 commissure of neuraxis neuraxis commissure Planarian_Anatomy PLANA:0000493 *not* the same as FMA:76741 Commissure nervous system commissure https://planosphere.stowers.org/ontology/PLANA_0000493 any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain[MP] UBERON:0005970 Planarian_Anatomy PLANA:0000494 brain commissure https://planosphere.stowers.org/ontology/PLANA_0000494 A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise AEO:0000192 BTO:0001638 CARO:0000010 EFO:0003658 FMA:50705 TAO:0001270 UBERON:0005306 XAO:0004060 ncithesaurus:Blastemal_Cell blastema cell Planarian_Anatomy PLANA:0000495 blastema https://planosphere.stowers.org/ontology/PLANA_0000495 OBSOLETE A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. UBERON:0000015 Planarian_Anatomy PLANA:0000496 non-material anatomical boundary obsolete anatomical boundary https://planosphere.stowers.org/ontology/PLANA_0000496 true OBSOLETE An anatomical structure that connects two structures junction FMA:5898 UBERON:0007651 http://www.snomedbrowser.com/Codes/Details/91833003 anatomical junction Planarian_Anatomy PLANA:0000497 replacing with UBERON term obsolete anatomical junction https://planosphere.stowers.org/ontology/PLANA_0000497 true A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FMA:68646 GO:0005623 KUPO:0000002 VHOG:0001533 WBbt:0004017 XAO:0003012 Planarian_Anatomy PLANA:0000499 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell https://planosphere.stowers.org/ontology/PLANA_0000499 Anatomical structure that is a direct part of the cell. TODO - move metadata to GO and obsolete this class once homes have been found for existing children. Note the inconsistency between the usage of the label 'cell component' in GO and CARO cell component AAO:0010271 BILA:0000014 C34070 CARO:0000014 FBbt:00007012 FMA:86454 GO:0044464 HAO:0000014 NIF_Subcellular:sao-1337158144 OpenCyc:Mx4rwQwkcZwpEbGdrcN5Y29ycA TGMA:0001834 UBERON:0000470 UMLS:C1178969 http://linkedlifedata.com/resource/umls/id/C1178969 Planarian_Anatomy PLANA:0000500 cell part https://planosphere.stowers.org/ontology/PLANA_0000500 A prolongation or process extending from a cell. GO_0042995 Planarian_Anatomy PLANA:0000501 cell projection https://planosphere.stowers.org/ontology/PLANA_0000501 A cell projection supported by an assembly of actin filaments. GO_0098858 Planarian_Anatomy PLANA:0000502 actin-based cell projection https://planosphere.stowers.org/ontology/PLANA_0000502 A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GO_0005929 Planarian_Anatomy PLANA:0000503 cilium https://planosphere.stowers.org/ontology/PLANA_0000503 Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. GO:0005902 Planarian_Anatomy PLANA:0000504 microvillus https://planosphere.stowers.org/ontology/PLANA_0000504 Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions. GO_0044291 Planarian_Anatomy PLANA:0000505 cell-cell contact zone https://planosphere.stowers.org/ontology/PLANA_0000505 A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. GO:0030054 Planarian_Anatomy PLANA:0000506 cell junction https://planosphere.stowers.org/ontology/PLANA_0000506 A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals. GO:0005911 Planarian_Anatomy PLANA:0000507 cell-cell junction https://planosphere.stowers.org/ontology/PLANA_0000507 The attachment of one cell to another cell via adhesion molecules. GO:0098609 Planarian_Anatomy PLANA:0000508 cell-cell adhesion https://planosphere.stowers.org/ontology/PLANA_0000508 Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. GO:0044424 Planarian_Anatomy PLANA:0000509 intracellular part https://planosphere.stowers.org/ontology/PLANA_0000509 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures GO:0005737 Planarian_Anatomy PLANA:0000510 cytoplasm https://planosphere.stowers.org/ontology/PLANA_0000510 Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions. eosinophilic tmeehan 2009-12-22T04:23:25Z CP_0000027 Planarian_Anatomy PLANA:0000511 acidophilic cytoplasm https://planosphere.stowers.org/ontology/PLANA_0000511 Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. tmeehan 2009-12-22T04:24:54Z CP_0000028 Planarian_Anatomy PLANA:0000512 basophilic cytoplasm https://planosphere.stowers.org/ontology/PLANA_0000512 Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO_0044444 Planarian_Anatomy PLANA:0000513 cytoplasmic part https://planosphere.stowers.org/ontology/PLANA_0000513 Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell. GO:0044433 Planarian_Anatomy PLANA:0000514 cytoplasmic vesicle part https://planosphere.stowers.org/ontology/PLANA_0000514 A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. GO:0005773 Planarian_Anatomy PLANA:0000515 vacuole https://planosphere.stowers.org/ontology/PLANA_0000515 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. GO_0007010 Planarian_Anatomy PLANA:0000516 cytoskeleton organization https://planosphere.stowers.org/ontology/PLANA_0000516 Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GO_0043229 Planarian_Anatomy PLANA:0000518 intracellular organelle https://planosphere.stowers.org/ontology/PLANA_0000518 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes GO_0043232 Planarian_Anatomy PLANA:0000519 intracellular non-membrane-bounded organelle https://planosphere.stowers.org/ontology/PLANA_0000519 A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. GO_0016020 Planarian_Anatomy PLANA:0000520 membrane https://planosphere.stowers.org/ontology/PLANA_0000520 Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes. GO_0098588 Planarian_Anatomy PLANA:0000521 bounding membrane of organelle https://planosphere.stowers.org/ontology/PLANA_0000521 Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. GO_0044425 Planarian_Anatomy PLANA:0000522 membrane part https://planosphere.stowers.org/ontology/PLANA_0000522 Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO_0044459 Planarian_Anatomy PLANA:0000523 plasma membrane part https://planosphere.stowers.org/ontology/PLANA_0000523 A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. GO_0031090 Planarian_Anatomy PLANA:0000524 organelle membrane https://planosphere.stowers.org/ontology/PLANA_0000524 Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. GO_0043226 Planarian_Anatomy PLANA:0000525 organelle https://planosphere.stowers.org/ontology/PLANA_0000525 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GO:0043227 Planarian_Anatomy PLANA:0000526 membrane-bounded organelle https://planosphere.stowers.org/ontology/PLANA_0000526 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GO_0043231 Planarian_Anatomy PLANA:0000527 intracellular membrane-bounded organelle https://planosphere.stowers.org/ontology/PLANA_0000527 A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. GO_0005794 Planarian_Anatomy PLANA:0000528 Golgi apparatus https://planosphere.stowers.org/ontology/PLANA_0000528 A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. GO_0005634 Planarian_Anatomy PLANA:0000529 nucleus https://planosphere.stowers.org/ontology/PLANA_0000529 A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. GO_0099503 Planarian_Anatomy PLANA:0000530 secretory vesicle https://planosphere.stowers.org/ontology/PLANA_0000530 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. GO_0043228 Planarian_Anatomy PLANA:0000531 non-membrane-bounded organelle https://planosphere.stowers.org/ontology/PLANA_0000531 Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. GO_0044428 Planarian_Anatomy PLANA:0000532 nuclear part https://planosphere.stowers.org/ontology/PLANA_0000532 A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. GO_0005730 Planarian_Anatomy PLANA:0000533 nucleolus https://planosphere.stowers.org/ontology/PLANA_0000533 The ordered and organized complex of DNA, protein (histones), and sometimes RNA, that forms the chromosome. GO_0000785 Planarian_Anatomy PLANA:0000534 chromatin https://planosphere.stowers.org/ontology/PLANA_0000534 A compact and highly condensed form of chromatin. GO_0000792 Planarian_Anatomy PLANA:0000535 heterochromatin https://planosphere.stowers.org/ontology/PLANA_0000535 A dispersed and relatively uncompacted form of chromatin. GO_0000791 Planarian_Anatomy PLANA:0000536 euchromatin https://planosphere.stowers.org/ontology/PLANA_0000536 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. GO_0005840 Planarian_Anatomy PLANA:0000537 ribosome https://planosphere.stowers.org/ontology/PLANA_0000537 A group of axons linking two or more neuropils and having a common origin, termination UBERON:0001018 Planarian_Anatomy PLANA:0000538 axon tract https://planosphere.stowers.org/ontology/PLANA_0000538 A cell whose function is determined by its response to an electric signal. CL:0000393 Planarian_Anatomy PLANA:0000539 electrically responsive cell https://planosphere.stowers.org/ontology/PLANA_0000539 A cell that initiates an electrical signal and passes that signal to another cell. CL:0000404 Planarian_Anatomy PLANA:0000540 electrically signaling cell https://planosphere.stowers.org/ontology/PLANA_0000540 An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. neural subtree UBERON:0001021 nerves peripheral nerve Planarian_Anatomy PLANA:0000541 nerve https://planosphere.stowers.org/ontology/PLANA_0000541 A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 Planarian_Anatomy PLANA:0000543 neuron projection bundle https://planosphere.stowers.org/ontology/PLANA_0000543 A neuron which conveys sensory information centrally from the periphery. CL:0000526 FMA:87653 input neuron Planarian_Anatomy PLANA:0000545 afferent neuron https://planosphere.stowers.org/ontology/PLANA_0000545 A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body. CL:0000103 FMA:67282 Planarian_Anatomy PLANA:0000546 bipolar neuron https://planosphere.stowers.org/ontology/PLANA_0000546 A neuron that has an axon which crosses the midline. CL:0000678 Planarian_Anatomy PLANA:0000547 commissural neuron https://planosphere.stowers.org/ontology/PLANA_0000547 A neuron which sends impulses peripherally to activate muscles or secretory cells. CL:0000527 output neuron Planarian_Anatomy PLANA:0000548 efferent neuron https://planosphere.stowers.org/ontology/PLANA_0000548 A motor neuron that is capable of directly inducing muscle contraction. CL:0008014 Planarian_Anatomy PLANA:0000549 In vertebrates, all motor neurons are excitatory, but various types of inhibitory motor neurons exist in invertebrates. excitatory motor neuron https://planosphere.stowers.org/ontology/PLANA_0000549 Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. BTO:0003811 CL:0000099 FBbt:00005125 FMA:67313 WBbt:0005113 Planarian_Anatomy PLANA:0000550 interneuron https://planosphere.stowers.org/ontology/PLANA_0000550 Any neuron having a sensory function; an afferent neuron conveying sensory impulses. BTO:0001037 CL:0000101 FBbt:00005124 FMA:84649 WBbt:0005759 Planarian_Anatomy PLANA:0000552 sensory neuron https://planosphere.stowers.org/ontology/PLANA_0000552 An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement. BTO:0000312 CL:0000100 FMA:83617 WBbt:0005409 motoneuron Planarian_Anatomy PLANA:0000553 motor neuron https://planosphere.stowers.org/ontology/PLANA_0000553 Neuronal cells which synthesize, store and release neurohormones. CL:0000381 FBbt:00005130 Planarian_Anatomy PLANA:0000556 neurosecretory neuron https://planosphere.stowers.org/ontology/PLANA_0000556 Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides. CL:0011103 Planarian_Anatomy PLANA:0000558 sympathetic neuron https://planosphere.stowers.org/ontology/PLANA_0000558 Neuron with one neurite that extends from the cell body. CL:0000106 FMA:67278 Planarian_Anatomy PLANA:0000559 unipolar neuron https://planosphere.stowers.org/ontology/PLANA_0000559 Neuron with one neurite that extends from the cell body. PMID:18499291 Neuron with an axon and two or more dendrites. CL:0000104 FMA:67287 Planarian_Anatomy PLANA:0000560 multipolar neuron https://planosphere.stowers.org/ontology/PLANA_0000560 Neuron with an axon and two or more dendrites. PMID:18499291 Cells that are in close proximity to neurons. CL:0000130 Planarian_Anatomy PLANA:0000561 neuron associated cell (sensu Nematoda and Protostomia) https://planosphere.stowers.org/ontology/PLANA_0000561 Any neuron that is part of a central nervous system. TermGenie 2014-06-25T01:17:43Z CL:2000029 Planarian_Anatomy PLANA:0000562 central nervous system neuron https://planosphere.stowers.org/ontology/PLANA_0000562 Any neuron that is part of a peripheral nervous system. TermGenie 2014-06-25T02:28:17Z CL:2000032 Planarian_Anatomy PLANA:0000564 peripheral nervous system neuron https://planosphere.stowers.org/ontology/PLANA_0000564 A neruon whose cell body is within an autonomic ganglion. CL:0000107 FMA:80121 Planarian_Anatomy PLANA:0000565 autonomic neuron https://planosphere.stowers.org/ontology/PLANA_0000565 Neuron that is part of the enteric nervous system. haendel 2012-06-28T08:20:31Z CL:0007011 Planarian_Anatomy PLANA:0000566 enteric neuron https://planosphere.stowers.org/ontology/PLANA_0000566 Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue. this class represents a continuous sheet of basal lamina which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal lamina' represents a portion of substance on the scale of a single cell. A basal lamina is certainly present in Bilateria and was evaluated as an autapomorphy of this taxon.[well established][VHOG] basal lamina basal laminae lamina basalis AAO:0010269 AEO:0000065 BILA:0000065 Basal:lamina C32186 CARO:0000065 EHDAA2:0003065 FMA:62918 HAO:0000065 MESH:D001485 NIF_Subcellular:sao1397492660 TAO:0001485 TGMA:0001850 UMLS:C0085872 VHOG:0001592 WBbt:0005756 XAO:0003163 ZFA:0001485 http://linkedlifedata.com/resource/umls/id/C0085872 basal lamina of connective tissue Planarian_Anatomy PLANA:0001005 Depicted by field is an electron micrograph of the dorsal epidermis in a transverse plane from an asexual adult animal. The basal lamina is noted with a magenta bracket. Scale bar is 5um. basal lamina of epithelium https://planosphere.stowers.org/ontology/PLANA_0001005 A fully formed, sexually mature organism. The sexually reproducing Schmidtea mediterranea biotype exists as an obligate cross-fertilizing hermaphrodite. Erin Davies 2017-04-24T02:52:06Z Schmidtea_mediterranea_Developmental_Stages PLANA:0004503 Depcited by field shows a light microscopy image of a sexually mature adult with a scale bar of 2 mm. sexually mature adult https://planosphere.stowers.org/ontology/PLANA_0004503 A fully formed, sexually mature organism. The sexually reproducing Schmidtea mediterranea biotype exists as an obligate cross-fertilizing hermaphrodite. PMID:19022767 PMID:11972158 The asexually reproducing Schmidtea mediterranea biotype exists as a constitutive adult, undergoing successive cycles of fission and whole animal regeneration. Asexual Schmidtea mediterranea contain primordial germ cells, but do not possess a reproductive system. Erin Davies 2017-04-24T02:59:06Z Schmidtea_mediterranea_Developmental_Stages PLANA:0004504 Depicted by field shows an asexual adult with a scale bar of 500um asexual adult https://planosphere.stowers.org/ontology/PLANA_0004504 The asexually reproducing Schmidtea mediterranea biotype exists as a constitutive adult, undergoing successive cycles of fission and whole animal regeneration. Asexual Schmidtea mediterranea contain primordial germ cells, but do not possess a reproductive system. PMID:11972158 PMID:17376870 dmd-1+ expressing somatic cells within the testis that promote male GSC maintenance. dmd-1+, ophis-1+ somatic gonadal cells ensheath germ cells via long cytoplasmic processes and promote differentiation. Erin Davies 2017-07-19T21:05:52Z Planarian_Anatomy PLANA:0004506 testis somatic gonadal cell https://planosphere.stowers.org/ontology/PLANA_0004506 dmd-1+ expressing somatic cells within the testis that promote male GSC maintenance. dmd-1+, ophis-1+ somatic gonadal cells ensheath germ cells via long cytoplasmic processes and promote differentiation. PMID:23652002 PMID:27163480 ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia. Erin Davies 2017-07-19T21:35:08Z Planarian_Anatomy PLANA:0004507 ovarian somatic gonadal cell https://planosphere.stowers.org/ontology/PLANA_0004507 ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia. PMID:27163480 Axis that runs from the oral pole and to the aboral pole of the spherical embryo (Stage 3 through early Stage 6). The oral pole is centered around the temporary embryonic pharynx; the aboral pole is located opposite the temporary embryonic pharynx. embryo of oral-aboral axis oral-aboral axis of the embryo Axis that runs from the oral pole and to the aboral pole of the spherical embryo (Stage 3 through early Stage 6). The oral pole is centered around the temporary embryonic pharynx; the aboral pole is located opposite the temporary embryonic pharynx. PMID:28072387 Depicted by is an illustration noting the oral-aboral axis in cyan double headed arrow. Note it starts at the temporary embryonic pharynx and extends to opposite. The apical surface of the single layered primitive ectoderm that is in contact with the environment. Erin Davies 2017-07-27T16:25:14Z Planarian_Anatomy PLANA:0004512 primitive ectoderm surface https://planosphere.stowers.org/ontology/PLANA_0004512 The apical surface of the single layered primitive ectoderm that is in contact with the environment. OCLC:20423827 OCLC:464776945 OCLC:82522822 PMID:28072387 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md The surface of the primitive gut cells in contact with the embryonic wall. Erin Davies 2017-07-27T16:25:35Z Planarian_Anatomy PLANA:0004513 primtive gut cell surface https://planosphere.stowers.org/ontology/PLANA_0004513 The surface of the primitive gut cells in contact with the embryonic wall. PMID:28072387 The surface of phagocytic embryonic gut cells in contact with ingested yolk cells. Erin Davies 2017-07-27T16:25:45Z Planarian_Anatomy PLANA:0004514 embryonic gut cell surface https://planosphere.stowers.org/ontology/PLANA_0004514 The surface of phagocytic embryonic gut cells in contact with ingested yolk cells. PMID:28072387 The epithelial cell surface lining the temporary embryonic pharynx lumen. Erin Davies 2017-07-27T16:26:16Z Planarian_Anatomy PLANA:0004516 temporary embryonic pharynx lumen epithelial surface https://planosphere.stowers.org/ontology/PLANA_0004516 The epithelial cell surface lining the temporary embryonic pharynx lumen. PMID:20100474 PMID:28072387 An undifferentiated, cycling embryonic cell in Stage 1-5 embryos that expresses piwi-1, numerous adult asexual neoblast enriched genes, and early embryo enriched genes. Erin Davies 2017-07-27T19:54:22Z Planarian_Anatomy PLANA:0004517 blastomere https://planosphere.stowers.org/ontology/PLANA_0004517 An undifferentiated, cycling embryonic cell in Stage 1-5 embryos that expresses piwi-1, numerous adult asexual neoblast enriched genes, and early embryo enriched genes. PMID:28072387 Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues. Erin Davies 2017-07-27T20:00:04Z Planarian_Anatomy PLANA:0004518 extraembryonic cell https://planosphere.stowers.org/ontology/PLANA_0004518 Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues. PMID:28072387 A neuronal cell innervating the temporary embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening. Erin Davies 2017-07-27T20:01:15Z Planarian_Anatomy PLANA:0004519 temporary embryonic pharynx neuron https://planosphere.stowers.org/ontology/PLANA_0004519 A neuronal cell innervating the temporary embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening. PMID:28072387 Differentiated radial muscle cell present in the temporary embryonic pharynx. Erin Davies 2017-07-27T20:01:39Z Planarian_Anatomy PLANA:0004520 temporary embryonic pharynx radial muscle cell https://planosphere.stowers.org/ontology/PLANA_0004520 Differentiated radial muscle cell present in the temporary embryonic pharynx. PMID:16932928 foxA1+ epithelial cell contained in the temporary embryonic pharynx. Erin Davies 2017-07-27T20:02:04Z Planarian_Anatomy PLANA:0004521 temporary embryonic pharynx epithelial cell https://planosphere.stowers.org/ontology/PLANA_0004521 foxA1+ epithelial cell contained in the temporary embryonic pharynx. PMID:20100474 PMID:28072387 Differentiated muscle cell present in a circular muscle fiber of the temporary embryonic pharynx. Erin Davies 2017-07-27T20:43:26Z Planarian_Anatomy PLANA:0004524 temporary embryonic pharynx circular muscle fiber https://planosphere.stowers.org/ontology/PLANA_0004524 Differentiated muscle cell present in a circular muscle fiber of the temporary embryonic pharynx. PMID:16932928 Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus. Erin Davies 2017-08-28T18:20:43Z Planarian_Anatomy PLANA:0004527 Depicted by field contains diagram representation of body region. copulatory region https://planosphere.stowers.org/ontology/PLANA_0004527 Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus. PMID:22074376 Epithelia associated with the pharynx organ. Erin Davies 2017-08-31T14:53:38Z Planarian_Anatomy PLANA:0004528 pharyngeal epithelium https://planosphere.stowers.org/ontology/PLANA_0004528 Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. Erin Davies 2017-08-31T19:21:09Z UBERON:0002416 Planarian_Anatomy PLANA:0004529 integumental system https://planosphere.stowers.org/ontology/PLANA_0004529 Anatomical space enclosed by the oviduct epithelium. Erin Davies 2017-09-01T17:52:16Z Planarian_Anatomy PLANA:0004530 oviduct lumen https://planosphere.stowers.org/ontology/PLANA_0004530 Anatomical space enclosed by the oviduct epithelium. PMID:22074376 Anatomical space enclosed by the sperm duct epithelium. Erin Davies 2017-09-02T22:26:19Z Planarian_Anatomy PLANA:0004531 sperm duct lumen https://planosphere.stowers.org/ontology/PLANA_0004531 Anatomical space enclosed by the sperm duct epithelium. PMID:19022767 PMID:22074376 Ciliated epithelium lining the oviduct. Erin Davies 2017-09-02T22:35:10Z Planarian_Anatomy PLANA:0004532 oviduct epithelium https://planosphere.stowers.org/ontology/PLANA_0004532 Ciliated epithelium lining the oviduct. PMID:22074376 Ciliated epithelium lining the sperm duct. Erin Davies 2017-09-02T22:43:04Z Planarian_Anatomy PLANA:0004533 sperm duct epithelium https://planosphere.stowers.org/ontology/PLANA_0004533 Ciliated epithelium lining the sperm duct. PMID:19022767 PMID:22074376 Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct. Erin Davies 2017-09-02T22:55:44Z Planarian_Anatomy PLANA:0004534 tuba lumen https://planosphere.stowers.org/ontology/PLANA_0004534 Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct. PMID:19022767 PMID:20844018 PMID:22074376 PMID:27149082 Anatomial plane which divides the body into ventral and dorsal regions. This plane always includes the midline and is also known as the frontal plane. Steph Nowotarski 2017-04-26T19:32:04Z Planarian_Anatomy PLANA:0007502 Depicted by field contains hematoxylin and eosin staining of a coronal plane section of a asexual adult animal. Scale bar = 250um coronal plane https://planosphere.stowers.org/ontology/PLANA_0007502 Anatomical plane which divides the body into right and left parts. This plane passes through the midline. whole organism of sagittal plane sagittal plane of the whole animal Anatomical plane which divides the body into right and left parts. This plane passes through the midline. Three dimensional compartment along the dorsoventral axis that is above the anteroposterior axis, containing the eyes. Steph Nowotarski 2017-04-27T16:38:48Z BSPO:0000089 FBcv:0000035 FBql:00005876 Planarian_Anatomy PLANA:0007504 dorsal compartment https://planosphere.stowers.org/ontology/PLANA_0007504 Compartment along the dorsoventral axis that is below the anteroposterior axis. Steph Nowotarski 2017-04-27T16:38:59Z BSPO:0000091 FBql:00005877 Planarian_Anatomy PLANA:0007505 ventral compartment https://planosphere.stowers.org/ontology/PLANA_0007505 Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus. Steph Nowotarski 2017-04-27T16:39:34Z BSPO:0000087 FBql:00005874 Planarian_Anatomy PLANA:0007506 anterior compartment https://planosphere.stowers.org/ontology/PLANA_0007506 Three dimensional compartment along the anteroposterior axis that is closer to the tail rather than the head, from the anterior boundary of the pharyngeal pouch to the tip of the tail. Steph Nowotarski 2017-04-27T16:39:59Z BSPO:0000090 FBcv:0000036 FBql:00005875 Planarian_Anatomy PLANA:0007507 posterior compartment https://planosphere.stowers.org/ontology/PLANA_0007507 Anatomical structures that exist outside of cells; non-cellular. Steph Nowotarski 2017-05-03T13:48:26Z WBbt:0005732 Planarian_Anatomy PLANA:0007508 extracellular component https://planosphere.stowers.org/ontology/PLANA_0007508 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. Steph Nowotarski 2017-05-03T13:48:41Z GO:0005886 Planarian_Anatomy PLANA:0007509 plasma membrane https://planosphere.stowers.org/ontology/PLANA_0007509 Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi. Steph Nowotarski 2017-05-03T18:08:16Z GO:0043230 Planarian_Anatomy PLANA:0007511 extracellular organelle https://planosphere.stowers.org/ontology/PLANA_0007511 A spherical to rod shaped organelle that generates the majority of a cell's supply of ATP via cellular respiration. Mitochondria have their own genome and consist of outer and inner membranes, the latter folds inward to form cristae. This folding increases the surface area of the membrane and thus increases the space available to produce ATP. The inner and outer membranes are separated by an intermembrane space, and the inner membrane encloses the matrix. Steph Nowotarski 2017-05-03T18:19:46Z Planarian_Anatomy PLANA:0007512 mitochondrion https://planosphere.stowers.org/ontology/PLANA_0007512 Network of interconnected, flattened, and/or tubular membrane, known as cisternae. This membrane is contiguous with the outer nuclear membrane. The endoplasmic reticulum is involved in both protein and lipid synthesis. Steph Nowotarski 2017-05-04T14:46:22Z Planarian_Anatomy PLANA:0007513 endoplasmic reticulum https://planosphere.stowers.org/ontology/PLANA_0007513 Endoplasmic reticululum that is studded with ribosomes, leading to a "rough" or "granular" appearance. Steph Nowotarski 2017-05-04T14:47:41Z Planarian_Anatomy PLANA:0007514 rough endoplasmic reticulum https://planosphere.stowers.org/ontology/PLANA_0007514 Endoplamic reticulum that does not contain ribosomes, which synthesizes lipids, phospholipids, and steroids. Steph Nowotarski 2017-05-04T14:48:11Z Planarian_Anatomy PLANA:0007515 smooth endoplasmic reticulum https://planosphere.stowers.org/ontology/PLANA_0007515 Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined. Steph Nowotarski 2017-05-04T14:49:17Z GO:0005643 Planarian_Anatomy PLANA:0007516 nuclear pore https://planosphere.stowers.org/ontology/PLANA_0007516 The digestive component of the cell. They are homogenous, dense, membrane bound organelles filled with acid hydrolases which break down polymers. Steph Nowotarski 2017-05-04T15:35:23Z Planarian_Anatomy PLANA:0007518 lysosome https://planosphere.stowers.org/ontology/PLANA_0007518 The digestive component of the cell. They are homogenous, dense, membrane bound organelles filled with acid hydrolases which break down polymers. ISBN:0-71677033-4 PMID:4853064 Axis that runs along the long axis of the animal from anterior (head) to posterior (tail). It is perpendicular to the dorsoventral axis and as such, it splits dorsal and ventral regions of the animal to either side. whole organism of anterior-posterior axis anterior-posterior axis of the whole animal Axis that runs along the long axis of the animal from anterior (head) to posterior (tail). It is perpendicular to the dorsoventral axis and as such, it splits dorsal and ventral regions of the animal to either side. Depiction shows an asexual with the term annoated in yellow. Scale bar =500um Axis that runs along the short axis of the animal, perpendicular to the anteroposterior axis, running from the dorsal (back) side of the animal to the ventral (belly) side of the animal. This axis splits anterior and posterior regions of the animal to either side. whole organism of dorsal-ventral axis dorsal-ventral axis of the whole animal Axis that runs along the short axis of the animal, perpendicular to the anteroposterior axis, running from the dorsal (back) side of the animal to the ventral (belly) side of the animal. This axis splits anterior and posterior regions of the animal to either side. Axis perpendicular to both the anteroposterior and dorsoventral axis that runs from the left side of the animal, through the medial region (center) and out to the right side. whole organism of left-right axis dextro-sinister axis of the whole animal Axis perpendicular to both the anteroposterior and dorsoventral axis that runs from the left side of the animal, through the medial region (center) and out to the right side. Depiction shows an asexual with the term annoated in yellow. Scale bar =500um Axis that runs from the center of the body, starting at the anteroposterior axis and out to the lateral (left, right, dorsal or ventral) surface of the animal. whole organism of medial-lateral axis medial-lateral axis of the whole animal Axis that runs from the center of the body, starting at the anteroposterior axis and out to the lateral (left, right, dorsal or ventral) surface of the animal. Depiction shows an asexual with the term annoated in yellow. Scale bar =500um Axis that starts at the distal part of an appendage, closest to the body, and runs to the proximal part of an appendage, farthest from the body. whole organism of proximal-distal axis proximal-distal axis of the whole animal Axis that starts at the distal part of an appendage, closest to the body, and runs to the proximal part of an appendage, farthest from the body. Depicted by shows a planarian pharynx exposed by tricaine treatment. The proximodistal axis is denoted with the double headed magenta arrow. Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD. Steph Nowotarski 2017-05-15T18:28:35Z Planarian_Anatomy PLANA:0007524 anterior pole https://planosphere.stowers.org/ontology/PLANA_0007524 Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD. PMID:21566195 PMID:23297191 PMID:24040508 PMID:24415944 PMID:24704339 PMID:24992682 Distinct posterior cluster of muscle cells located at the midline which express wnt1. Steph Nowotarski 2017-05-15T18:28:47Z Planarian_Anatomy PLANA:0007525 posterior pole https://planosphere.stowers.org/ontology/PLANA_0007525 Distinct posterior cluster of muscle cells located at the midline which express wnt1. PMID:18063755 PMID:21680047 A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu, guide neuronal migration during development, and exchange metabolites with neurons. Steph Nowotarski 2017-06-22T17:12:28Z CL:0000125 Planarian_Anatomy PLANA:0007528 glial cell https://planosphere.stowers.org/ontology/PLANA_0007528 A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu, guide neuronal migration during development, and exchange metabolites with neurons. PMID:27612384 A biological tissue mass of nerve cell bodies. Steph Nowotarski 2017-06-22T18:29:52Z UBERON:0000045 Planarian_Anatomy PLANA:0007529 ganglion https://planosphere.stowers.org/ontology/PLANA_0007529 Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft. Steph Nowotarski 2017-07-24T19:28:03Z Planarian_Anatomy PLANA:0007534 inner pharyngeal epithelium https://planosphere.stowers.org/ontology/PLANA_0007534 Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft. doi:10.1002/jmor.1051550208 OCLC:16809160 Pharynx muscle fibers running parallel to the diameter of the pharynx. Steph Nowotarski 2017-07-24T19:39:14Z Planarian_Anatomy PLANA:0007535 pharyngeal circular muscle fiber https://planosphere.stowers.org/ontology/PLANA_0007535 Pharynx muscle fibers running parallel to the diameter of the pharynx. ASIN:B000M4NK9M The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell. Steph Nowotarski 2017-09-05T14:18:21Z UBERON:0000955 Planarian_Anatomy PLANA:0007537 brain https://planosphere.stowers.org/ontology/PLANA_0007537 Specialized epithelial cells located along the dorsoventral margin. Adhesion glands are comprised of three cell types, the viscid and releasing gland cells which penetrate through an epithelial anchor cell and terminate at the epithelial surface. Steph Nowotarski 2017-09-05T14:32:51Z Planarian_Anatomy PLANA:0007538 adhesion gland https://planosphere.stowers.org/ontology/PLANA_0007538 Specialized epithelial cells located along the dorsoventral margin. Adhesion glands are comprised of three cell types, the viscid and releasing gland cells which penetrate through an epithelial anchor cell and terminate at the epithelial surface. OCLC:16809160 PMID:20865784 Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells. Steph Nowotarski 2017-09-05T15:08:27Z Planarian_Anatomy PLANA:0007539 anchor cell https://planosphere.stowers.org/ontology/PLANA_0007539 Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells. OCLC:16809160 PMID:20865784 A specialized insunk epithelial cell that is part of the adhesion glands which is responsible for production and excretion of the viscid substance allowing adherence to a substrate. Steph Nowotarski 2017-09-05T15:08:38Z Planarian_Anatomy PLANA:0007540 viscid gland cell https://planosphere.stowers.org/ontology/PLANA_0007540 A specialized insunk epithelial cell that is part of the adhesion glands which is responsible for production and excretion of the viscid substance allowing adherence to a substrate. OCLC:16809160 PMID:20865784 Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance. Steph Nowotarski 2017-09-05T15:08:48Z Planarian_Anatomy PLANA:0007541 releasing gland cell https://planosphere.stowers.org/ontology/PLANA_0007541 Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance. OCLC:16809160 PMID:20865784 A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2. Planarian_Anatomy PLANA:0007543 TrpA+ central nervous system neuron https://planosphere.stowers.org/ontology/PLANA_0007543 A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2. PMID:22549959 A subset of sensory neurons located along the dorsal head margin. Planarian_Anatomy PLANA:0007544 cintillo+ sensory neuron https://planosphere.stowers.org/ontology/PLANA_0007544 A subset of sensory neurons located along the dorsal head margin. PMID:12557210 The outermost region of the deep-superficial axis. This anatomical compartment contains definitive epidermis, basal lamina and subepidermal nerve plexus. epidermal surface epidermis surface Planarian_Anatomy PLANA:0007545 epidermal compartment https://planosphere.stowers.org/ontology/PLANA_0007545 piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons. Planarian_Anatomy PLANA:0007546 TrpA+ neural progenitor cell https://planosphere.stowers.org/ontology/PLANA_0007546 piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons. PMID:25254346 PMID:22549959 piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole. Planarian_Anatomy PLANA:0007547 anterior pole progenitor cell https://planosphere.stowers.org/ontology/PLANA_0007547 piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole. PMID:24415944  Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords. Planarian_Anatomy PLANA:0007548 transverse commissure https://planosphere.stowers.org/ontology/PLANA_0007548 Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords. PMID:17999079 An anatomical compartment of the deep-superficial axis containing the body wall musculature and underlying submuscular nerve plexus. Planarian_Anatomy PLANA:0007549 body wall musculature compartment https://planosphere.stowers.org/ontology/PLANA_0007549 piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons. Planarian_Anatomy PLANA:0007550 serotonergic neural progenitor cell https://planosphere.stowers.org/ontology/PLANA_0007550 piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons. PMID:23903188 PMID:24131630 PMID:25254346 piwi-1+, klf+ progenitor neoblasts required for production of cintillo+ sensory neurons. Planarian_Anatomy PLANA:0007551 klf+ sensory neuron progenitor cell https://planosphere.stowers.org/ontology/PLANA_0007551 piwi-1+, klf+ progenitor neoblasts required for production of cintillo+ sensory neurons. PMID:25254346 A population of piwi-2+, ston-2+, elav-2+, ptprd-9+ and msi-1+ progenitors that give rise to one or more neuronal (pc-2+, synapsin+) lineages. Planarian_Anatomy PLANA:0007552 nu neoblast https://planosphere.stowers.org/ontology/PLANA_0007552 A population of piwi-2+, ston-2+, elav-2+, ptprd-9+ and msi-1+ progenitors that give rise to one or more neuronal (pc-2+, synapsin+) lineages. PMID:27150006 A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus. Planarian_Anatomy PLANA:0007553 lateral nerve https://planosphere.stowers.org/ontology/PLANA_0007553 A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus. PMID:17999079 An anatomical compartment of the deep-superficial axis between the gastrodermal nerve plexus and submuscular nerve plexus. mesenchyme Planarian_Anatomy PLANA:0007554 parenchymal compartment https://planosphere.stowers.org/ontology/PLANA_0007554 piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons. Planarian_Anatomy PLANA:0007555 pax3/7+ neural progenitor cell https://planosphere.stowers.org/ontology/PLANA_0007555 piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons. PMID: 25254346 Anatomical space enclosed by the temporary embryonic pharynx epithelial cells. Lumen through which yolk cells are transported into the embryonic gut cavity. Erin Davies Planarian_Anatomy PLANA:0007556 temporary embryonic pharynx cavity https://planosphere.stowers.org/ontology/PLANA_0007556 Anatomical space enclosed by the temporary embryonic pharynx epithelial cells. Lumen through which yolk cells are transported into the embryonic gut cavity. PMID:28072387 Nerve plexus surrounding the testis. Planarian_Anatomy PLANA:0007557 testis nerve plexus https://planosphere.stowers.org/ontology/PLANA_0007557 Nerve plexus surrounding the testis. PMID:7833618 PMID:17999079 Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs. Erin Davies Planarian_Anatomy PLANA:0007558 fission plane https://planosphere.stowers.org/ontology/PLANA_0007558 Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs. OCLC:16809160 PMID:11972158 Nerve plexus surrounding the ovary. Planarian_Anatomy PLANA:0007559 ovary nerve plexus https://planosphere.stowers.org/ontology/PLANA_0007559 Nerve plexus surrounding the ovary. PMID:7833618 PMID:17999079 The innermost anatomical compartment of the deep-superficial axis, extending from the definitive gut lumen to the gastrodermal nerve plexus. Planarian_Anatomy PLANA:0007560 gastrovascular compartment https://planosphere.stowers.org/ontology/PLANA_0007560 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 biological structure connected biological structure uberon UBERON:0000061 anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 connected biological structure CARO:0000003 A life cycle stage that starts with fertilization and ends with the fully formed embryo. BilaDO:0000002 EV:0300001 FBdv:00005289 FMA:72652 HsapDv:0000002 MmusDv:0000002 OGES:000000 OGES:000022 WBls:0000003 WBls:0000092 WBls:0000102 XAO:1000012 embryonic stage uberon embryogenesis UBERON:0000068 embryo stage A life cycle stage that starts with fertilization and ends with the fully formed embryo. stage succeeding embryo, including mature structure In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 OGES:000024 WBls:0000022 WBls:0000093 WBls:0000103 postembryonic stage post-hatching stage uberon postembryonic UBERON:0000092 post-embryonic stage stage succeeding embryo, including mature structure An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. FBdv:00000000 HsapDv:0000001 MmusDv:0000001 OGES:000011 ncithesaurus:Life entire life cycle entire lifespan life lifespan uberon UBERON:0000104 life cycle An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. A spatiotemporal region encompassing some part of the life cycle of an organism. this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here the WBls class 'all stages' belongs here as it is the superclass of other WBls stages we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 FMA:24120 HsapDv:0000000 MmusDv:0000000 OlatDv:0000010 PdumDv:0000090 WBls:0000002 XAO:1000000 ZFS:0000000 ZFS:0100000 ncithesaurus:Developmental_Stage developmental stage stage uberon UBERON:0000105 life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. A stage at which the organism is a single cell produced by means of sexual reproduction. As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 NCIT:C12601 PdumDv:0000100 VHOG:0000745 XAO:1000001 ZFS:0000001 1-cell stage fertilized egg stage one cell stage uberon fertilized egg stage one-cell stage zygote zygotum UBERON:0000106 zygote stage A stage at which the organism is a single cell produced by means of sexual reproduction. As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] 2012-09-17 VHOG:0000745 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 fertilized egg stage BTO:0000854 one-cell stage VHOG:0000745 zygote VHOG:0000745 zygotum A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. BILS:0000111 BilaDO:0000010 HsapDv:0000015 MmusDv:0000018 OGES:000005 OGES:000032 uberon segmentation stage UBERON:0000111 organogenesis stage A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. lumen space AAO:0010110 AEO:0000005 BILA:0000005 CARO:0000005 EHDAA2:0003005 FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 TAO:0001668 TGMA:0001825 UMLS:C0524461 VHOG:0001728 XAO:0003190 ZFA:0001643 lumen space uberon anatomical spaces UBERON:0000464 anatomical space Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. UMLS:C0524461 ncithesaurus:Lumen_Space anatomical spaces ZFA:0001643 Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity Anatomical entity that has mass. Anatomical entity that has no mass. AAO:0010265 AEO:0000007 BILA:0000007 CARO:0000007 EHDAA2:0003007 FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 TGMA:0001827 VHOG:0001727 immaterial physical anatomical entity uberon UBERON:0000466 immaterial anatomical entity Anatomical entity that has no mass. immaterial physical anatomical entity FMA:67112 Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency AAO:0010053 AEO:0000032 BILA:0000032 CALOHA:TS-2084 CARO:0000032 EFO:0000808 EHDAA2:0003032 EMAPA:36031 FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 MAT:0000293 MESH:D001829 MIAA:0000293 NCIT:C32221 OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA TAO:0001308 TGMA:0001840 UMLS:C0229962 VHOG:0001758 XAO:0003013 ZFA:0001308 galen:BodyPart anatomic region uberon body part body region cardinal body part UBERON:0000475 organism subdivision Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. CARO:0000032 CARO:DOS UMLS:C0229962 ncithesaurus:Body_Part anatomic region MA:0002433 body region FMA:7153 cardinal body part FMA:7153 Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. AAO:0010268 AEO:0000040 BILA:0000040 CARO:0000040 EHDAA2:0003040 FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 TGMA:0001841 XAO:0003162 ZFA:0000382 uberon acellular anatomical structures UBERON:0000476 acellular anatomical structure Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. acellular anatomical structures ZFA:0000382 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. AAO:0010841 AEO:0000000 BILA:0000000 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FBbt_root:00000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 uberon UBERON:0001062 anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. FMA:62955 UMLS:C1515976 ncithesaurus:Anatomic_Structure_System_or_Substance Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. cavity EMAPA:37442 FMA:67552 MA:0002447 NCIT:C34007 galen:Cavity uberon UBERON:0002553 anatomical cavity Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. FMA:67552 EMAPA:37442 MA:th AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 FBbt:00007006 FMA:292313 MIAA:0000019 uberon developing structure developmental structure developmental tissue UBERON:0005423 developing anatomical structure developmental tissue MIAA:0000019 An anatomical structure that is undergoing regeneration. we define this in terms of active participation in regeneration, rather that capabilities. In this sense it is different from the AEO structure. A portion of tissue that is regrowing after damage or amputation.[TAO] EHDAA2:0003233 AEO:0000200 EHDAA2:0003233 TAO:0005147 XAO:0004059 ZFA:0005147 uberon regenerating tissue regenerating tissues regenerative tissue UBERON:0007567 regenerating anatomical structure An anatomical structure that is undergoing regeneration. A portion of tissue that is regrowing after damage or amputation.[TAO] 2012-08-14 TAO:0005147 TAO ZFIN:curator regenerating tissue ZFA:0005147 regenerating tissues ZFA:0005147 example to be eventually removed The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core placeholder removed An editor note should explain what were the merged terms and the reason for the merge. terms merged This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. We expect to be able to mine these new reasons and add instances as required. other true Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP From ligand activity to has_ligand This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction From has_ligand to ligand activity