CARO part_of NCBITaxon:79327; CL part_of NCBITaxon:79327 Planarian_Anatomy 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 IAO:0000115 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 IAO:0100001 term replaced by definiton 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 IAO:0100001 synonym typically used in the context of human anatomy IAO:0100001 synonym typically used in the context of vertebrate anatomy IAO:0100001 namespace-id-rule IAO:0100001 synonym_type_property has_broad_synonym IAO:0100001 database_cross_reference IAO:0100001 has_exact_synonym IAO:0100001 has_narrow_synonym IAO:0100001 has_obo_format_version IAO:0100001 has_obo_namespace IAO:0100001 has_related_synonym IAO:0100001 has_scope IAO:0100001 has_synonym_type IAO:0100001 shorthand Sofia Robb 2017-07-26T18:19:59Z treat-xrefs-as-genus-differentia Sofia Robb 2017-09-11T16:38:22Z depiction is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part_of BFO:0000050 Planarian_Anatomy part of 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. This object Property is transitive and as such will be entailed. anterior_to cjm 2009-07-31T02:15:46Z BSPO:0000096 Planarian_Anatomy 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 Planarian_Anatomy distal_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). BSPO:cjm x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). dorsal_to BSPO:0000098 Planarian_Anatomy 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. This object Property is transitive and as such will be entailed. caudal_to posterior_to BSPO:0000099 caudal_to Planarian_Anatomy posterior_to caudal_to x proximal_to y iff x is closer to the point of attachment with the body than y. proximal_to BSPO:0000100 Planarian_Anatomy The elbow is proximal to the hand, but distal to the shoulder. proximal_to x proximal_to y iff x is closer to the point of attachment with the body than y. BSPO:cjm x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 Planarian_Anatomy ventral_to x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm On the same side as. For example, the left arm is ipsilateral to the left leg. BSPO:0000105 Planarian_Anatomy ipsilateral_to On the same side as. For example, the left arm is ipsilateral to the left leg. BSPO:cjm On the opposite side from. For example, the left arm is contralateral to the right arm (and the right leg). BSPO:0000106 Planarian_Anatomy contralateral_to On the opposite side from. For example, the left arm is contralateral to the right arm (and the right leg). BSPO:cjm Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 Planarian_Anatomy deep_to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:cjm Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 Planarian_Anatomy superficial_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:cjm Closer to the left side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left_of Y <=> every instance x of X is left_of some instance y of Y, and there exists some organism o such that x part_of o and y part_of o. BSPO:0000110 Planarian_Anatomy left_of Closer to the left side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left_of Y <=> every instance x of X is left_of some instance y of Y, and there exists some organism o such that x part_of o and y part_of o. BSPO:cjm Closer to the right side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left_of Y <=> every instance x of X is right_of some instance y of Y, and there exists some organism o such that x part_of o and y part_of o. BSPO:0000111 Planarian_Anatomy right_of Closer to the right side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left_of Y <=> every instance x of X is right_of some instance y of Y, and there exists some organism o such that x part_of o and y part_of o. BSPO:cjm Direcly opposite to. i.e. on the opposite side through the axis. BSPO:0000113 Planarian_Anatomy opposite_to Direcly opposite to. i.e. on the opposite side through the axis. BSPO:cjm X in_left_side_of Y <=> if Y is subdivided into two left and right portions, X is part_of the left portion. BSPO:0000120 Planarian_Anatomy in_left_side_of X in_left_side_of Y <=> if Y is subdivided into two left and right portions, X is part_of the left portion. BSPO:PATO_mtg_2009 X in_right_side_of Y <=> if Y is subdivided into two left and right portions, X is part_of the right portion. BSPO:0000121 Planarian_Anatomy in_right_side_of X in_right_side_of Y <=> if Y is subdivided into two left and right portions, X is part_of the right portion. BSPO:PATO_mtg_2009 X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:0000122 Planarian_Anatomy in_posterior_side_of X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:PATO_mtg_2009 X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:0000123 Planarian_Anatomy in_anterior_side_of X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:PATO_mtg_2009 x in_proximal_side_of y <=> if y is subdivided into two proximal and distal portions, y is part_of the proximal portion. BSPO:0000124 Planarian_Anatomy in_proximal_side_of x in_proximal_side_of y <=> if y is subdivided into two proximal and distal portions, y is part_of the proximal portion. BSPO:PATO_mtg_2009 x in_distal_side_of y <=> if y is subdivided into two proximal and distal portions, y is part_of the distal portion. BSPO:0000125 Planarian_Anatomy in_distal_side_of x in_distal_side_of y <=> if y is subdivided into two proximal and distal portions, y is part_of the distal portion. BSPO:PATO_mtg_2009 X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure BSPO:0000126 Planarian_Anatomy in_lateral_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 UBERON:cjm X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the superficial portion. BSPO:0001100 Planarian_Anatomy in_superficial_part_of X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the superficial portion. BSPO:cjm X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. BSPO:0001101 Planarian_Anatomy in_deep_part_of X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. BSPO:cjm X proximalmost_part_of Y <=> X is in_proximal_side_of Y and X is adjacent_to the proximal boundary of Y BSPO:0001106 Planarian_Anatomy proximalmost_part_of X proximalmost_part_of Y <=> X is in_proximal_side_of Y and X is adjacent_to the proximal boundary of Y https://orcid.org/0000-0002-6601-2165 x immediately_deep_to y iff x deep_to y and x is contiguous with y. This relation holds when both the deep_to and ajdacent_to relationship similarly hold. immediately_deep_to BSPO:0001107 Planarian_Anatomy immediately_deep_to x immediately_deep_to y iff x deep_to y and x is contiguous with y. This relation holds when both the deep_to and ajdacent_to relationship similarly hold. BSPO:curators X distalmost_part_of Y <=> X is in_distal_side_of Y and X is adjacent_to the distal boundary of Y distalmost_part_of BSPO:0001108 Planarian_Anatomy distalmost_part_of X distalmost_part_of Y <=> X is in_distal_side_of Y and X is adjacent_to the distal boundary of Y https://orcid.org/0000-0002-6601-2165 BSPO:0001113 Planarian_Anatomy preaxialmost_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 Planarian_Anatomy posterior_to (developmentally) postaxial_to x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side. http://medical-dictionary.thefreedictionary.com/postaxial posterior_to (developmentally) MA:th BSPO:0001115 Planarian_Anatomy postaxialmost_part_of X intersects_median_plane of iff X crosses the midine plane of Y. BSPO:0005001 Planarian_Anatomy intersects_midsagittal_plane_of BSPO:0015001 Planarian_Anatomy A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. If s finishes_axis x, and x has_end_point p, then x overlaps p finishes_axis BSPO:0015002 Planarian_Anatomy follows_axis BSPO:0015003 Planarian_Anatomy has_axis A relation between an axis and a part of an organism, in which the part defines the initial point of the axis. BSPO:0015004 Planarian_Anatomy Axes can be defined in a given species by subtyping the relevant axis type and stating a end and end point has_end_point A relation between an axis and a part of an organism, in which the part defines the initial point of the axis. BSPO:cjm crossing at right angles BSPO:0015005 Planarian_Anatomy orthogonal_to crossing at right angles BSPO:cjm Intersects at two points. BSPO:0015006 Planarian_Anatomy passes_through Intersects at two points. BSPO:cjm BSPO:0015007 Planarian_Anatomy A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. . If s starts_axis x, and x has_start_point p, then x overlaps p starts_axis BSPO:0015008 Planarian_Anatomy placeholder. used for relation between anatomical surface and an anatomical side. surface_of x immediately_anterior_to y iff x anterior_to y and x is contiguous with y. immediately_anterior_to BSPO:0015009 Planarian_Anatomy immediately_anterior_to x immediately_anterior_to y iff x anterior_to y and x is contiguous with y. BSPO:curators x immediately_distal_to y iff x distal_to y and x is contiguous with y. BSPO:0015010 Planarian_Anatomy immediately_distal_to x immediately_distal_to y iff x distal_to y and x is contiguous with y. BSPO:curators x immediately_dorsal_to y iff x dorsal_to y and x is contiguous with y. BSPO:0015011 Planarian_Anatomy immediately_dorsal_to x immediately_dorsal_to y iff x dorsal_to y and x is contiguous with y. BSPO:curators x immediately_posterior_to y iff x posterior_to y and x is contiguous with y. immediately_posterior_to BSPO:0015012 Planarian_Anatomy immediately_posterior_to x immediately_posterior_to y iff x posterior_to y and x is contiguous with y. BSPO:curators x immediately_proximal_to y iff x proximal_to y and x is contiguous with y. BSPO:0015013 Planarian_Anatomy immediately_proximal_to x immediately_proximal_to y iff x proximal_to y and x is contiguous with y. BSPO:curators x immediately_superficial_to y iff x superficial_to y and x is contiguous with y. immediately_superficial_to BSPO:0015014 Planarian_Anatomy immediately_superficial_to x immediately_superficial_to y iff x superficial_to y and x is contiguous with y. BSPO:curators x immediately_ventral_to y iff x ventral_to y and x is contiguous with y. BSPO:0015015 Planarian_Anatomy immediately_ventral_to x immediately_ventral_to y iff x ventral_to y and x is contiguous with y. BSPO:curators x immediately_left_of y iff x left_of y and x is contiguous with y. BSPO:0015016 Planarian_Anatomy immediately_left_of x immediately_left_of y iff x left_of y and x is contiguous with y. BSPO:curators x immediately_right_of y iff x right_of y and x is contiguous with y. BSPO:0015017 Planarian_Anatomy immediately_right_of x immediately_right_of y iff x right_of y and x is contiguous with y. BSPO:curators nearer to the oral opening of the organism, on the oral-aboral axis. This object Property is transitive and as such will be entailed. oral_to BSPO:0015201 Planarian_Anatomy oral_to nearer to the aboral opening of the organism, on the oral-aboral axis. This object Property is transitive and as such will be entailed. aboral_to BSPO:0015202 Planarian_Anatomy aboral_to x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the front. This object Property is transitive and as such will be entailed. anterior_to (developmentally) lateral (radial) to medial (tibial) to preaxial_to BSPO:1000000 Planarian_Anatomy anterior_to (developmentally) lateral (radial) to medial (tibial) to preaxial_to x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the front. This object Property is transitive and as such will be entailed. http://medical-dictionary.thefreedictionary.com/preaxial anterior_to (developmentally) MA:th feature restricted to Steph Nowotarski 2017-07-24T20:21:09Z Planarian_Anatomy specific_to specific to 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 Planarian_Anatomy contained in x overlaps y iff they have some part in common. RO:0002131 Planarian_Anatomy "(forall (x y) (iff (overlaps x y) (exists (z) (and (part_of z x) (part_of z y)))))" CLIF [] overlaps x overlaps y iff they have some part in common. BSPO:cjm x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y. This object Property is transitive and as such will be entailed. Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan develops_from RO:0002202 Planarian_Anatomy This is the transitive form of the develops from relation develops from 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 object Property is symmetric as as such will be applied 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 Planarian_Anatomy adjacent to x develops_in y if x is located in y whilst x is developing Chris Mungall EHDAA2 Jonathan Bard, EHDAA2 develops_in RO:0002226 Planarian_Anatomy This relation take from EHDAA2 - precise semantics yet to be defined develops in 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 Planarian_Anatomy developmentally replaces 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 Planarian_Anatomy developmentally related to 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 Planarian_Anatomy branching part of 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 Planarian_Anatomy 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). This object Property is transitive and as such will be entailed. Chris Mungall existence_starts_with RO:0002489 Planarian_Anatomy 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 Planarian_Anatomy 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 Planarian_Anatomy 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 Planarian_Anatomy 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 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 Planarian_Anatomy 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 Planarian_Anatomy 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 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. Planarian_Anatomy existence starts at point 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. Planarian_Anatomy existence ends at point a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel produced_by RO:0003001 Planarian_Anatomy produced by A relation between an axis and a part of an organism, in which the part defines the initial point of the axis. :has_start_point RO:0002220 Planarian_Anatomy Axes can be defined in a given species by subtyping the relevant axis type and stating a start and end point. has_start_point A relation between an axis and a part of an organism, in which the part defines the initial point of the axis. BSPO:cjm x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. RO:0002220 Planarian_Anatomy parallel_to x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. BSPO:curators Planarian_Anatomy existence starts and ends during placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B. PLANA uses this objectProperty specifically for body region relations. For example, anterior pole subdivision_of anterior. Planarian_Anatomy placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision of The side of an organism that is left of the sagittal plane. BSPO:0000000 left Planarian_Anatomy BSPO:0000000 left side The side of an organism that is left of the sagittal plane. BSPO:cjm A 2D surface of an 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. BSPO:0000005 FMA:24137 surface Planarian_Anatomy BSPO:0000005 to be merged into CARO anatomical surface Fiat anatomical region extending a short distance from the boundary of an object inwards. BSPO:0000006 edge margin Planarian_Anatomy BSPO:0000006 anatomical margin Fiat anatomical region extending a short distance from the boundary of an object inwards. BSPO:cjm The side of an organism that is right of the sagittal plane. BSPO:0000007 right Planarian_Anatomy BSPO:0000007 right side The side of an organism that is right of the sagittal plane. BSPO:cjm BSPO:wd Sagittal plane that divides a bilateral body into unequal left and right parts. Steph Nowotarski BSPO:0000008 parasagittal section Planarian_Anatomy BSPO:0000008 Image depicts a hemotoxylin and eosin stained sagittal section of an asexual adult animal. This slice does not run through the midline of the animal, as the photoreceptors are apparent. Scale bar: 500um parasagittal plane Sagittal plane that divides a bilateral body into unequal left and right parts. BSPO:mah Sagittal plane that divides bilateral body into equal left and right parts. BSPO:0000009 FMA:74563 median sagittal plane midline plane midsagittal section Planarian_Anatomy median plane BSPO:0000009 only in bilaterally symmetrical organisms midsagittal plane Sagittal plane that divides bilateral body into equal left and right parts. BSPO:mah median sagittal plane FMA:74563 A straight line through space, intersecting an anatomical entity. BSPO:0000010 http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG Planarian_Anatomy BSPO:0000010 Axis directions are defined in terms of axes. anatomical axis A straight line through space, intersecting an anatomical entity. BSPO:cjm An axis that extends from an internal position to a more external position in the body or body part. BSPO:0000012 Planarian_Anatomy BSPO:0000012 Muscles are frequently categorized as 'deep', 'intermediate', and 'superficial'. deep-superficial axis An axis that extends from an internal position to a more external position in the body or body part. BSPO:PM Anatomical plane that divides bilateral body into dorsal and ventral parts. BSPO:0000019 FMA:52810 frontal plane horizontal anatomical plane horizontal section Planarian_Anatomy coronal section frontal section BSPO:0000019 horizontal plane Anatomical plane that divides bilateral body into dorsal and ventral parts. BSPO:mah horizontal anatomical plane FMA:52810 Anatomical gradient that is distributed along the deep-superficial axis. BSPO:0000021 Planarian_Anatomy BSPO:0000021 deep-superficial gradient Anatomical gradient that is distributed along the deep-superficial axis. BSPO:wd Anatomical gradient that is distributed along the apical-basal axis. BSPO:0000023 Planarian_Anatomy BSPO:0000023 apical-basal gradient Anatomical gradient that is distributed along the apical-basal axis. BSPO:wd Anatomical gradient that is distributed along the proximal-distal axis. BSPO:0000024 Planarian_Anatomy BSPO:0000024 proximal-distal gradient Anatomical gradient that is distributed along the proximal-distal axis. BSPO:wd Anatomical region that overlaps the posterior and lateral regions of the body or body part. Melissa Haendel 2009-06-15T01:06:01Z BSPO:0000028 posterolateral region Planarian_Anatomy BSPO:0000028 postero-lateral region Anatomical region that overlaps the posterior and lateral regions of the body or body part. BSPO:wd Anatomical region that overlaps the anterior and lateral regions of a body or body part. Melissa Haendel 2009-06-15T01:07:18Z BSPO:0000029 anterolateral region Planarian_Anatomy BSPO:0000029 antero-lateral region Anatomical region that overlaps the anterior and lateral regions of a body or body part. BSPO:wd Anatomical region located deep within an organism or structure. BSPO:0000033 Planarian_Anatomy BSPO:0000033 deep region Anatomical region located deep within an organism or structure. BSPO:wd Anatomical region superficially located on the body or body part. BSPO:0000034 Planarian_Anatomy BSPO:0000034 superficial region Anatomical region superficially located on the body or body part. BSPO:wd Melissa Haendel 2009-06-16T08:49:03Z BSPO:0000036 anterior-most anteriormost Planarian_Anatomy BSPO:0000036 anterior-most region Melissa Haendel 2009-06-16T08:49:50Z BSPO:0000037 posterior-most posteriormost Planarian_Anatomy BSPO:0000037 posterior-most region Melissa Haendel 2009-06-16T08:50:26Z BSPO:0000038 dorsal-most dorsalmost Planarian_Anatomy BSPO:0000038 dorsal-most region Melissa Haendel 2009-06-16T08:51:07Z BSPO:0000039 ventral-most ventralmost Planarian_Anatomy BSPO:0000039 ventral-most region BSPO:0000041 Planarian_Anatomy BSPO:0000041 deep/superficial compartment boundary Anatomical margin that is located on the antero-medial region of the body or body part. Melissa Haendel 2009-09-10T08:49:57Z BSPO:0000042 anteromedial margin Planarian_Anatomy BSPO:0000042 antero-medial margin Anatomical margin that is located on the antero-medial region of the body or body part. BSPO:wd<new dbxref> BSPO:0000043 Planarian_Anatomy BSPO:0000043 apical/basal compartment boundary BSPO:0000044 Planarian_Anatomy BSPO:0000044 proximal/distal compartment boundary Anatomical margin that is located on the antero-lateral region of the body or body part. Melissa Haendel 2009-09-10T08:50:37Z BSPO:0000045 anterolateral margin Planarian_Anatomy BSPO:0000045 antero-lateral margin Anatomical margin that is located on the antero-lateral region of the body or body part. BSPO:wd Anatomical margin that is located on the postero-medial region of the body or body part. Melissa Haendel 2009-09-10T08:51:07Z BSPO:0000046 posteromedial margin Planarian_Anatomy BSPO:0000046 postero-medial margin Anatomical margin that is located on the postero-medial region of the body or body part. BSPO:wd Anatomical margin that is located on the postero-lateral region of the body or body part. Melissa Haendel 2009-09-10T08:51:42Z BSPO:0000047 posterolateral margin Planarian_Anatomy BSPO:0000047 postero-lateral margin Anatomical margin that is located on the postero-lateral region of the body or body part. BSPO:wd Anatomical margin that is located on the dorso-medial region of the body or body part. Melissa Haendel 2009-09-10T08:52:04Z BSPO:0000048 dorso-medial margin Planarian_Anatomy BSPO:0000048 dorso-medial margin Anatomical margin that is located on the dorso-medial region of the body or body part. BSPO:wd Anatomical margin that is located on the ventro-medial region of the body or body part. Melissa Haendel 2009-09-10T08:52:48Z BSPO:0000049 ventromedial margin Planarian_Anatomy BSPO:0000049 ventro-medial margin Anatomical margin that is located on the ventro-medial region of the body or body part. BSPO:wd Material anatomical entity defined by change in the value of some quantity per unit of distance across some spatial axis. BSPO:0000051 FBql:00005254 Planarian_Anatomy BSPO:0000051 anatomical gradient Material anatomical entity defined by change in the value of some quantity per unit of distance across some spatial axis. BSPO:cjm Anatomical gradient that is distributed along the anterior-posterior axis. BSPO:0000052 FBcv:0000142 FBql:00005256 Planarian_Anatomy BSPO:0000052 anterior-posterior gradient Anatomical gradient that is distributed along the anterior-posterior axis. BSPO:wd Anatomical gradient that is distributed along the dorsal-ventral axis. BSPO:0000053 FBcv:0000143 FBql:00005255 Planarian_Anatomy BSPO:0000053 dorsal-ventral gradient Anatomical gradient that is distributed along the dorsal-ventral axis. BSPO:wd An anatomical region bounded by a plane perpendicular to an axis through the middle. BSPO:0000054 FBql:00005841 Planarian_Anatomy BSPO:0000054 anatomical side An anatomical region bounded by a plane perpendicular to an axis through the middle. BSPO:cjm An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:0000055 FBcv:0000053 FBql:00005848 anterior rostral Planarian_Anatomy BSPO:0000055 anterior side An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:RW An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:0000056 FBcv:0000065 FBql:00005849 posterior caudal Planarian_Anatomy BSPO:0000056 posterior side An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:RW BSPO:wd caudal Anatomical side that is located on the apical end of an organism or structure. BSPO:0000057 FBcv:0000054 FBql:00005854 apical Planarian_Anatomy BSPO:0000057 apical side Anatomical side that is located on the apical end of an organism or structure. BSPO:wd Anatomical side that is located on the basal end of an organism or structure. BSPO:0000058 FBcv:0000055 FBql:00005855 basal Planarian_Anatomy BSPO:0000058 The part of the organism attached to a substrate. Axis of symmetry. basal side Anatomical side that is located on the basal end of an organism or structure. BSPO:wd An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane. BSPO:0000063 FBcv:0000059 FBql:00005842 dorsal Planarian_Anatomy BSPO:0000063 dorsal side An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane. BSPO:wd BSPO:0000067 FBcv:0000064 FBql:00005847 medial Planarian_Anatomy BSPO:0000067 a point in the centre of the organism (where the left-right axis intersects the midsagittal plane) medial side An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. BSPO:0000068 FBcv:0000070 FBql:00005843 ventral Planarian_Anatomy BSPO:0000068 ventral side An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. BSPO:RW BSPO:wd A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. BSPO:0000070 FBql:00005841 Planarian_Anatomy BSPO:0000070 to be merged into CARO anatomical region A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. BSPO:cjm Anatomical region anteriorly located on the body or body part. BSPO:0000071 FBql:00005848 Planarian_Anatomy BSPO:0000071 anterior region Anatomical region anteriorly located on the body or body part. BSPO:wd Anatomical region posteriorly located on the body or body part. BSPO:0000072 FBql:00005849 Planarian_Anatomy BSPO:0000072 posterior region Anatomical region posteriorly located on the body or body part. BSPO:wd Anatomical region located on the apical end on the body or body part. BSPO:0000073 FBql:00005854 Planarian_Anatomy BSPO:0000073 apical region Anatomical region located on the apical end on the body or body part. BSPO:wd Anatomical region located basally on the body or body part. BSPO:0000074 FBql:00005855 Planarian_Anatomy BSPO:0000074 basal region Anatomical region located basally on the body or body part. BSPO:wd Anatomical region centrally located on the body or body part. BSPO:0000075 FBql:00015851 Planarian_Anatomy BSPO:0000075 central region Anatomical region centrally located on the body or body part. BSPO:wd BSPO:0000076 FBql:00005851 Planarian_Anatomy BSPO:0000076 inherited from flybase cv. not clear how this would be used contralateral region Anatomical region proximally located on the body or body part. BSPO:0000077 FBql:00005852 Planarian_Anatomy BSPO:0000077 proximal region Anatomical region proximally located on the body or body part. BSPO:wd Anatomical region distally located on the body or body part. BSPO:0000078 FBql:00005853 Planarian_Anatomy BSPO:0000078 distal region Anatomical region distally located on the body or body part. BSPO:wd Anatomical region dorsally located on the body or body part. BSPO:0000079 FBql:00005842 Planarian_Anatomy BSPO:0000079 dorsal region Anatomical region dorsally located on the body or body part. BSPO:wd Anatomical region that overlaps the dorsal and lateral regions of a body or body part. BSPO:0000080 FBql:00005845 dorsolateral region Planarian_Anatomy BSPO:0000080 dorso-lateral region Anatomical region that overlaps the dorsal and lateral regions of a body or body part. BSPO:wd BSPO:0000081 FBql:00005850 Planarian_Anatomy BSPO:0000081 ipsilateral region Anatomical region laterally located on the body or body part. BSPO:0000082 FBql:00005844 Planarian_Anatomy BSPO:0000082 lateral region Anatomical region laterally located on the body or body part. BSPO:wd Anatomical region medially located on the body or body part. BSPO:0000083 FBql:00005847 Planarian_Anatomy BSPO:0000083 medial region Anatomical region medially located on the body or body part. BSPO:wd Anatomical region ventrally located on the body or body part. BSPO:0000084 FBql:00005843 Planarian_Anatomy BSPO:0000084 ventral region Anatomical region ventrally located on the body or body part. BSPO:wd Anatomical region that overlaps the ventral and lateral regions of a body or body part. BSPO:0000085 FBql:00005846 ventrolateral region Planarian_Anatomy BSPO:0000085 This is an example of a composition of two axis positions. ventro-lateral region Anatomical region that overlaps the ventral and lateral regions of a body or body part. BSPO:wd A broad, three dimensional body region, defined in relation to the anteroposterior, dorsoventral or mediolateral axis. BSPO:0000086 FBql:00005873 FMA:9647 Planarian_Anatomy BSPO:0000086 to be merged into CARO anatomical compartment BSPO:0000092 FBql:00005881 Planarian_Anatomy BSPO:0000092 to be merged into CARO anatomical compartment boundary BSPO:0000093 FBcv:0000033 FBql:00005880 Planarian_Anatomy BSPO:0000093 anterior/posterior compartment boundary BSPO:0000094 FBcv:0000034 FBql:00005879 Planarian_Anatomy BSPO:0000094 dorsal/ventral compartment boundary Anatomical region peripherally located on the body or body part. BSPO:0000127 Planarian_Anatomy BSPO:0000127 peripheral region Anatomical region peripherally located on the body or body part. BSPO:wd BSPO:0000128 Planarian_Anatomy BSPO:0000128 axial region An anatomical axis that extends from the center of the body outwards or externally. wasila.dahdul 2013-07-02T11:21:42Z BSPO:0000196 Planarian_Anatomy proximal-distal axis BSPO:0000196 The medial-external axis could apply to a sphere-shaped body. medial-external axis An anatomical axis that extends from the center of the body outwards or externally. BSPO:curators An anatomical axis that is perpendicular to an apical/basal axis or proximal/distal axis and extends from the center of an axis (shoot axis or root in the case of plants) to any point on the exterior of the axis. wasila.dahdul 2013-07-02T11:23:31Z BSPO:0000197 M-R axis MR axis Planarian_Anatomy BSPO:0000197 In plants, lateral growth (http://purl.obolibrary.org/obo/GO_0080190) run is along the medial/radial axis (from medial to radial) [RW]. Also applies to radially symmetrical animals such as sea urchins, cnidarians [PM] or applies to more-or-less cylindrical body parts in animals, like limbs. medial-radial axis An anatomical axis that is perpendicular to an apical/basal axis or proximal/distal axis and extends from the center of an axis (shoot axis or root in the case of plants) to any point on the exterior of the axis. BSPO:curators Anatomical plane that is perpendicular to a radial plane. wasila.dahdul 2014-01-22T15:34:31Z BSPO:0000201 Planarian_Anatomy BSPO:0000201 Need to add logical definitions. tangential plane Anatomical plane that is perpendicular to a radial plane. BSPO:wd Anatomical plane that follows the two dimensions specified by an apical-basal axis relative to direction of growth and a medial-lateral axis. wasila.dahdul 2014-01-22T15:34:02Z BSPO:0000202 Planarian_Anatomy BSPO:0000202 Need to add logical definitions. radial plane Anatomical plane that follows the two dimensions specified by an apical-basal axis relative to direction of growth and a medial-lateral axis. BSPO:wd Anatomical surface that is located on the anterior side of the body or body part. BSPO:0000371 FBql:00005848 Planarian_Anatomy BSPO:0000371 anterior surface Anatomical surface that is located on the anterior side of the body or body part. BSPO:wd Anatomical surface that is located on the posterior side of the body or body part. BSPO:0000372 FBql:00005849 Planarian_Anatomy BSPO:0000372 posterior surface Anatomical surface that is located on the posterior side of the body or body part. BSPO:wd Anatomical surface that is located on the apical side of the body or body part. BSPO:0000373 FBql:00005854 Planarian_Anatomy BSPO:0000373 apical surface Anatomical surface that is located on the apical side of the body or body part. BSPO:wd Anatomical surface that is located on the basal side of the body or body part. BSPO:0000374 FBql:00005855 Planarian_Anatomy BSPO:0000374 basal surface Anatomical surface that is located on the basal side of the body or body part. BSPO:wd Anatomical surface on the side opposite to another structure BSPO:0000376 FBql:00005851 Planarian_Anatomy BSPO:0000376 contralateral surface Anatomical surface that is located on the proximal side of the body or body part. BSPO:0000377 FBql:00005852 Planarian_Anatomy BSPO:0000377 proximal surface Anatomical surface that is located on the proximal side of the body or body part. BSPO:wd Anatomical surface that is located on the distal side of the body or body part. BSPO:0000378 FBql:00005853 Planarian_Anatomy BSPO:0000378 distal surface Anatomical surface that is located on the distal side of the body or body part. BSPO:wd Anatomical surface that located on the dorsal side of the body or body part. BSPO:0000379 FBql:00005842 Planarian_Anatomy BSPO:0000379 dorsal surface Anatomical surface that located on the dorsal side of the body or body part. BSPO:wd Anatomical surface that is located on the same side of an organism or structure. BSPO:0000381 FBql:00005850 Planarian_Anatomy BSPO:0000381 ipsilateral surface Anatomical surface that is located on the same side of an organism or structure. BSPO:wd Anatomical surface that located on the lateral side of the body or body part. BSPO:0000382 FBql:00005844 Planarian_Anatomy BSPO:0000382 lateral surface Anatomical surface that located on the lateral side of the body or body part. BSPO:wd Anatomical surface that located on the medial side of the body or body part. BSPO:0000383 FBql:00005847 Planarian_Anatomy BSPO:0000383 medial surface Anatomical surface that located on the medial side of the body or body part. BSPO:wd Anatomical surface that is located on the ventral side of the body or body part. BSPO:0000384 FBql:00005843 Planarian_Anatomy BSPO:0000384 ventral surface Anatomical surface that is located on the ventral side of the body or body part. BSPO:wd Anatomical margin that is located on the anterior side of a body or body part. BSPO:0000671 Planarian_Anatomy BSPO:0000671 anterior margin Anatomical margin that is located on the anterior side of a body or body part. BSPO:wd Anatomical margin that is located on the posterior side of the body or body part. BSPO:0000672 Planarian_Anatomy BSPO:0000672 posterior margin Anatomical margin that is located on the posterior side of the body or body part. BSPO:wd Anatomical margin that is located on the apical side of the body or body part. BSPO:0000673 Planarian_Anatomy BSPO:0000673 apical margin Anatomical margin that is located on the apical side of the body or body part. BSPO:wd Anatomical margin that is located on the basal side of the body or body part. BSPO:0000674 Planarian_Anatomy BSPO:0000674 basal margin Anatomical margin that is located on the basal side of the body or body part. BSPO:wd Anatomical margin that is located on the proximal region of the body or body part. BSPO:0000677 Planarian_Anatomy BSPO:0000677 proximal margin Anatomical margin that is located on the proximal region of the body or body part. BSPO:wd Anatomical margin that is located on the distal side of the body or body part. BSPO:0000678 Planarian_Anatomy BSPO:0000678 distal margin Anatomical margin that is located on the distal side of the body or body part. BSPO:wd Anatomical margin that is located on the dorsal side of body or body part. BSPO:0000679 Planarian_Anatomy BSPO:0000679 dorsal margin Anatomical margin that is located on the dorsal side of body or body part. BSPO:wd Anatomical margin that is located on the dorso-lateral region of the body or body part. BSPO:0000680 dorsolateral margin Planarian_Anatomy BSPO:0000680 dorso-lateral margin Anatomical margin that is located on the dorso-lateral region of the body or body part. BSPO:wd Anatomical margin that is located on the lateral side of the body or body part. BSPO:0000682 Planarian_Anatomy BSPO:0000682 lateral margin Anatomical margin that is located on the lateral side of the body or body part. BSPO:wd Anatomical margin that is located on the medial side of the body or body part. BSPO:0000683 Planarian_Anatomy BSPO:0000683 medial margin Anatomical margin that is located on the medial side of the body or body part. BSPO:wd Anatomical margin that is located on the ventral side of the body or body part. BSPO:0000684 Planarian_Anatomy BSPO:0000684 ventral margin Anatomical margin that is located on the ventral side of the body or body part. BSPO:wd Anatomical margin that is located on the ventro-lateral region of the body or body part. BSPO:0000685 ventrolateral margin Planarian_Anatomy BSPO:0000685 This is an example of a composition of two axis positions ventro-lateral margin Anatomical margin that is located on the ventro-lateral region of the body or body part. BSPO:wd Anatomical margin that is located on the antero-dorso region of the body or body part. BSPO:0000686 anterodorsal margin Planarian_Anatomy BSPO:0000686 antero-dorsal margin Anatomical margin that is located on the antero-dorso region of the body or body part. BSPO:wd Anatomical margin that is located on the postero-dorsal region of the body or body part. BSPO:0000687 posterodorsal margin Planarian_Anatomy BSPO:0000687 postero-dorsal margin Anatomical margin that is located on the postero-dorsal region of the body or body part. BSPO:wd Anatomical margin that is located on the antero-ventral region of the body or body part. BSPO:0000688 anteroventral margin Planarian_Anatomy BSPO:0000688 antero-ventral margin Anatomical margin that is located on the antero-ventral region of the body or body part. BSPO:wd Anatomical margin that is located on the postero-ventral region of the body or body part. BSPO:0000689 posteroventral margin Planarian_Anatomy BSPO:0000689 postero-ventral margin Anatomical margin that is located on the postero-ventral region of the body or body part. BSPO:wd D0-D2. Zygote and dispersed blastomere cleavage in a yolk syncytium. Days 0-2 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000001 Stage 1 https://planosphere.stowers.org/ontology/PLANA_0000001 D0-D2. Zygote and dispersed blastomere cleavage in a yolk syncytium. Days 0-2 post-egg capsule deposition at 20˚C. PMID:28072387 D2-D3. Sphere formation. A fraction of the blastomeres differentiate into temporary embryonic tissues that provide form and function to the embryo. Undifferentiated blastomeres remain in the embryonic wall. Days 2-3 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000002 Depicted by field contains hematoxylin and eosin staining section of a stage 2 embryo. Scale bar = 100um Stage 2 https://planosphere.stowers.org/ontology/PLANA_0000002 D2-D3. Sphere formation. A fraction of the blastomeres differentiate into temporary embryonic tissues that provide form and function to the embryo. Undifferentiated blastomeres remain in the embryonic wall. Days 2-3 post-egg capsule deposition at 20˚C. PMID:28072387 D2-D4. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity. Days 2-4 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000003 Depicted by field contains hematoxylin and eosin staining section of a stage 3 embryo. Scale bar = 100um Stage 3 https://planosphere.stowers.org/ontology/PLANA_0000003 D2-D4. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity. Days 2-4 post-egg capsule deposition at 20˚C. PMID:28072387 D3-D5. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation. Days 3-5 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000004 Depicted by field contains hematoxylin and eosin staining section of a stage 4 embryo. Scale bar = 100um Stage 4 https://planosphere.stowers.org/ontology/PLANA_0000004 D3-D5. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation. Days 3-5 post-egg capsule deposition at 20˚C. PMID:28072387 D5-D7. Organogenesis onset. Downregulation of early embryo enriched transcripts and birth of adult lineages within the blastomere population. Early embryonic gut formation continues. Yolk ingestion into the gut cavity. Days 5-7 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000005 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo. Scale bar = 100um Stage 5 https://planosphere.stowers.org/ontology/PLANA_0000005 D5-D7. Organogenesis onset. Downregulation of early embryo enriched transcripts and birth of adult lineages within the blastomere population. Early embryonic gut formation continues. Yolk ingestion into the gut cavity. Days 5-7 post-egg capsule deposition at 20˚C. PMID:28072387 D7-D9. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation. Days 7-9 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000006 Depicted by field contains hematoxylin and eosin staining section of a stage 6 embryo. Scale bar = 100um Stage 6 https://planosphere.stowers.org/ontology/PLANA_0000006 D7-D9. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation. Days 7-9 post-egg capsule deposition at 20˚C. PMID:28072387 D9-D11. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility. Days 9-11 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000007 Depicted by field contains hematoxylin and eosin staining section of a stage 7 embryo. Scale bar = 100um Stage 7 https://planosphere.stowers.org/ontology/PLANA_0000007 D9-D11. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility. Days 9-11 post-egg capsule deposition at 20˚C. PMID:28072387 D13-D15. Organogenesis and organ maturation continues. Hatching. Days 13-15 post-egg capsule deposition at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000008 Depicted by field contains hematoxylin and eosin staining section of a stage 8 embryo. Scale bar = 100um Stage 8 https://planosphere.stowers.org/ontology/PLANA_0000008 D13-D15. Organogenesis and organ maturation continues. Hatching. Days 13-15 post-egg capsule deposition at 20˚C. PMID:28072387 A heterogeneous subpopulation of neoblasts with enriched expression of SoxP-1 and SoxP-2 thought to contain both pluripotent stem cells and tissue-specific progenitors. Planarian_Anatomy PLANA:0000009 sigma neoblast https://planosphere.stowers.org/ontology/PLANA_0000009 A heterogeneous subpopulation of neoblasts with enriched expression of SoxP-1 and SoxP-2 thought to contain both pluripotent stem cells and tissue-specific progenitors. PMID:25017721 Neoblasts and post-mitotic, differentiating daughters coexpressing POU2-3, six1/2-2, Sal1, Eya and Osr, required for maintenance and regeneration of protonephridial cell types. Planarian_Anatomy PLANA:0000011 protonephridial progenitor https://planosphere.stowers.org/ontology/PLANA_0000011 Neoblasts and post-mitotic, differentiating daughters coexpressing POU2-3, six1/2-2, Sal1, Eya and Osr, required for maintenance and regeneration of protonephridial cell types. PMID:21937596 Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system. Planarian_Anatomy PLANA:0000012 neural progenitor https://planosphere.stowers.org/ontology/PLANA_0000012 Musculature surrounding internal organs of the body. Erin Davies Planarian_Anatomy PLANA:0000013 visceral musculature https://planosphere.stowers.org/ontology/PLANA_0000013 Musculature surrounding internal organs of the body. PMID: 26904543 An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s). Planarian_Anatomy PLANA:0000014 zeta neoblast https://planosphere.stowers.org/ontology/PLANA_0000014 An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s). PMID:25017721 An epithelial cell lacking cilia. Planarian_Anatomy PLANA:0000015 non ciliated epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000015 A plicate and protrusible organ that is the sole point of entry and exit for the Triclad gut. It contains epithelial, muscular, secretory and neuronal cell types. Planarian_Anatomy PLANA:0000016 definitive pharynx https://planosphere.stowers.org/ontology/PLANA_0000016 A plicate and protrusible organ that is the sole point of entry and exit for the Triclad gut. It contains epithelial, muscular, secretory and neuronal cell types. OCLC:16809160 Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain. Planarian_Anatomy PLANA:0000017 photoreceptor neuron https://planosphere.stowers.org/ontology/PLANA_0000017 Bipolar photoreceptor neurons with dendritic projections into the optic cup and axons that innervate the underlying brain. PMID:21852957 PMID:22884275 Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells. Planarian_Anatomy PLANA:0000018 Category 4 cell https://planosphere.stowers.org/ontology/PLANA_0000018 Post-mitotic, mesenchymally and epidermally located progenitors downstream of the Category 3 cells. PMID:25017721 PMID:26457503 Progenitor neoblasts implicated in the maintenance and regeneration of muscle fibers. Planarian_Anatomy PLANA:0000019 muscle progenitor https://planosphere.stowers.org/ontology/PLANA_0000019 Progenitor neoblasts implicated in the maintenance and regeneration of muscle fibers. PMID:25017721 Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct. Planarian_Anatomy PLANA:0000020 protonephridia https://planosphere.stowers.org/ontology/PLANA_0000020 Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct. OCLC:16809160 PMID:21828097 PMID:26057828 Organisms sharing a specified genotype or karyotype. Planarian_Anatomy PLANA:0000021 biotype https://planosphere.stowers.org/ontology/PLANA_0000021 Post-mitotic, ciliated epidermal cells. Planarian_Anatomy PLANA:0000022 Category 5 cell https://planosphere.stowers.org/ontology/PLANA_0000022 Post-mitotic, ciliated epidermal cells. PMID:25017721 An innervated, muscular pump that ingests yolk cells into the gut cavity. The temporary embryonic pharynx is an extraembryonic tissue that forms during Stage 2, functions during Stages 3-5, and degenerates during Stages 6-7. PMID:28072387 Planarian_Anatomy PLANA:0000023 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo with anatomical feature noted with black indicators. temporary embryonic pharynx https://planosphere.stowers.org/ontology/PLANA_0000023 Obligate asexual animals that reproduce solely through fission followed by whole body regeneration. Asexual Smed are stable diploids that harbor a chromosome translocation, making them karyotypically distinct from sexual Smed. Planarian_Anatomy PLANA:0000024 Smed asexual biotype https://planosphere.stowers.org/ontology/PLANA_0000024 Obligate asexual animals that reproduce solely through fission followed by whole body regeneration. Asexual Smed are stable diploids that harbor a chromosome translocation, making them karyotypically distinct from sexual Smed. PMID:11972158 The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organisms, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. UBERON:0001016 Planarian_Anatomy PLANA:0000025 nervous system https://planosphere.stowers.org/ontology/PLANA_0000025 The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organisms, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. UBERON:0001016 The planarian triclad gut contains a central anterior gut branch connected to two posterior gut branches arranged around the definitive pharynx. Secondary gut branches extend laterally from the primary gut branches, while tertiary gut branches extend from the secondary branches. Food and waste enter and exit the definitive gut through the defintive pharynx. Planarian_Anatomy PLANA:0000026 definitive gut https://planosphere.stowers.org/ontology/PLANA_0000026 The planarian triclad gut contains a central anterior gut branch connected to two posterior gut branches arranged around the definitive pharynx. Secondary gut branches extend laterally from the primary gut branches, while tertiary gut branches extend from the secondary branches. Food and waste enter and exit the definitive gut through the defintive pharynx. PMID:21664348 Cross-fertilizing hemaphrodites that reproduce sexually and do not undergo fission. After mating, each parent lays an egg capsule containing one or more embryos. Sexual Smed are stable diploids. Planarian_Anatomy PLANA:0000027 Smed sexual biotype https://planosphere.stowers.org/ontology/PLANA_0000027 Cross-fertilizing hemaphrodites that reproduce sexually and do not undergo fission. After mating, each parent lays an egg capsule containing one or more embryos. Sexual Smed are stable diploids. PMID:11972158 Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts. Planarian_Anatomy PLANA:0000028 Category 2 cell https://planosphere.stowers.org/ontology/PLANA_0000028 Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts. PMID:18786419 PMID:20040488 PMID:22385657 PMID:25017721 PMID:26114597 A single cell layer of extraembryonic, post-mitotic ectodermal cells bounding the embryo. The primitive ectoderm forms during Stage 2 and is thought to degenerate as the definitive epidermis forms during Stages 5-7. Planarian_Anatomy PLANA:0000029 primitive ectoderm https://planosphere.stowers.org/ontology/PLANA_0000029 A single cell layer of extraembryonic, post-mitotic ectodermal cells bounding the embryo. The primitive ectoderm forms during Stage 2 and is thought to degenerate as the definitive epidermis forms during Stages 5-7. OCLC:20423827 OCLC:464776945 OCLC:82522822 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md The median line/ plane of bilateral symmetry along the anteroposterior axis. edge Planarian_Anatomy PLANA:0000030 midline https://planosphere.stowers.org/ontology/PLANA_0000030 Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup. Planarian_Anatomy PLANA:0000031 pigment cup cell https://planosphere.stowers.org/ontology/PLANA_0000031 Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup. PMID:21852957 PMID:22884275 The median line/ plane of bilateral symmetry along the anteroposterior axis on the dorsal surface of the animal. Planarian_Anatomy PLANA:0000032 dorsal midline https://planosphere.stowers.org/ontology/PLANA_0000032 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 https://planosphere.stowers.org/ontology/PLANA_0000033 Mitotically active zeta neoblasts and their post-mitotic descendants which undergo progressive differentiation and outward directed movement through the mesenchyme prior to incorporation into the epidermis, where terminal differentiation occurs. PMID:18786419 PMID:20040488 PMID:22385657 PMID:25017721 PMID:26114597 PMID:26457503 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 https://planosphere.stowers.org/ontology/PLANA_0000034 A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal. OCLC:16809160 Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells. Planarian_Anatomy PLANA:0000035 Category 3 cell https://planosphere.stowers.org/ontology/PLANA_0000035 Post-mitotic, mesenchymally located epidermal progenitors downstream of the Category 2 cells. PMID:18786419 PMID:20040488 PMID:26114597 PMID:26457503 An organ that detects light. UBERON:0000970 Planarian_Anatomy PLANA:0000036 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The eyes are indicated by arrows. Scale bar = 250um eye https://planosphere.stowers.org/ontology/PLANA_0000036 Adult tissues built during organogenesis that are present in juveniles at birth. Planarian_Anatomy PLANA:0000037 definitive tissue https://planosphere.stowers.org/ontology/PLANA_0000037 Adult tissues built during organogenesis that are present in juveniles at birth. PMID:28072387 PMID:2888018 The median line/ plane of bilateral symmetry along the anteroposterior axis on the ventral surface of the animal. Planarian_Anatomy PLANA:0000038 ventral midline https://planosphere.stowers.org/ontology/PLANA_0000038 An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut. Planarian_Anatomy PLANA:0000039 gamma neoblast https://planosphere.stowers.org/ontology/PLANA_0000039 An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut. PMID:25017721 A stage of embryonic development defined by a unique gene expression signature, morphology and chronological time post-egg capsule deposition for hermaphrodites reared at 20˚C. Schmidtea_mediterranea_Developmental_Stages PLANA:0000040 Schmidtea mediterranea developmental stage https://planosphere.stowers.org/ontology/PLANA_0000040 A stage of embryonic development defined by a unique gene expression signature, morphology and chronological time post-egg capsule deposition for hermaphrodites reared at 20˚C. PMID:28072387 Stage 3-5 embryo hemisphere centered around the pole opposite the temporary embryonic pharynx. Planarian_Anatomy PLANA:0000041 aboral hemisphere https://planosphere.stowers.org/ontology/PLANA_0000041 Stage 3-5 embryo hemisphere centered around the pole opposite the temporary embryonic pharynx. PMID:28072387 The single, central gut branch of the triclad gut anterior to the definitive pharynx. Planarian_Anatomy PLANA:0000042 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. Anterior primary gut branch indicated by arrows. Scale bar = 250um anterior primary gut branch https://planosphere.stowers.org/ontology/PLANA_0000042 The single, central gut branch of the triclad gut anterior to the definitive pharynx. PMID:21664348 Region along the edge of the animal where the dorsal and ventral surfaces meet. edge Planarian_Anatomy PLANA:0000043 dorsoventral margin https://planosphere.stowers.org/ontology/PLANA_0000043 The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head. brain Planarian_Anatomy PLANA:0000044 cephalic ganglia https://planosphere.stowers.org/ontology/PLANA_0000044 The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head. OCLC:16809160 PMID:17999079 Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema. Planarian_Anatomy PLANA:0000045 circular muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000045 Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md Pluripotent piwi-1+ stem cells that self-renew, form expanding colonies and produce differentiating daughters that contribute to multiple organ systems. cNeoblasts are predicted to be broadly distributed across the anteroposterior axis of the adult worm. Planarian_Anatomy PLANA:0000046 clonogenic neoblast https://planosphere.stowers.org/ontology/PLANA_0000046 Pluripotent piwi-1+ stem cells that self-renew, form expanding colonies and produce differentiating daughters that contribute to multiple organ systems. cNeoblasts are predicted to be broadly distributed across the anteroposterior axis of the adult worm. PMID:21566185 Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis. collection duct Planarian_Anatomy PLANA:0000047 collecting duct https://planosphere.stowers.org/ontology/PLANA_0000047 Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis. PMID:26057828 Body wall muscle fibers arrayed diagonally along the anteroposterior axis. Planarian_Anatomy PLANA:0000048 diagonal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000048 Body wall muscle fibers arrayed diagonally along the anteroposterior axis. PMID:26904543 Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. UBERON:0001007 Planarian_Anatomy PLANA:0000049 digestive system https://planosphere.stowers.org/ontology/PLANA_0000049 Embryonic development producing juvenile animals with body plans and feeding behavior similar to adults. Juveniles grow and mature into adults without undergoing metamorphosis. Schmidtea_mediterranea_Developmental_Terms PLANA:0000051 direct development https://planosphere.stowers.org/ontology/PLANA_0000051 Embryonic development producing juvenile animals with body plans and feeding behavior similar to adults. Juveniles grow and mature into adults without undergoing metamorphosis. PMID: 12888018 A derived form of early embryonic cleavage present in ectolecithal embryos. Blastomeres divide asynchronously within a yolk syncytium, and division progeny do not remain in direct contact with one another. Schmidtea_mediterranea_Developmental_Terms PLANA:0000052 dispersed cleavage https://planosphere.stowers.org/ontology/PLANA_0000052 A derived form of early embryonic cleavage present in ectolecithal embryos. Blastomeres divide asynchronously within a yolk syncytium, and division progeny do not remain in direct contact with one another. OCLC:20423827 OCLC:42792751 OCLC:464776945 OCLC:82522822 PMID:15599763 PMID:19197510 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells. Planarian_Anatomy PLANA:0000053 distal tubule https://planosphere.stowers.org/ontology/PLANA_0000053 Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells. PMID:21828097 Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe. Planarian_Anatomy PLANA:0000054 dorsal epidermis https://planosphere.stowers.org/ontology/PLANA_0000054 Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe. OCLC:16809160 Ciliated epithelial cells along the dorsal midline. racing stripe Planarian_Anatomy PLANA:0000055 dorsal stripe https://planosphere.stowers.org/ontology/PLANA_0000055 Ciliated epithelial cells along the dorsal midline. PMID: 17553481 Turbellarian (freshwater flatworm) embryos that undergo a modified form of cleavage due to separation of oocyte and yolk. Yolk is not contained within oocytes, and is produced by somatic vitellogenic gland cells. Schmidtea_mediterranea_Developmental_Terms PLANA:0000056 ectolecithal embryo https://planosphere.stowers.org/ontology/PLANA_0000056 Turbellarian (freshwater flatworm) embryos that undergo a modified form of cleavage due to separation of oocyte and yolk. Yolk is not contained within oocytes, and is produced by somatic vitellogenic gland cells. PMID:22074376 PMID:27149082 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000002.md The first few specialized divisions of an activated animal egg. GO:0040016 Schmidtea_mediterranea_Developmental_Terms PLANA:0000057 embryonic cleavage https://planosphere.stowers.org/ontology/PLANA_0000057 A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the temporary embryonic pharynx and primitive gut cells. Embryonic gut cells, likely produced from blastomeres, form a phagocytic tissue layer surrounding the inner gut cavity during Stages 4-6. It is not known whether the embryonic gut is temporary embryonic tissue or a definitive tissue. For convenience, the embryonic gut is currently designated as an extraembryonic structure because cell type specific markers for the embryonic gut do not stain the definitive gut in hatchlings or adult animals. Planarian_Anatomy PLANA:0000058 embryonic digestive system https://planosphere.stowers.org/ontology/PLANA_0000058 A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the temporary embryonic pharynx and primitive gut cells. Embryonic gut cells, likely produced from blastomeres, form a phagocytic tissue layer surrounding the inner gut cavity during Stages 4-6. It is not known whether the embryonic gut is temporary embryonic tissue or a definitive tissue. For convenience, the embryonic gut is currently designated as an extraembryonic structure because cell type specific markers for the embryonic gut do not stain the definitive gut in hatchlings or adult animals. PMID:28072387 Dispersed, phagocytic gut cells that appear during Stage 4 and ultimately generate a honeycomb-like lattice surrounding the central gut cavity in Stage 5 embryos. Early embryonic gut cell specific transcripts are expressed from Stage 4-6, and are downregulated during Stage 7. Planarian_Anatomy PLANA:0000059 embryonic gut cell https://planosphere.stowers.org/ontology/PLANA_0000059 Dispersed, phagocytic gut cells that appear during Stage 4 and ultimately generate a honeycomb-like lattice surrounding the central gut cavity in Stage 5 embryos. Early embryonic gut cell specific transcripts are expressed from Stage 4-6, and are downregulated during Stage 7. PMID:28072387 The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos. Planarian_Anatomy PLANA:0000060 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo with anatomical feature noted with black indicators. embryonic wall https://planosphere.stowers.org/ontology/PLANA_0000060 The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos. OCLC:16809160 PMID:12888018 Visceral muscle surrounding the definitive gut. Planarian_Anatomy PLANA:0000061 enteric musculature https://planosphere.stowers.org/ontology/PLANA_0000061 Visceral muscle surrounding the definitive gut. PMID: 26904543 Attachment between the triclad gut and the proximal end of the definitive pharynx. Planarian_Anatomy PLANA:0000062 esophagus https://planosphere.stowers.org/ontology/PLANA_0000062 Attachment between the triclad gut and the proximal end of the definitive pharynx. PMID: 24737865 OCLC:16809160 A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. UBERON:0000478 Planarian_Anatomy PLANA:0000063 extraembryonic structure https://planosphere.stowers.org/ontology/PLANA_0000063 Terminal structure of protonephridia unit; consists of flame cells. Planarian_Anatomy PLANA:0000064 flame bulb https://planosphere.stowers.org/ontology/PLANA_0000064 Terminal structure of protonephridia unit; consists of flame cells. PMID:21828097 PMID:26057828 Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the ‘filtration weir’, which consists of closely apposed strands of cytoplasm surrounding a central cilia bundle, and by numerous microvilli between weir and cilia. Positive for acetyated tubulin. Planarian_Anatomy PLANA:0000065 flame cell https://planosphere.stowers.org/ontology/PLANA_0000065 Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the ‘filtration weir’, which consists of closely apposed strands of cytoplasm surrounding a central cilia bundle, and by numerous microvilli between weir and cilia. Positive for acetyated tubulin. OCLC:16809160 PMID:21828097 PMID:26057828 The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle. Planarian_Anatomy PLANA:0000066 gastrodermis https://planosphere.stowers.org/ontology/PLANA_0000066 The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle. PMID:21664348 Secretory cells that release digestive enzymes into the lumen of the intestine. Planarian_Anatomy PLANA:0000067 goblet cell https://planosphere.stowers.org/ontology/PLANA_0000067 Secretory cells that release digestive enzymes into the lumen of the intestine. PMID:21664348 Lumen of embryonic digestive tract, prior to formation of the branched defintive gut. Planarian_Anatomy PLANA:0000068 embryonic gut cavity https://planosphere.stowers.org/ontology/PLANA_0000068 Lumen of embryonic digestive tract, prior to formation of the branched defintive gut. PMID:28072387 Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole. Planarian_Anatomy PLANA:0000069 inner longitudinal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000069 Inner most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thicker than the outer longitudinal muscle fibers. The pattern of these muscles differs along the dorsoventral axis, with the dorsal arrangement converging at the central zone of the anterior pole. The ventral arrangement is more parallel or may diverge slightly as it approaches the ventral pole. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md Absorptive digestive cells that engulf food particles for intracellular digestion. Planarian_Anatomy PLANA:0000070 intestinal phagocyte https://planosphere.stowers.org/ontology/PLANA_0000070 Absorptive digestive cells that engulf food particles for intracellular digestion. PMID:21664348 Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers. Planarian_Anatomy PLANA:0000071 longitudinal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000071 Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md The sole point of entry and exit for the Triclad planarian flatworm gut. The mouth is connected to the pharyngeal pouch to allow for exit and re-entry of the definitive pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells. Manus Planarian_Anatomy PLANA:0000072 mouth https://planosphere.stowers.org/ontology/PLANA_0000072 The sole point of entry and exit for the Triclad planarian flatworm gut. The mouth is connected to the pharyngeal pouch to allow for exit and re-entry of the definitive pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells. OCLC:16809160 Manus https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000006.md A female germ cell that has entered meiosis. CL:0000023 Planarian_Anatomy PLANA:0000074 oocyte https://planosphere.stowers.org/ontology/PLANA_0000074 A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons. Planarian_Anatomy PLANA:0000075 optic cup https://planosphere.stowers.org/ontology/PLANA_0000075 A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons. PMID:21852957 PMID:22884275 Stage 3-5 embryo hemisphere centered around the temporary embryonic pharynx. Planarian_Anatomy PLANA:0000076 oral hemisphere https://planosphere.stowers.org/ontology/PLANA_0000076 Stage 3-5 embryo hemisphere centered around the temporary embryonic pharynx. PMID:28072387 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 https://planosphere.stowers.org/ontology/PLANA_0000077 Outer most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thinner than the inner longitudinal muscle fibers. Planarian_Anatomy PLANA:0000078 outer longitudinal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000078 Outer most body wall muscle fibers arrayed along the anteroposterior axis. These fibers are thinner than the inner longitudinal muscle fibers. PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md Dorsal-ventral muscle fibers present through the mesenchyme. dorsoventral muscle fibers Planarian_Anatomy PLANA:0000079 The depicted by field is a hemotoxylin and eosin stained sagittal section with the dorsal side up and anterior to the right. The parenchymal musculature, or dorsal ventral muscle fibers are the periodic vertical strands apparent in the middle of the image. Scale bar is 200um. parenchymal musculature https://planosphere.stowers.org/ontology/PLANA_0000079 Dorsal-ventral muscle fibers present through the mesenchyme. OCLC:16809160 A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. UBERON:0000010 Planarian_Anatomy PLANA:0000080 peripheral nervous system https://planosphere.stowers.org/ontology/PLANA_0000080 An epithelial structure housing the definitive pharynx, connected to the esophagus and mouth. Planarian_Anatomy PLANA:0000081 pharyngeal pouch https://planosphere.stowers.org/ontology/PLANA_0000081 An epithelial structure housing the definitive pharynx, connected to the esophagus and mouth. OCLC:16809160 Ciliated epidermal cells located along the dorsal midline. Planarian_Anatomy PLANA:0000082 racing stripe https://planosphere.stowers.org/ontology/PLANA_0000082 Ciliated epidermal cells located along the dorsal midline. PMID: 17553481 The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch. Planarian_Anatomy PLANA:0000084 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The posterior primary gut branch is indicated by arrows. Scale bar = 250um posterior primary gut branch https://planosphere.stowers.org/ontology/PLANA_0000084 The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch. PMID:21664348 Four large phagocytic cells associated with the temporary embryonic pharynx. Planarian_Anatomy PLANA:0000085 primitive gut cell https://planosphere.stowers.org/ontology/PLANA_0000085 Four large phagocytic cells associated with the temporary embryonic pharynx. PMID:28072387 Stage 2 embryo undergoing the process of sphere formation. Schmidtea_mediterranea_Developmental_Terms PLANA:0000086 protosphere https://planosphere.stowers.org/ontology/PLANA_0000086 Stage 2 embryo undergoing the process of sphere formation. PMID:28072387 Ciliated epithelial cells form tubules, generating coiled, branching units terminating in flame bulbs. Tubules are formed via intercellular junctions between two epithelial cells. Proximal tubules are connected to non-ciliated distal tubules within the parenchyma. Planarian_Anatomy PLANA:0000087 proximal tubule https://planosphere.stowers.org/ontology/PLANA_0000087 Ciliated epithelial cells form tubules, generating coiled, branching units terminating in flame bulbs. Tubules are formed via intercellular junctions between two epithelial cells. Proximal tubules are connected to non-ciliated distal tubules within the parenchyma. PMID:21828097 The renal system is an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. UBERON:0001008 Planarian_Anatomy PLANA:0000088 renal system https://planosphere.stowers.org/ontology/PLANA_0000088 Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge. Planarian_Anatomy PLANA:0000089 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The secondary gut branch is indicated by arrows. Scale bar = 250um secondary gut branch https://planosphere.stowers.org/ontology/PLANA_0000089 Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge. PMID:21664348 A mature male germ cell that develops from a spermatid. CL:0000019 spermatozoa Planarian_Anatomy PLANA:0000090 sperm https://planosphere.stowers.org/ontology/PLANA_0000090 Generation of a multilayered spherical embryo comprised of temporary extraembryonic tissues and undifferentiated blastomeres. Schmidtea_mediterranea_Developmental_Terms PLANA:0000091 sphere formation https://planosphere.stowers.org/ontology/PLANA_0000091 Generation of a multilayered spherical embryo comprised of temporary extraembryonic tissues and undifferentiated blastomeres. OCLC:20423827 OCLC:464776945 PMID:12888018 PMID:15599763 PMID:28072387 Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2. Schmidtea_mediterranea_Developmental_Terms PLANA:0000092 syncytial yolk cell https://planosphere.stowers.org/ontology/PLANA_0000092 Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2. PMID:15599763 Gut branches originating from and connected to the secondary gut branches. Planarian_Anatomy PLANA:0000093 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The tertiary gut branch indicated is by arrows. Scale bar = 250um tertiary gut branch https://planosphere.stowers.org/ontology/PLANA_0000093 Gut branches originating from and connected to the secondary gut branches. PMID:21664348 The process in which the anatomical structures of a tissue are generated and organized. GO:0048729 Schmidtea_mediterranea_Developmental_Terms PLANA:0000094 tissue morphogenesis https://planosphere.stowers.org/ontology/PLANA_0000094 Ovo+ neoblasts and post-mitotic eye progenitors that simultaneously migrate and differentiate into photoreceptor neurons and non-neuronal pigment cup cells comprising the optic cup. Planarian_Anatomy PLANA:0000095 trail cell https://planosphere.stowers.org/ontology/PLANA_0000095 Ovo+ neoblasts and post-mitotic eye progenitors that simultaneously migrate and differentiate into photoreceptor neurons and non-neuronal pigment cup cells comprising the optic cup. PMID:22884275 Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells Planarian_Anatomy PLANA:0000096 ventral epidermis https://planosphere.stowers.org/ontology/PLANA_0000096 The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO]. A cluster of neurons that extends posteriorly from the embryonic and larval brain and is surrounded by a connective tissue sheath. The ventral nerve cords make up the nervous system of some phyla of the invertebrates, particularly within the nematodes, annelids and the arthropods. It usually consists of cerebral ganglia anteriorly with the nerve cords running down the ventral ('belly', as opposed to back) plane of the organism. This characteristic is important in qualifying the difference compared to the chordates, which have a dorsal nerve cord. Ventral nerve cords from anterior to posterior (the thoracic and abdominal tagma in the arthropods) are made up of segmented ganglia that are connected by a tract of nerve fibers passing from one side to the other of the nerve cord called commissures. The complete system bears some likeness to a rope ladder. In some animals the bilateral ganglia are fused into a single large ganglion per segment. This characteristic is found mostly in the insects. BTO:0002328 EFO:0000896 FBbt:00001102 MAT:0000339 MIAA:0000339 UBERON:0000934 WBbt:0005829 http://en.wikipedia.org/wiki/Ventral_nerve_cord nlx:146329 ventral cord Planarian_Anatomy PLANA:0000097 ventral nerve cord https://planosphere.stowers.org/ontology/PLANA_0000097 Diploid cell produced by the fusion of sperm cell nucleus and egg cell. CL:0000365 Planarian_Anatomy PLANA:0000098 zygote https://planosphere.stowers.org/ontology/PLANA_0000098 The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. neural cell CL:0000540 Planarian_Anatomy PLANA:0000099 neuron https://planosphere.stowers.org/ontology/PLANA_0000099 A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where the apical part is directed towards the lumen and the basal part to the basal lamina. CL:0000066 Planarian_Anatomy PLANA:0000100 epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000100 A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. CL:0000187 Planarian_Anatomy PLANA:0000101 muscle cell https://planosphere.stowers.org/ontology/PLANA_0000101 A subdivision of an anatomical compartment. Planarian_Anatomy PLANA:0000102 anatomical compartment subdivision https://planosphere.stowers.org/ontology/PLANA_0000102 The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. UBERON:0001017 Planarian_Anatomy PLANA:0000103 central nervous system https://planosphere.stowers.org/ontology/PLANA_0000103 Straight or curved rod-like structures within the epidermal cells, oriented with long axis at right angles to the epidermal surface, that are discharged into mucous secretions. Planarian_Anatomy PLANA:0000104 rhabdite https://planosphere.stowers.org/ontology/PLANA_0000104 Straight or curved rod-like structures within the epidermal cells, oriented with long axis at right angles to the epidermal surface, that are discharged into mucous secretions. OCLC:16809160 A cell that specializes in controlled release of one or more substances. CL:0000151 Planarian_Anatomy PLANA:0000105 secretory cell https://planosphere.stowers.org/ontology/PLANA_0000105 An epithelial cell that has cilia. CL:0000067 Planarian_Anatomy PLANA:0000106 ciliated epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000106 An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo. CL:0000428 Planarian_Anatomy PLANA:0000107 yolk cell https://planosphere.stowers.org/ontology/PLANA_0000107 An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo. PMID:27149082 Feature of an organism that is a subdivision of a local region. For example, the anterior pole is a subdivision of the head. Planarian_Anatomy PLANA:0000109 anatomical compartment subdivision feature https://planosphere.stowers.org/ontology/PLANA_0000109 foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the definitive pharynx. Planarian_Anatomy PLANA:0000110 definitive pharynx progenitor https://planosphere.stowers.org/ontology/PLANA_0000110 foxA1+ neoblasts and their post-mitotic, differentiating daughters required for maintenance and regeneration of the definitive pharynx. PMID:24737865 PMID:25254346 Ciliated epithelial cells that assemble into proximal tubules. Planarian_Anatomy PLANA:0000111 proximal tubule epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000111 Ciliated epithelial cells that assemble into proximal tubules. PMID:21828097 A term used to describe a developmental process during Schmidtea mediterranea embryogenesis. Schmidtea_mediterranea_Developmental_Terms PLANA:0000112 Schmidtea mediterranea developmental term https://planosphere.stowers.org/ontology/PLANA_0000112 A term used to describe a developmental process during Schmidtea mediterranea embryogenesis. https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000000.md Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. Planarian_Anatomy PLANA:0000113 tissue https://planosphere.stowers.org/ontology/PLANA_0000113 Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. UBERON:0000479 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000000.md Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. UBERON:0000467 Planarian_Anatomy PLANA:0000114 anatomical system https://planosphere.stowers.org/ontology/PLANA_0000114 Nonciliated epithelial cells that assemble into protonephridial proximal tubules. Planarian_Anatomy PLANA:0000115 distal tubule epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000115 Nonciliated epithelial cells that assemble into protonephridial proximal tubules. PMID:21828097 Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. UBERON:0000922 Planarian_Anatomy PLANA:0000116 embryo https://planosphere.stowers.org/ontology/PLANA_0000116 Anatomical structure that is part of an embryo. UBERON:0002050 Planarian_Anatomy PLANA:0000117 embryonic structure https://planosphere.stowers.org/ontology/PLANA_0000117 Nonciliated epithelial cells that assemble into collecting ducts. Planarian_Anatomy PLANA:0000118 collecting duct epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000118 Nonciliated epithelial cells that assemble into collecting ducts. PMID:26057828 A post-mitotic, terminally differentiated cell type found in planarian embryos, juveniles and/or adult animals. Planarian_Anatomy PLANA:0000119 terminally differentiated cell https://planosphere.stowers.org/ontology/PLANA_0000119 A cycling neoblast and/or post-mitotic cell that is primed or irreversibly committed to a tissue-specific differentation program precursor cell Planarian_Anatomy PLANA:0000120 progenitor cell https://planosphere.stowers.org/ontology/PLANA_0000120 A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. CL:0000034 Planarian_Anatomy PLANA:0000121 stem cell https://planosphere.stowers.org/ontology/PLANA_0000121 A mature sexual reproductive cell having a single set of unpaired chromosomes. CL:0000300 Planarian_Anatomy PLANA:0000122 gamete https://planosphere.stowers.org/ontology/PLANA_0000122 A cell of the embryo. CL:0002321 Planarian_Anatomy PLANA:0000123 embryonic cell https://planosphere.stowers.org/ontology/PLANA_0000123 The sensory system subserving the sense of vision. UBERON:0002104 Planarian_Anatomy PLANA:0000124 visual system https://planosphere.stowers.org/ontology/PLANA_0000124 Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. UBERON:0001032 Planarian_Anatomy PLANA:0000125 sensory system https://planosphere.stowers.org/ontology/PLANA_0000125 Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. UBERON:0001032 Anatomical system that has as its parts the organs concerned with reproduction. UBERON:0000990 Planarian_Anatomy PLANA:0000126 reproductive system https://planosphere.stowers.org/ontology/PLANA_0000126 Ciliated epithelial cells that assemble into the oviduct. Planarian_Anatomy PLANA:0000127 oviduct epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000127 Ciliated epithelial cells that assemble into the oviduct. PMID:22074376 Ciliated epithelial cells comprising the sperm ducts. Planarian_Anatomy PLANA:0000128 sperm duct epithelial cell https://planosphere.stowers.org/ontology/PLANA_0000128 Ciliated epithelial cells comprising the sperm ducts. PMID:19022767 PMID:22074376 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 https://planosphere.stowers.org/ontology/PLANA_0000129 piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers. Planarian_Anatomy PLANA:0000130 circular muscle progenitor cell https://planosphere.stowers.org/ontology/PLANA_0000130 piwi-1+, nkx1-1+ progenitor neoblasts required for specification of circular muscle fibers. PMID:29168507 Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue. UBERON:0001048 Planarian_Anatomy PLANA:0000131 primordium https://planosphere.stowers.org/ontology/PLANA_0000131 The production of haploid germ cells from diploid precursor cells through meiosis. Schmidtea_mediterranea_Developmental_Terms PLANA:0000132 gametogenesis https://planosphere.stowers.org/ontology/PLANA_0000132 The production of haploid germ cells from diploid precursor cells through meiosis. PMID: 19022767 A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. mechanoreceptor Planarian_Anatomy PLANA:0000133 mechanoreceptor cell https://planosphere.stowers.org/ontology/PLANA_0000133 A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. PMID: 7466176 PMID: 18202849 piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers. Planarian_Anatomy PLANA:0000134 longitudinal muscle progenitor cell https://planosphere.stowers.org/ontology/PLANA_0000134 piwi-1+, myoD+, snail-1+ progenitor neoblasts required for specification and creation of longitudinal muscle fibers. PMID:29168507 Definition forthcoming Planarian_Anatomy PLANA:0000135 female primordial germ cell https://planosphere.stowers.org/ontology/PLANA_0000135 The passageway connecting the gonopore to the bursa (genital atrium). Part of the copulatory apparatus. During mating, sperm from a partner is deposited into the bursal canal, where it collects in the bursa before travelling up the oviducts to the bursa. Egg capsules pass through the bursal canal as they are laid through the gonopore. Planarian_Anatomy PLANA:0000201 bursal canal https://planosphere.stowers.org/ontology/PLANA_0000201 The passageway connecting the gonopore to the bursa (genital atrium). Part of the copulatory apparatus. During mating, sperm from a partner is deposited into the bursal canal, where it collects in the bursa before travelling up the oviducts to the bursa. Egg capsules pass through the bursal canal as they are laid through the gonopore. PMID:22074376 The gonopore, a component of the copulatory apparatus, is an opening located on the ventral side of the animal posterior to the definitive pharynx. The gonopore is the sole point of exit and entry for the reproductive system, allowing from reciprocal exchange of sperm during copulation and egg capsule laying. genital pore Planarian_Anatomy PLANA:0000203 gonopore https://planosphere.stowers.org/ontology/PLANA_0000203 The gonopore, a component of the copulatory apparatus, is an opening located on the ventral side of the animal posterior to the definitive pharynx. The gonopore is the sole point of exit and entry for the reproductive system, allowing from reciprocal exchange of sperm during copulation and egg capsule laying. PMID:22074376 A gonad containing female germline stem cells which fuel oocyte production. Two ovaries are located ventally, underneath the body wall musculature, immediately posterior to the cephalic ganglia (brain) and adjacent to the ventral nerve cords. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuel formation of the ovaries during juvenile development. Planarian_Anatomy PLANA:0000204 ovary https://planosphere.stowers.org/ontology/PLANA_0000204 A gonad containing female germline stem cells which fuel oocyte production. Two ovaries are located ventally, underneath the body wall musculature, immediately posterior to the cephalic ganglia (brain) and adjacent to the ventral nerve cords. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuel formation of the ovaries during juvenile development. PMID:17376870 Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium. Planarian_Anatomy PLANA:0000205 oviduct https://planosphere.stowers.org/ontology/PLANA_0000205 Ciliated tubes adjacent to the ventral nerve cords, adjoining the tuba and the bursal canal, that transport fertilized oocytes to the genital atrium. PMID:22074376 A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal. Planarian_Anatomy PLANA:0000206 penis papilla https://planosphere.stowers.org/ontology/PLANA_0000206 A rounded protuberance, connected to the seminal vesicles, responsible for transferring semen into a mating partner's bursal canal. PMID:22074376 A network of tubes that transport sperm from the testes to the seminal vesicles. Tubes connect each testis to ducts that run along the ventral nerve cords. The ducts bifurcate immediately posterior to the pharynx, where they connect to the seminal vesicles. Planarian_Anatomy PLANA:0000207 sperm duct https://planosphere.stowers.org/ontology/PLANA_0000207 A network of tubes that transport sperm from the testes to the seminal vesicles. Tubes connect each testis to ducts that run along the ventral nerve cords. The ducts bifurcate immediately posterior to the pharynx, where they connect to the seminal vesicles. PMID:19022767 PMID:22074376 A gonad containing male germline stem cells which fuel sperm production. Testes are located dorsolaterally, and are excluded from the head. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuels formation of testes during juvenile development and regeneration. Planarian_Anatomy PLANA:0000208 testis https://planosphere.stowers.org/ontology/PLANA_0000208 A gonad containing male germline stem cells which fuel sperm production. Testes are located dorsolaterally, and are excluded from the head. The neoblast compartment, including piwi-1+, nanos+ primordial germ cells, fuels formation of testes during juvenile development and regeneration. PMID:19022767 Anatomical structure that is present during embryonic development. UBERON:0005423 Planarian_Anatomy PLANA:0000209 developing anatomical structure https://planosphere.stowers.org/ontology/PLANA_0000209 Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2. Planarian_Anatomy PLANA:0000211 primitive ectoderm cell https://planosphere.stowers.org/ontology/PLANA_0000211 Primitive ectoderm cells differentiate from the blastomere population, exit the cell cycle and interact to boud the embryo during Stage 2. OCLC:20423827 OCLC:464776945 OCLC:82522822 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md Undifferentiated, zygote-derived cleavage progeny that give rise to temporary embryonic tissues during Stage 2, continue dividing asynchronously in the embryonic wall, and ultimately give rise to neoblasts and adult lineage progenitors beginning in Stage 5. Planarian_Anatomy PLANA:0000212 blastomere compartment https://planosphere.stowers.org/ontology/PLANA_0000212 Undifferentiated, zygote-derived cleavage progeny that give rise to temporary embryonic tissues during Stage 2, continue dividing asynchronously in the embryonic wall, and ultimately give rise to neoblasts and adult lineage progenitors beginning in Stage 5. PMID:28072387 A sexually immature member of the Schmidtea mediterranea sexuallly reproducing biotype. Schmidtea_mediterranea_Developmental_Stages PLANA:0000214 juvenile https://planosphere.stowers.org/ontology/PLANA_0000214 Products of the reproductive system include gametes, zygotes, yolk cells and egg capsules. Planarian_Anatomy PLANA:0000215 reproductive system product https://planosphere.stowers.org/ontology/PLANA_0000215 A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos. Egg capsules are anchored to a substrate via a stalk. Planarian_Anatomy PLANA:0000216 Depicted by field shows a light microscopy image of egg capsules with a scale bar of 3mm egg capsule https://planosphere.stowers.org/ontology/PLANA_0000216 A proteinaceous, semi-permeable shell housing yolk cells and one or more embryos. Egg capsules are anchored to a substrate via a stalk. PMID:18942102 Reproductive organ that produces and releases eggs (ovary) or sperm (testis). UBERON:0000991 Planarian_Anatomy PLANA:0000217 gonad https://planosphere.stowers.org/ontology/PLANA_0000217 Neoblasts coexpressing piwi-1 and nanos that are required for male and female gonad formation. Primordial germ cells are present in both asexual and sexual adults. Planarian_Anatomy PLANA:0000218 male primordial germ cell https://planosphere.stowers.org/ontology/PLANA_0000218 Neoblasts coexpressing piwi-1 and nanos that are required for male and female gonad formation. Primordial germ cells are present in both asexual and sexual adults. PMID:17376870 gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm. spermatogonial stem cell (SSC) Planarian_Anatomy PLANA:0000219 male germline stem cell https://planosphere.stowers.org/ontology/PLANA_0000219 gh4+, nanos+ cells residing at the testis periphery that self-renew and give rise to differentiating daughters that will ultimately produce haploid sperm. PMID: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 https://planosphere.stowers.org/ontology/PLANA_0000220 An euploid male germ cell of an early stage of spermatogenesis. In planaria, the gh4+ stem cell daughter exiting the niche undergoes three rounds of transit amplifying division with incomplete cytokinesis prior to transitioning to terminal differentiation. PMID:27163480, PMID:27330085 A tektin-1+ male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. CL:0000017 Planarian_Anatomy PLANA:0000221 spermatocyte https://planosphere.stowers.org/ontology/PLANA_0000221 A tektin-1+ male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. PMID:27330085 A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa. CL:0000018 Planarian_Anatomy PLANA:0000222 spermatid https://planosphere.stowers.org/ontology/PLANA_0000222 A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes. Planarian_Anatomy PLANA:0000223 female germline stem cell https://planosphere.stowers.org/ontology/PLANA_0000223 A piwi-1+, nanos+ cell residing in the ovary that self-renews and give rise to oogonial cells that differentiate into oocytes. PMID: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 https://planosphere.stowers.org/ontology/PLANA_0000224 Glands surrounding the copulatory bursa that are required for production of the proteinaceous egg capsule shell and stalk. 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 https://planosphere.stowers.org/ontology/PLANA_0000225 A reproductive strategy in which eggs are laid, with most embryonic development occurring outside of the parent. PMID:19022767 Fertilization of an oocyte by sperm from a different individual. Reciprocal exchange of sperm occurs during Schmidtea mediterranea copulation. Schmidtea_mediterranea_Developmental_Terms PLANA:0000226 cross-fertilization https://planosphere.stowers.org/ontology/PLANA_0000226 Fertilization of an oocyte by sperm from a different individual. Reciprocal exchange of sperm occurs during Schmidtea mediterranea copulation. PMID:19022767 PMID:28812561 1. A gamete (as an egg or sperm cell) or one of its antecedent cells. 2. A mature male or female germ cell usually possessing a haploid chromosome set and capable of initiating formation of a new diploid individual by fusion with a gamete of the opposite sex. BTO:0000535 Planarian_Anatomy PLANA:0000227 germ cell https://planosphere.stowers.org/ontology/PLANA_0000227 A male germ cell is a germ cell that supports male gamete production. CL:0000015 Planarian_Anatomy PLANA:0000228 male germ cell https://planosphere.stowers.org/ontology/PLANA_0000228 Female germ cell is a germ cell that supports female gamete production. CL:0000021 Planarian_Anatomy PLANA:0000229 female germ cell https://planosphere.stowers.org/ontology/PLANA_0000229 A sperm storage organ located immediately posterior to the ovary, at the anterior end of the oviduct. Oocytes exiting the ovary are fertilized in the tuba as they enter the oviduct. Planarian_Anatomy PLANA:0000230 tuba https://planosphere.stowers.org/ontology/PLANA_0000230 A sperm storage organ located immediately posterior to the ovary, at the anterior end of the oviduct. Oocytes exiting the ovary are fertilized in the tuba as they enter the oviduct. PMID:19022767 PMID:20844018 PMID:22074376 PMID:27149082 Glands surrounding the oviducts which produce yolk cells. Yolk cells deposited into the oviducts travel to the genital atrium where they are packaged, along with one or more zygotes, into developing egg capsules. Planarian_Anatomy PLANA:0000231 vitelline gland https://planosphere.stowers.org/ontology/PLANA_0000231 Glands surrounding the oviducts which produce yolk cells. Yolk cells deposited into the oviducts travel to the genital atrium where they are packaged, along with one or more zygotes, into developing egg capsules. PMID:16932928 PMID:18942102 PMID:27149082 Accessory reproductive structures involved in copulation, egg capsule development and laying. Planarian_Anatomy PLANA:0000232 copulatory apparatus https://planosphere.stowers.org/ontology/PLANA_0000232 Accessory reproductive structures involved in copulation, egg capsule development and laying. PMID:22074376 A chamber where egg capsules are formed. One or more zygotes and yolk cells produced by the vitelline glands collect in the copulatory bursa; glands surrounding the copulatory bursa produce the egg capsule shell. Nascent egg capsules exit the body by passing through the bursal canal and gonopore. The copulatory bursa is synonymous with the term genital atrium. bursa genital atrium Planarian_Anatomy PLANA:0000233 copulatory bursa https://planosphere.stowers.org/ontology/PLANA_0000233 A chamber where egg capsules are formed. One or more zygotes and yolk cells produced by the vitelline glands collect in the copulatory bursa; glands surrounding the copulatory bursa produce the egg capsule shell. Nascent egg capsules exit the body by passing through the bursal canal and gonopore. The copulatory bursa is synonymous with the term genital atrium. PMID:22074376 Glandular pouches adjoining the sperm ducts which produce seminal fluid. Planarian_Anatomy PLANA:0000234 seminal vesicle https://planosphere.stowers.org/ontology/PLANA_0000234 Glandular pouches adjoining the sperm ducts which produce seminal fluid. PMID: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 https://planosphere.stowers.org/ontology/PLANA_0000237 A cyst of 8 interconnected spermatocytes undergoes meiosis, producing 32 haploid round spermatids. Round spermatids express protein kinase A, and undergo morphogenesis to produce mature sperm. PMID:27163480, PMID:27330085 Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm. Planarian_Anatomy PLANA:0000238 elongate spermatid https://planosphere.stowers.org/ontology/PLANA_0000238 Spermatids expressing protein kinase A undergoing morphogenic changes to make mature sperm. PMID:27163480, PMID:27330085 An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes. FMA:83673 Planarian_Anatomy PLANA:0000239 oogonial cell https://planosphere.stowers.org/ontology/PLANA_0000239 Any collection of muscles that is part of a body wall [Automatically generated definition]. define generically to encompass both vertebrates and invertebrates body wall muscles BSA:0000058 BTO:0001863 FMA:86931 UBERON:0004462 WBbt:0005813 Planarian_Anatomy PLANA:0000240 body wall musculature https://planosphere.stowers.org/ontology/PLANA_0000240 Pharynx muscle fibers running anteroposterior (proximal to distal). Planarian_Anatomy PLANA:0000241 pharyngeal longitudinal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000241 Pharynx muscle fibers running anteroposterior (proximal to distal). ASIN:B000M4NK9M Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. UBERON:0002553 Planarian_Anatomy PLANA:0000242 anatomical cavity https://planosphere.stowers.org/ontology/PLANA_0000242 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 https://planosphere.stowers.org/ontology/PLANA_0000400 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 https://planosphere.stowers.org/ontology/PLANA_0000401 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 https://planosphere.stowers.org/ontology/PLANA_0000402 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 https://planosphere.stowers.org/ontology/PLANA_0000403 A anatomical space that is enclosed by a pharynx. UBERON:0001731 Planarian_Anatomy PLANA:0000404 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. Cavity of pharynx is indicated by arrows. Scale bar = 250um cavity of pharynx https://planosphere.stowers.org/ontology/PLANA_0000404 An anatomical space that is surrounded by a digestive tract. UBERON:0006909 Planarian_Anatomy PLANA:0000405 Depicted by field contains hematoxylin and eosin staining on a coronal section of a asexual adult animal. The lumen of the digestive tract is indicated by arrows. Scale bar = 250um lumen of digestive tract https://planosphere.stowers.org/ontology/PLANA_0000405 An anatomical space that is surrounded by a digestive tract. PMID:21664348 The orifice that connects the mouth to the exterior of the body. UBERON:0000166 Planarian_Anatomy PLANA:0000406 oral opening https://planosphere.stowers.org/ontology/PLANA_0000406 Anatomical space between the definitive pharynx and the epithelial cells comprising parapharyngeal pouch. Planarian_Anatomy PLANA:0000407 Depicted by field contains hematoxylin and eosin staining coronal section section of a asexual adult animal. Parapharyngeal pouch cavity is indicated by arrows. Scale bar = 250um pharnygeal pouch cavity https://planosphere.stowers.org/ontology/PLANA_0000407 Anatomical space between the definitive pharynx and the epithelial cells comprising parapharyngeal pouch. OCLC:16809160 The apical surface of the single layered epidermis that is in contact with the environment. Planarian_Anatomy PLANA:0000409 Depicted by field is an electron micrograph of the dorsal epidermis in a transverse plane from an asexual adult animal. The apical epidermis surface is noted with magenta arrows. Scale bar is 5um. apical epidermis surface https://planosphere.stowers.org/ontology/PLANA_0000409 The basal surface of the epidermal epithelium in direct contact with the basal lamina. Planarian_Anatomy PLANA:0000410 The depicted by field is an electron micrograph of the dorsal epidermis in a transverse plane. The basal epidermis surface is noted with magenta arrows. Scale bar is 5um. basal epidermis surface https://planosphere.stowers.org/ontology/PLANA_0000410 The surface of the gut lumen in contact with ingested food. Planarian_Anatomy PLANA:0000411 The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the anterior primary gut branch. The lumen gut surface is marked by black arrows. Scale bar is 200um. lumen gut surface https://planosphere.stowers.org/ontology/PLANA_0000411 The surface of the gut lumen in contact with ingested food. PMID:21664348 The epithelial surface lining the interior of the pharynx, facing the lumen. Planarian_Anatomy PLANA:0000412 The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the pharynx and surrounding tissues. The pharynx lumen epithelial surface is marked by black arrows. Scale bar is 200um. pharynx lumen epithelial surface https://planosphere.stowers.org/ontology/PLANA_0000412 The epithelial surface lining the interior of the pharynx, facing the lumen. UBERON:0001731 Epithelial surface covering the outside of the pharynx. Planarian_Anatomy PLANA:0000413 The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the pharynx and surrounding tissues. The pharynx outer epithelial surface is marked by black arrows. Scale bar is 200um. pharynx outer epithelial surface https://planosphere.stowers.org/ontology/PLANA_0000413 Epithelial surface covering the outside of the pharynx. doi:10.1002/jmor.1052060308 PMID:29865769 The surface of the parapharyngeal pouch facing the pharynx. Planarian_Anatomy PLANA:0000414 The depicted by field is a hemotoxylin and eosin stained coronal section encompassing the pharynx and surrounding tissues. Anterior is up. The parapharyngeal pouch surface is marked by black arrows. Scale bar is 200um. pharyngeal pouch surface https://planosphere.stowers.org/ontology/PLANA_0000414 The surface of the parapharyngeal pouch facing the pharynx. OCLC:16809160 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 https://planosphere.stowers.org/ontology/PLANA_0000416 Anatomical structure which is a subdivision of a whole adult or juvenile organism, consisting of components of multiple anatomical systems. Planarian_Anatomy PLANA:0000417 definitive organism subdivision https://planosphere.stowers.org/ontology/PLANA_0000417 The head is the anterior-most division of the body [GO]. A three dimensional compartment bounded by the anterior margin or the head and the posterior boundary of the cephalic ganglia (brain). UBERON:0000033 Planarian_Anatomy PLANA:0000418 head https://planosphere.stowers.org/ontology/PLANA_0000418 Region of the juvenile or adult animal between the posterior end of the cephalic ganglia and the anterior end of the definitive pharynx. Planarian_Anatomy PLANA:0000419 neck https://planosphere.stowers.org/ontology/PLANA_0000419 Region of the animal lateral to and surrounding the definitive pharynx. trunk Planarian_Anatomy PLANA:0000420 Trunk is a synonym here because the parapharyngeal region is always contained in a trunk fragment. However, a trunk fragment may also contain some neck and some tail. parapharyngeal region https://planosphere.stowers.org/ontology/PLANA_0000420 Caudal region, beginning at the mouth and ending at posterior pole. Planarian_Anatomy PLANA:0000421 tail https://planosphere.stowers.org/ontology/PLANA_0000421 Medial region of the tail; the parenchymal space between the posterior primary gut branches. Planarian_Anatomy PLANA:0000422 tail stripe https://planosphere.stowers.org/ontology/PLANA_0000422 Anatomical structure which is a subdivision of a whole developing/ embryonic organism, consisting of components of multiple anatomical systems. Planarian_Anatomy PLANA:0000423 embryonic subdivision https://planosphere.stowers.org/ontology/PLANA_0000423 Anatomical entity that has mass. UBERON:0000465 Planarian_Anatomy PLANA:0000424 material anatomical entity https://planosphere.stowers.org/ontology/PLANA_0000424 Anatomical structure present in juvenile and adult planaria. Planarian_Anatomy PLANA:0000425 definitive anatomical structure https://planosphere.stowers.org/ontology/PLANA_0000425 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 https://planosphere.stowers.org/ontology/PLANA_0000426 An anatomical structure that has more than one cell as a part. UBERON:0010000 Planarian_Anatomy PLANA:0000427 multicellular anatomical structure https://planosphere.stowers.org/ontology/PLANA_0000427 Total musculature of the planarian body. http://purl.obolibrary.org/obo/UBERON_0001015 Planarian_Anatomy PLANA:0000428 musculature system https://planosphere.stowers.org/ontology/PLANA_0000428 A heterogeneous population of pluripotent, somatic adult stem cells and lineage primed progenitors that are required for maintenance and regeneration of all cell types in planaria, including the germline. Planarian_Anatomy PLANA:0000429 neoblast compartment https://planosphere.stowers.org/ontology/PLANA_0000429 A heterogeneous population of pluripotent, somatic adult stem cells and lineage primed progenitors that are required for maintenance and regeneration of all cell types in planaria, including the germline. PMID:16311336 PMID:21566185 PMID:22899852 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000004.md A part of an epithelial cell. Planarian_Anatomy PLANA:0000430 epithelial cell component https://planosphere.stowers.org/ontology/PLANA_0000430 Anatomical structure that performs a specific function or group of functions. UBERON:0000062 Planarian_Anatomy PLANA:0000431 organ https://planosphere.stowers.org/ontology/PLANA_0000431 An anatomical structure that is undergoing regeneration. UBERON:0007567 Planarian_Anatomy PLANA:0000432 regenerating anatomical structure https://planosphere.stowers.org/ontology/PLANA_0000432 The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. Source: NIF_Subcellular:sao-1337158144, GOC:go_curators GO:0005575 Planarian_Anatomy PLANA:0000433 cellular component https://planosphere.stowers.org/ontology/PLANA_0000433 A decussation of the diencephalon where the fibers of the optic nerve cross The point at which fibers of the optic nerves cross.[AAO] The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG] chiasma chiasma nervorum opticorum optic chiasm (Rufus of Ephesus) AAO:0010622 BAMS:DC BAMS:OC BAMS:och BAMS:ox BM:Tel-OCX C90609 DHBA:10644 DMBA:17783 EHDAA2:0001302 EHDAA:10227 EMAPA:17603 FMA:62045 GAID:832 HBA:9310 MA:0001098 MBA:117 MESH:D009897 Optic:chiasm TAO:0000556 UBERON:0000959 UMLS:C0029126 VHOG:0000190 XAO:0004071 ZFA:0000556 birnlex:1416 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=459 http://linkedlifedata.com/resource/umls/id/C0029126 http://www.snomedbrowser.com/Codes/Details/244453006 chiasma opticum decussation of optic nerve fibers optic chiasm Planarian_Anatomy PLANA:0000459 optic chiasma https://planosphere.stowers.org/ontology/PLANA_0000459 A decussation of the diencephalon where the fibers of the optic nerve cross PMID:18466009 A bundle of nerve fibers connecting the two cephalic ganglia. UBERON:0000935 Planarian_Anatomy PLANA:0000460 anterior commissure https://planosphere.stowers.org/ontology/PLANA_0000460 Nerve branches that extend from the lateral side of each cephalic ganglia lobe. Each lobe has nine lateral branches which terminate in sensory organs. Evidence suggests they play a role in chemosensation. Planarian_Anatomy PLANA:0000461 lateral branches https://planosphere.stowers.org/ontology/PLANA_0000461 Nerve branches that extend from the lateral side of each cephalic ganglia lobe. Each lobe has nine lateral branches which terminate in sensory organs. Evidence suggests they play a role in chemosensation. PMID:12128224, PMID:9493832, PMID:4452894, PMID:18466009, PMID:27612384 A cell that performs a sensory function. Planarian_Anatomy PLANA:0000462 sensory cell https://planosphere.stowers.org/ontology/PLANA_0000462 Neurons that express choline acetyltransferase. Planarian_Anatomy PLANA:0000463 cholinergic neuron https://planosphere.stowers.org/ontology/PLANA_0000463 Neurons that express choline acetyltransferase. PMID:20338223 Neurons that express glutamine decarboxylase. Planarian_Anatomy PLANA:0000464 GABAergic neuron https://planosphere.stowers.org/ontology/PLANA_0000464 Neurons that express glutamine decarboxylase. PMID:18440152 Plexus of nerves located in the definitive pharynx comprised of inner and outer wall rings. Planarian_Anatomy PLANA:0000465 pharynx nerve plexus https://planosphere.stowers.org/ontology/PLANA_0000465 Plexus of nerves located just between the definitive epidermis and the body wall musculature. Planarian_Anatomy PLANA:0000466 subepidermal nerve plexus https://planosphere.stowers.org/ontology/PLANA_0000466 Plexus of nerves located just between the definitive epidermis and the body wall musculature. PMID:27612384 doi:10.1002/jmor.1051550208 Plexus of nerves that innervate the body wall muscles. Planarian_Anatomy PLANA:0000467 submuscular nerve plexus https://planosphere.stowers.org/ontology/PLANA_0000467 A thin net of single nerve fibers located around the gut. Planarian_Anatomy PLANA:0000468 gastrodermal plexus https://planosphere.stowers.org/ontology/PLANA_0000468 A thin net of single nerve fibers located around the gut. PMID: 17999079 doi.org/10.1002/jmor.1051550208 A cluster of neurites that is part of a nervous system and forms a network of dendrites and axons where synapses are present and in which neuronal somata do not occur. Multi-cell component structure of the central nervous system consisting largely of neuron projections (tracts and synaptic neuropil domains) and associated glial cells. This corresponds to the part of the CNS that is enclosed by the cortex. neuropilus BTO:0005268 C12617 CALOHA:TS-2403 FBbt:00005139 FMA:261269 GAID:740 MESH:D019581 NIF_Subcellular:sao205380252 UBERON:0002606 UMLS:C0228081 birnlex:1142 http://en.wikipedia.org/wiki/Neuropil http://linkedlifedata.com/resource/umls/id/C0228081 http://www.snomedbrowser.com/Codes/Details/67146008 Planarian_Anatomy PLANA:0000470 neuropil https://planosphere.stowers.org/ontology/PLANA_0000470 A cluster of neurites that is part of a nervous system and forms a network of dendrites and axons where synapses are present and in which neuronal somata do not occur. PMID:27612384 Heavily ciliated epidermal cells covering the outer surface of the pharynx shaft. These are "insunk" epidermal cells in which the nuclei reside behind the layers of longitudinal and circumferential muscles and the epithelial cell body sends out a ciliated projection to the surface to cover and encase the shaft. Planarian_Anatomy PLANA:0000472 outer pharyngeal epithelium https://planosphere.stowers.org/ontology/PLANA_0000472 Heavily ciliated epidermal cells covering the outer surface of the pharynx shaft. These are "insunk" epidermal cells in which the nuclei reside behind the layers of longitudinal and circumferential muscles and the epithelial cell body sends out a ciliated projection to the surface to cover and encase the shaft. ASIN:B000M4NK9M Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles. Planarian_Anatomy PLANA:0000473 outer pharyngeal circular muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000473 Pharynx muscle fibers thar run circumferentially about the pharynx and lie just beneath the outer longitudinal pharynx muscles. ASIN:B000M4NK9M Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers. Planarian_Anatomy PLANA:0000474 inner pharyngeal circular muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000474 Pharynx muscle fiber that runs circumferentially about the pharynx and lies just beneath the inner logitudinal pharynx muscle fibers. ASIN:B000M4NK9M Pharynx muscle fibers running anteroposterior which lie beneath both the inner circular muscle fibers and the apical, ciliated portion of the epithium lining the lumenal surface. Planarian_Anatomy PLANA:0000475 inner pharyngeal longitudinal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000475 Pharynx muscle fibers running anteroposterior which lie beneath both the inner circular muscle fibers and the apical, ciliated portion of the epithium lining the lumenal surface. ASIN:B000M4NK9M Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium. Planarian_Anatomy PLANA:0000476 outer pharyngeal longitudinal muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000476 Pharynx muscle fibers running anteroposterior which lie just underneath the apical, cilaited portion of the outer epithelium. ASIN:B000M4NK9M Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts. Planarian_Anatomy PLANA:0000477 pharyngeal radial muscle fiber https://planosphere.stowers.org/ontology/PLANA_0000477 Pharynx muscle fibers that run radially, connecting the outer muscle fibers and epithelia with their inner counterparts. ASIN:B000M4NK9M The total musculature within the pharynx. UBERON:0004467 Planarian_Anatomy PLANA:0000478 musculature of pharynx https://planosphere.stowers.org/ontology/PLANA_0000478 The total musculature within the pharynx. PMID: 26904543 Ring of the pharynx nerve plexus that is proximal to the lumen. Planarian_Anatomy PLANA:0000479 inner pharynx nerve plexus https://planosphere.stowers.org/ontology/PLANA_0000479 Ring of the pharynx nerve plexus that is proximal to the exterior surface. Planarian_Anatomy PLANA:0000480 outer pharynx nerve plexus https://planosphere.stowers.org/ontology/PLANA_0000480 Ring of the pharynx nerve plexus that is proximal to the exterior surface. doi:10.1002/jmor.1051550208 PMID:27612384 Neurons that express the neurotransmitter serotonin. Planarian_Anatomy PLANA:0000481 serotonergic neuron https://planosphere.stowers.org/ontology/PLANA_0000481 Neurons that express the neurotransmitter serotonin. PMID:17624455 A neuron that expresses the neurotransmitter dopamine. Planarian_Anatomy PLANA:0000482 dopaminergic neuron https://planosphere.stowers.org/ontology/PLANA_0000482 A neuron that expresses the neurotransmitter dopamine. PMID:17565705 Neurons that express the biogenic amine octopamine. Planarian_Anatomy PLANA:0000483 octopaminergic neuron https://planosphere.stowers.org/ontology/PLANA_0000483 Neurons that express the biogenic amine octopamine. PMID:18926867 Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus. Planarian_Anatomy PLANA:0000484 secretory system https://planosphere.stowers.org/ontology/PLANA_0000484 Anatomical system that has as its parts cells and glands devoted to the discharge of substances such as mucus. PMID:20865784 Specialized insunk epithelial cells located in the mesenchyme that participate in mucus secretion. They are characterized by elongated cell bodies with long cytoplasmic projections that terminate between, or penetrate directly through epithelial cells and form a secretory pore at the surface. Planarian_Anatomy PLANA:0000485 gland cell https://planosphere.stowers.org/ontology/PLANA_0000485 Specialized insunk epithelial cells located in the mesenchyme that participate in mucus secretion. They are characterized by elongated cell bodies with long cytoplasmic projections that terminate between, or penetrate directly through epithelial cells and form a secretory pore at the surface. PMID:20865784 The opening by which the gland cells secrete mucus to the exterior of the animal. Planarian_Anatomy PLANA:0000486 secretory pore https://planosphere.stowers.org/ontology/PLANA_0000486 The opening by which the gland cells secrete mucus to the exterior of the animal. PMID:20865784 One of two distinct histochemical classes of gland cells, these can be found throughout the body but primarily form clusters of subepidermal marginal adhesive glands along the dorsalventral border of the animal. eosinophilic gland cell Planarian_Anatomy PLANA:0000487 acidophilic gland cell https://planosphere.stowers.org/ontology/PLANA_0000487 One of two distinct histochemical classes of gland cells, these can be found throughout the body but primarily form clusters of subepidermal marginal adhesive glands along the dorsalventral border of the animal. PMID:20865784 One of two distinct histochemical classes of gland cells, these are found near the ventral mesenchyme, the pharynx and in the dorsal region of the head. May also be called cyanophilic gland cells. Planarian_Anatomy PLANA:0000488 basophilic gland cell https://planosphere.stowers.org/ontology/PLANA_0000488 One of two distinct histochemical classes of gland cells, these are found near the ventral mesenchyme, the pharynx and in the dorsal region of the head. May also be called cyanophilic gland cells. PMID:20865784 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 https://planosphere.stowers.org/ontology/PLANA_0000489 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 https://planosphere.stowers.org/ontology/PLANA_0000490 An anatomical plane that bisects a zone of weakness in an appendage. When autotomy occurs, the appendage divides along this plane. this class is intended for autotomy that bisects an appendage. Other forms of autotomy are possible: for example, a sea cucumber and autotomitize internal organs UBERON:0035086 Planarian_Anatomy PLANA:0000491 plane of autotomy https://planosphere.stowers.org/ontology/PLANA_0000491 Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA]. in FMA this is a subtype of junction rather than tissue plexus AEO:0000138 BTO:0000205 C12929 EHDAA2:0003138 EHDAA:3780 FMA:5901 MA:0002407 UBERON:0001810 UMLS:C0501403 http://en.wikipedia.org/wiki/Nervous_system_plexus http://linkedlifedata.com/resource/umls/id/C0501403 http://www.snomedbrowser.com/Codes/Details/122455009 Planarian_Anatomy PLANA:0000492 nerve plexus https://planosphere.stowers.org/ontology/PLANA_0000492 Axon tract that crosses the midline of the central nervous system[NIF, modified]. In the context of Drosophila refers to a broad band of axons connecting equivalent neuropils each side of the brain[FBbt]. White matter fiber bundle that crosses the midline of the brain or spinal cord, that connects similar structures on both sides. (CUMBO; Heimer, L. The Human Brain, 2nd ed., 1995, pg 6) commissural white matter commissure commissure C32349 FBbt:00005103 FMA:83906 OpenCyc:Mx4rdBrmE6gOEdudWQACs5b6Bw TADS:0000201 UBERON:0001020 UMLS:C1185742 http://en.wikipedia.org/wiki/Commissure http://linkedlifedata.com/resource/umls/id/C1185742 nlx:110 nlx_anat:20090513 commissure of neuraxis neuraxis commissure Planarian_Anatomy PLANA:0000493 *not* the same as FMA:76741 Commissure nervous system commissure https://planosphere.stowers.org/ontology/PLANA_0000493 any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain[MP] UBERON:0005970 Planarian_Anatomy PLANA:0000494 brain commissure https://planosphere.stowers.org/ontology/PLANA_0000494 A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise AEO:0000192 BTO:0001638 CARO:0000010 EFO:0003658 FMA:50705 TAO:0001270 UBERON:0005306 XAO:0004060 ncithesaurus:Blastemal_Cell blastema cell Planarian_Anatomy PLANA:0000495 blastema https://planosphere.stowers.org/ontology/PLANA_0000495 A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. UBERON:0000015 Planarian_Anatomy PLANA:0000496 anatomical boundary https://planosphere.stowers.org/ontology/PLANA_0000496 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 https://planosphere.stowers.org/ontology/PLANA_0000497 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. anteroposterior axis UBERON:0013701 Planarian_Anatomy PLANA:0000498 Depiction shows an asexual with the term annoated in yellow. Scale bar =500um main body axis https://planosphere.stowers.org/ontology/PLANA_0000498 A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FMA:68646 GO:0005623 KUPO:0000002 VHOG:0001533 WBbt:0004017 XAO:0003012 Planarian_Anatomy PLANA:0000499 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell https://planosphere.stowers.org/ontology/PLANA_0000499 Anatomical structure that is a direct part of the cell. TODO - move metadata to GO and obsolete this class once homes have been found for existing children. Note the inconsistency between the usage of the label 'cell component' in GO and CARO cell component AAO:0010271 BILA:0000014 C34070 CARO:0000014 FBbt:00007012 FMA:86454 GO:0044464 HAO:0000014 NIF_Subcellular:sao-1337158144 OpenCyc:Mx4rwQwkcZwpEbGdrcN5Y29ycA TGMA:0001834 UBERON:0000470 UMLS:C1178969 http://linkedlifedata.com/resource/umls/id/C1178969 Planarian_Anatomy PLANA:0000500 cell part https://planosphere.stowers.org/ontology/PLANA_0000500 A prolongation or process extending from a cell. GO_0042995 Planarian_Anatomy PLANA:0000501 cell projection https://planosphere.stowers.org/ontology/PLANA_0000501 A cell projection supported by an assembly of actin filaments. GO_0098858 Planarian_Anatomy PLANA:0000502 actin-based cell projection https://planosphere.stowers.org/ontology/PLANA_0000502 A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GO_0005929 Planarian_Anatomy PLANA:0000503 cilium https://planosphere.stowers.org/ontology/PLANA_0000503 Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. GO:0005902 Planarian_Anatomy PLANA:0000504 microvillus https://planosphere.stowers.org/ontology/PLANA_0000504 Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions. GO_0044291 Planarian_Anatomy PLANA:0000505 cell-cell contact zone https://planosphere.stowers.org/ontology/PLANA_0000505 A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. GO:0030054 Planarian_Anatomy PLANA:0000506 cell junction https://planosphere.stowers.org/ontology/PLANA_0000506 A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals. GO:0005911 Planarian_Anatomy PLANA:0000507 cell-cell junction https://planosphere.stowers.org/ontology/PLANA_0000507 The attachment of one cell to another cell via adhesion molecules. GO:0098609 Planarian_Anatomy PLANA:0000508 cell-cell adhesion https://planosphere.stowers.org/ontology/PLANA_0000508 Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. GO:0044424 Planarian_Anatomy PLANA:0000509 intracellular part https://planosphere.stowers.org/ontology/PLANA_0000509 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures GO:0005737 Planarian_Anatomy PLANA:0000510 cytoplasm https://planosphere.stowers.org/ontology/PLANA_0000510 Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions. eosinophilic tmeehan 2009-12-22T04:23:25Z CP_0000027 Planarian_Anatomy PLANA:0000511 acidophilic cytoplasm https://planosphere.stowers.org/ontology/PLANA_0000511 Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. tmeehan 2009-12-22T04:24:54Z CP_0000028 Planarian_Anatomy PLANA:0000512 basophilic cytoplasm https://planosphere.stowers.org/ontology/PLANA_0000512 Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO_0044444 Planarian_Anatomy PLANA:0000513 cytoplasmic part https://planosphere.stowers.org/ontology/PLANA_0000513 Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell. GO:0044433 Planarian_Anatomy PLANA:0000514 cytoplasmic vesicle part https://planosphere.stowers.org/ontology/PLANA_0000514 A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. GO:0005773 Planarian_Anatomy PLANA:0000515 vacuole https://planosphere.stowers.org/ontology/PLANA_0000515 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. GO_0007010 Planarian_Anatomy PLANA:0000516 cytoskeleton organization https://planosphere.stowers.org/ontology/PLANA_0000516 Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GO_0043229 Planarian_Anatomy PLANA:0000518 intracellular organelle https://planosphere.stowers.org/ontology/PLANA_0000518 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes GO_0043232 Planarian_Anatomy PLANA:0000519 intracellular non-membrane-bounded organelle https://planosphere.stowers.org/ontology/PLANA_0000519 A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. GO_0016020 Planarian_Anatomy PLANA:0000520 membrane https://planosphere.stowers.org/ontology/PLANA_0000520 Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes. GO_0098588 Planarian_Anatomy PLANA:0000521 bounding membrane of organelle https://planosphere.stowers.org/ontology/PLANA_0000521 Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. GO_0044425 Planarian_Anatomy PLANA:0000522 membrane part https://planosphere.stowers.org/ontology/PLANA_0000522 Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO_0044459 Planarian_Anatomy PLANA:0000523 plasma membrane part https://planosphere.stowers.org/ontology/PLANA_0000523 A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. GO_0031090 Planarian_Anatomy PLANA:0000524 organelle membrane https://planosphere.stowers.org/ontology/PLANA_0000524 Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. GO_0043226 Planarian_Anatomy PLANA:0000525 organelle https://planosphere.stowers.org/ontology/PLANA_0000525 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GO:0043227 Planarian_Anatomy PLANA:0000526 membrane-bounded organelle https://planosphere.stowers.org/ontology/PLANA_0000526 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GO_0043231 Planarian_Anatomy PLANA:0000527 intracellular membrane-bounded organelle https://planosphere.stowers.org/ontology/PLANA_0000527 A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. GO_0005794 Planarian_Anatomy PLANA:0000528 Golgi apparatus https://planosphere.stowers.org/ontology/PLANA_0000528 A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. GO_0005634 Planarian_Anatomy PLANA:0000529 nucleus https://planosphere.stowers.org/ontology/PLANA_0000529 A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. GO_0099503 Planarian_Anatomy PLANA:0000530 secretory vesicle https://planosphere.stowers.org/ontology/PLANA_0000530 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. GO_0043228 Planarian_Anatomy PLANA:0000531 non-membrane-bounded organelle https://planosphere.stowers.org/ontology/PLANA_0000531 Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. GO_0044428 Planarian_Anatomy PLANA:0000532 nuclear part https://planosphere.stowers.org/ontology/PLANA_0000532 A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. GO_0005730 Planarian_Anatomy PLANA:0000533 nucleolus https://planosphere.stowers.org/ontology/PLANA_0000533 The ordered and organized complex of DNA, protein (histones), and sometimes RNA, that forms the chromosome. GO_0000785 Planarian_Anatomy PLANA:0000534 chromatin https://planosphere.stowers.org/ontology/PLANA_0000534 A compact and highly condensed form of chromatin. GO_0000792 Planarian_Anatomy PLANA:0000535 heterochromatin https://planosphere.stowers.org/ontology/PLANA_0000535 A dispersed and relatively uncompacted form of chromatin. GO_0000791 Planarian_Anatomy PLANA:0000536 euchromatin https://planosphere.stowers.org/ontology/PLANA_0000536 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. GO_0005840 Planarian_Anatomy PLANA:0000537 ribosome https://planosphere.stowers.org/ontology/PLANA_0000537 A group of axons linking two or more neuropils and having a common origin, termination UBERON:0001018 Planarian_Anatomy PLANA:0000538 axon tract https://planosphere.stowers.org/ontology/PLANA_0000538 A cell whose function is determined by its response to an electric signal. CL:0000393 Planarian_Anatomy PLANA:0000539 electrically responsive cell https://planosphere.stowers.org/ontology/PLANA_0000539 A cell that initiates an electrical signal and passes that signal to another cell. CL:0000404 Planarian_Anatomy PLANA:0000540 electrically signaling cell https://planosphere.stowers.org/ontology/PLANA_0000540 An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. neural subtree UBERON:0001021 nerves peripheral nerve Planarian_Anatomy PLANA:0000541 nerve https://planosphere.stowers.org/ontology/PLANA_0000541 A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 Planarian_Anatomy PLANA:0000543 neuron projection bundle https://planosphere.stowers.org/ontology/PLANA_0000543 A neuron which conveys sensory information centrally from the periphery. CL:0000526 FMA:87653 input neuron Planarian_Anatomy PLANA:0000545 afferent neuron https://planosphere.stowers.org/ontology/PLANA_0000545 A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body. CL:0000103 FMA:67282 Planarian_Anatomy PLANA:0000546 bipolar neuron https://planosphere.stowers.org/ontology/PLANA_0000546 A neuron that has an axon which crosses the midline. CL:0000678 Planarian_Anatomy PLANA:0000547 commissural neuron https://planosphere.stowers.org/ontology/PLANA_0000547 A neuron which sends impulses peripherally to activate muscles or secretory cells. CL:0000527 output neuron Planarian_Anatomy PLANA:0000548 efferent neuron https://planosphere.stowers.org/ontology/PLANA_0000548 A motor neuron that is capable of directly inducing muscle contraction. CL:0008014 Planarian_Anatomy PLANA:0000549 In vertebrates, all motor neurons are excitatory, but various types of inhibitory motor neurons exist in invertebrates. excitatory motor neuron https://planosphere.stowers.org/ontology/PLANA_0000549 Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. BTO:0003811 CL:0000099 FBbt:00005125 FMA:67313 WBbt:0005113 Planarian_Anatomy PLANA:0000550 interneuron https://planosphere.stowers.org/ontology/PLANA_0000550 Any neuron having a sensory function; an afferent neuron conveying sensory impulses. BTO:0001037 CL:0000101 FBbt:00005124 FMA:84649 WBbt:0005759 Planarian_Anatomy PLANA:0000552 sensory neuron https://planosphere.stowers.org/ontology/PLANA_0000552 An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement. BTO:0000312 CL:0000100 FMA:83617 WBbt:0005409 motoneuron Planarian_Anatomy PLANA:0000553 motor neuron https://planosphere.stowers.org/ontology/PLANA_0000553 Neuronal cells which synthesize, store and release neurohormones. CL:0000381 FBbt:00005130 Planarian_Anatomy PLANA:0000556 neurosecretory neuron https://planosphere.stowers.org/ontology/PLANA_0000556 Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides. CL:0011103 Planarian_Anatomy PLANA:0000558 sympathetic neuron https://planosphere.stowers.org/ontology/PLANA_0000558 Neuron with one neurite that extends from the cell body. CL:0000106 FMA:67278 Planarian_Anatomy PLANA:0000559 unipolar neuron https://planosphere.stowers.org/ontology/PLANA_0000559 Neuron with one neurite that extends from the cell body. PMID:18499291 Neuron with an axon and two or more dendrites. CL:0000104 FMA:67287 Planarian_Anatomy PLANA:0000560 multipolar neuron https://planosphere.stowers.org/ontology/PLANA_0000560 Neuron with an axon and two or more dendrites. PMID:18499291 Cells that are in close proximity to neurons. CL:0000130 Planarian_Anatomy PLANA:0000561 neuron associated cell (sensu Nematoda and Protostomia) https://planosphere.stowers.org/ontology/PLANA_0000561 Any neuron that is part of a central nervous system. TermGenie 2014-06-25T01:17:43Z CL:2000029 Planarian_Anatomy PLANA:0000562 central nervous system neuron https://planosphere.stowers.org/ontology/PLANA_0000562 Any neuron that is part of a peripheral nervous system. TermGenie 2014-06-25T02:28:17Z CL:2000032 Planarian_Anatomy PLANA:0000564 peripheral nervous system neuron https://planosphere.stowers.org/ontology/PLANA_0000564 A neruon whose cell body is within an autonomic ganglion. CL:0000107 FMA:80121 Planarian_Anatomy PLANA:0000565 autonomic neuron https://planosphere.stowers.org/ontology/PLANA_0000565 Neuron that is part of the enteric nervous system. haendel 2012-06-28T08:20:31Z CL:0007011 Planarian_Anatomy PLANA:0000566 enteric neuron https://planosphere.stowers.org/ontology/PLANA_0000566 Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue. this class represents a continuous sheet of basal lamina which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal lamina' represents a portion of substance on the scale of a single cell. A basal lamina is certainly present in Bilateria and was evaluated as an autapomorphy of this taxon.[well established][VHOG] basal lamina basal laminae lamina basalis AAO:0010269 AEO:0000065 BILA:0000065 Basal:lamina C32186 CARO:0000065 EHDAA2:0003065 FMA:62918 HAO:0000065 MESH:D001485 NIF_Subcellular:sao1397492660 TAO:0001485 TGMA:0001850 UMLS:C0085872 VHOG:0001592 WBbt:0005756 XAO:0003163 ZFA:0001485 http://linkedlifedata.com/resource/umls/id/C0085872 basal lamina of connective tissue Planarian_Anatomy PLANA:0001005 Depicted by field is an electron micrograph of the dorsal epidermis in a transverse plane from an asexual adult animal. The basal lamina is noted with a magenta bracket. Scale bar is 5um. basal lamina of epithelium https://planosphere.stowers.org/ontology/PLANA_0001005 A fully formed, sexually mature organism. The sexually reproducing Schmidtea mediterranea biotype exists as an obligate cross-fertilizing hermaphrodite. Erin Davies 2017-04-24T02:52:06Z Schmidtea_mediterranea_Developmental_Stages PLANA:0004503 Depcited by field shows a light microscopy image of a sexually mature adult with a scale bar of 2 mm. sexually mature adult https://planosphere.stowers.org/ontology/PLANA_0004503 A fully formed, sexually mature organism. The sexually reproducing Schmidtea mediterranea biotype exists as an obligate cross-fertilizing hermaphrodite. PMID:19022767 PMID:11972158 The asexually reproducing Schmidtea mediterranea biotype exists as a constitutive adult, undergoing successive cycles of fission and whole animal regeneration. Asexual Schmidtea mediterranea contain primordial germ cells, but do not possess a reproductive system. Erin Davies 2017-04-24T02:59:06Z Schmidtea_mediterranea_Developmental_Stages PLANA:0004504 Depicted by field shows an asexual adult with a scale bar of 500um asexual adult https://planosphere.stowers.org/ontology/PLANA_0004504 The asexually reproducing Schmidtea mediterranea biotype exists as a constitutive adult, undergoing successive cycles of fission and whole animal regeneration. Asexual Schmidtea mediterranea contain primordial germ cells, but do not possess a reproductive system. PMID:11972158 PMID:17376870 dmd-1+ expressing somatic cells within the testis that promote male GSC maintenance. dmd-1+, ophis-1+ somatic gonadal cells ensheath germ cells via long cytoplasmic processes and promote differentiation. Erin Davies 2017-07-19T21:05:52Z Planarian_Anatomy PLANA:0004506 testis somatic gonadal cell https://planosphere.stowers.org/ontology/PLANA_0004506 dmd-1+ expressing somatic cells within the testis that promote male GSC maintenance. dmd-1+, ophis-1+ somatic gonadal cells ensheath germ cells via long cytoplasmic processes and promote differentiation. PMID:23652002, PMID:27163480 ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia. Erin Davies 2017-07-19T21:35:08Z Planarian_Anatomy PLANA:0004507 ovarian somatic gonadal cell https://planosphere.stowers.org/ontology/PLANA_0004507 ophis+ somatic cells (gh4-, nanos-) in the ovary that may provide trophic support to female germline stem cells and differentiating oogonia. PMID:27163480 Axis that runs 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 Planarian_Anatomy PLANA:0004511 oral-aboral axis https://planosphere.stowers.org/ontology/PLANA_0004511 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 Planarian_Anatomy PLANA:0004512 primitive ectoderm surface https://planosphere.stowers.org/ontology/PLANA_0004512 The apical surface of the single layered primitive ectoderm that is in contact with the environment. OCLC:20423827 OCLC:464776945 OCLC:82522822 PMID:28072387 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md The surface of the primitive gut cells in contact with the embryonic wall. Erin Davies 2017-07-27T16:25:35Z Planarian_Anatomy PLANA:0004513 primtive gut cell surface https://planosphere.stowers.org/ontology/PLANA_0004513 The surface of the primitive gut cells in contact with the embryonic wall. PMID:28072387 The surface of phagocytic embryonic gut cells in contact with ingested yolk cells. Erin Davies 2017-07-27T16:25:45Z Planarian_Anatomy PLANA:0004514 embryonic gut cell surface https://planosphere.stowers.org/ontology/PLANA_0004514 The surface of phagocytic embryonic gut cells in contact with ingested yolk cells. PMID:28072387 The epithelial cell surface lining the temporary embryonic pharynx lumen. Erin Davies 2017-07-27T16:26:16Z Planarian_Anatomy PLANA:0004516 temporary embryonic pharynx lumen epithelial surface https://planosphere.stowers.org/ontology/PLANA_0004516 The epithelial cell surface lining the temporary embryonic pharynx lumen. PMID:28072387, PMID:20100474 An undifferentiated, cycling embryonic cell in Stage 1-5 embryos that expresses piwi-1, numerous adult asexual neoblast enriched genes, and early embryo enriched genes. Erin Davies 2017-07-27T19:54:22Z Planarian_Anatomy PLANA:0004517 blastomere https://planosphere.stowers.org/ontology/PLANA_0004517 An undifferentiated, cycling embryonic cell in Stage 1-5 embryos that expresses piwi-1, numerous adult asexual neoblast enriched genes, and early embryo enriched genes. PMID:28072387 Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues. Erin Davies 2017-07-27T20:00:04Z Planarian_Anatomy PLANA:0004518 extraembryonic cell https://planosphere.stowers.org/ontology/PLANA_0004518 Post-mitotic, terminally differentiated cells which, give rise to temporary embryonic tissues. PMID: 28072387 A neuronal cell innervating the temporary embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening. Erin Davies 2017-07-27T20:01:15Z Planarian_Anatomy PLANA:0004519 temporary embryonic pharynx neuron https://planosphere.stowers.org/ontology/PLANA_0004519 A neuronal cell innervating the temporary embryonic pharynx. Four neurons innervate the radial muscle fibers that ring the oral opening. PMID:28072387 Differentiated radial muscle cell present in the temporary embryonic pharynx. Erin Davies 2017-07-27T20:01:39Z Planarian_Anatomy PLANA:0004520 temporary embryonic pharynx radial muscle cell https://planosphere.stowers.org/ontology/PLANA_0004520 Differentiated radial muscle cell present in the temporary embryonic pharynx. PMID:16932928 foxA1+ epithelial cell contained in the temporary embryonic pharynx. Erin Davies 2017-07-27T20:02:04Z Planarian_Anatomy PLANA:0004521 temporary embryonic pharynx epithelial cell https://planosphere.stowers.org/ontology/PLANA_0004521 foxA1+ epithelial cell contained in the temporary embryonic pharynx. PMID:28072387, PMID:20100474 Differentiated muscle cell present in a circular muscle fiber of the temporary embryonic pharynx. Erin Davies 2017-07-27T20:43:26Z Planarian_Anatomy PLANA:0004524 temporary embryonic pharynx circular muscle fiber https://planosphere.stowers.org/ontology/PLANA_0004524 Differentiated muscle cell present in a circular muscle fiber of the temporary embryonic pharynx. PMID:16932928 Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus. Erin Davies 2017-08-28T18:20:43Z Planarian_Anatomy PLANA:0004527 copulatory region https://planosphere.stowers.org/ontology/PLANA_0004527 Portion of the sexual biotype body plan immediately posterior to the parapharyngeal region, and immediately anterior to the tail. Encompasses the copulatory apparatus. PMID:22074376 Epithelia associated with the pharynx organ. Erin Davies 2017-08-31T14:53:38Z Planarian_Anatomy PLANA:0004528 pharyngeal epithelium https://planosphere.stowers.org/ontology/PLANA_0004528 Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. Erin Davies 2017-08-31T19:21:09Z UBERON:0002416 Planarian_Anatomy PLANA:0004529 integumental system https://planosphere.stowers.org/ontology/PLANA_0004529 Anatomical space enclosed by the oviduct epithelium. Erin Davies 2017-09-01T17:52:16Z Planarian_Anatomy PLANA:0004530 oviduct lumen https://planosphere.stowers.org/ontology/PLANA_0004530 Anatomical space enclosed by the oviduct epithelium. PMID:22074376 Anatomical space enclosed by the sperm duct epithelium. Erin Davies 2017-09-02T22:26:19Z Planarian_Anatomy PLANA:0004531 sperm duct lumen https://planosphere.stowers.org/ontology/PLANA_0004531 Anatomical space enclosed by the sperm duct epithelium. PMID:19022767 PMID:22074376 Ciliated epithelium lining the oviduct. Erin Davies 2017-09-02T22:35:10Z Planarian_Anatomy PLANA:0004532 oviduct epithelium https://planosphere.stowers.org/ontology/PLANA_0004532 Ciliated epithelium lining the oviduct. PMID:22074376 Ciliated epithelium lining the sperm duct. Erin Davies 2017-09-02T22:43:04Z Planarian_Anatomy PLANA:0004533 sperm duct epithelium https://planosphere.stowers.org/ontology/PLANA_0004533 Ciliated epithelium lining the sperm duct. PMID:19022767 PMID:22074376 Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct. Erin Davies 2017-09-02T22:55:44Z Planarian_Anatomy PLANA:0004534 tuba lumen https://planosphere.stowers.org/ontology/PLANA_0004534 Anatomical space enclosed by tuba. Oocyte(s) are fertilized in the tuba lumen by sperm that traveled up the oviduct. PMID:19022767 PMID:20844018 PMID:22074376 PMID:27149082 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 https://planosphere.stowers.org/ontology/PLANA_0007501 Anatomial plane which divides the body into ventral and dorsal regions. This plane always includes the midline and is also known as the frontal plane. Steph Nowotarski 2017-04-26T19:32:04Z Planarian_Anatomy PLANA:0007502 Depicted by field contains hematoxylin and eosin staining of a coronal plane section of a asexual adult animal. Scale bar = 250um coronal plane https://planosphere.stowers.org/ontology/PLANA_0007502 Anatomical plane which divides the body into right and left parts. This plane passes through the midline. Steph Nowotarski 2017-04-26T19:32:33Z Planarian_Anatomy PLANA:0007503 sagittal plane https://planosphere.stowers.org/ontology/PLANA_0007503 Three dimensional compartment along the dorsoventral axis that is above the anteroposterior axis, containing the eyes. Steph Nowotarski 2017-04-27T16:38:48Z BSPO:0000089 FBcv:0000035 FBql:00005876 Planarian_Anatomy PLANA:0007504 dorsal compartment https://planosphere.stowers.org/ontology/PLANA_0007504 Compartment along the dorsoventral axis that is below the anteroposterior axis. Steph Nowotarski 2017-04-27T16:38:59Z BSPO:0000091 FBql:00005877 Planarian_Anatomy PLANA:0007505 ventral compartment https://planosphere.stowers.org/ontology/PLANA_0007505 Compartment along the anteroposterior axis closer to the head rather than the tail, from the head margin to the esophagus. Steph Nowotarski 2017-04-27T16:39:34Z BSPO:0000087 FBql:00005874 Planarian_Anatomy PLANA:0007506 anterior compartment https://planosphere.stowers.org/ontology/PLANA_0007506 Three dimensional compartment along the anteroposterior axis that is closer to the tail rather than the head, from the anterior boundary of the pharyngeal pouch to the tip of the tail. Steph Nowotarski 2017-04-27T16:39:59Z BSPO:0000090 FBcv:0000036 FBql:00005875 Planarian_Anatomy PLANA:0007507 posterior compartment https://planosphere.stowers.org/ontology/PLANA_0007507 Anatomical structures that exist outside of cells; non-cellular. Steph Nowotarski 2017-05-03T13:48:26Z WBbt:0005732 Planarian_Anatomy PLANA:0007508 extracellular component https://planosphere.stowers.org/ontology/PLANA_0007508 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. Steph Nowotarski 2017-05-03T13:48:41Z GO:0005886 Planarian_Anatomy PLANA:0007509 plasma membrane https://planosphere.stowers.org/ontology/PLANA_0007509 Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi. Steph Nowotarski 2017-05-03T18:08:16Z GO:0043230 Planarian_Anatomy PLANA:0007511 extracellular organelle https://planosphere.stowers.org/ontology/PLANA_0007511 A spherical to rod shaped organelle that generates the majority of a cell's supply of ATP via cellular respiration. Mitochondria have their own genome and consist of outer and inner membranes, the latter folds inward to form cristae. This folding increases the surface area of the membrane and thus increases the space available to produce ATP. The inner and outer membranes are separated by an intermembrane space, and the inner membrane encloses the matrix. Steph Nowotarski 2017-05-03T18:19:46Z Planarian_Anatomy PLANA:0007512 mitochondrion https://planosphere.stowers.org/ontology/PLANA_0007512 Network of interconnected, flattened, and/or tubular membrane, known as cisternae. This membrane is contiguous with the outer nuclear membrane. The endoplasmic reticulum is involved in both protein and lipid synthesis. Steph Nowotarski 2017-05-04T14:46:22Z Planarian_Anatomy PLANA:0007513 endoplasmic reticulum https://planosphere.stowers.org/ontology/PLANA_0007513 Endoplasmic reticululum that is studded with ribosomes, leading to a "rough" or "granular" appearance. Steph Nowotarski 2017-05-04T14:47:41Z Planarian_Anatomy PLANA:0007514 rough endoplasmic reticulum https://planosphere.stowers.org/ontology/PLANA_0007514 Endoplamic reticulum that does not contain ribosomes, which synthesizes lipids, phospholipids, and steroids. Steph Nowotarski 2017-05-04T14:48:11Z Planarian_Anatomy PLANA:0007515 smooth endoplasmic reticulum https://planosphere.stowers.org/ontology/PLANA_0007515 Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined. Steph Nowotarski 2017-05-04T14:49:17Z GO:0005643 Planarian_Anatomy PLANA:0007516 nuclear pore https://planosphere.stowers.org/ontology/PLANA_0007516 The digestive component of the cell. They are homogenous, dense, membrane bound organelles filled with acid hydrolases which break down polymers. Steph Nowotarski 2017-05-04T15:35:23Z Planarian_Anatomy PLANA:0007518 lysosome https://planosphere.stowers.org/ontology/PLANA_0007518 The digestive component of the cell. They are homogenous, dense, membrane bound organelles filled with acid hydrolases which break down polymers. ISBN: 0-71677033-4 PMID:4853064 Axis that runs along the long axis of the animal from anterior (head) to posterior (tail). It is perpendicular to the dorsoventral axis and as such, it splits dorsal and ventral regions of the animal to either side. Steph Nowotarski 2017-05-04T17:59:38Z Planarian_Anatomy PLANA:0007519 Depiction shows an asexual with the term annoated in yellow. Scale bar =500um anteroposterior axis https://planosphere.stowers.org/ontology/PLANA_0007519 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 https://planosphere.stowers.org/ontology/PLANA_0007520 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 Depiction shows an asexual with the term annoated in yellow. Scale bar =500um dextro-sinister axis https://planosphere.stowers.org/ontology/PLANA_0007521 Axis that runs from the center of the body, starting at the anteroposterior axis and out to the lateral (left, right, dorsal or ventral) surface of the animal. Steph Nowotarski 2017-05-04T18:01:37Z Planarian_Anatomy PLANA:0007522 Depiction shows an asexual with the term annoated in yellow. Scale bar =500um mediolateral axis https://planosphere.stowers.org/ontology/PLANA_0007522 Axis that starts at the distal part of an appendage, closest to the body, and runs to the proximal part of an appendage, farthest from the body. Steph Nowotarski 2017-05-04T18:02:04Z Planarian_Anatomy PLANA:0007523 proximodistal axis https://planosphere.stowers.org/ontology/PLANA_0007523 Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD. Steph Nowotarski 2017-05-15T18:28:35Z Planarian_Anatomy PLANA:0007524 anterior pole https://planosphere.stowers.org/ontology/PLANA_0007524 Distinct anterior cluster of muscle cells located at the midline which express notum, follistatin, zic-1, and foxD. PMID:21566195 PMID:23297191 PMID:24040508 PMID:24415944 PMID:24704339 PMID:24992682 Distinct posterior cluster of muscle cells located at the midline which express wnt1. Steph Nowotarski 2017-05-15T18:28:47Z Planarian_Anatomy PLANA:0007525 posterior pole https://planosphere.stowers.org/ontology/PLANA_0007525 Distinct posterior cluster of muscle cells located at the midline which express wnt1. PMID:18063755 PMID:21680047 A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu, guide neuronal migration during development, and exchange metabolites with neurons. Steph Nowotarski 2017-06-22T17:12:28Z CL:0000125 Planarian_Anatomy PLANA:0007528 glial cell https://planosphere.stowers.org/ontology/PLANA_0007528 A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu, guide neuronal migration during development, and exchange metabolites with neurons. PMID:27612384 A biological tissue mass of nerve cell bodies. Steph Nowotarski 2017-06-22T18:29:52Z UBERON:0000045 Planarian_Anatomy PLANA:0007529 ganglion https://planosphere.stowers.org/ontology/PLANA_0007529 Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft. Steph Nowotarski 2017-07-24T19:28:03Z Planarian_Anatomy PLANA:0007534 inner pharyngeal epithelium https://planosphere.stowers.org/ontology/PLANA_0007534 Heavily ciliated epidermal cells covering the inner surface of the pharynx shaft. doi:10.1002/jmor.1051550208 OCLC:16809160 Pharynx muscle fibers running parallel to the diameter of the pharynx. Steph Nowotarski 2017-07-24T19:39:14Z Planarian_Anatomy PLANA:0007535 pharyngeal circular muscle fiber https://planosphere.stowers.org/ontology/PLANA_0007535 Pharynx muscle fibers running parallel to the diameter of the pharynx. ASIN:B000M4NK9M The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell. Steph Nowotarski 2017-09-05T14:18:21Z UBERON:0000955 Planarian_Anatomy PLANA:0007537 brain https://planosphere.stowers.org/ontology/PLANA_0007537 Specialized epithelial cells located along the dorsoventral margin. Adhesion glands are comprised of three cell types, the viscid and releasing gland cells which penetrate through an epithelial anchor cell and terminate at the epithelial surface. Steph Nowotarski 2017-09-05T14:32:51Z Planarian_Anatomy PLANA:0007538 adhesion gland https://planosphere.stowers.org/ontology/PLANA_0007538 Specialized epithelial cells located along the dorsoventral margin. Adhesion glands are comprised of three cell types, the viscid and releasing gland cells which penetrate through an epithelial anchor cell and terminate at the epithelial surface. OCLC:16809160 PMID: 20865784 Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells. Steph Nowotarski 2017-09-05T15:08:27Z Planarian_Anatomy PLANA:0007539 anchor cell https://planosphere.stowers.org/ontology/PLANA_0007539 Specialized epithelial cell located along the dorsoventral margin that surrounds the viscid and releasing gland cells. OCLC:16809160 PMID: 20865784 A specialized insunk epithelial cell that is part of the adhesion glands which is responsible for production and excretion of the viscid substance allowing adherence to a substrate. Steph Nowotarski 2017-09-05T15:08:38Z Planarian_Anatomy PLANA:0007540 viscid gland cell https://planosphere.stowers.org/ontology/PLANA_0007540 A specialized insunk epithelial cell that is part of the adhesion glands which is responsible for production and excretion of the viscid substance allowing adherence to a substrate. OCLC:16809160 PMID: 20865784 Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance. Steph Nowotarski 2017-09-05T15:08:48Z Planarian_Anatomy PLANA:0007541 releasing gland cell https://planosphere.stowers.org/ontology/PLANA_0007541 Specialized insunk epithelial cell that is part of the adhesion gland which is responsible for production of releasing substance. OCLC:16809160 PMID: 20865784 A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2. Planarian_Anatomy PLANA:0007543 TrpA+ central nervous system neuron https://planosphere.stowers.org/ontology/PLANA_0007543 A subset of TrpA+ neurons, located medially in the cephalic ganglia, whose formation is dependent on function of runt-1 and ap2. PMID:22549959 A subset of sensory neurons located along the dorsal head margin. Planarian_Anatomy PLANA:0007544 cintillo+ sensory neuron https://planosphere.stowers.org/ontology/PLANA_0007544 A subset of sensory neurons located along the dorsal head margin. PMID:12557210 The outermost region of the deep-superficial axis. This anatomical compartment contains definitive epidermis, basal lamina and subepidermal nerve plexus. Planarian_Anatomy PLANA:0007545 epidermal compartment https://planosphere.stowers.org/ontology/PLANA_0007545 piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons. Planarian_Anatomy PLANA:0007546 TrpA+ neural progenitor cell https://planosphere.stowers.org/ontology/PLANA_0007546 piwi-1+, runt-1+, ap2+ progenitor neoblasts required for production of TrpA+ neurons. PMID:25254346 PMID:22549959 piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole. Planarian_Anatomy PLANA:0007547 anterior pole progenitor cell https://planosphere.stowers.org/ontology/PLANA_0007547 piwi-1+, foxD+, prep+ progenitor neoblasts required for formation of the anterior pole. PMID:24415944  Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords. Planarian_Anatomy PLANA:0007548 transverse commissure https://planosphere.stowers.org/ontology/PLANA_0007548 Axon tracts from ganglia that cross the midline, connecting the two ventral nerve cords. PMID: 17999079 An anatomical compartment of the deep-superficial axis containing the body wall musculature and underlying submuscular nerve plexus. Planarian_Anatomy PLANA:0007549 body wall musculature compartment https://planosphere.stowers.org/ontology/PLANA_0007549 piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons. Planarian_Anatomy PLANA:0007550 serotonergic neural progenitor cell https://planosphere.stowers.org/ontology/PLANA_0007550 piwi-1+, lhx1/5-1+, pitx+ progenitor neoblasts required for specification of tph+ serotonergic neurons. PMID:23903188 PMID:24131630 PMID:25254346 piwi-1+, klf+ progenitor neoblasts required for production of cintillo+ sensory neurons. Planarian_Anatomy PLANA:0007551 klf+ sensory neuron progenitor cell https://planosphere.stowers.org/ontology/PLANA_0007551 piwi-1+, klf+ progenitor neoblasts required for production of cintillo+ sensory neurons. PMID:25254346 A population of piwi-2+, ston-2+, elav-2+, ptprd-9+ and msi-1+ progenitors that give rise to one or more neuronal (pc-2+, synapsin+) lineages. Planarian_Anatomy PLANA:0007552 nu neoblast https://planosphere.stowers.org/ontology/PLANA_0007552 A population of piwi-2+, ston-2+, elav-2+, ptprd-9+ and msi-1+ progenitors that give rise to one or more neuronal (pc-2+, synapsin+) lineages. PMID:27150006 A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus. Planarian_Anatomy PLANA:0007553 lateral nerve https://planosphere.stowers.org/ontology/PLANA_0007553 A nerve extending laterally from the ventral nerve cord that innervates the submuscular plexus. PMID: 17999079 An anatomical compartment of the deep-superficial axis between the gastrodermal nerve plexus and submuscular nerve plexus. mesenchyme Planarian_Anatomy PLANA:0007554 parenchymal compartment https://planosphere.stowers.org/ontology/PLANA_0007554 piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons. Planarian_Anatomy PLANA:0007555 pax3/7+ neural progenitor cell https://planosphere.stowers.org/ontology/PLANA_0007555 piwi-1+, pax3/7+ progenitor neoblasts implicated in the production of DBH+ ventral midline neurons. PMID: 25254346 Anatomical space enclosed by the temporary embryonic pharynx epithelial cells. Lumen through which yolk cells are transported into the embryonic gut cavity. Erin Davies Planarian_Anatomy PLANA:0007556 temporary embryonic pharynx cavity https://planosphere.stowers.org/ontology/PLANA_0007556 Anatomical space enclosed by the temporary embryonic pharynx epithelial cells. Lumen through which yolk cells are transported into the embryonic gut cavity. PMID:28072387 Nerve plexus surrounding the testis. Planarian_Anatomy PLANA:0007557 testis nerve plexus https://planosphere.stowers.org/ontology/PLANA_0007557 Nerve plexus surrounding the testis. PMID: 7833618 PMID: 17999079 Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs. Erin Davies Planarian_Anatomy PLANA:0007558 fission plane https://planosphere.stowers.org/ontology/PLANA_0007558 Transverse anatomical plane, located approximately 1-2 mm from the posterior extremity of an adult animal, at which fission occurs. PMID: 11972158; OCLC:16809160 Nerve plexus surrounding the ovary. Planarian_Anatomy PLANA:0007559 ovary nerve plexus https://planosphere.stowers.org/ontology/PLANA_0007559 Nerve plexus surrounding the ovary. PMID: 7833618 PMID: 17999079 The innermost anatomical compartment of the deep-superficial axis, extending from the definitive gut lumen to the gastrodermal nerve plexus. Planarian_Anatomy PLANA:0007560 gastrovascular compartment https://planosphere.stowers.org/ontology/PLANA_0007560