CARO part_of NCBITaxon:79327; CL part_of NCBITaxon:79327 1.2 The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) editor preferred term A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. example of usage has curation status definition An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. editor note Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people term editor An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) alternative term Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 definition source An administrative note of use for a curator but of no use for a user curator note For external terms/classes, the ontology from which the term was imported imported from expand expression to first order logic expression An alternative name for a class or property which is unique across the OBO Foundry. OBO foundry unique label elucidation An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p is symmetric relational form of process class Relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y is direct form of Relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y is indirect form of An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. external_definition Notes on the homology status of this class. homology_notes has_relational_adjective Notes on the how instances of this class vary across species. taxon_notes Notes on how similar or equivalent classes are represented in other ontologies. external_ontology_notes has_broad_synonym database_cross_reference has_exact_synonym has_obo_format_version has_obo_namespace Sofia Robb 2017-07-26T18:19:59Z treat-xrefs-as-genus-differentia Sofia Robb 2017-09-11T16:38:22Z depiction is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part_of BFO:0000050 uberon BFO:0000050 part of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has_part BFO:0000051 BFO:0000051 has part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) BFO:0000054 Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) BFO:0000055 Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes participates_in BFO:0000056 uberon BFO:0000056 participates in BFO:0000060 accidentally included in BFO 1.2 proposal - should have been BFO_0000062 obsolete preceded by preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 is preceded by takes place after uberon BFO:0000062 preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes BFO:0000063 uberon BFO:0000063 precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in BFO:0000066 Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t contains_process BFO:0000067 uberon BFO:0000067 Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer anterior_to cjm 2009-07-31T02:15:46Z BSPO:0000096 uberon BSPO:0000096 anterior_to x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). distal_to BSPO:0000097 uberon BSPO:0000097 distal_to x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). dorsal_to BSPO:0000098 uberon BSPO:0000098 dorsal_to x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. caudal_to posterior_to BSPO:0000099 uberon BSPO:0000099 posterior_to x proximal_to y iff x is closer to the point of attachment with the body than y. proximal_to BSPO:0000100 uberon BSPO:0000100 proximal_to x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). ventral_to BSPO:0000102 uberon BSPO:0000102 ventral_to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. deep_to BSPO:0000107 uberon BSPO:0000107 deep_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. superficial_to BSPO:0000108 uberon BSPO:0000108 superficial_to X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. in_posterior_side_of BSPO:0000122 uberon BSPO:0000122 in_posterior_side_of X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. in_anterior_side_of BSPO:0000123 uberon BSPO:0000123 in_anterior_side_of X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. in_proximal_side_of BSPO:0000124 uberon BSPO:0000124 in_proximal_side_of X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. in_distal_side_of BSPO:0000125 uberon BSPO:0000125 in_distal_side_of X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure in_lateral_side_of BSPO:0000126 uberon BSPO:0000126 in_lateral_side_of X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the superficial portion. in_superficial_part_of BSPO:0001100 uberon BSPO:0001100 in_superficial_part_of X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. in_deep_part_of BSPO:0001101 uberon BSPO:0001101 in_deep_part_of X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y proximalmost_part_of BSPO:0001106 uberon BSPO:0001106 proximalmost_part_of This relation holds when both the deep_to and ajdacent_to relationship similarly hold. immediately_deep_to BSPO:0001107 uberon BSPO:0001107 immediately_deep_to X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y distalmost_part_of BSPO:0001108 uberon BSPO:0001108 distalmost_part_of x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side. posterior_to (developmentally) postaxial_to BSPO:0001114 uberon BSPO:0001114 postaxial_to X intersects_median_plane of iff X crosses the midine plane of Y. intersects_midsagittal_plane_of BSPO:0005001 uberon BSPO:0005001 intersects_midsagittal_plane_of immediately_anterior_to BSPO:0015009 uberon BSPO:0015009 immediately_anterior_to immediately_posterior_to BSPO:0015012 uberon BSPO:0015012 immediately_posterior_to immediately_superficial_to BSPO:0015014 uberon BSPO:0015014 immediately_superficial_to in_dorsal_side_of BSPO:0015101 uberon BSPO:0015101 in_dorsal_side_of in_ventral_side_of BSPO:0015102 uberon BSPO:0015102 in_ventral_side_of nearer to the oral opening of the organism, on the oral-aboral axis. oral_to BSPO:0015201 uberon BSPO:0015201 oral_to nearer to the aboral opening of the organism, on the oral-aboral axis. aboral_to BSPO:0015202 uberon BSPO:0015202 aboral_to x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the front. anterior_to (developmentally) lateral (radial) to medial (tibial) to preaxial_to BSPO:1000000 uberon BSPO:1000000 preaxial_to feature restricted to Steph Nowotarski 2017-07-24T20:21:09Z PLANA:0007536 specific_to inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in RO:0000052 inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer_of RO:0000053 uberon RO:0000053 bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of RO:0000079 function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of RO:0000080 quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of RO:0000081 role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function RO:0000085 has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has_quality RO:0000086 uberon RO:0000086 has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role RO:0000087 has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence RO:0000091 has disposition inverse of has disposition RO:0000092 disposition of A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. David Osumi-Sutherland (forall (?x ?y) (iff (neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (or (synapsed_by ?x ?y) (synapsed_to ?x ?y))))) (forall (...s ?x ?y ?z) (iff (neural_circuit_path ...s ?x ?y ?z) (and (neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (or (synapsed_by ?y ?z) (synapsed_to ?y ?z))))) (forall (?x ?y) (iff (in_neural_circuit_with ?x ?y) (exists (...s) (neural_circuit_path ?x ...s ?y)))) RO:0000300 in neural circuit with A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. David Osumi-Sutherland (forall (?x ?y) (iff (upstream_neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (synapsed_to ?x ?y)))) (forall (...s ?x ?y ?z) (iff (upstream_neural_circuit_path ...s ?x ?y ?z ) (and (upstream_neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (synapsed_to ?y ?z)))) (forall (?x ?y) (iff (upstream_in_neural_circuit_with ?x ?y) (exists (...s) (upstream_neural_circuit_path ?x ...s ?y)))) RO:0000301 upstream in neural circuit with A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. David Osumi-Sutherland (forall (?x ?y) (iff (downstream_neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (synapsed_by ?x ?y)))) (forall (...s ?x ?y ?z) (iff (downstream_neural_circuit_path ...s ?x ?y ?z ) (and (downstream_neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (synapsed_by ?y ?z)))) (forall (?x ?y) (iff (downstream_in_neural_circuit_with ?x ?y) (exists (...s) (downstream_neural_circuit_path ?x ...s ?y)))) RO:0000302 downstream in neural circuit with this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. RO:0001000 derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into RO:0001001 derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of location_of RO:0001015 uberon RO:0001015 location of contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in RO:0001018 contained in contains contains RO:0001019 uberon RO:0001019 contains located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime located_in located_in http://www.obofoundry.org/ro/#OBO_REL:located_in RO:0001025 uberon RO:0001025 located in the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of boundary_of RO:0002000 uberon RO:0002000 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. David Osumi-Sutherland has boundary has_2D_boundary has_boundary RO:0002002 uberon RO:0002002 has 2D boundary A relation that holds between two neurons that are electrically coupled via gap junctions. David Osumi-Sutherland RO:0002003 electrically_synapsed_to The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). David Osumi-Sutherland RO:0002004 tracheates David Osumi-Sutherland innervated_by http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 nerve supply uberon RO:0002005 http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by David Osumi-Sutherland RO:0002006 has synaptic terminal of X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 David Osumi-Sutherland bounding_layer_of RO:0002007 uberon RO:0002007 A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label David Osumi-Sutherland RO:0002008 Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. coincident with A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. David Osumi-Sutherland x 'cell expresses' y iff: cell(x) AND gene(y) AND exists some 'transcription, DNA templated (GO_0006351)'(t) AND t occurs_in x AND t has_input y RO:0002009 cell expresses x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). David Osumi-Sutherland RO:0002010 regulates in other organism A relationship that holds between a process that regulates a transport process and the entity transported by that process. David Osumi-Sutherland RO:0002011 regulates transport of A part of relation that applies only between occurents. RO:0002012 occurent part of David Osumi-Sutherland <= RO:0002081 Primitive instance level timing relation between events before or simultaneous with Relation between occurrents, shares start and end boundaries. David Osumi-Sutherland simultaneous_with RO:0002082 coincides_with is_equal_to uberon RO:0002082 t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with David Osumi-Sutherland RO:0002083 t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before David Osumi-Sutherland RO:0002084 Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends David Osumi-Sutherland di RO:0002085 Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses David Osumi-Sutherland RO:0002086 X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. immediately_preceded_by RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of uberon RO:0002087 X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland RO:0002088 Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which starts David Osumi-Sutherland RO:0002089 starts before David Osumi-Sutherland ends_at_start_of meets RO:0002090 X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes David Osumi-Sutherland io RO:0002091 X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during RO:0002092 X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during David Osumi-Sutherland o overlaps RO:0002093 X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland BFO_0000051 some ( GO_0043025 and BFO_0000050 some ?Y) RO:0002100 has soma location relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. David Osumi-Sutherland fasciculates with (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) )))))) RO:0002101 fasciculates with Relation between a neuron and some structure its axon forms (chemical) synapses in. Chris Mungall David Osumi-Sutherland BFO_0000051 some ( GO_0030424 and BFO_0000051 some ( GO_0042734 and BFO_0000050 some ( GO_0045202 and BFO_0000050 some ?Y))) RO:0002102 axon synapses in Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. Chris Mungall David Osumi-Sutherland BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?))) synapsed_by RO:0002103 uberon RO:0002103 synapsed by Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. Alexander Diehl Chris Mungall Lindsay Cowell BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y) RO:0002104 has plasma membrane part A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. David Osumi-Sutherland Marta Costa BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002105 Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) synapsed_via_type_Ib_bouton_to A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. David Osumi-Sutherland Marta Costa BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002106 Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) synapsed_via_type_Is_bouton_to A relation between a motor neuron and a muscle that it synapses to via a type II bouton. David Osumi-Sutherland Marta Costa BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) synapsed_via_type_II_bouton_to Relation between a muscle and a motor neuron that synapses to it via a type II bouton. David Osumi-Sutherland Marta Costa BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) RO:0002108 Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) synapsed_by_via_type_II_bouton Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. David Osumi-Sutherland Marta Costa BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) RO:0002109 Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) synapsed_by_via_type_Ib_bouton Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. Chris Mungall David Osumi-Sutherland synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) RO:0002110 has postsynaptic terminal in has neurotransmitter RO:0002111 releases neurotransmitter Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. David Osumi-Sutherland Marta Costa BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) RO:0002112 Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) synapsed_by_via_type_Is_bouton Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapses in BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?) RO:0002113 has presynaptic terminal in A relation between a motor neuron and a muscle that it synapses to via a type III bouton. BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002114 Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) synapsed_via_type_III_bouton_to Relation between a muscle and a motor neuron that synapses to it via a type III bouton. BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) RO:0002115 Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) synapsed_by_via_type_III_bouton Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. Chris Mungall David Osumi-Sutherland BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?))) RO:0002120 N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) synapsed to Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. Chris Mungall David Osumi-Sutherland BFO_0000051 some ( GO_0030425 and BFO_0000051 some ( http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some ( GO_0045202 and BFO_0000050 some ?Y))) RO:0002121 dendrite synapsed in A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. David Osumi-Sutherland has synapse in RO_0002131 some (GO_0045202 that BFO_0000050 some Y?) RO:0002130 has synaptic terminal in x overlaps y if and only if there exists some z such that x has part z and z part of y BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps RO:0002131 uberon RO:0002131 overlaps The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. David Osumi-Sutherland has fasciculating component (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) )))))) RO:0002132 has fasciculating neuron projection Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. David Osumi-Sutherland RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?))) innervates RO:0002134 uberon RO:0002134 http://code.google.com/p/obo-relations/issues/detail?id=6 innervates X continuous_with Y if and only if X and Y share a fiat boundary. David Osumi-Sutherland connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) continuous_with RO:0002150 uberon RO:0002150 continuous with x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom proper overlaps (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x))))) RO:0002151 partially overlaps d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. ancestral_stucture_of evolutionarily_descended_from RO:0002156 derived by descent from inverse of derived by descent from RO:0002157 has derived by descendant two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. Consider obsoleting and merging with child relation, 'in homology relationship with' homologous_to homologous to RO:0002158 uberon RO:0002158 VBO calls this homologous_to shares ancestor with serially_homologous_to RO:0002159 uberon RO:0002159 serially homologous to lactation SubClassOf 'only in taxon' some 'Mammalia' X only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria Chris Mungall only_in_taxon RO:0002160 uberon RO:0002160 only in taxon x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. Chris Mungall Jennifer Deegan in_taxon RO:0002162 uberon RO:0002162 Connects a biological entity to its taxon of origin. in taxon A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) RO:0002163 spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). A is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b connected_to RO:0002170 uberon RO:0002170 Connection does not imply overlaps. connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) connects RO:0002176 uberon RO:0002176 connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attaches_to_part_of RO:0002177 uberon RO:0002177 attached to part of Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure supplies RO:0002178 arterial supply of uberon RO:0002178 source: FMA supplies drains RO:0002179 drains blood from drains from uberon RO:0002179 source: Wikipedia drains w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has_component RO:0002180 uberon RO:0002180 has component A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). Chris Mungall RO:0002200 has phenotype inverse of has phenotype Chris Mungall RO:0002201 phenotype of x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan develops_from RO:0002202 uberon RO:0002202 This is the transitive form of the develops from relation develops from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan develops_into RO:0002203 uberon RO:0002203 develops into definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. Chris Mungall RO:0002204 gene product of every HOTAIR lncRNA is the gene product of some HOXC gene every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y Chris Mungall RO:0002205 has gene product 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process Chris Mungall RO:0002206 expressed in Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y Chris Mungall David Osumi-Sutherland has developmental precursor FBbt directly_develops_from RO:0002207 uberon RO:0002207 TODO - add child relations from DOS directly develops from inverse of directly develops from developmental precursor of RO:0002210 directly develops into x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 regulates x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y Chris Mungall negatively regulates (process to process) RO:0002212 negatively regulates x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall positively regulates (process to process) RO:0002213 positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) capable_of RO:0002215 uberon RO:0002215 capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable_of_part_of RO:0002216 uberon RO:0002216 capable of part of x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in RO:0002217 actively participates in 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent RO:0002218 has active participant x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y Chris Mungall surrounded_by RO:0002219 uberon RO:0002219 surrounded by A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. X adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO x adjacent_to y iff: x and y share a boundary Chris Mungall adjacent_to RO:0002220 uberon RO:0002220 adjacent to inverse of surrounded by Chris Mungall surrounds RO:0002221 uberon RO:0002221 surrounds Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to inverse of starts with Relation between occurrents, shares a start boundary with. Chris Mungall Allen starts RO:0002223 uberon RO:0002223 starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by starts_with RO:0002224 uberon RO:0002224 starts with x develops from part of y if and only if there exists some z such that x develops from z and z is part of y Chris Mungall develops_from_part_of RO:0002225 uberon RO:0002225 develops from part of x develops_in y if x is located in y whilst x is developing Chris Mungall EHDAA2 Jonathan Bard, EHDAA2 develops_in RO:0002226 uberon RO:0002226 This relation take from EHDAA2 - precise semantics yet to be defined develops in inverse of ends with Chris Mungall Relation between occurrents, shares an end boundary with. ends RO:0002229 finishes uberon RO:0002229 ends x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by ends_with RO:0002230 uberon RO:0002230 ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y Chris Mungall starts with process that occurs in RO:0002231 has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y Chris Mungall ends with process that occurs in RO:0002232 has end location p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes RO:0002233 has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. Chris Mungall produces RO:0002234 has output A broad relationship between an exposure event or process and any entity (e.g., a human, human population, or a human organ) that interacts with an exposure stressor during the exposure event ExO:0000001 RO:0002240 has exposure receptor A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. ExO:0000000 RO:0002241 has exposure stressor A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor ExO:0000055 RO:0002242 has exposure route A broad relationship between an exposure event or process and a the material an agent takes from the source to the target. RO:0002243 has exposure transport path g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. RO:0002245 over-expressed in g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. RO:0002246 under-expressed in b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. RO:0002252 connecting branch of inverse of connecting branch of RO:0002253 has connecting branch Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall has_developmental_contribution_from RO:0002254 uberon RO:0002254 has developmental contribution from inverse of has developmental contribution from Chris Mungall developmentally_contributes_to RO:0002255 uberon RO:0002255 developmentally contributes to t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T Chris Mungall David Osumi-Sutherland Melissa Haendel induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) GO:0001759 We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] developmentally_induced_by RO:0002256 uberon RO:0002256 sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) developmentally induced by Inverse of developmentally induced by Chris Mungall RO:0002257 developmentally induces Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one developmentally_preceded_by RO:0002258 uberon RO:0002258 This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) RO:0002260 has biological role c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) RO:0002261 has application role c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) RO:0002262 has chemical role c involved in regulation of p if c enables 'p' and p' causally upstream of p RO:0002263 acts upstream of c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p affects RO:0002264 acts upstream of or within x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage Chris Mungall replaces developmentally_replaces RO:0002285 uberon RO:0002285 developmentally replaces Inverse of developmentally preceded by Chris Mungall RO:0002286 developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue Chris Mungall RO:0002287 part of developmental precursor of x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. Chris Mungall RO:0002291 ubiquitously expressed in Inverse of 'expressed in' Chris Mungall RO:0002292 expresses inverse of ubiquiotously expressed in Chris Mungall RO:0002293 ubiquitously expresses p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. Chris Mungall results_in_developmental_progression_of RO:0002295 results in developmental progression of every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. Chris Mungall http://www.geneontology.org/GO.doc.development.shtml results_in_development_of RO:0002296 results in development of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) Chris Mungall GOC:mtg_berkeley_2013 results_in_formation_of RO:0002297 results in formation of an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. Chris Mungall GOC:mtg_berkeley_2013 results_in_morphogenesis_of RO:0002298 results in morphogenesis of an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. Chris Mungall GOC:mtg_berkeley_2013 results_in_maturation_of RO:0002299 results in maturation of foramen ovale closure SubClassOf results in disappearance of foramen ovale Chris Mungall May be merged into parent relation results_in_disappearance_of RO:0002300 results in disappearance of every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) Chris Mungall May be merged into parent relation RO:0002301 results in developmental regression of Inverse of 'is substance that treats' cjm RO:0002302 is treated by substance cjm RO:0002304 holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm RO:0002305 holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect Chris Mungall RO:0002312 evolutionary variant of Holds between p and c when p is a transportation or localization process and the outcome of this process is to regulate the location of c Chris Mungall regulates location of transports RO:0002313 transports or maintains localization of q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall RO:0002314 inheres in part of an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall GOC:mtg_berkeley_2013 results_in_acquisition_of_features_of RO:0002315 results in acquisition of features of A relationship that holds via some environmental process Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. RO:0002320 evolutionarily related to An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. Chris Mungall adapted for adapted_for confers_advantage_in RO:0002322 uberon RO:0002322 confers advantage in A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development RO:0002324 developmentally related to Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium RO:0002325 colocalizes with ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 contributes to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. RO:0002327 enables Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally_related_to RO:0002328 uberon RO:0002328 functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part_of_structure_that_is_capable_of RO:0002329 uberon RO:0002329 part of structure that is capable of holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism RO:0002330 genomically related to c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of RO:0002331 involved in every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c Chris Mungall regulates levels of (process to entity) RO:0002332 regulates levels of inverse of enables Chris Mungall RO:0002333 enabled by inverse of regulates Chris Mungall regulated by (processual) RO:0002334 regulated by inverse of negatively regulates Chris Mungall RO:0002335 negatively regulated by inverse of positively regulates Chris Mungall RO:0002336 positively regulated by A relationship that holds via some process of localization Chris Mungall RO:0002337 related via localization to This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. Chris Mungall RO:0002338 has target start location This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. Chris Mungall RO:0002339 has target end location Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. Chris Mungall RO:0002340 imports Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l Chris Mungall RO:0002341 results in transport along Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. Chris Mungall RO:0002342 results in transport across 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 results in growth of 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) Chris Mungall RO:0002344 results in transport to from or in Chris Mungall RO:0002345 exports an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. Chris Mungall http://www.geneontology.org/GO.doc.development.shtml#fate RO:0002348 results in commitment to p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. Chris Mungall http://www.geneontology.org/GO.doc.development.shtml#fate RO:0002349 results in determination of An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member_of RO:0002350 uberon RO:0002350 member of has member is a mereological relation between a collection and an item. SIO has_member RO:0002351 uberon RO:0002351 has member inverse of has input Chris Mungall input_of RO:0002352 uberon RO:0002352 input of inverse of has output Chris Mungall output_of RO:0002353 uberon RO:0002353 output of Chris Mungall RO:0002354 formed as result of A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall RO:0002355 results in structural organization of The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. Chris Mungall http://www.geneontology.org/GO.doc.development.shtml#fate RO:0002356 results in specification of p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. Chris Mungall RO:0002357 results in developmental induction of Chris Mungall http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has dendrite location a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall attaches_to RO:0002371 uberon RO:0002371 attached to m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) has_muscle_origin RO:0002372 uberon RO:0002372 The origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscles has muscle origin m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002373 has muscle insertion false x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat Chris Mungall has_fused_element RO:0002374 uberon RO:0002374 A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. has fused element A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) RO:0002375 in branching relationship with https://github.com/obophenotype/uberon/issues/170 drains into tributary_of RO:0002376 uberon RO:0002376 tributary_of x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. Chris Mungall anastomoses with RO:0002378 anabranch of A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location Chris Mungall This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially coextensive with x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve Chris Mungall branching_part_of RO:0002380 uberon RO:0002380 branching part of x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. Chris Mungall RO:0002381 main stem of x proper_distributary_of y iff x distributary_of y and x does not flow back into y Chris Mungall RO:0002382 proper distributary of x proper_tributary_of y iff x tributary_of y and x does not originate from y Chris Mungall RO:0002383 proper tributary of x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall RO:0002384 has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y Chris Mungall has_potential_to_developmentally_contribute_to RO:0002385 uberon RO:0002385 has potential to developmentally contribute to x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y Chris Mungall RO:0002386 has potential to developmentally induce x has the potential to develop into y iff x develops into y or if x is capable of developing into y Chris Mungall has_potential_to_develop_into RO:0002387 uberon RO:0002387 has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y Chris Mungall has_potential_to_directly_develop_into RO:0002388 uberon RO:0002388 has potential to directly develop into 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 has direct input Chris Mungall RO:0002401 Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit obsolete has indirect input translation SubClassOf has_direct_output some protein p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. Chris Mungall directly produces RO:0002402 obsolete has direct output Chris Mungall RO:0002403 Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit obsolete has indirect output inverse of upstream of Chris Mungall RO:0002404 causally downstream of Chris Mungall RO:0002405 immediately causally downstream of p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q Chris Mungall directly positively regulates directly activates (process to process) RO:0002406 directly activates p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q Chris Mungall indirectly positively regulates RO:0002407 indirectly activates Chris Mungall directly negatively regulates directly inhibits (process to process) RO:0002408 directly inhibits Chris Mungall indirectly negatively regulates RO:0002409 indirectly inhibits This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall RO:0002411 causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall RO:0002412 immediately causally upstream of p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall directly provides input for (process to process) RO:0002413 directly provides input for transitive form of directly_provides_input_for Chris Mungall This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') transitively provides input for (process to process) RO:0002414 transitively provides input for p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects RO:0002418 causally upstream of or within false Chris Mungall RO:0002424 This is an exploratory relation differs in Chris Mungall RO:0002425 differs in attribute of Chris Mungall RO:0002426 differs in attribute inverse of causally upstream of or within Chris Mungall RO:0002427 causally downstream of or within c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall RO:0002428 involved in regulation of Chris Mungall RO:0002429 involved in positive regulation of Chris Mungall RO:0002430 involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p Chris Mungall involved in or reguates RO:0002431 involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d Chris Mungall executes activity in RO:0002432 enables activity in p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. Chris Mungall contributes_to_morphology_of RO:0002433 uberon RO:0002433 contributes to morphology of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with RO:0002434 interacts with https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) Chris Mungall RO:0002435 genetically interacts with An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. Chris Mungall binds molecularly binds with RO:0002436 molecularly interacts with An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. Chris Mungall interacts with on organism level RO:0002437 biotically interacts with An interaction relationship in which the partners are related via a feeding relationship. Chris Mungall RO:0002438 trophically interacts with A biotic interaction in which the two organisms live together in more or less intimate association. Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 symbiotically interacts with An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 commensually interacts with An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 mutualistically interacts with Chris Mungall has parasite parasitised by directly parasitized by RO:0002445 parasitized by Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. Chris Mungall semibiotically interacts with RO:0002446 participates in a abiotic-biotic interaction with Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b Chris Mungall RO:0002448 molecularly controls Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. Chris Mungall inhibits RO:0002449 molecularly decreases activity of Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b. Chris Mungall activates RO:0002450 molecularly increases activity of all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints Chris Mungall RO:0002451 transmitted by A relation that holds between a disease or an organism and a phenotype Chris Mungall RO:0002452 has symptom Chris Mungall RO:0002460 has vector Chris Mungall Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner in Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. RO:0002464 helper property Chris Mungall RO:0002465 is symbiosis Chris Mungall RO:0002466 is commensalism Chris Mungall RO:0002467 is mutualism Chris Mungall RO:0002468 is parasitism A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b. Chris Mungall RO:0002472 is evidence for 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. Chris Mungall composed_primarily_of RO:0002473 uberon RO:0002473 composed primarily of ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d Chris Mungall This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child nucleus of A child nucleus relationship in which the cells are part of a hermaphroditic organism Chris Mungall RO:0002477 child nucleus of in hermaphrodite A child nucleus relationship in which the cells are part of a male organism Chris Mungall RO:0002478 child nucleus of in male p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall RO:0002479 has part that occurs in An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later Chris Mungall RO:0002480 ubiquitinates Chris Mungall RO:0002481 is kinase activity Chris Mungall RO:0002482 is ubiquitination See notes for inverse relation Chris Mungall RO:0002485 receives input from This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. Chris Mungall RO:0002486 sends output to Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. RO:0002487 relation between structure and stage x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). Chris Mungall existence_starts_during RO:0002488 begins_to_exist_during uberon RO:0002488 existence starts during x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). Chris Mungall existence_starts_with RO:0002489 uberon RO:0002489 existence starts with x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) Chris Mungall RO:0002490 The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) Chris Mungall RO:0002491 The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). Chris Mungall existence_ends_during RO:0002492 ceases_to_exist_during uberon RO:0002492 The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). Chris Mungall existence_ends_with RO:0002493 uberon RO:0002493 The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships Chris Mungall transformation_of RO:0002494 transforms from uberon RO:0002494 transformation of x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t Chris Mungall immediate_transformation_of RO:0002495 direct_transformation_of immediately transforms from uberon RO:0002495 immediate transformation of x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). Chris Mungall existence_starts_during_or_after RO:0002496 uberon RO:0002496 The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. Chris Mungall existence_ends_during_or_before RO:0002497 uberon RO:0002497 The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before A relationship between a material entity and a process where the material entity has some causal role that influences the process RO:0002500 causal agent in p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 causal relation between processes Chris Mungall RO:0002502 depends on q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. Chris Mungall RO:0002503 towards 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c Chris Mungall has intermediate product RO:0002505 has intermediate A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future Chris Mungall determined by (system to material entity) Chris Mungall Pier Buttigieg RO:0002507 determined by inverse of determined by Chris Mungall determines (material entity to system) RO:0002508 determines s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. Chris Mungall RO:0002509 determined by part of x is transcribed from y if and only if x is synthesized from template y Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002510 transcribed from inverse of transcribed from Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002511 transcribed to x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002512 ribosomal translation of inverse of ribosomal translation of Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002513 ribosomally translates to A relation that holds between two entities that have the property of being sequences or having sequences. Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. RO:0002514 sequentially related to Every UTR is adjacent to a CDS of the same transcript Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 sequentially adjacent to Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence Chris Mungall started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002516 has start sequence inverse of has start sequence Chris Mungall starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 is start sequence of Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence Chris Mungall ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002518 has end sequence inverse of has end sequence Chris Mungall ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 is end sequence of x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 is consecutive sequence of Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering Chris Mungall RO:0002521 is sequentially aligned with The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y Chris Mungall RO:0002522 bounds sequence of inverse of bounds sequence of Chris Mungall RO:0002523 is bound by sequence of x has subsequence y iff all of the sequence parts of x are sequence parts of y Chris Mungall contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002524 has subsequence inverse of has subsequence Chris Mungall contained by RO:0002525 is subsequence of x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. Chris Mungall RO:0002526 overlaps sequence of x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. Chris Mungall disconnected from RO:0002527 does not overlap sequence of inverse of downstream of sequence of Chris Mungall RO:0002528 is upstream of sequence of x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. Chris Mungall RO:0002529 is downstream of sequence of A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y Chris Mungall RO:0002530 is immediately downstream of sequence of A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of Chris Mungall RO:0002531 is immediately upstream of sequence of A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. has sekeletal support has supporting framework has_skeleton RO:0002551 uberon RO:0002551 has skeleton p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall RO:0002552 results in ending of inverse of is evidence for Chris Mungall RO:0002558 x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. has evidence Chris Mungall causally influenced by (material entity to material entity) RO:0002559 causally influenced by Chris Mungall RO:0002563 interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall RO:0002564 molecular interaction relation helper property Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall RO:0002565 results in movement of Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall causally influences (material entity to material entity) RO:0002566 causally influences A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically related to m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. Chris Mungall Wikipedia:Antagonist_(muscle) has_muscle_antagonist RO:0002568 uberon RO:0002568 has muscle antagonist inverse of branching part of Chris Mungall has_branching_part RO:0002569 uberon RO:0002569 has branching part x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. Chris Mungall UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 conduit for x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. Chris Mungall GOC:cjm lumen_of RO:0002571 uberon RO:0002571 lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity Chris Mungall luminal_space_of RO:0002572 uberon RO:0002572 luminal space of A relation that holds between an attribute or a qualifier and another attribute. Chris Mungall This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. RO:0002573 has modifier Chris Mungall RO:0002574 participates in a biotic-biotic interaction with inverse of has skeleton Chris Mungall RO:0002576 skeleton of p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p Chris Mungall directly regulates (processual) RO:0002578 directly regulates x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. RO:0002583 existence starts at point gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall RO:0002584 has part structure that is capable of p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results in closure of p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p RO:0002586 results in breakdown of RO:0002587 results in synthesis of RO:0002588 results in assembly of p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. RO:0002589 results in catabolism of RO:0002590 results in disassembly of RO:0002591 results in remodeling of p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results in organization of x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. RO:0002593 existence ends at point A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall RO:0002595 causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. RO:0002596 capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. RO:0002597 capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. RO:0002598 capable of positively regulating c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. May be ceded to OBI RO:0002607 is marker for Inverse of 'causal agent in' RO:0002608 has causal agent A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. RO:0002609 related via dependence to A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Groups both positive and negative correlation RO:0002610 correlated with An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. RO:0002614 In the Gene Ontology association model, this corresponds to the With/From field is evidence with support from Inverse of is-model-of RO:0002615 has model RO:0002616 related via evidence or inference to p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p directly positively regulates (process to process) RO:0002629 directly positively regulates p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p directly negatively regulates (process to process) RO:0002630 directly negatively regulates inverse of intracellular endoparasite of RO:0002641 has intracellular endoparasite a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel produces RO:0003000 uberon RO:0003000 Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel produced_by RO:0003001 uberon RO:0003001 produced by Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b. Logical axioms to be added after the relevant branch of GO is MIREOTed in RO:0003002 represses expression of Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b. Logical axioms to be added after the relevant branch of GO is MIREOTed in RO:0003003 increases expression of Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? Matthew Brush RO:0003301 The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. is model of The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition. Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. RO:0003302 Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. causes or contributes to condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition. RO:0003303 causes condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition. RO:0003304 contributes to condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual. contributes to expressivity of condition RO:0003305 contributes to severity of condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population. contributes to penetrance of condition RO:0003306 contributes to frequency of condition A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. RO:0003308 correlated with condition An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 co-occurs Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. correspondence resemblance ECO:0000041 SO:similar_to sameness similar to RO:HOM0000000 in similarity relationship with Similarity that results from common evolutionary origin. homologous to RO:HOM0000001 This broad definition encompasses all the working definitions proposed so far in the literature. in homology relationship with Similarity that results from independent evolution. analogy homoplasous to RO:HOM0000002 in homoplasy relationship with Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. ECO:0000075 homocracous to RO:HOM0000003 Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. in homocracy relationship with Homoplasy that involves different underlying mechanisms or structures. analogy RO:HOM0000004 Convergence usually implies a notion of adaptation. in convergence relationship with Homoplasy that involves homologous underlying mechanisms or structures. parallel evolution RO:HOM0000005 Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. in parallelism relationship with Homology that is defined by similarity with regard to selected structural parameters. idealistic homology ECO:0000071 MI:2163 structural homologous to RO:HOM0000006 in structural homology relationship with Homology that is defined by common descent. true homology homology ECO:0000080 RO_proposed_relation:homologous_to SO:0000330 SO:0000853 SO:0000857 SO:homologous_to TAO:homologous_to cladistic homology historical homologous to phylogenetic homology taxic homology RO:HOM0000007 in historical homology relationship with Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. transformational homology ECO:0000067 biological homologous to RO:HOM0000008 Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. in biological homology relationship with Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. reversion atavism rudiment RO:HOM0000009 in reversal relationship with Structural homology that is detected by similarity in content and organization between chromosomes. synteny MeSH:Synteny SO:0000860 SO:0005858 syntenic homologous to RO:HOM0000010 in syntenic homology relationship with Historical homology that involves genes that diverged after a duplication event. SO:0000854 SO:0000859 SO:paralogous_to paralogous to RO:HOM0000011 in paralogy relationship with Paralogy that involves sets of syntenic blocks. duplicon paralogon syntenic paralogous to RO:HOM0000012 in syntenic paralogy relationship with Syntenic homology that involves chromosomes of different species. syntenic orthologous to RO:HOM0000013 in syntenic orthology relationship with Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. mixed homology modular homology partial correspondence percent homology fractional homology partial homologous to segmental homology RO:HOM0000014 in partial homology relationship with Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. MeSH:Structural_Homology,_Protein protein structural homologous to RO:HOM0000015 in protein structural homology relationship with Structural homology that involves a pseudogenic feature and its functional ancestor. pseudogene SO:non_functional_homolog_of non functional homologous to RO:HOM0000016 in non functional homology relationship with Historical homology that involves genes that diverged after a speciation event. ECO:00000060 SO:0000855 SO:0000858 SO:orthologous_to orthologous to RO:HOM0000017 The term is sometimes also used for anatomical structures. in orthology relationship with Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. xenologous to RO:HOM0000018 The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). in xenology relationship with Historical homology that involves two members sharing no other homologs in the lineages considered. 1 to 1 homologous to 1:1 homology one-to-one homology RO:HOM0000019 in 1 to 1 homology relationship with Orthology that involves two genes that did not experience any duplication after the speciation event that created them. 1 to 1 orthologous to 1:1 orthology one-to-one orthology RO:HOM0000020 in 1 to 1 orthology relationship with Paralogy that results from a whole genome duplication event. homoeology ohnologous to RO:HOM0000022 in ohnology relationship with Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. in-paralogous to inparalogy symparalogy RO:HOM0000023 in in-paralogy relationship with Paralogy that results from a duplication preceding a given speciation event. alloparalogy out-paralogous to outparalogy RO:HOM0000024 in out-paralogy relationship with 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. pro-orthologous to RO:HOM0000025 in pro-orthology relationship with 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. semi-orthologous to RO:HOM0000026 The converse of pro-orthologous. in semi-orthology relationship with Iterative homology that involves structures arranged along the main body axis. homonomy serial homologous to RO:HOM0000027 in serial homology relationship with Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. heterochronous homologous to heterochrony RO:HOM0000028 in heterochronous homology relationship with Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. juvenification pedomorphosis RO:HOM0000029 in paedomorphorsis relationship with Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. RO:HOM0000030 in peramorphosis relationship with Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. RO:HOM0000031 in progenesis relationship with Paedomorphosis that is produced by a retardation of somatic development. juvenilization neotenous to RO:HOM0000032 in neoteny relationship with Convergence that results from co-evolution usually involving an evolutionary arms race. mimicrous to RO:HOM0000033 in mimicry relationship with Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. co-orthology many to 1 orthology 1 to many orthologous to 1:many orthology one-to-many orthology RO:HOM0000034 in 1 to many orthology relationship with Historical homology that involves two members of a larger set of homologs. many to many homologous to many-to-many homology many:many homology RO:HOM0000036 in many to many homology relationship with Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. 1:many homology 1 to many homologous to one-to-many homology RO:HOM0000037 in 1 to many homology relationship with Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. synapomorphy apomorphous to RO:HOM0000042 in apomorphy relationship with Historical homology that is based on distant shared ancestry. symplesiomorphy plesiomorphous to RO:HOM0000043 This term is usually contrasted to apomorphy. in plesiomorphy relationship with Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. generative homology homoiology deep genetic homology deep homologous to RO:HOM0000044 Used for structures in distantly related taxa. in deep homology relationship with Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. hemiplasous to RO:HOM0000045 in hemiplasy relationship with Historical homology that involves not recombining and subsequently differentiated sex chromosomes. gametologous to RO:HOM0000046 in gametology relationship with Historical homology that involves the chromosomes able to pair (synapse) during meiosis. MeSH:Chromosome_Pairing chromosomal homologous to RO:HOM0000047 in chromosomal homology relationship with Orthology that involves two genes that experienced duplications more recent than the species split that created them. co-orthology trans-homology many to many orthologous to many-to-many orthology many:many orthology trans-orthology RO:HOM0000048 in many to many orthology relationship with Paralogy that involves genes from the same species. within-species paralogous to RO:HOM0000049 in within-species paralogy relationship with Paralogy that involves genes from different species. between-species paralogous to RO:HOM0000050 The genes have diverged before a speciation event. in between-species paralogy relationship with Paedomorphosis that is produced by delayed growth of immature structures into the adult form. post-displacement RO:HOM0000051 in postdisplacement relationship with Peramorphosis that is produced by a delay in the offset of development. RO:HOM0000052 in hypermorphosis relationship with Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. synologous to RO:HOM0000053 in synology relationship with Orthology that involves functional equivalent genes with retention of the ancestral function. ECO:0000080 isoorthologous to RO:HOM0000054 in isoorthology relationship with Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. iterative paralogy serial paralogy tandem paralogous to RO:HOM0000055 in tandem paralogy relationship with Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). homoiology homoplastic tendency re-awakening apomorphic tendency cryptic homology latent homologous to underlying synapomorphy RO:HOM0000057 Used for structures in closely related taxa. in latent homology relationship with Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. generative homology syngenous to RO:HOM0000058 Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. in syngeny relationship with Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. 1:1 paralogy apparent 1:1 orthology apparent orthologous to pseudoorthology RO:HOM0000060 The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. in apparent orthology relationship with Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. pseudoparalogous to RO:HOM0000061 These genes may come out as paralogs in a single-genome analysis. in pseudoparalogy relationship with Historical homology that involves functional equivalent genes with retention of the ancestral function. equivalogous to RO:HOM0000062 This may include examples of orthology, paralogy and xenology. in equivalogy relationship with Historical homology that involves orthologous pairs of interacting molecules in different organisms. interologous to RO:HOM0000063 in interology relationship with Similarity that is characterized by interchangeability in function. functional similarity RO:HOM0000065 in functional equivalence relationship with Biological homology that involves parts of the same organism. iterative homologous to RO:HOM0000066 in iterative homology relationship with Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. duplicate xenology multiple xenology paraxenologous to RO:HOM0000068 in paraxenology relationship with Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. plerologous to RO:HOM0000069 This phenomenon is usually due to gene conversion process. in plerology relationship with Structural homology that involves structures with the same or similar relative positions. homotopous to RO:HOM0000071 Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. in homotopy relationship with Biological homology that involves an ectopic structure and the normally positioned structure. heterotopy RO:HOM0000072 in homeosis relationship with Synology that results from allopolyploidy. homoeologous to RO:HOM0000073 On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. in homoeology relationship with Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. axis paramorphism RO:HOM0000074 in paramorphism relationship with Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. regulogous to RO:HOM0000075 in regulogy relationship with immediate_transformation_of http://semanticscience.org/resource/SIO_000658 direct_transformation_of immediately transforms from SIO:000658 immediate_transformation_of provenance_notes UBPROP:0000004 uberon UBPROP:0000004 obsolete provenance_notes true x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. uberon anteriorly_connected_to anteriorly connected to carries uberon channel_for channel for uberon channels_from channels_from uberon channels_into channels_into x is a conduit for y iff y passes through the lumen of x. uberon conduit_for conduit for x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to distally connected to uberon existence_starts_and_ends_during existence starts and ends during uberon extends_fibers_into extends_fibers_into has_completed has_completed A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_high_plasma_membrane_amount has_high_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_low_plasma_membrane_amount has_low_plasma_membrane_amount has_not_completed has_not_completed uberon has_start has_start X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides. uberon in_central_side_of in_central_side_of uberon in_innermost_side_of in_innermost_side_of uberon in_outermost_side_of in_outermost_side_of a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s add to RO uberon indirectly_supplies indirectly_supplies http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y lacks_part lacks_part uberon layer_part_of layer part of x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon posteriorly_connected_to posteriorly connected to uberon protects protects x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon proximally_connected_to proximally connected to c site_of p if c is the bearer of a disposition that is realized by a process that has p as part capable_of_has_part uberon site_of site_of uberon subdivision_of placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision of . uberon transitively_anteriorly_connected_to transitively anteriorly connected to uberon transitively_connected_to transitively_connected to . uberon transitively_distally_connected_to transitively distally connected to . uberon transitively_proximally_connected_to transitively proximally connected to uberon trunk_part_of trunk_part_of D0-D2. Zygote and dispersed blastomere cleavage in a yolk syncytium. Days 0-2 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000001 Stage 1 Planosphere [https://planosphere.stowers.org/stage1] D0-D2. Zygote and dispersed blastomere cleavage in a yolk syncytium. Days 0-2 post-egg capsule deposition at 20˚C. PMID:28072387 D2-D3. Sphere formation. A fraction of the blastomeres differentiate into temporary embryonic tissues that provide form and function to the embryo. Undifferentiated blastomeres remain in the embryonic wall. Days 2-3 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000002 Stage 2 Planosphere [https://planosphere.stowers.org/stage2] D2-D3. Sphere formation. A fraction of the blastomeres differentiate into temporary embryonic tissues that provide form and function to the embryo. Undifferentiated blastomeres remain in the embryonic wall. Days 2-3 post-egg capsule deposition at 20˚C. PMID:28072387 D2-D4. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity. Days 2-4 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000003 Stage 3 Planosphere [https://planosphere.stowers.org/stage3] D2-D4. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity. Days 2-4 post-egg capsule deposition at 20˚C. PMID:28072387 D3-D5. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation. Days 3-5 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000004 Stage 4 Planosphere [https://planosphere.stowers.org/stage4] D3-D5. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation. Days 3-5 post-egg capsule deposition at 20˚C. PMID:28072387 D5-D7. Organogenesis onset. Downregulation of early embryo enriched transcripts and birth of adult lineages within the blastomere population. Early embryonic gut formation continues. Yolk ingestion into the gut cavity. Days 5-7 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000005 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo. Stage 5 Planosphere [https://planosphere.stowers.org/stage5] D5-D7. Organogenesis onset. Downregulation of early embryo enriched transcripts and birth of adult lineages within the blastomere population. Early embryonic gut formation continues. Yolk ingestion into the gut cavity. Days 5-7 post-egg capsule deposition at 20˚C. PMID:28072387 D7-D9. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation. Days 7-9 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000006 Stage 6 Planosphere [https://planosphere.stowers.org/stage6] D7-D9. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation. Days 7-9 post-egg capsule deposition at 20˚C. PMID:28072387 D9-D11. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility. Days 9-11 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000007 Stage 7 Planosphere [https://planosphere.stowers.org/stage7] D9-D11. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility. Days 9-11 post-egg capsule deposition at 20˚C. PMID:28072387 D13-D15. Organogenesis and organ maturation continues. Hatching. Days 13-15 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000008 Stage 8 Planosphere [https://planosphere.stowers.org/stage8] D13-D15. Organogenesis and organ maturation continues. Hatching. Days 13-15 post-egg capsule deposition at 20˚C. PMID:28072387 A heterogeneous subpopulation of neoblasts with enriched expression of SoxP-1 and SoxP-2 thought to contain both pluripotent stem cells and tissue-specific progenitors. Planarian_Anatomy PLANA:0000009 sigma neoblast Planosphere [https://planosphere.stowers.org/sigmaneoblast] A heterogeneous subpopulation of neoblasts with enriched expression of SoxP-1 and SoxP-2 thought to contain both pluripotent stem cells and tissue-specific progenitors. PMID:25017721 Neoblasts and post-mitotic, differentiating daughters coexpressing POU2-3, six1/2-2, Sal1, Eya and Osr, required for maintenance and regeneration of protonephridial cell types. Planarian_Anatomy PLANA:0000011 protonephridial progenitor Planosphere [https://planosphere.stowers.org/protonephridialprogenitor] Neoblasts and post-mitotic, differentiating daughters coexpressing POU2-3, six1/2-2, Sal1, Eya and Osr, required for maintenance and regeneration of protonephridial cell types. PMID:21937596 Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system. Planarian_Anatomy PLANA:0000012 neural progenitor Planosphere [https://planosphere.stowers.org/neuralprogenitor] An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s). Planarian_Anatomy PLANA:0000014 zeta neoblast Planosphere [https://planosphere.stowers.org/zetaneoblast] An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s). PMID:25017721 A plicate and protrusible organ that is the sole point of entry and exit for the Triclad gut. It contains epithelial, muscular, secretory and neuronal cell types. Planarian_Anatomy PLANA:0000016 definitive pharynx Planosphere [https://planosphere.stowers.org/definitivepharynx] A plicate and protrusible organ that is the sole point of entry and exit for the Triclad gut. It contains epithelial, muscular, secretory and neuronal cell types. OCLC:16809160 Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain. Planarian_Anatomy PLANA:0000017 photoreceptor neuron Planosphere [https://planosphere.stowers.org/photoreceptorneuron] Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain. PMID:21852957 PMID:22884275 Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells. Planarian_Anatomy PLANA:0000018 Category 4 cell Planosphere [https://planosphere.stowers.org/category4cell] Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells. PMID:25017721 PMID:26457503 myoD+ neoblasts and their post-mitotic, differentiating daughters implicated in the maintenance and regeneration of muscles. Planarian_Anatomy PLANA:0000019 muscle progenitor Planosphere [https://planosphere.stowers.org/muscleprogenitor] myoD+ neoblasts and their post-mitotic, differentiating daughters implicated in the maintenance and regeneration of muscles. PMID:25017721 Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct. Planarian_Anatomy PLANA:0000020 protonephridia Planosphere [https://planosphere.stowers.org/protonephridia] Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct. OCLC:16809160 PMID:21828097 PMID:26057828 Post-mitotic, ciliated epidermal cells. Planarian_Anatomy PLANA:0000022 Category 5 cell Planosphere [https://planosphere.stowers.org/category5cell] Post-mitotic, ciliated epidermal cells. PMID:25017721 An innervated, muscular pump that ingests yolk cells into the gut cavity. The temporary embryonic pharynx is an extraembryonic tissue that forms during Stage 2, functions during Stages 3-5, and degenerates during Stages 6-7. PMID:28072387 Planarian_Anatomy PLANA:0000023 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo with anatomical feature noted with black indicators. temporary embryonic pharynx Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynx] The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organisms, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. UBERON:0001016 Planarian_Anatomy PLANA:0000025 nervous system Planosphere [https://planosphere.stowers.org/nervoussystem] The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organisms, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. UBERON:0001016 The planarian triclad gut contains a central anterior gut branch connected to two posterior gut branches arranged around the definitive pharynx. Secondary gut branches extend laterally from the primary gut branches, while tertiary gut branches extend from the secondary branches. Food and waste enter and exit the definitive gut through the defintive pharynx. Planarian_Anatomy PLANA:0000026 definitive gut Planosphere [https://planosphere.stowers.org/definitivegut] The planarian triclad gut contains a central anterior gut branch connected to two posterior gut branches arranged around the definitive pharynx. Secondary gut branches extend laterally from the primary gut branches, while tertiary gut branches extend from the secondary branches. Food and waste enter and exit the definitive gut through the defintive pharynx. PMID:3490491 Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts. Planarian_Anatomy PLANA:0000028 Category 2 cell Planosphere [https://planosphere.stowers.org/category2cell] Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts. PMID:18786419 PMID:20040488 PMID:22385657 PMID:25017721 PMID:26114597 A single cell layer of extraembryonic, post-mitotic ectodermal cells bounding the embryo. The primitive ectoderm forms during Stage 2 and is thought to degenerate as the definitive epidermis forms during Stages 5-7. Planarian_Anatomy PLANA:0000029 primitive ectoderm Planosphere [https://planosphere.stowers.org/primitiveectoderm] A single cell layer of extraembryonic, post-mitotic ectodermal cells bounding the embryo. The primitive ectoderm forms during Stage 2 and is thought to degenerate as the definitive epidermis forms during Stages 5-7. OCLC:20423827 OCLC:464776945 OCLC:82522822 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup. Planarian_Anatomy PLANA:0000031 pigment cup cell Planosphere [https://planosphere.stowers.org/pigmentcupcell] Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup. PMID:21852957 PMID:22884275 Mitotically active zeta neoblasts and their post-mitotic descendants which undergo progressive differentiation and outward directed movement through the mesenchyme prior to incorporation into the epidermis, where terminal differentiation occurs. Planarian_Anatomy PLANA:0000033 epidermal progenitor Planosphere [https://planosphere.stowers.org/epidermalprogenitor] Mitotically active zeta neoblasts and their post-mitotic descendants which undergo progressive differentiation and outward directed movement through the mesenchyme prior to incorporation into the epidermis, where terminal differentiation occurs. PMID:18786419 PMID:20040488 PMID:22385657 PMID:25017721 PMID:26114597 PMID:26457503 A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal. Planarian_Anatomy PLANA:0000034 At present, this definition does not apply to epithelial structures other than the dorsal and ventral epidermis (i.e., the pharyngeal epithelium). definitive epidermis Planosphere [https://planosphere.stowers.org/definitiveepidermis] A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal. OCLC:16809160 Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells. Planarian_Anatomy PLANA:0000035 Category 3 cell Planosphere [https://planosphere.stowers.org/category3cell] Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells. PMID:18786419 PMID:20040488 PMID:26114597 PMID:26457503 An organ that detects light. UBERON:0000970 Planarian_Anatomy PLANA:0000036 eye Planosphere [https://planosphere.stowers.org/eye] Adult tissues built during organogenesis that are present in juveniles at birth. Planarian_Anatomy PLANA:0000037 definitive tissue Planosphere [https://planosphere.stowers.org/definitivetissue] Adult tissues built during organogenesis that are present in juveniles at birth. PMID:28072387 PMID:2888018 An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut. Planarian_Anatomy PLANA:0000039 gamma neoblast Planosphere [https://planosphere.stowers.org/gammaneoblast] An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut. PMID:25017721 A stage of embryonic development defined by a unique gene expression signature, morphology and chronological time post-egg capsule deposition for hermaphrodites reared at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000040 Schmidtea mediterranea developmental stage Planosphere [https://planosphere.stowers.org/schmidteamediterraneadevelopmentalstage] A stage of embryonic development defined by a unique gene expression signature, morphology and chronological time post-egg capsule deposition for hermaphrodites reared at 20˚C. PMID:28072387 Stage 3-5 embryo hemisphere centered around the pole opposite the temporary embryonic pharynx. Planarian_Anatomy PLANA:0000041 aboral hemisphere Planosphere [https://planosphere.stowers.org/aboralhemisphere] Stage 3-5 embryo hemisphere centered around the pole opposite the temporary embryonic pharynx. PMID:28072387 The single, central gut branch of the triclad gut anterior to the definitive pharynx. Planarian_Anatomy PLANA:0000042 anterior primary gut branch Planosphere [https://planosphere.stowers.org/anteriorprimarygutbranch] The single, central gut branch of the triclad gut anterior to the definitive pharynx. PMID:3490491 The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head. brain Planarian_Anatomy PLANA:0000044 cephalic ganglia Planosphere [https://planosphere.stowers.org/cephalicganglia] Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema. Planarian_Anatomy PLANA:0000045 circular muscle fiber Planosphere [https://planosphere.stowers.org/circularmusclefiber] Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md Pluripotent piwi-1+ stem cells that self-renew, form expanding colonies and produce differentiating daughters that contribute to multiple organ systems. cNeoblasts are predicted to be broadly distributed across the anteroposterior axis of the adult worm. Planarian_Anatomy PLANA:0000046 clonogenic neoblast Planosphere [https://planosphere.stowers.org/clonogenicneoblast] Pluripotent piwi-1+ stem cells that self-renew, form expanding colonies and produce differentiating daughters that contribute to multiple organ systems. cNeoblasts are predicted to be broadly distributed across the anteroposterior axis of the adult worm. PMID:21566185 Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis. Planarian_Anatomy PLANA:0000047 collecting duct Planosphere [https://planosphere.stowers.org/collectingduct] Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis. PMID:26057828 Body wall muscle fibers arrayed diagonally along the anteroposterior axis. Planarian_Anatomy PLANA:0000048 diagonal muscle fiber Planosphere [https://planosphere.stowers.org/diagonalmusclefiber] Body wall muscle fibers arrayed diagonally along the anteroposterior axis. PMID:26904543 Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. UBERON:0001007 Planarian_Anatomy PLANA:0000049 digestive system Planosphere [https://planosphere.stowers.org/digestivesystem] Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. UBERON:0013765 Planarian_Anatomy PLANA:0000050 digestive system element Planosphere [https://planosphere.stowers.org/digestivesystemelement] Embryonic development producing juvenile animals with body plans and feeding behavior similar to adults. Juveniles grow and mature into adults without undergoing metamorphosis. Schmidtea_mediterranea_Developmental_Terms PLANA:0000051 direct development Planosphere [https://planosphere.stowers.org/directdevelopment] A derived form of early embryonic cleavage present in ectolecithal embryos. Blastomeres divide asynchronously within a yolk syncytium, and division progeny do not remain in direct contact with one another. Schmidtea_mediterranea_Developmental_Terms PLANA:0000052 dispersed cleavage Planosphere [https://planosphere.stowers.org/dispersedcleavage] A derived form of early embryonic cleavage present in ectolecithal embryos. Blastomeres divide asynchronously within a yolk syncytium, and division progeny do not remain in direct contact with one another. OCLC:20423827 OCLC:42792751 OCLC:464776945 OCLC:82522822 PMID:15599763 PMID:19197510 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells. Planarian_Anatomy PLANA:0000053 distal tubule Planosphere [https://planosphere.stowers.org/distaltubule] Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells. PMID:21828097 Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe. Planarian_Anatomy PLANA:0000054 dorsal epidermis Planosphere [https://planosphere.stowers.org/dorsalepidermis] Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe. OCLC:16809160 Ciliated epithelial cells along the dorsal midline. Planarian_Anatomy PLANA:0000055 dorsal stripe Planosphere [https://planosphere.stowers.org/dorsalstripe] Turbellarian (freshwater flatworm) embryos that undergo a modified form of cleavage due to separation of oocyte and yolk. Yolk is not contained within oocytes, and is produced by somatic vitellogenic gland cells. Schmidtea_mediterranea_Developmental_Terms PLANA:0000056 ectolecithal embryo Planosphere [https://planosphere.stowers.org/ectolecithalembryo] Turbellarian (freshwater flatworm) embryos that undergo a modified form of cleavage due to separation of oocyte and yolk. Yolk is not contained within oocytes, and is produced by somatic vitellogenic gland cells. PMID:22074376 PMID:27149082 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000002.md The first few specialized divisions of an activated animal egg. GO:0040016 Schmidtea_mediterranea_Developmental_Terms PLANA:0000057 embryonic cleavage Planosphere [https://planosphere.stowers.org/embryoniccleavage] A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the temporary embryonic pharynx and primitive gut cells. Embryonic gut cells, likely produced from blastomeres, form a phagocytic tissue layer surrounding the inner gut cavity during Stages 4-6. It is not known whether the embryonic gut is temporary embryonic tissue or a definitive tissue. For convenience, the embryonic gut is currently designated as an extraembryonic structure because cell type specific markers for the embryonic gut do not stain the definitive gut in hatchlings or adult animals. Planarian_Anatomy PLANA:0000058 embryonic digestive system Planosphere [https://planosphere.stowers.org/embryonicdigestivesystem] A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the temporary embryonic pharynx and primitive gut cells. Embryonic gut cells, likely produced from blastomeres, form a phagocytic tissue layer surrounding the inner gut cavity during Stages 4-6. It is not known whether the embryonic gut is temporary embryonic tissue or a definitive tissue. For convenience, the embryonic gut is currently designated as an extraembryonic structure because cell type specific markers for the embryonic gut do not stain the definitive gut in hatchlings or adult animals. PMID:28072387 Dispersed, phagocytic gut cells that appear during Stage 4 and ultimately generate a honeycomb-like lattice surrounding the central gut cavity in Stage 5 embryos. Early embryonic gut cell specific transcripts are expressed from Stage 4-6, and are downregulated during Stage 7. Planarian_Anatomy PLANA:0000059 embryonic gut cell Planosphere [https://planosphere.stowers.org/embryonicgutcell] Dispersed, phagocytic gut cells that appear during Stage 4 and ultimately generate a honeycomb-like lattice surrounding the central gut cavity in Stage 5 embryos. Early embryonic gut cell specific transcripts are expressed from Stage 4-6, and are downregulated during Stage 7. PMID:28072387 The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos. Planarian_Anatomy PLANA:0000060 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo with anatomical feature noted with black indicators. embryonic wall Planosphere [https://planosphere.stowers.org/embryonicwall] The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos. OCLC:16809160 PMID:12888018 Visceral muscle surrounding the definitive gut. Planarian_Anatomy PLANA:0000061 enteric muscle Planosphere [https://planosphere.stowers.org/entericmuscle] Attachment between the triclad gut and the proximal end of the definitive pharynx. Planarian_Anatomy PLANA:0000062 esophagus Planosphere [https://planosphere.stowers.org/esophagus] A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. UBERON:0000478 Planarian_Anatomy PLANA:0000063 extraembryonic structure Planosphere [https://planosphere.stowers.org/extraembryonicstructure] Terminal structure of protonephridia unit; consists of flame cells. Planarian_Anatomy PLANA:0000064 flame bulb Planosphere [https://planosphere.stowers.org/flamebulb] Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the ‘filtration weir’, which consists of closely apposed strands of cytoplasm surrounding a central cilia bundle, and by numerous microvilli between weir and cilia. Positive for acetyated tubulin. Planarian_Anatomy PLANA:0000065 flame cell Planosphere [https://planosphere.stowers.org/flamecell] Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the ‘filtration weir’, which consists of closely apposed strands of cytoplasm surrounding a central cilia bundle, and by numerous microvilli between weir and cilia. Positive for acetyated tubulin. OCLC:16809160 PMID:21828097 PMID:26057828 The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle. Planarian_Anatomy PLANA:0000066 gastrodermis Planosphere [https://planosphere.stowers.org/gastrodermis] The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle. PMID:3490491 Secretory cells that release digestive enzymes into the lumen of the intestine. Planarian_Anatomy PLANA:0000067 goblet cell Planosphere [https://planosphere.stowers.org/gobletcell] Secretory cells that release digestive enzymes into the lumen of the intestine. PMID:3490491 Lumen of embryonic digestive tract, prior to formation of the branched defintive gut. Planarian_Anatomy PLANA:0000068 embryonic gut cavity Planosphere [https://planosphere.stowers.org/embryonicgutcavity] Lumen of embryonic digestive tract, prior to formation of the branched defintive gut. PMID:28072387 Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole. Planarian_Anatomy PLANA:0000069 inner longitudinal muscle fiber Planosphere [https://planosphere.stowers.org/innerlongitudinalmusclefiber] Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md Absorptive digestive cells that engulf food particles for intracellular digestion. Planarian_Anatomy PLANA:0000070 intestinal phagocyte Planosphere [https://planosphere.stowers.org/intestinalphagocyte] Absorptive digestive cells that engulf food particles for intracellular digestion. PMID:3490491 Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers. Planarian_Anatomy PLANA:0000071 longitudinal muscle fiber Planosphere [https://planosphere.stowers.org/longitudinalmusclefiber] Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md The sole point of entry and exit for the Triclad planarian flatworm gut. The mouth is connected to the pharyngeal pouch to allow for exit and re-entry of the definitive pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells. Manus Planarian_Anatomy PLANA:0000072 mouth Planosphere [https://planosphere.stowers.org/mouth] The sole point of entry and exit for the Triclad planarian flatworm gut. The mouth is connected to the pharyngeal pouch to allow for exit and re-entry of the definitive pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells. OCLC:16809160 Manus https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000006.md A female germ cell that has entered meiosis. CL:0000023 Planarian_Anatomy PLANA:0000074 oocyte Planosphere [https://planosphere.stowers.org/oocyte] A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons. Planarian_Anatomy PLANA:0000075 optic cup Planosphere [https://planosphere.stowers.org/opticcup] A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons. PMID:21852957 PMID:22884275 Stage 3-5 embryo hemisphere centered around the temporary embryonic pharynx. Planarian_Anatomy PLANA:0000076 oral hemisphere Planosphere [https://planosphere.stowers.org/oralhemisphere] Stage 3-5 embryo hemisphere centered around the temporary embryonic pharynx. PMID:28072387 A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. UBERON:0000111 Schmidtea_mediterranea_Developmental_Terms PLANA:0000077 organogenesis Planosphere [https://planosphere.stowers.org/organogenesis] Outer most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thinner than the inner longitudinal muscle fibers. Planarian_Anatomy PLANA:0000078 outer longitudinal muscle fiber Planosphere [https://planosphere.stowers.org/outerlongitudinalmusclefiber] Outer most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thinner than the inner longitudinal muscle fibers. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md Dorsal-ventral muscle fibers present through the mesenchyme. dorsoventral muscle fibers Planarian_Anatomy PLANA:0000079 parenchymal musculature Planosphere [https://planosphere.stowers.org/parenchymalmusculature] Dorsal-ventral muscle fibers present through the mesenchyme. OCLC:16809160 A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. UBERON:0000010 Planarian_Anatomy PLANA:0000080 peripheral nervous system Planosphere [https://planosphere.stowers.org/peripheralnervoussystem] An epithelial structure housing the definitive pharynx, connected to the esophagus and mouth. Planarian_Anatomy PLANA:0000081 pharyngeal pouch Planosphere [https://planosphere.stowers.org/pharyngealpouch] An epithelial structure housing the definitive pharynx, connected to the esophagus and mouth. OCLC:16809160 The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch. Planarian_Anatomy PLANA:0000084 posterior primary gut branch Planosphere [https://planosphere.stowers.org/posteriorprimarygutbranch] The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch. PMID:3490491 Four large phagocytic cells associated with the temporary embryonic pharynx. Planarian_Anatomy PLANA:0000085 primitive gut cell Planosphere [https://planosphere.stowers.org/primitivegutcell] Four large phagocytic cells associated with the temporary embryonic pharynx. PMID:28072387 Stage 2 embryo undergoing the process of sphere formation. Schmidtea_mediterranea_Developmental_Terms PLANA:0000086 protosphere Planosphere [https://planosphere.stowers.org/protosphere] Stage 2 embryo undergoing the process of sphere formation. PMID:28072387 Ciliated epithelial cells form tubules, generating coiled, branching units terminating in flame bulbs. Tubules are formed via intercellular junctions between two epithelial cells. Proximal tubules are connected to non-ciliated distal tubules within the parenchyma. Planarian_Anatomy PLANA:0000087 proximal tubule Planosphere [https://planosphere.stowers.org/proximaltubule] Ciliated epithelial cells form tubules, generating coiled, branching units terminating in flame bulbs. Tubules are formed via intercellular junctions between two epithelial cells. Proximal tubules are connected to non-ciliated distal tubules within the parenchyma. PMID:21828097 The renal system is an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. UBERON:0001008 Planarian_Anatomy PLANA:0000088 renal system Planosphere [https://planosphere.stowers.org/renalsystem] Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge. Planarian_Anatomy PLANA:0000089 secondary gut branch Planosphere [https://planosphere.stowers.org/secondarygutbranch] Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge. PMID:3490491 A mature male germ cell that develops from a spermatid. CL:0000019 spermatozoa Planarian_Anatomy PLANA:0000090 sperm Planosphere [https://planosphere.stowers.org/sperm] Generation of a multilayered spherical embryo comprised of temporary extraembryonic tissues and undifferentiated blastomeres. Schmidtea_mediterranea_Developmental_Terms PLANA:0000091 sphere formation Planosphere [https://planosphere.stowers.org/sphereformation] Generation of a multilayered spherical embryo comprised of temporary extraembryonic tissues and undifferentiated blastomeres. OCLC:20423827 OCLC:464776945 PMID:12888018 PMID:15599763 PMID:28072387 Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2. Schmidtea_mediterranea_Developmental_Terms PLANA:0000092 syncytial yolk cell Planosphere [https://planosphere.stowers.org/syncytialyolkcell] Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2. PMID:15599763 Gut branches originating from and connected to the secondary gut branches. Planarian_Anatomy PLANA:0000093 tertiary gut branch Planosphere [https://planosphere.stowers.org/tertiarygutbranch] Gut branches originating from and connected to the secondary gut branches. PMID:3490491 The process in which the anatomical structures of a tissue are generated and organized. GO:0048729 Schmidtea_mediterranea_Developmental_Terms PLANA:0000094 tissue morphogenesis Planosphere [https://planosphere.stowers.org/tissuemorphogenesis] Ovo+ neoblasts and post-mitotic eye progenitors that simultaneously migrate and differentiate into photoreceptor neurons and non-neuronal pigment cup cells comprising the optic cup. Planarian_Anatomy PLANA:0000095 trail cell Planosphere [https://planosphere.stowers.org/trailcell] Ovo+ neoblasts and post-mitotic eye progenitors that simultaneously migrate and differentiate into photoreceptor neurons and non-neuronal pigment cup cells comprising the optic cup. PMID:22884275 Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells Planarian_Anatomy PLANA:0000096 ventral epidermis Planosphere [https://planosphere.stowers.org/ventralepidermis] The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO]. A cluster of neurons that extends posteriorly from the embryonic and larval brain and is surrounded by a connective tissue sheath. The ventral nerve cords make up the nervous system of some phyla of the invertebrates, particularly within the nematodes, annelids and the arthropods. It usually consists of cerebral ganglia anteriorly with the nerve cords running down the ventral ('belly', as opposed to back) plane of the organism. This characteristic is important in qualifying the difference compared to the chordates, which have a dorsal nerve cord. Ventral nerve cords from anterior to posterior (the thoracic and abdominal tagma in the arthropods) are made up of segmented ganglia that are connected by a tract of nerve fibers passing from one side to the other of the nerve cord called commissures. The complete system bears some likeness to a rope ladder. In some animals the bilateral ganglia are fused into a single large ganglion per segment. This characteristic is found mostly in the insects. BTO:0002328 EFO:0000896 FBbt:00001102 MAT:0000339 MIAA:0000339 UBERON:0000934 WBbt:0005829 http://en.wikipedia.org/wiki/Ventral_nerve_cord nlx:146329 ventral cord Planarian_Anatomy PLANA:0000097 ventral nerve cord Planosphere [https://planosphere.stowers.org/ventralnervecord] Diploid cell produced by the fusion of sperm cell nucleus and egg cell. CL:0000365 Planarian_Anatomy PLANA:0000098 zygote Planosphere [https://planosphere.stowers.org/zygote] The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. CL:0000540 Planarian_Anatomy PLANA:0000099 neuron Planosphere [https://planosphere.stowers.org/neuron] A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where the apical part is directed towards the lumen and the basal part to the basal lamina. CL:0000066 Planarian_Anatomy PLANA:0000100 epithelial cell Planosphere [https://planosphere.stowers.org/epithelialcell] A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. CL:0000187 Planarian_Anatomy PLANA:0000101 muscle cell Planosphere [https://planosphere.stowers.org/musclecell] The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. UBERON:0001017 Planarian_Anatomy PLANA:0000103 central nervous system Planosphere [https://planosphere.stowers.org/centralnervoussystem] Straight or curved rod-like structures within the epidermal cells, oriented with long axis at right angles to the epidermal surface, that are discharged into mucous secretions. Planarian_Anatomy PLANA:0000104 rhabdite Planosphere [https://planosphere.stowers.org/rhabdite] A cell that specializes in controlled release of one or more substances. CL:0000151 Planarian_Anatomy PLANA:0000105 secretory cell Planosphere [https://planosphere.stowers.org/secretorycell] An epithelial cell that has a cillia. CL:0000067 Planarian_Anatomy PLANA:0000106 ciliated epithelial cell Planosphere [https://planosphere.stowers.org/cilaitedepithelialcell] An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo. CL:0000428 Planarian_Anatomy PLANA:0000107 yolk cell Planosphere [https://planosphere.stowers.org/yolkcell] An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo. PMID:27149082 foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the definitive pharynx. Planarian_Anatomy PLANA:0000110 definitive pharynx progenitor cell Planosphere [https://planosphere.stowers.org/definitivepharynxprogenitorcell] foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the definitive pharynx. PMID:24737865 PMID:25254346 A term used to describe a developmental process during Schmidtea mediterranea embryogenesis. Schmidtea_mediterranea_Developmental_Terms PLANA:0000112 Schmidtea mediterranea developmental term Planosphere [https://planosphere.stowers.org/schmidteamediterraneadevelomentalterm] A term used to describe a developmental process during Schmidtea mediterranea embryogenesis. https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000000.md Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. Planarian_Anatomy PLANA:0000113 tissue Planosphere [https://planosphere.stowers.org/tissue] Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. UBERON:0000479 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000000.md Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. UBERON:0000467 Planarian_Anatomy PLANA:0000114 anatomical system Planosphere [https://planosphere.stowers.org/anatomicalsystem] Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. UBERON:0000922 Planarian_Anatomy PLANA:0000116 embryo Planosphere [https://planosphere.stowers.org/embryo] Anatomical structure that is part of an embryo. UBERON:0002050 Planarian_Anatomy PLANA:0000117 embryonic structure Planosphere [https://planosphere.stowers.org/embryonicstructure] A post-mitotic, terminally differentiated cell type found in planarian embryos, juveniles and/or adult animals. Planarian_Anatomy PLANA:0000119 terminally differentiated cell Planosphere [https://planosphere.stowers.org/terminallydifferentiatedcell] A cycling neoblast and/or post-mitotic cell that is primed or irreversibly committed to a tissue-specific differentation program Planarian_Anatomy PLANA:0000120 progenitor cell Planosphere [https://planosphere.stowers.org/progenitorcell] A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. CL:0000034 Planarian_Anatomy PLANA:0000121 stem cell Planosphere [https://planosphere.stowers.org/stemcell] A mature sexual reproductive cell having a single set of unpaired chromosomes. CL:0000300 Planarian_Anatomy PLANA:0000122 gamete Planosphere [https://planosphere.stowers.org/gamete] A cell of the embryo. CL:0002321 Planarian_Anatomy PLANA:0000123 embryonic cell Planosphere [https://planosphere.stowers.org/embryoniccell] The sensory system subserving the sense of vision. UBERON:0002104 Planarian_Anatomy PLANA:0000124 visual system Planosphere [https://planosphere.stowers.org/visualsystem] Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. UBERON:0001032 Planarian_Anatomy PLANA:0000125 sensory system Planosphere [https://planosphere.stowers.org/sensorysystem] Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. UBERON:0001032 Anatomical system that has as its parts the organs concerned with reproduction. UBERON:0000990 Planarian_Anatomy PLANA:0000126 reproductive system Planosphere [https://planosphere.stowers.org/reproductivesystem] A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CL:0000000 Planarian_Anatomy PLANA:0000127 definitive cell type Planosphere [https://planosphere.stowers.org/celltype] A cell that, by division or terminal differentiation, can give rise to other cell types. CL:0011115 Planarian_Anatomy PLANA:0000128 precursor cell Planosphere [https://planosphere.stowers.org/precursorcell] Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 Planarian_Anatomy PLANA:0000129 anatomical structure Planosphere [https://planosphere.stowers.org/anatomicalstructure] Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue. UBERON:0001048 Planarian_Anatomy PLANA:0000131 primordium Planosphere [https://planosphere.stowers.org/primordium] The production of haploid germ cells from diploid precursor cells through meiosis. Schmidtea_mediterranea_Developmental_Terms PLANA:0000132 gametogenesis Planosphere [https://planosphere.stowers.org/gametogenesis] A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. mechanoreceptor Planarian_Anatomy PLANA:0000133 mechanoreceptor cell Planosphere [https://planosphere.stowers.org/mechanoreceptorcell] Somatic male and female accessory organs and structures of the hermaphroditic reproductive system. Somatic reproductive elements are only made in the Smed sexual biotype and form during juvenile development. Planarian_Anatomy PLANA:0000200 somatic reproductive system element Planosphere [https://planosphere.stowers.org/somaticreproductivesystemelement] The passageway connecting the gonopore to the bursa (genital atrium). Part of the copulatory apparatus. During mating, sperm from a partner is deposited into the bursal canal, where it collects in the bursa before travelling up the oviducts to the bursa. Egg capsules pass through the bursal canal as they are laid through the gonopore. Planarian_Anatomy PLANA:0000201 bursal canal Planosphere [https://planosphere.stowers.org/bursalcanal] The passageway connecting the gonopore to the bursa (genital atrium). Part of the copulatory apparatus. During mating, sperm from a partner is deposited into the bursal canal, where it collects in the bursa before travelling up the oviducts to the bursa. Egg capsules pass through the bursal canal as they are laid through the gonopore. PMID:22074376 The gonopore, a component of the copulatory apparatus, is an opening located on the ventral side of the animal posterior to the definitive pharynx. The gonopore is the sole point of exit and entry for the reproductive system, allowing from reciprocal exchange of sperm during copulation and egg capsule laying. genital pore Planarian_Anatomy PLANA:0000203 gonopore Planosphere [https://planosphere.stowers.org/gonopore] The gonopore, a component of the copulatory apparatus, is an opening located on the ventral side of the animal posterior to the definitive pharynx. The gonopore is the sole point of exit and entry for the reproductive system, allowing from reciprocal exchange of sperm during copulation and egg capsule laying. PMID:22074376 A gonad containing female germline stem cells which fuel oocyte production. Two ovaries are located ventally, underneath the body wall musculature, immediately posterior to the cephalic ganglia (brain) and adjacent to the ventral nerve cords. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuel formation of the ovaries during juvenile development. Planarian_Anatomy PLANA:0000204 ovary Planosphere [https://planosphere.stowers.org/ovary] A gonad containing female germline stem cells which fuel oocyte production. Two ovaries are located ventally, underneath the body wall musculature, immediately posterior to the cephalic ganglia (brain) and adjacent to the ventral nerve cords. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuel formation of the ovaries during juvenile development. PMID:17376870 Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium. Planarian_Anatomy PLANA:0000205 oviduct Planosphere [https://planosphere.stowers.org/oviduct] Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium. PMID:22074376 A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal. Planarian_Anatomy PLANA:0000206 penis papilla Planosphere [https://planosphere.stowers.org/penispapilla] A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal. PMID:22074376 A network of tubes that transport sperm from the testes to the seminal vesicles. Tubes connect each testis to ducts that run along the ventral nerve cords. The ducts bifurcate immediately posterior to the pharynx, where they connect to the seminal vesicles. Planarian_Anatomy PLANA:0000207 sperm duct Planosphere [https://planosphere.stowers.org/spermduct] A network of tubes that transport sperm from the testes to the seminal vesicles. Tubes connect each testis to ducts that run along the ventral nerve cords. The ducts bifurcate immediately posterior to the pharynx, where they connect to the seminal vesicles. PMID:19022767 PMID:22074376 A gonad containing male germline stem cells which fuel sperm production. Testes are located dorsolaterally, and are excluded from the head. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuels formation of testes during juvenile development and regeneration. Planarian_Anatomy PLANA:0000208 testis Planosphere [https://planosphere.stowers.org/testis] A gonad containing male germline stem cells which fuel sperm production. Testes are located dorsolaterally, and are excluded from the head. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuels formation of testes during juvenile development and regeneration. PMID:19022767 Anatomical structure that is present during embryonic development. UBERON:0005423 Planarian_Anatomy PLANA:0000209 developing anatomical structure Planosphere [https://planosphere.stowers.org/developinganatomicalstructure] Any of the cell types, tissues, organs or elements that are part of the embryonic digestive system. Examples include the temporary embryonic pharynx, primitive gut cells, embryonic gut cells and the central gut cavity. Planarian_Anatomy PLANA:0000210 embryonic digestive system element Planosphere [https://planosphere.stowers.org/embryonicdigestivesystemelement] Any of the cell types, tissues, organs or elements that are part of the embryonic digestive system. Examples include the temporary embryonic pharynx, primitive gut cells, embryonic gut cells and the central gut cavity. PMID:28072387 Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2. Planarian_Anatomy PLANA:0000211 primitive ectoderm cell Planosphere [https://planosphere.stowers.org/primitiveectodermcell] Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2. OCLC:20423827 OCLC:464776945 OCLC:82522822 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md Undifferentiated, zygote-derived cleavage progeny that give rise to temporary embryonic tissues during Stage 2, continue dividing asynchronously in the embryonic wall, and ultimately give rise to neoblasts and adult lineage progenitors beginning in Stage 5. Planarian_Anatomy PLANA:0000212 blastomere compartment Planosphere [https://planosphere.stowers.org/blastomerecompartment] Undifferentiated, zygote-derived cleavage progeny that give rise to temporary embryonic tissues during Stage 2, continue dividing asynchronously in the embryonic wall, and ultimately give rise to neoblasts and adult lineage progenitors beginning in Stage 5. PMID:28072387 A sexually immature member of the Schmidtea mediterranea sexuallly reproducing biotype. Schmidtea_mediterranea_Developmental_Stages PLANA:0000214 juvenile Planosphere [https://planosphere.stowers.org/juvenile] Products of the reproductive system include gametes, zygotes, yolk cells and egg capsules. Planarian_Anatomy PLANA:0000215 reproductive system product Planosphere [https://planosphere.stowers.org/reproductivesystemproduct] A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos. Egg capsules are anchored to a substrate via a stalk. Planarian_Anatomy PLANA:0000216 egg capsule Planosphere [https://planosphere.stowers.org/eggcapsule] A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos. Egg capsules are anchored to a substrate via a stalk. PMID:18942102 Reproductive organ that produces and releases eggs (ovary) or sperm (testis). UBERON:0000991 Planarian_Anatomy PLANA:0000217 gonad Planosphere [https://planosphere.stowers.org/gonad] Neoblasts coexpressing piwi-1 and nanos that are required for male and female gonad formation. Primordial germ cells are present in both asexual and sexual adults. Planarian_Anatomy PLANA:0000218 primordial germ cell Planosphere [https://planosphere.stowers.org/primordialgermcell] Neoblasts coexpressing piwi-1 and nanos that are required for male and female gonad formation. Primordial germ cells are present in both asexual and sexual adults. PMID:17376870 gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm. spermatogonial stem cell (SSC) Planarian_Anatomy PLANA:0000219 male germline stem cell Planosphere [https://planosphere.stowers.org/malegermlinestemcell] gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm. PMID:20844018, PMID:19022767, PMID:27163480, PMID:27330085 An euploid male germ cell of an early stage of spermatogenesis. In planaria, the gh4+ stem cell daughter exiting the niche undergoes three rounds of transit amplifying division with incomplete cytokinesis prior to transitioning to terminal differentiation. CL:0000020 Planarian_Anatomy PLANA:0000220 spermatogonium Planosphere [https://planosphere.stowers.org/spermatogonium] An euploid male germ cell of an early stage of spermatogenesis. In planaria, the gh4+ stem cell daughter exiting the niche undergoes three rounds of transit amplifying division with incomplete cytokinesis prior to transitioning to terminal differentiation. PMID:27163480, PMID:27330085 A tektin-1+ male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. CL:0000017 Planarian_Anatomy PLANA:0000221 spermatocyte Planosphere [https://planosphere.stowers.org/spermatocyte] A tektin-1+ male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. PMID:27330085 A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa. CL:0000018 Planarian_Anatomy PLANA:0000222 spermatid Planosphere [https://planosphere.stowers.org/spermatid] A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes. Planarian_Anatomy PLANA:0000223 female germline stem cell Planosphere [https://planosphere.stowers.org/femalegermlinestemcell] A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes. PMID:20844018, PMID:19022767 Glands surrounding the copulatory bursa that are required for production of the proteinaceous egg capsule shell and stalk. Planarian_Anatomy PLANA:0000224 cement gland Planosphere [https://planosphere.stowers.org/cementgland] Glands surrounding the copulatory bursa that are required for production of the proteinaceous egg capsule shell and stalk. PMID:18942102, PMID:27149082, ASIN:B000M4NK9M, PMID:22074376 A reproductive strategy in which eggs are laid, with most embryonic development occurring outside of the parent. Schmidtea_mediterranea_Developmental_Terms PLANA:0000225 oviparity Planosphere [https://planosphere.stowers.org/oviparity] A reproductive strategy in which eggs are laid, with most embryonic development occurring outside of the parent. PMID:19022767 Fertilization of an oocyte by sperm from a different individual. Reciprocal exchange of sperm occurs during Schmidtea mediterranea copulation. Schmidtea_mediterranea_Developmental_Terms PLANA:0000226 cross-fertilization Planosphere [https://planosphere.stowers.org/cross-fertilization] Fertilization of an oocyte by sperm from a different individual. Reciprocal exchange of sperm occurs during Schmidtea mediterranea copulation. PMID:19022767 doi:10.1038/s41559-016-0019 1. A gamete (as an egg or sperm cell) or one of its antecedent cells. 2. A mature male or female germ cell usually possessing a haploid chromosome set and capable of initiating formation of a new diploid individual by fusion with a gamete of the opposite sex. BTO:0000535 Planarian_Anatomy PLANA:0000227 germ cell Planosphere [https://planosphere.stowers.org/germcell] A male germ cell is a germ cell that supports male gamete production. CL:0000015 Planarian_Anatomy PLANA:0000228 male germ cell Planosphere [https://planosphere.stowers.org/malegermcell] Female germ cell is a germ cell that supports female gamete production. CL:0000021 Planarian_Anatomy PLANA:0000229 female germ cell Planosphere [https://planosphere.stowers.org/femalegermcell] A sperm storage organ located immediately posterior to the ovary, at the anterior end of the oviduct. Oocytes exiting the ovary are fertilized in the tuba as they enter the oviduct. Planarian_Anatomy PLANA:0000230 tuba Planosphere [https://planosphere.stowers.org/tuba] A sperm storage organ located immediately posterior to the ovary, at the anterior end of the oviduct. Oocytes exiting the ovary are fertilized in the tuba as they enter the oviduct. PMID:19022767 PMID:20844018 PMID:22074376 PMID:27149082 Glands surrounding the oviducts which produce yolk cells. Yolk cells deposited into the oviducts travel to the genital atrium where they are packaged, along with one or more zygotes, into developing egg capsules. Planarian_Anatomy PLANA:0000231 vitelline gland Planosphere [https://planosphere.stowers.org/vitellinegland] Glands surrounding the oviducts which produce yolk cells. Yolk cells deposited into the oviducts travel to the genital atrium where they are packaged, along with one or more zygotes, into developing egg capsules. PMID:16932928 PMID:18942102 PMID:27149082 Accessory reproductive structures involved in copulation, egg capsule development and laying. Planarian_Anatomy PLANA:0000232 copulatory apparatus Planosphere [https://planosphere.stowers.org/copulatoryapparatus] Accessory reproductive structures involved in copulation, egg capsule development and laying. PMID:22074376 A chamber where egg capsules are formed. One or more zygotes and yolk cells produced by the vitelline glands collect in the copulatory bursa; glands surrounding the copulatory bursa produce the egg capsule shell. Nascent egg capsules exit the body by passing through the bursal canal and gonopore. The copulatory bursa is synonymous with the term genital atrium. genital atrium Planarian_Anatomy PLANA:0000233 copulatory bursa Planosphere [https://planosphere.stowers.org/copulatorybursa] A chamber where egg capsules are formed. One or more zygotes and yolk cells produced by the vitelline glands collect in the copulatory bursa; glands surrounding the copulatory bursa produce the egg capsule shell. Nascent egg capsules exit the body by passing through the bursal canal and gonopore. The copulatory bursa is synonymous with the term genital atrium. PMID:22074376 Glandular pouches adjoining the sperm ducts which produce seminal fluid. Planarian_Anatomy PLANA:0000234 seminal vesicle Planosphere [https://planosphere.stowers.org/seminalvesicle] Glandular pouches adjoining the sperm ducts which produce seminal fluid. PMID:22074376, PMID:19022767 A cyst of 8 interconnected spermatocytes undergoes meiosis, producing 32 haploid round spermatids. Round spermatids express protein kinase A, and undergo morphogenesis to produce mature sperm. Planarian_Anatomy PLANA:0000237 round spermatid Planosphere [https://planosphere.stowers.org/roundspermatid] A cyst of 8 interconnected spermatocytes undergoes meiosis, producing 32 haploid round spermatids. Round spermatids express protein kinase A, and undergo morphogenesis to produce mature sperm. PMID:27163480, PMID:27330085 Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm. Planarian_Anatomy PLANA:0000238 elongate spermatid Planosphere [https://planosphere.stowers.org/elongatespermatid] Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm. PMID:27163480, PMID:27330085 An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes. FMA:83673 Planarian_Anatomy PLANA:0000239 oogonial cell Planosphere [https://planosphere.stowers.org/oogonialcell] Any collection of muscles that is part of a body wall [Automatically generated definition]. define generically to encompass both vertebrates and invertebrates body wall muscles BSA:0000058 BTO:0001863 FMA:86931 UBERON:0004462 WBbt:0005813 body wall musculature Planarian_Anatomy PLANA:0000240 musculature of body wall Planosphere [https://planosphere.stowers.org/musculatureofbodywall] Pharynx muscle fibers running anteroposterior (proximal to distal). Planarian_Anatomy PLANA:0000241 pharyngeal longitudinal muscle fiber Planosphere [https://planosphere.stowers.org/pharyngeallongitudinalmusclefiber] Pharynx muscle fibers running anteroposterior (proximal to distal). ASIN:B000M4NK9M Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. UBERON:0002553 PLANA:0000242 anatomical cavity Planosphere [https://planosphere.stowers.org/anatomicalcavity] Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. UBERON:0001062 Planarian_Anatomy PLANA:0000400 anatomical entity Planosphere [https://planosphere.stowers.org/anatomicalentity] Anatomical entity that has no mass. AAO:0010265 AEO:0000007 BILA:0000007 CARO:0000007 EHDAA2:0003007 FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 TGMA:0001827 UBERON:0000466 VHOG:0001727 immaterial physical anatomical entity Planarian_Anatomy PLANA:0000401 immaterial anatomical entity Planosphere [https://planosphere.stowers.org/immaterialanatomicalentity] Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface. AAO:0010266 AEO:0000009 BILA:0000009 CARO:0000009 EHDAA2:0003009 FMA:9658 TAO:0001839 UBERON:0006983 Planarian_Anatomy PLANA:0000402 anatomical point Planosphere [https://planosphere.stowers.org/anatomicalpoint] Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. anatomical spaces lumen space AAO:0010110 AEO:0000005 BILA:0000005 C94478 CARO:0000005 EHDAA2:0003005 FBbt:00007017 FMA:5897 HAO:0000005 TAO:0001668 TGMA:0001825 UBERON:0000464 UMLS:C0524461 VHOG:0001728 XAO:0003190 ZFA:0001643 http://linkedlifedata.com/resource/umls/id/C0524461 lumen space Planarian_Anatomy PLANA:0000403 anatomical space Planosphere [https://planosphere.stowers.org/anatomicalspace] A anatomical space that is enclosed by a pharynx. UBERON:0001731 Planarian_Anatomy PLANA:0000404 cavity of pharynx Planosphere [https://planosphere.stowers.org/cavityofpharynx] An anatomical space that is surrounded by a digestive tract. UBERON:0006909 Planarian_Anatomy PLANA:0000405 lumen of digestive tract Planosphere [https://planosphere.stowers.org/lumenofdigestivetract] The orifice that connects the mouth to the exterior of the body. UBERON:0000166 Planarian_Anatomy PLANA:0000406 oral opening Planosphere [https://planosphere.stowers.org/oralopening] The space within the parapharyngeal pouch not occupied by the pharynx proper. Planarian_Anatomy PLANA:0000407 parapharnygeal pouch cavity Planosphere [https://planosphere.stowers.org/parapharyngealpouch] A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood. UBERON:0006984 Planarian_Anatomy PLANA:0000408 anatomical surface Planosphere [https://planosphere.stowers.org/anatomicalsurface] The apical surface of the single layered epithelium epidermis that is in contact with the environment. Planarian_Anatomy PLANA:0000409 apical epidermis surface Planosphere [https://planosphere.stowers.org/apicalepidermissurface] The basal surface of the epidermial epithelium in contact with the basal lamina. Planarian_Anatomy PLANA:0000410 basal epidermis surface Planosphere [https://planosphere.stowers.org/basalepidermissurface] The surface of the gut lumen in contact with ingested food. Planarian_Anatomy PLANA:0000411 lumen gut surface Planosphere [https://planosphere.stowers.org/lumengutsurface] The epithelial surface lining the interior of the pharynx, facing the lumen. Planarian_Anatomy PLANA:0000412 pharynx lumen epithelial surface Planosphere [https://planosphere.stowers.org/pharynxlumenepithelialsurface] Epithelial surface covering the outside of the pharynx. Planarian_Anatomy PLANA:0000413 pharynx outer epithelial surface Planosphere [https://planosphere.stowers.org/pharynxouterepithelialsurface] The surface of the parapharyngeal pouch facing the pharynx. Planarian_Anatomy PLANA:0000414 parapharyngeal pouch surface Planosphere [https://planosphere.stowers.org/parapharyngealpouchsurface] A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. UBERON:0000015 Planarian_Anatomy PLANA:0000415 non-material anatomical boundary Planosphere [https://planosphere.stowers.org/non-materialanatomicalboundary] Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. UBERON:0000475 Planarian_Anatomy PLANA:0000416 organism subdivision Planosphere [https://planosphere.stowers.org/organismsubdivision] Anatomical structure which is a subdivision of a whole adult or juvenile organism, consisting of components of multiple anatomical systems. Planarian_Anatomy PLANA:0000417 definitive organism subdivision Planosphere [https://planosphere.stowers.org/definitiveorganismsubdivision] The head is the anterior-most division of the body [GO]. UBERON:0000033 Planarian_Anatomy PLANA:0000418 head Planosphere [https://planosphere.stowers.org/head] Region of the juvenile or adult animal between the posterior end of the cephalic ganglia and the anterior end of the definitive pharynx. Planarian_Anatomy PLANA:0000419 neck Planosphere [https://planosphere.stowers.org/neck] Region of the animal lateral to and surrounding the pharyngeal pouch. Planarian_Anatomy PLANA:0000420 parapharyngeal region Planosphere [https://planosphere.stowers.org/parapharyngealregion] Caudal region, beginning at the mouth and ending at posterior pole. Planarian_Anatomy PLANA:0000421 tail Planosphere [https://planosphere.stowers.org/tail] Medial region of the tail; the parenchymal space between the posterior primary gut branches. Planarian_Anatomy PLANA:0000422 tail stripe Planosphere [https://planosphere.stowers.org/tailstripe] Anatomical structure which is a subdivision of a whole developing/ embryonic organism, consisting of components of multiple anatomical systems. Planarian_Anatomy PLANA:0000423 embryonic organism subdivision Planosphere [https://planosphere.stowers.org/embryonicorganismsubdivision] Anatomical entity that has mass. UBERON:0000465 Planarian_Anatomy PLANA:0000424 material anatomical entity Planosphere [https://planosphere.stowers.org/materialanatomicalentity] Anatomical structure present in juvenile and adult planaria. Planarian_Anatomy PLANA:0000425 definitive anatomical structure Planosphere [https://planosphere.stowers.org/definitiveanatomicalstructure] Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. acellular anatomical structures AAO:0010268 AEO:0000040 BILA:0000040 CARO:0000040 EHDAA2:0003040 FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 TGMA:0001841 XAO:0003162 ZFA:0000382 Planarian_Anatomy PLANA:0000426 acellular anatomical structure Planosphere [https://planosphere.stowers.org/acellularanatomicalstructure] An anatomical structure that has more than one cell as a part. UBERON:0010000 Planarian_Anatomy PLANA:0000427 multicellular anatomical structure Planosphere [https://planosphere.stowers.org/multicellularanatomicalstructure] Total musculature of the planarian body. Planarian_Anatomy PLANA:0000428 musculature system Planosphere [https://planosphere.stowers.org/musculaturesystem] A heterogeneous population of pluripotent, somatic adult stem cells and lineage primed progenitors that are required for maintenance and regeneration of all cell types in planaria, including the germline. Planarian_Anatomy PLANA:0000429 neoblast compartment Planosphere [https://planosphere.stowers.org/neoblastcompartment] A heterogeneous population of pluripotent, somatic adult stem cells and lineage primed progenitors that are required for maintenance and regeneration of all cell types in planaria, including the germline. PMID:16311336 PMID:21566185 PMID:22899852 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md A part of an epithelial cell. Planarian_Anatomy PLANA:0000430 epithelial cell component Planosphere [https://planosphere.stowers.org/epithelialcellcomponent] Anatomical structure that performs a specific function or group of functions. UBERON:0000062 Planarian_Anatomy PLANA:0000431 organ Planosphere [https://planosphere.stowers.org/organ] An anatomical structure that is undergoing regeneration. UBERON:0007567 Planarian_Anatomy PLANA:0000432 regenerating anatomical structure Planosphere [https://planosphere.stowers.org/regeneratinganatomicalstructure] The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. Source: NIF_Subcellular:sao-1337158144, GOC:go_curators GO:0005575 Planarian_Anatomy PLANA:0000433 cellular component Planosphere [https://planosphere.stowers.org/cellularcomponent] A decussation of the diencephalon where the fibers of the optic nerve cross The point at which fibers of the optic nerves cross.[AAO] The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG] chiasma chiasma nervorum opticorum optic chiasm (Rufus of Ephesus) AAO:0010622 BAMS:DC BAMS:OC BAMS:och BAMS:ox BM:Tel-OCX C90609 DHBA:10644 DMBA:17783 EHDAA2:0001302 EHDAA:10227 EMAPA:17603 FMA:62045 GAID:832 HBA:9310 MA:0001098 MBA:117 MESH:D009897 Optic:chiasm TAO:0000556 UBERON:0000959 UMLS:C0029126 VHOG:0000190 XAO:0004071 ZFA:0000556 birnlex:1416 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=459 http://linkedlifedata.com/resource/umls/id/C0029126 http://www.snomedbrowser.com/Codes/Details/244453006 chiasma opticum decussation of optic nerve fibers optic chiasm Planarian_Anatomy PLANA:0000459 optic chiasma Planosphere [https://planosphere.stowers.org/opticchiasma] A decussation of the diencephalon where the fibers of the optic nerve cross PMID:18466009 A bundle of nerve fibers connecting the two cephalic ganglia. UBERON:0000935 Planarian_Anatomy PLANA:0000460 anterior commissure Planosphere [https://planosphere.stowers.org/anteriorcommissure] Nerve branches that extend from the lateral side of each cephalic ganglia lobe. Each lobe has nine lateral branches which terminate in sensory organs. Evidence suggests they play a role in chemosensation. Planarian_Anatomy PLANA:0000461 lateral branches Planosphere [https://planosphere.stowers.org/lateralbranches] Nerve branches that extend from the lateral side of each cephalic ganglia lobe. Each lobe has nine lateral branches which terminate in sensory organs. Evidence suggests they play a role in chemosensation. PMID:12128224, PMID:9493832, PMID:4452894, PMID:18466009, PMID:27612384 A cell that performs a sensory function. Planarian_Anatomy PLANA:0000462 sensory cell Planosphere [https://planosphere.stowers.org/sensorycell] Neurons that express choline acetyltransferase. Planarian_Anatomy PLANA:0000463 cholinergic neuron Planosphere [https://planosphere.stowers.org/cholinergricneuron] Neurons that express choline acetyltransferase. PMID:20338223 Neurons that express glutamine decarboxylase. Planarian_Anatomy PLANA:0000464 GABAergic neuron Planosphere [https://planosphere.stowers.org/gabaergicneuron] Neurons that express glutamine decarboxylase. PMID:18440152 Plexus of nerves located in the definitive pharynx comprised of inner and outer wall rings. Planarian_Anatomy PLANA:0000465 pharynx nerve plexus Planosphere [https://planosphere.stowers.org/pharynxnerveplexus] Plexus of nerves located just between the definitive epidermis and the body wall musculature. Planarian_Anatomy PLANA:0000466 subepidermal nerve plexus Planosphere [https://planosphere.stowers.org/subepidermalnerveplexus] Plexus of nerves that innervate the body wall muscles. Planarian_Anatomy PLANA:0000467 submuscular nerve plexus Planosphere [https://planosphere.stowers.org/submuscularplexus] A thin net of single nerve fibers located around the gut. Planarian_Anatomy PLANA:0000468 gastrodermal plexus Planosphere [https://planosphere.stowers.org/gastrodermalplexus] A cluster of neurites that is part of a nervous system and forms a network of dendrites and axons where synapses are present and in which neuronal somata do not occur. Multi-cell component structure of the central nervous system consisting largely of neuron projections (tracts and synaptic neuropil domains) and associated glial cells. This corresponds to the part of the CNS that is enclosed by the cortex. neuropilus BTO:0005268 C12617 CALOHA:TS-2403 FBbt:00005139 FMA:261269 GAID:740 MESH:D019581 NIF_Subcellular:sao205380252 UBERON:0002606 UMLS:C0228081 birnlex:1142 http://en.wikipedia.org/wiki/Neuropil http://linkedlifedata.com/resource/umls/id/C0228081 http://www.snomedbrowser.com/Codes/Details/67146008 Planarian_Anatomy PLANA:0000470 neuropil Planosphere [https://planosphere.stowers.org/neuropil] A cluster of neurites that is part of a nervous system and forms a network of dendrites and axons where synapses are present and in which neuronal somata do not occur. PMID:27612384 Heavily ciliated epidermal cells covering the outer surface of the pharynx shaft. These are "insunk" epidermal cells in which the nuclei reside behind the layers of longitudinal and circumferential muscles and the epithelial cell body sends out a ciliated projection to the surface to cover and encase the shaft. Planarian_Anatomy PLANA:0000472 outer pharyngeal epithelium Planosphere [https://planosphere.stowers.org/outerpharyngealepithelium] Heavily ciliated epidermal cells covering the outer surface of the pharynx shaft. These are "insunk" epidermal cells in which the nuclei reside behind the layers of longitudinal and circumferential muscles and the epithelial cell body sends out a ciliated projection to the surface to cover and encase the shaft. ASIN:B000M4NK9M Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles. Planarian_Anatomy PLANA:0000473 outer pharyngeal circular muscle fiber Planosphere [https://planosphere.stowers.org/outerpharyngealcircularmusclefiber] Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles. ASIN:B000M4NK9M Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers. Planarian_Anatomy PLANA:0000474 inner pharyngeal circular muscle fiber Planosphere [https://planosphere.stowers.org/innerpharyngealcircularmusclefiber] Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers. ASIN:B000M4NK9M Pharynx muscle fibers running anteroposterior which lie beneath both the inner circular muscle fibers and the apical, ciliated portion of the epithium lining the lumenal surface. Planarian_Anatomy PLANA:0000475 inner pharyngeal longitudinal muscle fiber Planosphere [https://planosphere.stowers.org/innerpharyngeallongitudinalmusclefiber] Pharynx muscle fibers running anteroposterior which lie beneath both the inner circular muscle fibers and the apical, ciliated portion of the epithium lining the lumenal surface. ASIN:B000M4NK9M Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium. Planarian_Anatomy PLANA:0000476 outer pharyngeal longitudinal muscle fiber Planosphere [https://planosphere.stowers.org/outerpharyngeallongitudinalmusclefiber] Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium. ASIN:B000M4NK9M Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts. Planarian_Anatomy PLANA:0000477 pharyngeal radial muscle fiber Planosphere [https://planosphere.stowers.org/pharyngealradialmusclefiber] Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts. ASIN:B000M4NK9M The total musculature within the pharynx. UBERON:0004467 Planarian_Anatomy PLANA:0000478 musculature of pharynx Planosphere [https://planosphere.stowers.org/musculatureofpharynx] Ring of the pharynx nerve plexus that is proximal to the lumen. Planarian_Anatomy PLANA:0000479 inner pharynx nerve plexus Planosphere [https://planosphere.stowers.org/innerpharynxnerveplexus] Ring of the pharynx nerve plexus that is proximal to the exterior surface. Planarian_Anatomy PLANA:0000480 outer pharynx nerve plexus Planosphere [https://planosphere.stowers.org/outerpharynxnerveplexus] Neurons that express the neurotransmitter serotonin. Planarian_Anatomy PLANA:0000481 serotonergic neuron Planosphere [https://planosphere.stowers.org/serotonergicneuron] Neurons that express the neurotransmitter serotonin. PMID:17624455 A neuron that expresses the neurotransmitter dopamine. Planarian_Anatomy PLANA:0000482 dopaminergic neuron Planosphere [https://planosphere.stowers.org/dopaminergicneuron] A neuron that expresses the neurotransmitter dopamine. PMID:17565705 Neurons that express the biogenic amine octopamine. Planarian_Anatomy PLANA:0000483 octopaminergic neuron Planosphere [https://planosphere.stowers.org/octopaminergicneuron] Neurons that express the biogenic amine octopamine. PMID:18926867 Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus. Planarian_Anatomy PLANA:0000484 secretory system Planosphere [https://planosphere.stowers.org/secretorysystem] Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus. PMID:20865784 Specialized insunk epithelial cells located in the mesenchyme that participate in mucus secretion. They are characterized by elongated cell bodies with long cytoplasmic projections that terminate between, or penetrate directly through epithelial cells and form a secretory pore at the surface. Planarian_Anatomy PLANA:0000485 gland cell Planosphere [https://planosphere.stowers.org/glandcell] Specialized insunk epithelial cells located in the mesenchyme that participate in mucus secretion. They are characterized by elongated cell bodies with long cytoplasmic projections that terminate between, or penetrate directly through epithelial cells and form a secretory pore at the surface. PMID:20865784 The opening by which the gland cells secrete mucus to the exterior of the animal. Planarian_Anatomy PLANA:0000486 secretory pore Planosphere [https://planosphere.stowers.org/secretorypore] The opening by which the gland cells secrete mucus to the exterior of the animal. PMID:20865784 One of two distinct histochemical classes of gland cells, these can be found throughout the body but primarily form clusters of subepidermal marginal adhesive glands along the dorsal/ ventral border of the animal. May also be referred to as eosinophilic gland cells. Planarian_Anatomy PLANA:0000487 acidophilic gland cell Planosphere [https://planosphere.stowers.org/acidophilicglandcell] One of two distinct histochemical classes of gland cells, these can be found throughout the body but primarily form clusters of subepidermal marginal adhesive glands along the dorsal/ ventral border of the animal. May also be referred to as eosinophilic gland cells. PMID:20865784 One of two distinct histochemical classes of gland cells, these are found near the ventral mesenchyme, the pharynx and in the dorsal region of the head. May also be called cyanophilic gland cells. Planarian_Anatomy PLANA:0000488 basophilic gland cell Planosphere [https://planosphere.stowers.org/basophilicglandcell] One of two distinct histochemical classes of gland cells, these are found near the ventral mesenchyme, the pharynx and in the dorsal region of the head. May also be called cyanophilic gland cells. PMID:20865784 Non-material anatomical entity of one dimension, which forms a boundary of an anatomical surface or is a modulation of an anatomical surface. AAO:0010267 AEO:0000008 BILA:0000008 CARO:0000008 EHDAA2:0003008 FMA:9657 HAO:0000008 TAO:0001837 TGMA:0001828 UBERON:0006800 XAO:0004003 ZFA:0001689 Planarian_Anatomy PLANA:0000489 anatomical line Planosphere [https://planosphere.stowers.org/anatomicalline] A flat anatomical 2D surface that bisects an anatomical structure or an anatomical space. fiat anatomical surface CARO:0001013 FMA:242982 UBERON:0035085 Planarian_Anatomy PLANA:0000490 All anatomical planes are fiat anatomical boundaries - no morphological boundary could ever be a perfect plane. anatomical plane Planosphere [https://planosphere.stowers.org/anatomicalplane] An anatomical plane that bisects a zone of weakness in an appendage. When autotomy occurs, the appendage divides along this plane. this class is intended for autotomy that bisects an appendage. Other forms of autotomy are possible: for example, a sea cucumber and autotomitize internal organs UBERON:0035086 Planarian_Anatomy PLANA:0000491 plane of autotomy Planosphere [https://planosphere.stowers.org/planeofautotomy] Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA]. in FMA this is a subtype of junction rather than tissue plexus AEO:0000138 BTO:0000205 C12929 EHDAA2:0003138 EHDAA:3780 FMA:5901 MA:0002407 UBERON:0001810 UMLS:C0501403 http://en.wikipedia.org/wiki/Nervous_system_plexus http://linkedlifedata.com/resource/umls/id/C0501403 http://www.snomedbrowser.com/Codes/Details/122455009 Planarian_Anatomy PLANA:0000492 nerve plexus Planosphere [https://planosphere.stowers.org/nerveplexus] Axon tract that crosses the midline of the central nervous system[NIF, modified]. In the context of Drosophila refers to a broad band of axons connecting equivalent neuropils each side of the brain[FBbt]. White matter fiber bundle that crosses the midline of the brain or spinal cord, that connects similar structures on both sides. (CUMBO; Heimer, L. The Human Brain, 2nd ed., 1995, pg 6) commissural white matter commissure commissure C32349 FBbt:00005103 FMA:83906 OpenCyc:Mx4rdBrmE6gOEdudWQACs5b6Bw TADS:0000201 UBERON:0001020 UMLS:C1185742 http://en.wikipedia.org/wiki/Commissure http://linkedlifedata.com/resource/umls/id/C1185742 nlx:110 nlx_anat:20090513 commissure of neuraxis neuraxis commissure Planarian_Anatomy PLANA:0000493 *not* the same as FMA:76741 Commissure nervous system commissure Planosphere [https://planosphere.stowers.org/nervoussystemcommissure] any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain[MP] UBERON:0005970 Planarian_Anatomy PLANA:0000494 brain commissure Planosphere [https://planosphere.stowers.org/braincommissure] A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise AEO:0000192 BTO:0001638 CARO:0000010 EFO:0003658 FMA:50705 TAO:0001270 UBERON:0005306 XAO:0004060 ncithesaurus:Blastemal_Cell blastema cell Planarian_Anatomy PLANA:0000495 blastema Planosphere [https://planosphere.stowers.org/blastema] A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. UBERON:0000015 Planarian_Anatomy PLANA:0000496 anatomical boundary Planosphere [https://planosphere.stowers.org/anatomicalboundary] An anatomical structure that connects two structures junction FMA:5898 UBERON:0007651 http://www.snomedbrowser.com/Codes/Details/91833003 anatomical junction Planarian_Anatomy PLANA:0000497 anatomical junction Planosphere [https://planosphere.stowers.org/anatomicaljunction] A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. UBERON:0013701 Planarian_Anatomy PLANA:0000498 main body axis Planosphere [https://planosphere.stowers.org/mainbodyaxis] A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FMA:68646 GO:0005623 KUPO:0000002 VHOG:0001533 WBbt:0004017 XAO:0003012 Planarian_Anatomy PLANA:0000499 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell Planosphere [https://planosphere.stowers.org/cell] Anatomical structure that is a direct part of the cell. TODO - move metadata to GO and obsolete this class once homes have been found for existing children. Note the inconsistency between the usage of the label 'cell component' in GO and CARO cell component AAO:0010271 BILA:0000014 C34070 CARO:0000014 FBbt:00007012 FMA:86454 GO:0044464 HAO:0000014 NIF_Subcellular:sao-1337158144 OpenCyc:Mx4rwQwkcZwpEbGdrcN5Y29ycA TGMA:0001834 UBERON:0000470 UMLS:C1178969 http://linkedlifedata.com/resource/umls/id/C1178969 Planarian_Anatomy PLANA:0000500 cell part Planosphere [https://planosphere.stowers.org/cellpart] A prolongation or process extending from a cell. GO_0042995 Planarian_Anatomy PLANA:0000501 cell projection Planosphere [https://planosphere.stowers.org/cellprojection] A cell projection supported by an assembly of actin filaments. GO_0098858 Planarian_Anatomy PLANA:0000502 actin-based cell projection Planosphere [https://planosphere.stowers.org/actin-basedcellprojection] A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GO_0005929 Planarian_Anatomy PLANA:0000503 cilium Planosphere [https://planosphere.stowers.org/cilium] Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. GO:0005902 Planarian_Anatomy PLANA:0000504 microvillus Planosphere [https://planosphere.stowers.org/microvillus] Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions. GO_0044291 Planarian_Anatomy PLANA:0000505 cell-cell contact zone Planosphere [https://planosphere.stowers.org/cell-cellcontactzone] A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. GO:0030054 Planarian_Anatomy PLANA:0000506 cell junction Planosphere [https://planosphere.stowers.org/celljunction] A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals. GO:0005911 Planarian_Anatomy PLANA:0000507 cell-cell junction Planosphere [https://planosphere.stowers.org/cell-celljunction] The attachment of one cell to another cell via adhesion molecules. GO:0098609 Planarian_Anatomy PLANA:0000508 cell-cell adhesion Planosphere [https://planosphere.stowers.org/cell-celladhesion] Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. GO:0044424 Planarian_Anatomy PLANA:0000509 intracellular part Planosphere [https://planosphere.stowers.org/intracellularpart] All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures GO:0005737 Planarian_Anatomy PLANA:0000510 cytoplasm Planosphere [https://planosphere.stowers.org/cytoplasm] Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions. eosinophilic tmeehan 2009-12-22T04:23:25Z CP_0000027 Planarian_Anatomy PLANA:0000511 acidophilic cytoplasm Planosphere [https://planosphere.stowers.org/acidophiliccytoplasm] Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. tmeehan 2009-12-22T04:24:54Z CP_0000028 Planarian_Anatomy PLANA:0000512 basophilic cytoplasm Planosphere [https://planosphere.stowers.org/basophiliccytoplasm] Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO_0044444 Planarian_Anatomy PLANA:0000513 cytoplasmic part Planosphere [https://planosphere.stowers.org/cytoplasmicpart] Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell. GO:0044433 Planarian_Anatomy PLANA:0000514 cytoplasmic vesicle part Planosphere [https://planosphere.stowers.org/cytoplasmicvesiclepart] A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. GO:0005773 Planarian_Anatomy PLANA:0000515 vacuole Planosphere [https://planosphere.stowers.org/vacuole] A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. GO_0007010 Planarian_Anatomy PLANA:0000516 cytoskeleton organization Planosphere [https://planosphere.stowers.org/cytoskeletonorganization] Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GO_0043229 Planarian_Anatomy PLANA:0000518 intracellular organelle Planosphere [https://planosphere.stowers.org/intracellularorganelle] Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes GO_0043232 Planarian_Anatomy PLANA:0000519 intracellular non-membrane-bounded organelle Planosphere [https://planosphere.stowers.org/intracellularnon-membrane-boundedorganelle] A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. GO_0016020 Planarian_Anatomy PLANA:0000520 membrane Planosphere [https://planosphere.stowers.org/membrane] Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes. GO_0098588 Planarian_Anatomy PLANA:0000521 bounding membrane of organelle Planosphere [https://planosphere.stowers.org/boundingmembraneoforganelle] Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. GO_0044425 Planarian_Anatomy PLANA:0000522 membrane part Planosphere [https://planosphere.stowers.org/membranepart] Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO_0044459 Planarian_Anatomy PLANA:0000523 plasma membrane part Planosphere [https://planosphere.stowers.org/plasmamembranepart] A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. GO_0031090 Planarian_Anatomy PLANA:0000524 organelle membrane Planosphere [https://planosphere.stowers.org/organellemembrane] Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. GO_0043226 Planarian_Anatomy PLANA:0000525 organelle Planosphere [https://planosphere.stowers.org/organelle] Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GO:0043227 Planarian_Anatomy PLANA:0000526 membrane-bounded organelle Planosphere [https://planosphere.stowers.org/membrane-boundedorganelle] Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GO_0043231 Planarian_Anatomy PLANA:0000527 intracellular membrane-bounded organelle Planosphere [https://planosphere.stowers.org/intracellularmembrane-boundedorganelle] A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. GO_0005794 Planarian_Anatomy PLANA:0000528 Golgi apparatus Planosphere [https://planosphere.stowers.org/golgiapparatus] A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. GO_0005634 Planarian_Anatomy PLANA:0000529 nucleus Planosphere [https://planosphere.stowers.org/nucleus] A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. GO_0099503 Planarian_Anatomy PLANA:0000530 secretory vesicle Planosphere [https://planosphere.stowers.org/secretoryvesicle] Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. GO_0043228 Planarian_Anatomy PLANA:0000531 non-membrane-bounded organelle Planosphere [https://planosphere.stowers.org/non-membrane-boundedorganelle] Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. GO_0044428 Planarian_Anatomy PLANA:0000532 nuclear part Planosphere [https://planosphere.stowers.org/nuclearpart] A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. GO_0005730 Planarian_Anatomy PLANA:0000533 nucleolus Planosphere [https://planosphere.stowers.org/nucleolus] The ordered and organized complex of DNA, protein (histones), and sometimes RNA, that forms the chromosome. GO_0000785 Planarian_Anatomy PLANA:0000534 chromatin Planosphere [https://planosphere.stowers.org/chromatin] A compact and highly condensed form of chromatin. GO_0000792 Planarian_Anatomy PLANA:0000535 heterochromatin Planosphere [https://planosphere.stowers.org/heterochromatin] A dispersed and relatively uncompacted form of chromatin. GO_0000791 Planarian_Anatomy PLANA:0000536 euchromatin Planosphere [https://planosphere.stowers.org/euchromatin] An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. GO_0005840 Planarian_Anatomy PLANA:0000537 ribosome Planosphere [https://planosphere.stowers.org/ribosome] A group of axons linking two or more neuropils and having a common origin, termination UBERON:0001018 Planarian_Anatomy PLANA:0000538 axon tract Planosphere [https://planosphere.stowers.org/axontract] A cell whose function is determined by its response to an electric signal. CL:0000393 Planarian_Anatomy PLANA:0000539 electrically responsive cell Planosphere [https://planosphere.stowers.org/electricallyresponsivecell] A cell that initiates an electrical signal and passes that signal to another cell. CL:0000404 Planarian_Anatomy PLANA:0000540 electrically signaling cell Planosphere [https://planosphere.stowers.org/electricallysignalingcell] An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. neural subtree UBERON:0001021 nerves peripheral nerve Planarian_Anatomy PLANA:0000541 nerve Planosphere [https://planosphere.stowers.org/nerve] A cell that is part of the nervous system. tmeehan 2010-09-15T01:34:57Z CALOHA:TS-2040 CL:0002319 FMA:70333 Planarian_Anatomy PLANA:0000542 neural cell Planosphere [https://planosphere.stowers.org/neuralcell] A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 Planarian_Anatomy PLANA:0000543 neuron projection bundle Planosphere [https://planosphere.stowers.org/neuronprojectionbundle] Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. UBERON_0000073 part of nervous system Planarian_Anatomy PLANA:0000544 regional part of nervous system Planosphere [https://planosphere.stowers.org/regionalpartofnervoussystem] A neuron which conveys sensory information centrally from the periphery. CL:0000526 FMA:87653 input neuron Planarian_Anatomy PLANA:0000545 afferent neuron Planosphere [https://planosphere.stowers.org/afferentneuron] A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body. CL:0000103 FMA:67282 Planarian_Anatomy PLANA:0000546 bipolar neuron Planosphere [https://planosphere.stowers.org/bipolarneuron] A neuron that has an axon which crosses the midline. CL:0000678 Planarian_Anatomy PLANA:0000547 commissural neuron Planosphere [https://planosphere.stowers.org/commissuralneuron] A neuron which sends impulses peripherally to activate muscles or secretory cells. CL:0000527 output neuron Planarian_Anatomy PLANA:0000548 efferent neuron Planosphere [https://planosphere.stowers.org/efferentneuron] A motor neuron that is capable of directly inducing muscle contraction. CL:0008014 Planarian_Anatomy PLANA:0000549 In vertebrates, all motor neurons are excitatory, but various types of inhibitory motor neurons exist in invertebrates. excitatory motor neuron Planosphere [https://planosphere.stowers.org/excitatorymotorneuron] Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. BTO:0003811 CL:0000099 FBbt:00005125 FMA:67313 WBbt:0005113 Planarian_Anatomy PLANA:0000550 interneuron Planosphere [https://planosphere.stowers.org/interneuron] Any neuron having a sensory function; an afferent neuron conveying sensory impulses. BTO:0001037 CL:0000101 FBbt:00005124 FMA:84649 WBbt:0005759 Planarian_Anatomy PLANA:0000552 sensory neuron Planosphere [https://planosphere.stowers.org/sensoryneuron] An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement. BTO:0000312 CL:0000100 FMA:83617 WBbt:0005409 motoneuron Planarian_Anatomy PLANA:0000553 motor neuron Planosphere [https://planosphere.stowers.org/motorneuron] Neuronal cells which synthesize, store and release neurohormones. CL:0000381 FBbt:00005130 Planarian_Anatomy PLANA:0000556 neurosecretory neuron Planosphere [https://planosphere.stowers.org/neurosecretoryneuron] A neuron that is part of nerve found outside the central nervous system. CL:0000111 FMA:84664 Planarian_Anatomy PLANA:0000557 peripheral neuron Planosphere [https://planosphere.stowers.org/peripheralneuron] Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides. CL:0011103 Planarian_Anatomy PLANA:0000558 sympathetic neuron Planosphere [https://planosphere.stowers.org/sympatheticneuron] Neuron with one neurite that extends from the cell body. CL:0000106 FMA:67278 Planarian_Anatomy PLANA:0000559 unipolar neuron Planosphere [https://planosphere.stowers.org/unipolarneuron] Neuron with one neurite that extends from the cell body. PMID:18499291 Neuron with an axon and two or more dendrites. CL:0000104 FMA:67287 Planarian_Anatomy PLANA:0000560 multipolar neuron Planosphere [https://planosphere.stowers.org/multipolarneuron] Neuron with an axon and two or more dendrites. PMID:18499291 Cells that are in close proximity to neurons. CL:0000130 Planarian_Anatomy PLANA:0000561 neuron associated cell (sensu Nematoda and Protostomia) Planosphere [https://planosphere.stowers.org/neuronassociatedcell] Any neuron that is part of a central nervous system. TermGenie 2014-06-25T01:17:43Z CL:2000029 Planarian_Anatomy PLANA:0000562 central nervous system neuron Planosphere [https://planosphere.stowers.org/centralnervoussystemneuron] Any neuron that is part of a peripheral nervous system. TermGenie 2014-06-25T02:28:17Z CL:2000032 Planarian_Anatomy PLANA:0000564 peripheral nervous system neuron Planosphere [https://planosphere.stowers.org/peripheralnervoussystemneuron] A neruon whose cell body is within an autonomic ganglion. CL:0000107 FMA:80121 Planarian_Anatomy PLANA:0000565 autonomic neuron Planosphere [https://planosphere.stowers.org/autonomicneuron] Neuron that is part of the enteric nervous system. haendel 2012-06-28T08:20:31Z CL:0007011 Planarian_Anatomy PLANA:0000566 enteric neuron Planosphere [https://planosphere.stowers.org/entericneuron] Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue. this class represents a continuous sheet of basal lamina which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal lamina' represents a portion of substance on the scale of a single cell. A basal lamina is certainly present in Bilateria and was evaluated as an autapomorphy of this taxon.[well established][VHOG] basal lamina basal laminae lamina basalis AAO:0010269 AEO:0000065 BILA:0000065 Basal:lamina C32186 CARO:0000065 EHDAA2:0003065 FMA:62918 HAO:0000065 MESH:D001485 NIF_Subcellular:sao1397492660 TAO:0001485 TGMA:0001850 UMLS:C0085872 VHOG:0001592 WBbt:0005756 XAO:0003163 ZFA:0001485 http://linkedlifedata.com/resource/umls/id/C0085872 basal lamina of connective tissue Planarian_Anatomy PLANA:0001005 basal lamina of epithelium Planosphere [https://planosphere.stowers.org/basallaminaofepithelium] A fully formed, sexually mature organism. The sexually reproducing Schmidtea mediterranea biotype exists as an obligate cross-fertilizing hermaphrodite. Erin Davies 2017-04-24T02:52:06Z Schmidtea_mediterranea_Developmental_Stages PLANA:0004503 sexually mature adult Planosphere [https://planosphere.stowers.org/sexuallymatureadult] A fully formed, sexually mature organism. The sexually reproducing Schmidtea mediterranea biotype exists as an obligate cross-fertilizing hermaphrodite. PMID:19022767 PMID:11972158 The asexually reproducing Schmidtea mediterranea biotype exists as a constitutive adult, undergoing successive cycles of fission and whole animal regeneration. Asexual Schmidtea mediterranea contain primordial germ cells, but do not possess a reproductive system. Erin Davies 2017-04-24T02:59:06Z Schmidtea_mediterranea_Developmental_Stages PLANA:0004504 asexual adult Planosphere [https://planosphere.stowers.org/asexualadult] The asexually reproducing Schmidtea mediterranea biotype exists as a constitutive adult, undergoing successive cycles of fission and whole animal regeneration. Asexual Schmidtea mediterranea contain primordial germ cells, but do not possess a reproductive system. PMID:11972158 PMID:17376870 dmd-1+ expressing somatic cells within the testis that promote male GSC maintenance. dmd-1+, ophis-1+ somatic gonadal cells ensheath germ cells via long cytoplasmic processes and promote differentiation. Erin Davies 2017-07-19T21:05:52Z PLANA:0004506 testis somatic gonadal cell Planosphere [https://planosphere.stowers.org/testissomaticgonadalcell] dmd-1+ expressing somatic cells within the testis that promote male GSC maintenance. dmd-1+, ophis-1+ somatic gonadal cells ensheath germ cells via long cytoplasmic processes and promote differentiation. PMID:23652002, PMID:27163480 ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia. Erin Davies 2017-07-19T21:35:08Z PLANA:0004507 ovarian somatic gonadal cell Planosphere [https://planosphere.stowers.org/ovariansomaticgonadalcell] ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia. PMID:27163480 Axis that runs between the oral and aboral poles of the spherical embryo (Stage 3 through early Stage 6). The oral pole is centered around the temporary embryonic pharynx; the aboral pole is located opposite the temporary embryonic pharynx. Erin Davies 2017-07-27T14:55:23Z oral-aboral axis Planosphere [https://planosphere.stowers.org/oral-aboralaxis] Axis that runs between the oral and aboral poles of the spherical embryo (Stage 3 through early Stage 6). The oral pole is centered around the temporary embryonic pharynx; the aboral pole is located opposite the temporary embryonic pharynx. PMID:28072387 The apical surface of the single layered primitive ectoderm that is in contact with the environment. Erin Davies 2017-07-27T16:25:14Z primitive ectoderm surface Planosphere [https://planosphere.stowers.org/primitiveectodermsurface] The apical surface of the single layered primitive ectoderm that is in contact with the environment. OCLC:20423827 OCLC:464776945 OCLC:82522822 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md The surface of the primitive gut cells in contact with the embryonic wall. Erin Davies 2017-07-27T16:25:35Z primtive gut surface Planosphere [https://planosphere.stowers.org/primitivegutsurface] The surface of the primitive gut cells in contact with the embryonic wall. PMID:28072387 The surface of phagocytic embryonic gut cells in contact with ingested yolk cells. Erin Davies 2017-07-27T16:25:45Z embryonic gut cell surface Planosphere [https://planosphere.stowers.org/embryonicgutcellsurface] The surface of phagocytic embryonic gut cells in contact with ingested yolk cells. PMID:28072387 The epithelial surface lining the interior of the temporary embryonic pharynx, facing the lumen. Erin Davies 2017-07-27T16:26:16Z temporary embryonic pharynx lumen epithelial surface Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxlumenepithelialsurface] An undifferentiated, cycling embryonic cell in Stage 1-5 embryos that expresses piwi-1, numerous adult asexual neoblast enriched genes, and early embryo enriched genes. Erin Davies 2017-07-27T19:54:22Z blastomere Planosphere [https://planosphere.stowers.org/blastomere] An undifferentiated, cycling embryonic cell in Stage 1-5 embryos that expresses piwi-1, numerous adult asexual neoblast enriched genes, and early embryo enriched genes. PMID:28072387 Erin Davies 2017-07-27T20:00:04Z extraembryonic cell Planosphere [https://planosphere.stowers.org/extraembryoniccell] A neuronal cell innervating the temporary embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening. Erin Davies 2017-07-27T20:01:15Z temporary embryonic pharynx neuronal cell Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxneuronalcell] A neuronal cell innervating the temporary embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening. PMID:28072387 Differentiated radial muscle cell present in the temporary embryonic pharynx. Erin Davies 2017-07-27T20:01:39Z temporary embryonic pharynx radial muscle cell Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxradialmusclecell] Differentiated radial muscle cell present in the temporary embryonic pharynx. PMID:16932928 foxA1+ epithelial cell contained in the temporary embryonic pharynx. Erin Davies 2017-07-27T20:02:04Z temporary embryonic pharynx epithelial cell Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxepithelialcell] foxA1+ epithelial cell contained in the temporary embryonic pharynx. PMID:28072387, PMID:20100474 A muscle fiber that connects and runs perpendicular to a circular muscle fiber surrounding the luminal opening of the temporary embryonic pharynx. Erin Davies 2017-07-27T20:11:31Z temporary embryonic pharynx radial muscle fiber Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxradialmusclefiber] A muscle fiber that connects and runs perpendicular to a circular muscle fiber surrounding the luminal opening of the temporary embryonic pharynx. PMID:16932928 A muscle fiber that encircles the luminal opening of the temporary embryonic pharynx. Erin Davies 2017-07-27T20:43:07Z temporary embryonic pharynx circular muscle fiber Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxcircularmusclefiber] A muscle fiber that encircles the luminal opening of the temporary embryonic pharynx. PMID:16932928 Differentiated muscle cell present in a circular muscle fiber of the temporary embryonic pharynx. Erin Davies 2017-07-27T20:43:26Z temporary embryonic pharynx circular muscle cell Planosphere [https://planosphere.stowers.org/temporaryembryonicpharynxcircularmusclecell] Differentiated muscle cell present in a circular muscle fiber of the temporary embryonic pharynx. PMID:16932928 Erin Davies 2017-08-28T18:16:26Z sexual tail Planosphere [https://planosphere.stowers.org/sexualtail] Erin Davies 2017-08-28T18:16:47Z asexual tail Planosphere [https://planosphere.stowers.org/asexualtail] Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus. Erin Davies 2017-08-28T18:20:43Z copulatory region Planosphere [https://planosphere.stowers.org/copulatoryregion] Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus. PMID:22074376 Epithelia associated with the pharynx organ. Erin Davies 2017-08-31T14:53:38Z Planarian_Anatomy pharyngeal epithelium Planosphere [https://planosphere.stowers.org/pharyngealepithelium] Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. Erin Davies 2017-08-31T19:21:09Z UBERON:0002416 Planarian_Anatomy integumental system Planosphere [https://planosphere.stowers.org/integumentalsystem] Anatomical space enclosed by the oviduct epithelium. Erin Davies 2017-09-01T17:52:16Z Planarian_Anatomy oviduct lumen Planosphere [https://planosphere.stowers.org/oviductlumen] Anatomical space enclosed by the sperm duct epithelium. Erin Davies 2017-09-02T22:26:19Z Planarian_Anatomy sperm duct lumen Planosphere [https://planosphere.stowers.org/spermductlumen] Ciliated epithelium lining the oviduct. Erin Davies 2017-09-02T22:35:10Z Planarian_Anatomy oviduct epithelium Planosphere [https://planosphere.stowers.org/oviductepithelium] Ciliated epithelium lining the sperm duct. Erin Davies 2017-09-02T22:43:04Z Planarian_Anatomy sperm duct epithelium Planosphere [https://planosphere.stowers.org/spermductepithelium] Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct. Erin Davies 2017-09-02T22:55:44Z Planarian_Anatomy tuba lumen Planosphere [https://planosphere.stowers.org/tubalumen] Anatomical plane which divides the body into superior and inferior parts. It always contains the midline and is perpendicular to the coronal and sagittal planes. It is also known as the horizontal plane, axial plane, or transaxial plane. Steph Nowotarski 2017-04-26T19:31:44Z Planarian_Anatomy PLANA:0007501 transverse plane Planosphere [https://planosphere.stowers.org/transverseplane] Anatomial plane which divides the body into ventral and dorsal regions. This plane always includes the midline and is also known as the frontal plane. Steph Nowotarski 2017-04-26T19:32:04Z Planarian_Anatomy PLANA:0007502 coronal plane Planosphere [https://planosphere.stowers.org/coronalplane] Anatomical plane which divides the body into right and left parts. This plane passes through the midline. Steph Nowotarski 2017-04-26T19:32:33Z Planarian_Anatomy PLANA:0007503 sagittal plane Planosphere [https://planosphere.stowers.org/sagittalplane] Position along the dorsoventral axis that is above the anteroposterior axis, or closer to the back. Steph Nowotarski 2017-04-27T16:38:48Z Planarian_Anatomy PLANA:0007504 dorsal Planosphere [https://planosphere.stowers.org/dorsal] Position along the dorsoventral axis that is below the anteroposterior axis, or closer to the belly. Steph Nowotarski 2017-04-27T16:38:59Z Planarian_Anatomy PLANA:0007505 ventral Planosphere [https://planosphere.stowers.org/ventral] Position along the anteroposterior axis closer to the head rather than the tail. Steph Nowotarski 2017-04-27T16:39:34Z Planarian_Anatomy PLANA:0007506 anterior Planosphere [https://planosphere.stowers.org/anterior] Position along the anteroposterior axis that is closer to the tail rather than the head. Steph Nowotarski 2017-04-27T16:39:59Z Planarian_Anatomy PLANA:0007507 posterior Planosphere [https://planosphere.stowers.org/posterior] Anatomical structures that exist outside of cells; non-cellular. Steph Nowotarski 2017-05-03T13:48:26Z WBbt:0005732 Planarian_Anatomy PLANA:0007508 extracellular component Planosphere [https://planosphere.stowers.org/extracellularcomponent] The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. Steph Nowotarski 2017-05-03T13:48:41Z GO:0005886 Planarian_Anatomy PLANA:0007509 plasma membrane Planosphere [https://planosphere.stowers.org/plasmamembrane] Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi. Steph Nowotarski 2017-05-03T18:08:16Z GO:0043230 Planarian_Anatomy PLANA:0007511 extracellular organelle Planosphere [https://planosphere.stowers.org/extracellularorganelle] A spherical to rod shaped organelle that generates the majority of a cell's supply of ATP via cellular respiration. Mitochondria have their own genome and consist of outer and inner membranes, the latter folds inward to form cristae. This folding increases the surface area of the membrane and thus increases the space available to produce ATP. The inner and outer membranes are separated by an intermembrane space, and the inner membrane encloses the matrix. Steph Nowotarski 2017-05-03T18:19:46Z Planarian_Anatomy PLANA:0007512 mitochondrion Planosphere [https://planosphere.stowers.org/mitochondrion] Network of interconnected, flattened, and/or tubular membrane, known as cisternae. This membrane is contiguous with the outer nuclear membrane. The endoplasmic reticulum is involved in both protein and lipid synthesis. Steph Nowotarski 2017-05-04T14:46:22Z Planarian_Anatomy PLANA:0007513 endoplasmic reticulum Planosphere [https://planosphere.stowers.org/endoplasmicreticulum] Endoplasmic reticululum that is studded with ribosomes, leading to a "rough" or "granular" appearance. Steph Nowotarski 2017-05-04T14:47:41Z Planarian_Anatomy PLANA:0007514 rough endoplasmic reticulum Planosphere [https://planosphere.stowers.org/roughendoplasmicreticulum] Endoplamic reticulum that does not contain ribosomes, which synthesizes lipids, phospholipids, and steroids. Steph Nowotarski 2017-05-04T14:48:11Z Planarian_Anatomy PLANA:0007515 smooth endoplasmic reticulum Planosphere [https://planosphere.stowers.org/smoothendoplasmicreticulum] Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined. Steph Nowotarski 2017-05-04T14:49:17Z GO:0005643 Planarian_Anatomy PLANA:0007516 nuclear pore Planosphere [https://planosphere.stowers.org/nuclearpore] The digestive component of the cell. They are homogenous, dense, membrane bound organelles filled with acid hydrolases which break down polymers. Steph Nowotarski 2017-05-04T15:35:23Z Planarian_Anatomy PLANA:0007518 lysosome Planosphere [https://planosphere.stowers.org/lysosome] The digestive component of the cell. They are homogenous, dense, membrane bound organelles filled with acid hydrolases which break down polymers. ISBN: 0-71677033-4 PMID:4853064 Axis that runs along the long axis of the animal from anterior (head) to posterior (tail). It is perpendicular to the dorsoventral axis and as such, it splits dorsal and ventral regions of the animal to either side. Steph Nowotarski 2017-05-04T17:59:38Z Planarian_Anatomy PLANA:0007519 anteroposterior axis Planosphere [https://planosphere.stowers.org/anteroposterioraxis] Axis that runs along the short axis of the animal, perpendicular to the anteroposterior axis, running from the dorsal (back) side of the animal to the ventral (belly) side of the animal. This axis splits anterior and posterior regions of the animal to either side. Steph Nowotarski 2017-05-04T18:00:07Z Planarian_Anatomy PLANA:0007520 dorsoventral axis Planosphere [https://planosphere.stowers.org/dorsoventralaxis] Axis perpendicular to both the anteroposterior and dorsoventral axis that runs from the left side of the animal, through the medial region (center) and out to the right side. Steph Nowotarski 2017-05-04T18:00:51Z Planarian_Anatomy PLANA:0007521 dextro-sinister axis Planosphere [https://planosphere.stowers.org/dextro-sinisteraxis] Axis that runs from the center of the body, starting at the anteroposterior axis and out the the lateral (left, right, dorsal or ventral) surface of the animal. Steph Nowotarski 2017-05-04T18:01:37Z Planarian_Anatomy PLANA:0007522 mediolateral axis Planosphere [https://planosphere.stowers.org/mediolateralaxis] Axis that starts at the distal (close to the body) part of an appendage and runs to the proximal (farthest from the body) part of an appendage. Steph Nowotarski 2017-05-04T18:02:04Z Planarian_Anatomy PLANA:0007523 proximodistal axis Planosphere [https://planosphere.stowers.org/proximodistralaxis] Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD. Steph Nowotarski 2017-05-15T18:28:35Z Planarian_Anatomy PLANA:0007524 anterior pole Planosphere [https://planosphere.stowers.org/anteriorpole] Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD. PMID:21566195 PMID:23297191 PMID:24040508 PMID:24415944 PMID:24704339 PMID:24992682 Distinct posterior cluster of muscle cells located at the midline which express wnt1. Steph Nowotarski 2017-05-15T18:28:47Z Planarian_Anatomy PLANA:0007525 posterior pole Planosphere [https://planosphere.stowers.org/posteriorpole] Distinct posterior cluster of muscle cells located at the midline which express wnt1. PMID:18063755 PMID:21680047 A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu, guide neuronal migration during development, and exchange metabolites with neurons. Steph Nowotarski 2017-06-22T17:12:28Z CL:0000125 Planarian_Anatomy PLANA:0007528 glial cell Planosphere [https://planosphere.stowers.org/glialcell] A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu, guide neuronal migration during development, and exchange metabolites with neurons. PMID:27612384 A biological tissue mass of nerve cell bodies. Steph Nowotarski 2017-06-22T18:29:52Z UBERON:0000045 Planarian_Anatomy PLANA:0007529 ganglion Planosphere [https://planosphere.stowers.org/ganglion] Region of the sexual biotype animal lateral to and surrounding the pharyngeal pouch. Steph Nowotarski 2017-07-24T18:38:16Z Planarian_Anatomy PLANA:0007530 sexual parapharyngeal region Planosphere [https://planosphere.stowers.org/sexualparapharyngealregion] Region of the asexual biotype animal lateral to and surrounding the pharyngeal pouch. Steph Nowotarski 2017-07-24T18:38:28Z Planarian_Anatomy PLANA:0007531 asexual parapharyngeal region Planosphere [https://planosphere.stowers.org/asexualparapharyngealregion] Region of the asexual biotype animal between the posterior end of the cephalic ganglia and the anterior end of the definitive pharynx. Steph Nowotarski 2017-07-24T18:41:25Z Planarian_Anatomy PLANA:0007532 asexual neck Planosphere [https://planosphere.stowers.org/asexualneck] Region of the juvenile or adult sexual biotype animal between the posterior end of the cephalic ganglia and the anterior end of the definitive pharynx. Steph Nowotarski 2017-07-24T18:41:33Z Planarian_Anatomy PLANA:0007533 sexual neck Planosphere [https://planosphere.stowers.org/sexualneck] Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft. Steph Nowotarski 2017-07-24T19:28:03Z Planarian_Anatomy PLANA:0007534 inner pharyngeal epithelium Planosphere [https://planosphere.stowers.org/innerpharyngealepithelium] Pharynx muscle fibers running parallel to the diameter of the pharynx. Steph Nowotarski 2017-07-24T19:39:14Z Planarian_Anatomy PLANA:0007535 pharyngeal circular muscle fiber Planosphere [https://planosphere.stowers.org/pharyngealcircularmusclefiber] Pharynx muscle fibers running parallel to the diameter of the pharynx. ASIN:B000M4NK9M The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell. Steph Nowotarski 2017-09-05T14:18:21Z UBERON:0000955 Planarian_Anatomy brain Planosphere [https://planosphere.stowers.org/brain] Specialized epithelial cells located along the body margin lining the dorsoventral margin. Adhesion glands are comprised of three cell types, the viscid and relasing gland cells which penetrate through an epithelial anchor cell and terminate at the epithelial surface. Steph Nowotarski 2017-09-05T14:32:51Z Planarian_Anatomy adhesion glands Planosphere [https://planosphere.stowers.org/adhesionglands] Specialized epithelial cells located along the body margin lining the dorsoventral margin. Adhesion glands are comprised of three cell types, the viscid and relasing gland cells which penetrate through an epithelial anchor cell and terminate at the epithelial surface. OCLC:16809160 PMID: 20865784 Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells. Steph Nowotarski 2017-09-05T15:08:27Z Planarian_Anatomy anchor cell Planosphere [https://planosphere.stowers.org/anchorcell] Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells. OCLC:16809160 PMID: 20865784 A specialized insunk epithelial cell that is part of the adhesion glands which is responsible for production and excretion of the viscid substance allowing adherence to a substrate. Steph Nowotarski 2017-09-05T15:08:38Z viscid gland cell Planosphere [https://planosphere.stowers.org/viscidglandcell] A specialized insunk epithelial cell that is part of the adhesion glands which is responsible for production and excretion of the viscid substance allowing adherence to a substrate. OCLC:16809160 PMID: 20865784 Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance. Steph Nowotarski 2017-09-05T15:08:48Z releasing gland cell Planosphere [https://planosphere.stowers.org/releasingglandcell] Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance. OCLC:16809160 PMID: 20865784