PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea. Planarian Anatomy Ontology (PLANA) Planarian_Anatomy 1.2 CARO part_of NCBITaxon:79327; CL part_of NCBITaxon:79327 2023-03-13 definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by Relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y is indirect form of If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. external_definition Notes on the homology status of this class. homology_notes has_relational_adjective Notes on the how instances of this class vary across species. taxon_notes Notes on how similar or equivalent classes are represented in other ontologies. external_ontology_notes IAO:0100001 synonym typically used in the context of human anatomy IAO:0100001 synonym typically used in the context of vertebrate anatomy http://purl.org/dc/elements/1.1/creator uberon dc-creator true dc-creator creator http://purl.org/dc/elements/1.1/description uberon dc-description true dc-description description http://purl.org/dc/elements/1.1/title uberon dc-title true dc-title title http://purl.org/dc/terms/license uberon dcterms-license true dcterms-license license IAO:0100001 namespace-id-rule IAO:0100001 synonym_type_property has_alternative_id An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 IAO:0100001 database_cross_reference An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 IAO:0100001 has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 IAO:0100001 has narrow synonym has_narrow_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 IAO:0100001 has_obo_format_version IAO:0100001 has_obo_namespace An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 IAO:0100001 has related synonym has_related_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 IAO:0100001 has_scope IAO:0100001 has_synonym_type in_subset IAO:0100001 shorthand Sofia Robb 2017-07-26T18:19:59Z treat-xrefs-as-genus-differentia 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 external quality spatial uberon part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 external quality spatial uberon has_part has_part has part has part has_part preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:0000096 rostral_to spatial anterior_to anterior_to anterior to x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 spatial dorsal_to dorsal_to dorsal to x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:0000099 caudal to spatial posterior_to posterior_to posterior to x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm caudal to x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 spatial ventral_to ventral_to ventral to x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole. BSPO:0000104 spatial approximately_perpendicular_to approximately_perpendicular_to approximately perpendicular to Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole. BSPO:cjm Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 spatial deep_to deep_to deep to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:cjm Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 spatial superficial_to superficial_to superficial to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:cjm Direcly opposite to. i.e. on the opposite side through the axis. BSPO:0000113 spatial opposite_to opposite_to opposite to Direcly opposite to. i.e. on the opposite side through the axis. BSPO:cjm X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. BSPO:0000120 spatial in_left_side_of in_left_side_of in left side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern 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 spatial in_right_side_of in_right_side_of in right side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern 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 in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure BSPO:0000126 spatial in_lateral_side_of in_lateral_side_of in lateral side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure UBERON:cjm x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. spatial parallel_to parallel to x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. BSPO:curators x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:0001107 spatial immediately_deep_to immediately_deep_to immediately deep to x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:curators BSPO:0015001 spatial finishes_axis finishes_axis A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. If s finishes axis x, and x has end point p, then x overlaps p finishes axis crossing at right angles BSPO:0015005 spatial orthogonal_to orthogonal_to orthogonal to crossing at right angles BSPO:cjm Intersects at two points. BSPO:0015006 spatial passes_through passes_through passes through Intersects at two points. BSPO:cjm BSPO:0015007 spatial starts_axis starts_axis A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. . If s starts axis x, and x has start point p, then x overlaps p starts axis BSPO:0015008 spatial surface_of surface_of placeholder. used for relation between anatomical surface and an anatomical side. surface of x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:0015014 spatial immediately_superficial_to immediately_superficial_to immediately superficial to x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:curators This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes inverse of the relation 'denotes' Person: Jie Zheng, Chris Stoeckert, Mike Conlon denoted by has_specified_output has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains contains A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes RO:0002092 external happens_during happens_during happens during RO:0002093 external ends_during ends_during ends during x overlaps y if and only if there exists some z such that x has part z and z part of y x overlaps y iff they have some part in common. http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 spatial overlaps overlaps "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF [] overlaps overlaps true x overlaps y iff they have some part in common. BSPO:cjm A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y This is the transitive form of the develops from relation develops from inverse of develops from develops into p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in capable of part of true A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall RO:0002220 spatial adjacent_to adjacent_to adjacent to adjacent to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y has developmental contribution from inverse of has developmental contribution from developmentally contributes to Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within Inverse of developmentally preceded by developmentally succeeded by p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. cjm causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of Chris Mungall inheres in part of characteristic of part of true A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of involved in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by inverse of has input Chris Mungall input of x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y has potential to developmentally contribute to x has the potential to develop into y iff x develops into y or if x is capable of developing into y has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y has potential to directly develop into inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall indirectly activates indirectly positively regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall indirectly inhibits indirectly negatively regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. executes activity in enables activity in is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall Vasundra Touré molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly activates molecularly increases activity of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. has part that occurs in true Chris Mungall is kinase activity Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). 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. The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities Chris Mungall causally influenced by (entity-centric) causally influenced by Chris Mungall interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ Chris Mungall molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Chris Mungall Vasundra Touré causally influences (entity-centric) causally influences x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. GOC:cjm lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity luminal space of p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) directly positively regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) directly negatively regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. 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. produced by Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. Vasundra Touré regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. pg 2022-09-26T06:07:17Z indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. pg 2022-09-26T06:08:01Z indirectly regulates A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. https://orcid.org/0000-0001-9625-1899 https://orcid.org/0000-0003-2620-0345 A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] immaterial entity A 2D surface of an anatomical continuant. FMA:24137 surface spatial BSPO:0000005 to be merged into CARO anatomical surface A 2D surface of an anatomical continuant. BSPO:cjm A straight line through space, intersecting an anatomical entity. http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG spatial BSPO:0000010 Axis directions are defined in terms of axes. anatomical axis A straight line through space, intersecting an anatomical entity. BSPO:cjm An axis that extends through an organism from head end to opposite end of body or tail. A-P axis AP axis anteroposterior axis cephalocaudal axis craniocaudal axis rostral/caudal rostrocaudal axis spatial longitudinal axis BSPO:0000013 In sponges, AP is used to indicate the direction of movement [in larval stage] (as it is in other metazoans that move, e.g., the basal bilaterians). [PM] anterior-posterior axis An axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm cephalocaudal axis http://en.wikipedia.org/wiki/Anatomical_terms_of_location craniocaudal axis rostral/caudal rostrocaudal axis An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure. apical/basal spatial longitudinal axis BSPO:0000014 apical-basal axis relative to substrate An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure. BSPO:mah An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal). proximal/distal proximodistal spatial BSPO:0000015 In some communities, proximal and distal are used when specifying the position of parts of elements that are contained within the body, such as gill arches or vertebral spines. In these cases, use of the classes medial-lateral axis or medial-external axis are more appropriate. proximal-distal axis An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal). BSPO:curators http://en.wikipedia.org/wiki/Anatomical_terms_of_location An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body. D-V axis DV axis dorsoventral axis anterior-posterior axis spatial BSPO:0000016 dorsal-ventral axis An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body. BSPO:curators anterior-posterior axis An axis that bisects an organism from left to right sides of body, through a sagittal plane. L-R axis LR axis R-L axis RL axis dextro-sinister axis left to right axis right to left axis right-left axis spatial BSPO:0000017 left-right axis An axis that bisects an organism from left to right sides of body, through a sagittal plane. BSPO:cjm Anatomical plane that divides body into anterior and posterior parts. FMA:12247 axial plane axial section transverse section spatial cross-section BSPO:0000018 transverse plane Anatomical plane that divides body into anterior and posterior parts. BSPO:mah Anatomical plane that divides bilateral body into dorsal and ventral parts. FMA:52810 frontal plane horizontal anatomical plane horizontal section spatial coronal section frontal section BSPO:0000019 horizontal plane Anatomical plane that divides bilateral body into dorsal and ventral parts. BSPO:mah horizontal anatomical plane FMA:52810 Anatomical region that overlaps the anterior and dorsal regions of a body or body part. Melissa Haendel 2009-06-15T01:01:38Z anterodorsal region spatial BSPO:0000026 antero-dorsal region Anatomical region that overlaps the anterior and dorsal regions of a body or body part. BSPO:wd Anatomical region that overlaps the anterior and ventral regions of a body or body part. Melissa Haendel 2009-06-15T01:04:59Z anteroventral region spatial BSPO:0000027 antero-ventral region Anatomical region that overlaps the anterior and ventral regions of a body or body part. BSPO:wd Anatomical region that overlaps the posterior and lateral regions of the body or body part. Melissa Haendel 2009-06-15T01:06:01Z posterolateral region spatial BSPO:0000028 postero-lateral region Anatomical region that overlaps the posterior and lateral regions of the body or body part. BSPO:wd Anatomical region that overlaps the anterior and lateral regions of a body or body part. Melissa Haendel 2009-06-15T01:07:18Z anterolateral region spatial BSPO:0000029 antero-lateral region Anatomical region that overlaps the anterior and lateral regions of a body or body part. BSPO:wd Anatomical region that overlaps the posterior and dorsal regions of the body or body part. Melissa Haendel 2009-06-15T01:08:13Z posterodorsal region spatial BSPO:0000030 postero-dorsal region Anatomical region that overlaps the posterior and dorsal regions of the body or body part. BSPO:wd Anatomical region that overlaps the posterior and ventral regions of a body or body part. Melissa Haendel 2009-06-15T01:08:38Z posteroventral region spatial BSPO:0000035 postero-ventral region Anatomical region that overlaps the posterior and ventral regions of a body or body part. BSPO:wd An anatomical region bounded by a plane perpendicular to an axis through the middle. FBql:00005841 spatial BSPO:0000054 anatomical side An anatomical region bounded by a plane perpendicular to an axis through the middle. BSPO:cjm An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane. FBcv:0000053 FBql:00005848 anterior rostral spatial BSPO:0000055 anterior side An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:RW An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane. FBcv:0000065 FBql:00005849 posterior caudal spatial BSPO:0000056 posterior side An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:RW BSPO:wd caudal Anatomical side that is located on the apical end of an organism or structure. FBcv:0000054 FBql:00005854 apical spatial BSPO:0000057 apical side Anatomical side that is located on the apical end of an organism or structure. BSPO:wd Anatomical side that is located on the basal end of an organism or structure. FBcv:0000055 FBql:00005855 basal spatial BSPO:0000058 The part of the organism attached to a substrate. Axis of symmetry. basal side Anatomical side that is located on the basal end of an organism or structure. BSPO:wd An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane. FBcv:0000059 FBql:00005842 dorsal spatial BSPO:0000063 dorsal side An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane. BSPO:wd FBcv:0000063 FBql:00005844 lateral spatial BSPO:0000066 lateral side An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. FBcv:0000070 FBql:00005843 ventral spatial BSPO:0000068 ventral side An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. BSPO:RW BSPO:wd A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. FBql:00005841 spatial BSPO:0000070 to be merged into CARO anatomical region A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. BSPO:cjm Anatomical region anteriorly located on the body or body part. FBql:00005848 spatial BSPO:0000071 anterior region Anatomical region anteriorly located on the body or body part. BSPO:wd Anatomical region posteriorly located on the body or body part. FBql:00005849 spatial BSPO:0000072 posterior region Anatomical region posteriorly located on the body or body part. BSPO:wd Anatomical region located on the apical end on the body or body part. FBql:00005854 spatial BSPO:0000073 apical region Anatomical region located on the apical end on the body or body part. BSPO:wd Anatomical region located basally on the body or body part. FBql:00005855 spatial BSPO:0000074 basal region Anatomical region located basally on the body or body part. BSPO:wd Anatomical region dorsally located on the body or body part. FBql:00005842 spatial BSPO:0000079 dorsal region Anatomical region dorsally located on the body or body part. BSPO:wd Anatomical region that overlaps the dorsal and lateral regions of a body or body part. FBql:00005845 dorsolateral region spatial BSPO:0000080 dorso-lateral region Anatomical region that overlaps the dorsal and lateral regions of a body or body part. BSPO:wd Anatomical region laterally located on the body or body part. FBql:00005844 spatial BSPO:0000082 lateral region Anatomical region laterally located on the body or body part. BSPO:wd Anatomical region ventrally located on the body or body part. FBql:00005843 spatial BSPO:0000084 ventral region Anatomical region ventrally located on the body or body part. BSPO:wd Anatomical region that overlaps the ventral and lateral regions of a body or body part. FBql:00005846 ventrolateral region spatial BSPO:0000085 This is an example of a composition of two axis positions. ventro-lateral region Anatomical region that overlaps the ventral and lateral regions of a body or body part. BSPO:wd FBql:00005873 FMA:9647 spatial BSPO:0000086 to be merged into CARO anatomical compartment FBql:00005881 spatial BSPO:0000092 to be merged into CARO anatomical compartment boundary FBcv:0000034 FBql:00005879 spatial BSPO:0000094 dorsal/ventral compartment boundary An anatomical axis that extends from the center of the body outwards or externally. wasila.dahdul 2013-07-02T11:21:42Z spatial proximal-distal axis BSPO:0000196 The medial-external axis could apply to a sphere-shaped body. medial-external axis An anatomical axis that extends from the center of the body outwards or externally. BSPO:curators An axis that extends from the oral opening to the furthest point in an organism that is directly opposite. wasila.dahdul 2013-07-02T11:29:33Z spatial BSPO:0000198 oral-aboral axis An axis that extends from the oral opening to the furthest point in an organism that is directly opposite. BSPO:PM Anatomical surface that is located on the anterior side of the body or body part. FBql:00005848 spatial BSPO:0000371 anterior surface Anatomical surface that is located on the anterior side of the body or body part. BSPO:wd Anatomical surface that is located on the posterior side of the body or body part. FBql:00005849 spatial BSPO:0000372 posterior surface Anatomical surface that is located on the posterior side of the body or body part. BSPO:wd Anatomical surface that is located on the apical side of the body or body part. FBql:00005854 spatial BSPO:0000373 apical surface Anatomical surface that is located on the apical side of the body or body part. BSPO:wd Anatomical surface that is located on the basal side of the body or body part. FBql:00005855 spatial BSPO:0000374 basal surface Anatomical surface that is located on the basal side of the body or body part. BSPO:wd Anatomical surface that located on the dorsal side of the body or body part. FBql:00005842 spatial BSPO:0000379 dorsal surface Anatomical surface that located on the dorsal side of the body or body part. BSPO:wd Anatomical surface that located on the lateral side of the body or body part. FBql:00005844 spatial BSPO:0000382 lateral surface Anatomical surface that located on the lateral side of the body or body part. BSPO:wd Anatomical surface that is located on the ventral side of the body or body part. FBql:00005843 spatial BSPO:0000384 ventral surface Anatomical surface that is located on the ventral side of the body or body part. BSPO:wd A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions. FMA:242982 anatomical cross-section anatomical section plane section spatial cross-section BSPO:0000400 These anatomical sections are applicable to most bilaterally symmetrical animals, but bipedal animals such as humans have more complex usage of these terms. For example, in post-embryonic humans a coronal plane is vertical and a transverse plane is horizontal, but for embryos and quadrupeds a coronal plane is horizontal and a transverse plane is vertical. anatomical plane A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions. BSPO:cjm Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size. FMA:11361 left/right plane median plane sagittal section spatial BSPO:0000417 sagittal plane Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size. BSPO:DOS BSPO:cjm BSPO:mah An axis that extends from the center of organism to one or other side. http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG M-L axis ML axis medio-lateral axis mediolateral axis spatial proximal-distal axis BSPO:0001001 Properly, the ML axis is a half axis; practically, its usage is less clumsy and less linguistically biased than "left-right". The terms may still be used relatively to describe locations along the LR axis. The gills are medial to the operculum, but lateral to the heart. medial-lateral axis An axis that extends from the center of organism to one or other side. BSPO:cjm A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. spatial CARO:0000000 Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. anatomical entity anatomical entity A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. CAROC:Brownsville2014 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. CARO:MAH Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. spatial CARO:0000003 anatomical structure connected anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CC:DOS An anatomical entity that has mass. spatial CARO:0000006 material anatomical entity material anatomical entity An anatomical entity that has mass. CC:DOS An anatomical entity that has no mass. spatial CARO:0000007 immaterial anatomical entity An anatomical entity that has no mass. CC:DOS A one dimensional, immaterial anatomical entity. spatial CARO:0000008 anatomical line A one dimensional, immaterial anatomical entity. CC:DOS A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. spatial CARO:0000010 anatomical boundary A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. CC:DOS biological entity The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GO:0019952 GO:0050876 Wikipedia:Reproduction reproductive physiological process biological_process GO:0000003 reproduction The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GOC:go_curators GOC:isa_complete GOC:jl ISBN:0198506732 The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis. G1 phase of mitotic cell cycle biological_process GO:0000080 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic G1 phase The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis. GOC:mtg_cell_cycle The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle. S phase of mitotic cell cycle S-phase of mitotic cell cycle biological_process GO:0000084 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic S phase The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle. GOC:mtg_cell_cycle The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis. G2 phase of mitotic cell cycle biological_process GO:0000085 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic G2 phase The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis. GOC:mtg_cell_cycle A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle. M phase of mitotic cell cycle M-phase of mitotic cell cycle biological_process GO:0000087 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic M phase A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle. GOC:mtg_cell_cycle The cell cycle phase which is the first stage of M phase of mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. biological_process GO:0000088 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic prophase The cell cycle phase which is the first stage of M phase of mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. GOC:mtg_cell_cycle The cell cycle phase, following prophase, during which chromosomes become aligned on the equatorial plate of the cell as part of a mitotic cell cycle. biological_process GO:0000089 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic metaphase The cell cycle phase, following prophase, during which chromosomes become aligned on the equatorial plate of the cell as part of a mitotic cell cycle. GOC:mtg_cell_cycle The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of a mitotic cell cycle. biological_process GO:0000090 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic anaphase The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of a mitotic cell cycle. GOC:mtg_cell_cycle The cell cycle phase which follows anaphase during M phase of mitosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. biological_process GO:0000093 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic telophase The cell cycle phase which follows anaphase during M phase of mitosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. GOC:mtg_cell_cycle The cell cycle phase which is the first stage of prophase I in meiosis, and during which the chromosomes first become visible. Wikipedia:Leptotene Wikipedia:Meiosis#Leptotene biological_process GO:0000237 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). leptotene The cell cycle phase which is the first stage of prophase I in meiosis, and during which the chromosomes first become visible. GOC:mtg_cell_cycle The cell cycle phase which follows leptotene during prophase I of meiosis, and during which each chromosome pairs with its homolog; the two become aligned and crossing over may occur. Wikipedia:Meiosis#Zygotene Wikipedia:Zygotene biological_process GO:0000238 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). zygotene The cell cycle phase which follows leptotene during prophase I of meiosis, and during which each chromosome pairs with its homolog; the two become aligned and crossing over may occur. GOC:mtg_cell_cycle The cell cycle phase which follows zygotene during prophase I of meiosis, and during which crossing over occurs between a chromatid in one partner and another chromatid in the homologous chromosome. Wikipedia:Meiosis#Pachytene Wikipedia:Pachytene biological_process GO:0000239 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). pachytene The cell cycle phase which follows zygotene during prophase I of meiosis, and during which crossing over occurs between a chromatid in one partner and another chromatid in the homologous chromosome. GOC:mtg_cell_cycle The cell cycle phase which follows pachytene during prophase I of meiosis, during which the homologous chromosomes begin to separate and the synaptonemal complex dissolves. Wikipedia:Diplotene Wikipedia:Meiosis#Diplotene biological_process GO:0000240 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). diplotene The cell cycle phase which follows pachytene during prophase I of meiosis, during which the homologous chromosomes begin to separate and the synaptonemal complex dissolves. GOC:mtg_cell_cycle The cell cycle phase which follows diplotene during prophase I of meiosis, the separation of homologous chromosomes is complete and crossing over has occurred. Wikipedia:Diakinesis Wikipedia:Meiosis#Diakinesis biological_process GO:0000241 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). diakinesis The cell cycle phase which follows diplotene during prophase I of meiosis, the separation of homologous chromosomes is complete and crossing over has occurred. GOC:mtg_cell_cycle Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GO:0007067 Wikipedia:Mitosis biological_process mitosis GO:0000278 Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. mitotic cell cycle Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 Reactome:69278 A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase. Wikipedia:M_phase M-phase biological_process GO:0000279 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). M phase A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase. GOC:mtg_cell_cycle The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. biological_process karyokinesis GO:0000280 nuclear division The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. GOC:mah A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring. puberty biological_process reproductive developmental process GO:0003006 developmental process involved in reproduction A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring. GOC:dph GOC:isa_complete puberty GOC:dph reproductive developmental process GOC:dph GOC:tb A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. molecular process molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. GOC:pdt catalytic activity A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). GOC:pdt NIF_Subcellular:sao1337158144 subcellular entity NIF_Subcellular:nlx_subcell_100315 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. jl 2013-12-19T15:25:51Z GO:1902589 organelle organisation single organism organelle organization biological_process organelle organization and biogenesis single-organism organelle organization GO:0006996 organelle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:mah single organism organelle organization GOC:TermGenie organelle organization and biogenesis GOC:dph GOC:jl GOC:mah The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. Wikipedia:Cell_cycle cell-division cycle biological_process GO:0007049 cell cycle The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. GOC:go_curators GOC:mtg_cell_cycle The cell cycle phase which is the first stage of meiosis I and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. biological_process GO:0007128 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic prophase I The cell cycle phase which is the first stage of meiosis I and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. GOC:mtg_cell_cycle The cell cycle phase, following prophase I, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis I. biological_process GO:0007132 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic metaphase I The cell cycle phase, following prophase I, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis I. GOC:mtg_cell_cycle The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis I. biological_process GO:0007133 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic anaphase I The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis I. GOC:mtg_cell_cycle The cell cycle phase which follows anaphase I of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. biological_process GO:0007134 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic telophase I The cell cycle phase which follows anaphase I of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. GOC:mtg_cell_cycle The cell cycle phase which is the first stage of meiosis II and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. biological_process GO:0007136 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic prophase II The cell cycle phase which is the first stage of meiosis II and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. GOC:mtg_cell_cycle The cell cycle phase, following prophase II, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis II. biological_process GO:0007137 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic metaphase II The cell cycle phase, following prophase II, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis II. GOC:mtg_cell_cycle The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis II. biological_process GO:0007138 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic anaphase II The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of meiosis II. GOC:mtg_cell_cycle The cell cycle phase which follows anaphase II of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. biological_process GO:0007139 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic telophase II The cell cycle phase which follows anaphase II of meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. GOC:mtg_cell_cycle A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. jl 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0044235 GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism biological_process cell organization and biogenesis GO:0016043 cellular component organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:ai GOC:jl GOC:mah cellular component organisation at cellular level GOC:mah cellular component organisation in other organism GOC:mah cell organization and biogenesis GOC:mah true Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines transferase activity transferase activity, transferring phosphorus-containing groups A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid). https://github.com/geneontology/go-ontology/issues/22929 Wikipedia:Sexual_reproduction biological_process GO:0019953 Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times. sexual reproduction A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid). Wikipedia:Sexual_reproduction The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. biological_process GO:0022402 cell cycle process The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. GOC:isa_complete GOC:mtg_cell_cycle One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. biological_process GO:0022403 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). cell cycle phase One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. GOC:mtg_cell_cycle A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. jl 2012-09-19T15:56:06Z GO:0044702 biological_process single organism reproductive process GO:0022414 reproductive process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:dph GOC:isa_complete A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. jl 2012-12-19T12:21:31Z GO:0044767 development biological_process single-organism developmental process GO:0032502 developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. GOC:isa_complete The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. biological_process GO:0043473 pigmentation The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. GOC:jl A distinct period or stage in a biological process or cycle. jl 2014-07-16T13:12:40Z biological_process GO:0044848 Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase. biological phase A distinct period or stage in a biological process or cycle. GOC:jl The creation of two or more organelles by division of one organelle. biological_process GO:0048285 organelle fission The creation of two or more organelles by division of one organelle. GOC:jid The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. development of an anatomical structure biological_process GO:0048856 anatomical structure development The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GO_REF:0000021 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. Wikipedia:Cell_division biological_process GO:0051301 Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. cell division The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. GOC:di GOC:go_curators GOC:pr The cell cycle 'gap' phase which is the interval between the completion of DNA segregation (usually by mitosis or meiosis) and the beginning of DNA synthesis. Wikipedia:G1_phase biological_process GO:0051318 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). G1 phase The cell cycle 'gap' phase which is the interval between the completion of DNA segregation (usually by mitosis or meiosis) and the beginning of DNA synthesis. GOC:mtg_cell_cycle The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation (usually by mitosis or meiosis). Wikipedia:G2_phase biological_process GO:0051319 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). G2 phase The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation (usually by mitosis or meiosis). GOC:mtg_cell_cycle The cell cycle phase, following G1, during which DNA synthesis takes place. Wikipedia:S_phase S-phase biological_process GO:0051320 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). S phase The cell cycle phase, following G1, during which DNA synthesis takes place. GOC:mtg_cell_cycle Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. https://github.com/geneontology/go-ontology/issues/24599 GO:0007126 Wikipedia:Meiosis biological_process meiosis GO:0051321 Note that this term should not be confused with 'GO:0140013 ; meiotic nuclear division'. 'GO:0051321 ; meiotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140013 meiotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. meiotic cell cycle Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. GOC:ai The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle. Wikipedia:Anaphase biological_process GO:0051322 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). anaphase The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle. GOC:mtg_cell_cycle The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell. Wikipedia:Metaphase biological_process GO:0051323 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). metaphase The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell. GOC:mtg_cell_cycle The cell cycle phase which is the first stage of M phase of meiosis and mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. Wikipedia:Prophase biological_process GO:0051324 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). prophase The cell cycle phase which is the first stage of M phase of meiosis and mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell. GOC:mtg_cell_cycle The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs. resting phase Wikipedia:Interphase karyostasis biological_process GO:0051325 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). interphase The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs. GOC:mtg_cell_cycle The cell cycle phase which follows anaphase during M phase of mitosis and meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. Wikipedia:Telophase biological_process GO:0051326 note that this term should not be used for direct annotation. if you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic s-phase). to capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). telophase The cell cycle phase which follows anaphase during M phase of mitosis and meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts. GOC:mtg_cell_cycle A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a meiotic cell cycle. M phase of meiotic cell cycle biological_process GO:0051327 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic M phase A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a meiotic cell cycle. GOC:mtg_cell_cycle The cell cycle phase which begins after cytokinesis and ends when meiotic prophase begins. Meiotic cells have an interphase after each meiotic division, but only interphase I involves replication of the cell's DNA. interphase of meiotic cell cycle biological_process GO:0051328 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic interphase The cell cycle phase which begins after cytokinesis and ends when meiotic prophase begins. Meiotic cells have an interphase after each meiotic division, but only interphase I involves replication of the cell's DNA. GOC:mtg_cell_cycle The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs. interphase of mitotic cell cycle biological_process GO:0051329 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic interphase The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs. GOC:mtg_cell_cycle The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by meiosis and the beginning of DNA synthesis. G1 phase of meiotic cell cycle biological_process GO:0051330 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic G1 phase The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by meiosis and the beginning of DNA synthesis. GOC:mtg_cell_cycle The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by meiosis. G2 phase of meiotic cell cycle biological_process GO:0051331 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic G2 phase The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by meiosis. GOC:mtg_cell_cycle The cell cycle phase, following G1, during which DNA synthesis takes place as part of a meiotic cell cycle. S phase of meiotic cell cycle S-phase of meiotic cell cycle premeiotic S-phase biological_process GO:0051332 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic S phase The cell cycle phase, following G1, during which DNA synthesis takes place as part of a meiotic cell cycle. GOC:mtg_cell_cycle A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. mah 2010-09-10T01:39:16Z GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level biological_process GO:0071840 cellular component organization or biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:mah cellular component organisation or biogenesis GOC:mah cellular component organisation or biogenesis at cellular level GOC:mah One of the distinct periods or stages into which the meiotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. biological_process GO:0098762 This term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation should be to 'regulation of x/y phase transition' or to a process which occurs during the reported phase (e.g. mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiotic cell cycle phase One of the distinct periods or stages into which the meiotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. GOC:dos One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. biological_process GO:0098763 This term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation should be to 'regulation of x/y phase transition' or to a process which occurs during the reported phase (e.g. mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). mitotic cell cycle phase One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events. GOC:dos A meiotic cell cycle phase prior to a during which some part of meiosis I nuclear division or the proceeding cytokinesis occurs. biological_process GO:0098764 Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiosis I cell cycle phase A meiotic cell cycle phase prior to a during which some part of meiosis I nuclear division or the proceeding cytokinesis occurs. GOC:dos A meiotic cell cycle phase that occurs after meiosis I (the first meiotic nuclear division). biological_process GO:0098765 This term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation should be to 'regulation of x/y phase transition' or to a process which occurs during the reported phase (e.g. mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). meiosis II cell cycle phase A meiotic cell cycle phase that occurs after meiosis I (the first meiotic nuclear division). GOC:dos One of the two nuclear divisions that occur as part of the meiotic cell cycle. https://github.com/geneontology/go-ontology/issues/19910 pg 2017-03-23T09:40:00Z meiosis biological_process GO:0140013 meiotic nuclear division One of the two nuclear divisions that occur as part of the meiotic cell cycle. PMID:9334324 A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. https://github.com/geneontology/go-ontology/issues/19910 pg 2017-03-23T14:44:23Z mitosis biological_process GO:0140014 mitotic nuclear division A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. ISBN:0198547684 A process that is part of the meiotic cell cycle. jl 2014-05-22T14:22:28Z biological_process GO:1903046 meiotic cell cycle process A process that is part of the meiotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 A process that is part of the mitotic cell cycle. jl 2014-05-22T14:22:34Z biological_process GO:1903047 mitotic cell cycle process A process that is part of the mitotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles. A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. Justin Whorton PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls https://github.com/information-artifact-ontology/IAO/issues/237 centrally registered identifier registry identifier An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. Justin Whorton Mathias Brochhausen proper name https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB) identifier A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. Justin Whorton Mathias Brochhausen dubbing process naming https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen identifier creating process An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. Alan Ruttenberg Justin Whorton Mathias Brochhausen code map code system codeset coding system controlled vocabulary https://github.com/information-artifact-ontology/IAO/issues/237 Alan Ruttenberg Clint Dowland Matt Diller Sarah Bost William R. Hogan Code sets might include non-entities/things (e.g. missing thumbs). Does not imply absence vs. presence of any taxonomy. Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities. Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs). For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets. Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain. The information content entities do not denote each other. code set planned process A process that realizes a plan which is the concretization of a plan specification. planned process A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality (PATO) PATO:0000072 quality PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. quality PATO:0000051 morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATO:0001647 relational shape quality quality PATO:0000052 Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. shape A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's placement which is defined by the angle between the bearer and an axis, or the angle between the bearer and another object. PATO:0000137 angular placement quality amount of rotation angle angular magnitude plane angle PATO:0000133 orientation A spatial quality inhering in a bearer by virtue of the bearer's placement which is defined by the angle between the bearer and an axis, or the angle between the bearer and another object. PATOC:JE A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATO:0001032 PATO:0001631 location placement relational spatial quality quality PATO:0000140 position A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATOC:GVG A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality quality PATO:0001018 physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality A quality which inheres in a continuant. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's having three angles. deltoid quality delta shaped triangle triangle-shaped PATO:0001875 triangular A shape quality inhering in a bearer by virtue of the bearer's having three angles. wordreference:wordreference A shape quality inhering in a bearer by virtue of the bearer's being narrowly triangular, wider at the apex and tapering toward the base. wedge-shaped quality PATO:0001955 cuneate A shape quality inhering in a bearer by virtue of the bearer's being narrowly triangular, wider at the apex and tapering toward the base. wordreference:wordreference A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. quality 2-D projection cross-sectional PATO:0002006 2-D shape A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. PATOC:CJM An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed along the longitudinal or anterior-posterior axis. 2014-10-17T14:24:19Z quality PATO:0005024 longitudinal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed along the longitudinal or anterior-posterior axis. PATOC:WD A shape that is in the form of a plug, being tube-like and expanded on one end. 2018-11-12T18:24:41Z plug like quality PATO:0040012 plug shaped A shape that is in the form of a plug, being tube-like and expanded on one end. https://orcid.org/0000-0003-3162-7490 A stage of Smed embryonic development, 0 - 2 days post-egg capsule deposition at 20˚C. Zygote and dispersed blastomere cleavage in a yolk syncytium. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Schmidtea_mediterranea_Developmental_Stages Stage 1 A stage of Smed embryonic development, 0 - 2 days post-egg capsule deposition at 20˚C. Zygote and dispersed blastomere cleavage in a yolk syncytium. PMID:28072387 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 3 days post-egg capsule deposition at 20˚C. 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 protosphere Schmidtea_mediterranea_Developmental_Stages Stage 2 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 3 days post-egg capsule deposition at 20˚C. 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. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 2 embryo. Scale bar = 100um A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 4 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Schmidtea_mediterranea_Developmental_Stages Stage 3 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 2 - 4 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall of nascent spheres. Yolk ingestion into the gut cavity. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 3 embryo. Scale bar = 100um A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 3 - 5 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Schmidtea_mediterranea_Developmental_Stages Stage 4 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 3 - 5 days post-egg capsule deposition at 20˚C. Dispersed blastomere cleavage in the embryonic wall. Yolk ingestion into the gut cavity. Early embryonic gut formation. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 4 embryo. Scale bar = 100um A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 5-7 days post-egg capsule deposition at 20˚C. 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Schmidtea_mediterranea_Developmental_Stages Stage 5 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 5-7 days post-egg capsule deposition at 20˚C. 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. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo. Scale bar = 100um A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 7 - 9 days post-egg capsule deposition at 20˚C. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Schmidtea_mediterranea_Developmental_Stages Stage 6 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 7 - 9 days post-egg capsule deposition at 20˚C. Organogenesis and morphogenesis. Definitive organ formation. Temporary embryonic cell types degenerate. Embryo elongation. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 6 embryo. Scale bar = 100um A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 9 - 11 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 PMID:28812561 Schmidtea_mediterranea_Developmental_Stages Stage 7 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 9 - 11 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Embryos elongated. Eyes just visible. Onset of gliding motility. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 7 embryo. Scale bar = 100um A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 13 - 15 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Hatching. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 hatchling newborn hatchling Schmidtea_mediterranea_Developmental_Stages Stage 8 A stage of Smed embryonic development defined by a unique gene expression signature and morphology, 13 - 15 days post-egg capsule deposition at 20˚C. Organogenesis and organ maturation continues. Hatching. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 8 embryo. Scale bar = 100um 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:15972844 PMID:25017721 PMID:25956527 PMID:26457503 PMID:26651295 PMID:27013241 PMID:27150006 PMID:27542689 PMID:28287248 PMID:28686611 PMID:28757112 PMID:29557542 PMID:29674432 PMID:29906446 sigma class neoblast sigma-class neoblast Planarian_Anatomy sigma neoblast 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 cell 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:24523458 PMID:28072387 Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system. neural committed stem cell neural precursor cell neural progenitor cell neuronal progenitor Planarian_Anatomy PLANA:0000012 neural progenitor cell Neoblasts and their differentiating daughters implicated in maintenance and regeneration of different tissues in the nervous system. PMID:21282632 PMID:24173799 PMID:25356635 PMID:26057828 PMID:26525673 PMID:28072387 PMID:29674432 Musculature surrounding internal organs of the body. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 FBbt:00005070 PMID:26904543 PMID:30471994 visceral muscle Planarian_Anatomy visceral musculature Musculature surrounding internal organs of the body. PMID:26904543 PMID:30471994 Image is an electron micrograph depicting the visceral musculature (arrowheads) that lies beneath the gut. The gut is identifiable by the collection of darkly stained lipid droplets in the top right corner and the white of the lumen at the top of the image. Scale bar is 10um An abundant neoblast subclass consisting of p53+, zfp1+ progenitors required for maintenance and regeneration of epidermal cell type(s). https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:25017721 PMID:25956527 PMID:26457503 PMID:26651295 PMID:27013241 PMID:27150006 PMID:27542689 PMID:28292427 PMID:28757112 PMID:28807897 PMID:29158443 PMID:29557542 PMID:29674431 PMID:29674432 PMID:29906446 zeta zeta class zeta class neoblast zeta-class neoblast zeta-neoblast Planarian_Anatomy zeta neoblast 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 XAO:0004225 Planarian_Anatomy non ciliated epithelial cell Image is an electron micrograph of the dorsal side of the animal where there is a transition from nonciliated epidermal cells to ciliated ones. On the left side of the image are the ciliated cells and on the right are the nonciliated. A few nonciliated have been marked with arrowheads. Scale bar is 10um. 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:15866156 PMID:16033796 PMID:16311336 PMID:16890156 PMID:17251262 PMID:17376870 PMID:17390146 PMID:17670787 PMID:17905225 PMID:17942485 PMID:18063755 PMID:18063757 PMID:18202849 PMID:18287199 PMID:18456843 PMID:18786419 PMID:19048075 PMID:19174194 PMID:19211673 PMID:19247960 PMID:19766622 PMID:19852954 PMID:19933103 PMID:20215344 PMID:20223763 PMID:20422023 PMID:20511647 PMID:20599901 PMID:20707997 PMID:20865784 PMID:20967238 PMID:21179478 PMID:21282632 PMID:21295483 PMID:21356107 PMID:21458439 PMID:21664348 PMID:21747960 PMID:21806978 PMID:21828097 PMID:21852957 PMID:21894189 PMID:21937596 PMID:22125640 PMID:22339734 PMID:22371573 PMID:22385657 PMID:22411224 PMID:22439894 PMID:22451003 PMID:22543868 PMID:22884275 PMID:23079596 PMID:23123964 PMID:23250205 PMID:23297191 PMID:23318635 PMID:23405188 PMID:23629965 PMID:23652002 PMID:23954785 PMID:24040508 PMID:24063805 PMID:24120894 PMID:24131630 PMID:24173799 PMID:24238224 PMID:24704339 PMID:24737865 PMID:24922054 PMID:25017721 PMID:25254346 PMID:25356635 PMID:25558068 PMID:25725068 PMID:25956527 PMID:26062938 PMID:26114597 PMID:26457503 PMID:26459857 PMID:26525673 PMID:26711341 PMID:27034770 PMID:27063937 PMID:27074666 PMID:27122174 PMID:27150006 PMID:27163480 PMID:27240733 PMID:27441386 PMID:27501047 PMID:27551436 PMID:27612382 PMID:27612384 PMID:27654173 PMID:28072387 PMID:28126842 PMID:28171748 PMID:28245923 PMID:28287248 PMID:28292427 PMID:28434803 PMID:28461239 PMID:28495872 PMID:28686611 PMID:28807897 PMID:28893948 PMID:29291981 PMID:29674431 PMID:29906446 PMID:30194301 PMID:30237141 PMID:30282036 PMID:30383829 PMID:30399335 PMID:30471994 PMID:30485821 PMID:30729158 PMID:30962434 https://doi.org/10.1101/279364 definitive pharynx Planarian_Anatomy pharynx 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:16033796 PMID:17251262 PMID:17390146 PMID:17553481 PMID:17905225 PMID:17942485 PMID:18202849 PMID:19048075 PMID:20967238 PMID:21282632 PMID:21852957 PMID:22339734 PMID:22411224 PMID:22427692 PMID:22445864 PMID:22549959 PMID:22884275 PMID:23250205 PMID:23318641 PMID:24063805 PMID:24922054 PMID:25254346 PMID:25356635 PMID:25493551 PMID:25772472 PMID:26017970 PMID:26618653 PMID:27068018 PMID:27606067 PMID:27612384 PMID:27800171 PMID:28137894 PMID:28216315 PMID:28245923 PMID:28495872 PMID:28976975 PMID:29547123 PMID:29674431 PMID:29674432 PMID:30143032 PMID:30399335 PMID:30471994 PMID:30485821 UBERON:0006562 PRN neuronal photoreceptive cell optical neuron photoreceptive neuron photoreceptor cell photosensitive cell visual neuron Planarian_Anatomy photoreceptor neuron 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:18786419 PMID:22439894 PMID:25017721 PMID:26457503 PMID:28072387 Planarian_Anatomy Category 4 cell 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:29674431 PMID:29674432 PMID:30471994 Planarian_Anatomy muscle progenitor cell 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:19852954 PMID:19933103 PMID:21828097 PMID:21937596 PMID:22479207 PMID:23318635 PMID:23318641 PMID:23954785 PMID:24063805 PMID:24523458 PMID:24737865 PMID:24992682 PMID:25017721 PMID:25254346 PMID:26057828 PMID:26457503 PMID:26651295 PMID:26711341 PMID:27068018 PMID:27150006 PMID:27501047 PMID:27551436 PMID:27612384 PMID:28245923 PMID:28292427 PMID:28807897 PMID:29100657 PMID:29158443 PMID:29674431 PMID:29674432 UBERON:0006973 excretory organ nephridia osmoregulatory duct protonephridial tubule Planarian_Anatomy protonephridia Excretory organs consisting of flame cells, proximal tubules, and distal tubules connected to a mesenchymal collecting duct. OCLC:16809160 PMID:21828097 PMID:26057828 http://purl.obolibrary.org/obo/Depicted by field contains a whole-mount acetylated tubulin (AcTub) staining. Scale bars_ 500 um. Inset to right shows depth-coded projection of AcTub staining. Superficial structures are in blue and deeper structures are in red. Scale bars: 50 um Organisms sharing a specified genotype or karyotype. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 Planarian_Anatomy biotype Post-mitotic, ciliated epidermal cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:25017721 PMID:28072387 Planarian_Anatomy Category 5 cell Post-mitotic, ciliated epidermal cells. PMID:25017721 An innervated, muscular pump that ingests yolk cells into the gut cavity. The embryonic pharynx is an extraembryonic tissue that forms during Stage 2, functions during Stages 3-5, and degenerates during Stages 6-7. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 FBbt:00001866 ISBN:9780070316607 PMID:28072387 temporary embryonic pharynx Planarian_Anatomy embryonic pharynx An innervated, muscular pump that ingests yolk cells into the gut cavity. The embryonic pharynx is an extraembryonic tissue that forms during Stage 2, functions during Stages 3-5, and degenerates during Stages 6-7. PMID:28072387 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo that zooms in on the embryonic pharynx. Asexual animal strains 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:11972158 PMID:28812561 asexual asexual adult asexual biotype Planarian_Anatomy Smed asexual biotype Asexual animal strains that reproduce solely through fission followed by whole body regeneration. Asexual Smed are stable diploids that harbor a chromosome translocation, making them karyotypically distinct from sexual Smed. PMID:11972158 PMID:17376870 Image is an scanning electron micrograph of the dorsal side of an entire animal. This is an adult asexual Schmidtea mediterranea. Anterior is to the right and posterior is to the left. Scale bar is 500um. 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]. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:16033796 PMID:16311336 PMID:17251262 PMID:18202849 PMID:19048075 PMID:19211673 PMID:19247960 PMID:20223763 PMID:20707997 PMID:20967238 PMID:21806978 PMID:22339734 PMID:22427692 PMID:22445864 PMID:22549959 PMID:22696458 PMID:23079596 PMID:23250205 PMID:23297191 PMID:23318641 PMID:23903188 PMID:24131630 PMID:24173799 PMID:24737865 PMID:24950970 PMID:25254346 PMID:25278423 PMID:25725068 PMID:26062938 PMID:26114597 PMID:26556349 PMID:27013241 PMID:27068018 PMID:27163480 PMID:27501047 PMID:27523733 PMID:27551436 PMID:27612384 PMID:27864883 PMID:28292427 PMID:29357350 PMID:29557542 PMID:29674431 PMID:30399335 UBERON:0001016 nerve system Planarian_Anatomy nervous system 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 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 gut through the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:17553481 PMID:17942485 PMID:18063757 PMID:18287199 PMID:19174194 PMID:19247960 PMID:19933103 PMID:20707997 PMID:20865784 PMID:20967238 PMID:21179478 PMID:21282632 PMID:21356107 PMID:21458439 PMID:21566185 PMID:21566195 PMID:21664348 PMID:21806978 PMID:21828097 PMID:22411224 PMID:22439894 PMID:22451003 PMID:22899852 PMID:23079596 PMID:23235145 PMID:23250205 PMID:23318635 PMID:23318641 PMID:23405188 PMID:23903188 PMID:23954785 PMID:24040508 PMID:24063805 PMID:24120894 PMID:24173799 PMID:24238224 PMID:24415944 PMID:24737865 PMID:24950970 PMID:24992682 PMID:25017721 PMID:25254346 PMID:25356635 PMID:25558068 PMID:25956527 PMID:26062938 PMID:26114597 PMID:26457503 PMID:26556349 PMID:26651295 PMID:27034770 PMID:27063937 PMID:27074666 PMID:27122174 PMID:27150006 PMID:27163480 PMID:27240733 PMID:27441386 PMID:27501047 PMID:27542689 PMID:27551436 PMID:27612382 PMID:27612384 PMID:27864883 PMID:28072387 PMID:28216315 PMID:28245923 PMID:28287248 PMID:28292427 PMID:28461239 PMID:28686611 PMID:28807897 PMID:29100657 PMID:29158443 PMID:29547123 PMID:29674431 PMID:29674432 PMID:29906446 PMID:30143032 PMID:30194301 PMID:30282036 PMID:30297872 PMID:30383829 PMID:30471994 PMID:30962434 UBERON:0000160 https://doi.org/10.1101/279364 adult gut blind gut definitive gut digestive tract gastrovascular digestive tract gastrovascular tract intestinal tract intestine three-branched gut triclad gut Planarian_Anatomy gut The planarian triclad gut contains a central anterior gut branch connected to two posterior gut branches arranged around the 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 gut through the pharynx. PMID:3490491 Strains of 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:11972158 PMID:19022767 PMID:28812561 hermaphroditic biotype sexual sexual hermaphrodite Planarian_Anatomy Smed sexual biotype Strains of cross-fertilizing hemaphrodites that reproduce sexually and do not undergo fission. After mating, each parent lays an egg capsule containing one or more embryos. Sexual Smed are stable diploids. PMID:11972158 PMID:19022767 Depicted by field contains light micrscope image of asexual and sexual biotypes of Schmidtea meditteranea with their respective karyotypes. Note that the asexual bioptype has a chromosome inversion compared to the sexual. Post-mitotic, mesenchymally located epidermal progenitors downstream of the zeta neoblasts. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:18786419 PMID:20040488 PMID:21894189 PMID:22385657 PMID:22427692 PMID:22439894 PMID:22899852 PMID:23318635 PMID:23629965 PMID:24063805 PMID:24173799 PMID:24367277 PMID:25017721 PMID:26114597 PMID:26651295 PMID:27013241 PMID:27068018 PMID:27542689 PMID:28072387 PMID:29674431 Category 2 gene expressing cell NB.21.11e expressing cell Smed-NB.21.11e+ cell early division progeny early epidermal progenitor early neoblast progeny early post-mitotic progeny early progeny prog-1+ epidermal progenitor cell Planarian_Anatomy Category 2 cell 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:20423827 OCLC:464776945 OCLC:82522822 PMID:28072387 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000001.md Planarian_Anatomy primitive ectoderm 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 NCIT:C81170 Planarian_Anatomy midline Illustration of the midline (in green). Non-neuronal, pigmented cells arrayed along the proximal side of the optic cup. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17251262 PMID:17390146 PMID:17553481 PMID:17905225 PMID:20967238 PMID:21282632 PMID:21458439 PMID:21852957 PMID:22339734 PMID:22445864 PMID:22884275 PMID:23250205 PMID:23318641 PMID:24063805 PMID:25254346 PMID:25493551 PMID:26017970 PMID:27122174 PMID:27551436 PMID:27606067 PMID:28137894 PMID:28245923 PMID:28287248 PMID:28495872 PMID:28976975 PMID:29158443 PMID:29674431 PMID:29674432 PMID:30471994 eye pigment cell eye pigment cup cell eye pigment producing cell eye pigmented cell melanin pigment cell optic cup cell photoceptor pigmented cell Planarian_Anatomy pigment cup cell 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. dorsal region of midline Planarian_Anatomy PLANA:0000032 dorsal midline Illustration of the dorsal midline (in green). 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. epithelial progenitor Planarian_Anatomy PLANA:0000033 epidermal progenitor cell 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:27150006 PMID:27606067 PMID:29674432 PMID:30282036 A single cell layer of post-mitotic epithelial cells containing ciliated and non-ciliated cell types forming the exterior surface of the animal. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:15866156 PMID:16311336 PMID:18786419 PMID:19048075 PMID:19247960 PMID:19852954 PMID:20215344 PMID:20511647 PMID:20599901 PMID:20865784 PMID:21179478 PMID:21282632 PMID:21295483 PMID:22252539 PMID:22549959 PMID:23235145 PMID:23297191 PMID:23954785 PMID:24120894 PMID:24173799 PMID:24922054 PMID:24950970 PMID:25558068 PMID:25772472 PMID:26114597 PMID:26457503 PMID:26651295 PMID:26711341 PMID:27034770 PMID:27074666 PMID:27150006 PMID:27163480 PMID:27240733 PMID:27501047 PMID:27612384 PMID:28137894 PMID:28216315 PMID:28245923 PMID:28292427 PMID:28686611 PMID:28757112 PMID:28976975 PMID:29100657 PMID:29158443 PMID:29273738 PMID:29674431 PMID:29674432 PMID:29906446 PMID:30194301 PMID:30282036 PMID:30962434 UBERON:0001003 definitive epidermis epidermal layer epidermis epithelium mature epidermis tegument Planarian_Anatomy At present, this definition does not apply to epithelial structures other than the dorsal and ventral epidermis (i.e., the pharyngeal epithelium). epidermis 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:18786419 PMID:20040488 PMID:21894189 PMID:22252539 PMID:22427692 PMID:22439894 PMID:22899852 PMID:23297191 PMID:23318635 PMID:23629965 PMID:23954785 PMID:24063805 PMID:24173799 PMID:24367277 PMID:26114597 PMID:26457503 PMID:26651295 PMID:27013241 PMID:27068018 PMID:28072387 AGAT-1 expressing cell AGAT1 expressing cell Category 3 gene expressing cell Smed-AGAT-1+ cell late division progeny late epidermal progenitor late neoblast progeny late postmitotic progeny late progeny Planarian_Anatomy Category 3 cell 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:15866156 PMID:15972844 PMID:16311336 PMID:16890156 PMID:17251262 PMID:17553481 PMID:17905225 PMID:17942485 PMID:18063755 PMID:18063757 PMID:18202849 PMID:18287199 PMID:18456843 PMID:18786419 PMID:19048075 PMID:19174194 PMID:19211673 PMID:19247960 PMID:19766622 PMID:19805089 PMID:19852954 PMID:20040488 PMID:20215344 PMID:20223763 PMID:20422023 PMID:20599901 PMID:20707997 PMID:20865784 PMID:20967238 PMID:21179478 PMID:21282632 PMID:21295481 PMID:21295483 PMID:21356107 PMID:21458439 PMID:21566185 PMID:21566195 PMID:21747960 PMID:21806978 PMID:21828097 PMID:21852957 PMID:21894189 PMID:21937596 PMID:22125640 PMID:22318224 PMID:22339734 PMID:22385657 PMID:22411224 PMID:22439894 PMID:22445864 PMID:22479207 PMID:22549959 PMID:22884275 PMID:22899852 PMID:23235145 PMID:23297191 PMID:23318635 PMID:23318641 PMID:23405188 PMID:23629965 PMID:23903188 PMID:24063805 PMID:24120894 PMID:24131630 PMID:24173799 PMID:24238224 PMID:24415944 PMID:24704339 PMID:24737865 PMID:24922054 PMID:24950970 PMID:24992682 PMID:25017721 PMID:25254346 PMID:25356635 PMID:25493551 PMID:25558068 PMID:25725068 PMID:25772472 PMID:25956527 PMID:26017970 PMID:26062938 PMID:26114597 PMID:26457503 PMID:26525673 PMID:26556349 PMID:26618653 PMID:26711341 PMID:26884331 PMID:27034770 PMID:27063937 PMID:27150006 PMID:27240733 PMID:27542689 PMID:27551436 PMID:27606067 PMID:27654173 PMID:27800171 PMID:28171748 PMID:28216315 PMID:28287248 PMID:28292427 PMID:28495872 PMID:28686611 PMID:28893948 PMID:28976975 PMID:29100657 PMID:29158443 PMID:29273738 PMID:29291974 PMID:29291981 PMID:29357350 PMID:29547123 PMID:29674431 PMID:30237141 PMID:30282036 PMID:30297872 PMID:30383829 PMID:30485821 PMID:30962434 UBERON:0000970 https://doi.org/10.1101/279364 cerebral eye eye spot eye-spot eyespot ocelli photoreceptor Planarian_Anatomy Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. The eyes are indicated by arrows. Scale bar = 250um eye An organ that detects light. UBERON:0000970 we will move forward using "tissue" instead. We have not listed anything as a regenerating or developing tissue, so this seems unnecessary obsolete definitive tissue true The median line/ plane of bilateral symmetry along the anteroposterior axis on the ventral surface of the animal. ventral region of midline Planarian_Anatomy PLANA:0000038 ventral midline Illustration of the ventral midline (in green). An abundant neoblast subclass, exhibiting enriched expression of gata456a, hnf4, prox-1 and nkx2.2, implicated in maintenance and regeneration of the definitive gut. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:25017721 PMID:26651295 PMID:27013241 PMID:27150006 PMID:27542689 PMID:28287248 PMID:28757112 PMID:28807897 PMID:29674431 PMID:29674432 PMID:29906446 gamma gamma class neoblast gamma-neoblast gut progenitor cell Planarian_Anatomy gamma neoblast 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 this term is not needed. All previous children of this term (Stage 1, Sage 2, etc) are now children of GO life cycle stage or zygote stage obsolete Schmidtea mediterranea developmental stage true Stage 3-5 embryo hemisphere centered around the pole opposite the embryonic pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 UBERON:0008259 Planarian_Anatomy aboral hemisphere Stage 3-5 embryo hemisphere centered around the pole opposite the embryonic pharynx. PMID:28072387 The single, central gut branch of the triclad gut anterior to the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21664348 PMID:3490491 Planarian_Anatomy anterior primary gut branch The single, central gut branch of the triclad gut anterior to the pharynx. PMID:3490491 Depicted by field contains hematoxylin and eosin staining section of a asexual adult animal. Anterior primary gut branch indicated by arrows. Scale bar = 250um Region along the edge of the animal where the dorsal and ventral surfaces meet. D/V boundary DV border DV boundary DV domain DV margin body edge body margin body periphery dorsal ventral boundary dorsal-ventral boundary dorsal/ventral compartment boundary of whole organism dorsoventral margin edge Planarian_Anatomy PLANA:0000043 dorsal ventral margin of the whole animal Region along the edge of the animal where the dorsal and ventral surfaces meet. ISBN:9780070316607 PMID:17905225 PMID:19174194 PMID:20865784 PMID:21295481 PMID:21295483 PMID:21458439 PMID:22549959 PMID:22696458 PMID:24415944 PMID:26457503 PMID:28216315 PMID:29357350 PMID:29674431 PMID:29674432 PMID:30399335 PMID:30485821 The planarian brain, consisting of two bilaterally symmetric lobes occupying a ventral position in the head. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:15866156 PMID:16033796 PMID:16344473 PMID:16890156 PMID:17251262 PMID:17376870 PMID:17553481 PMID:17670787 PMID:17905225 PMID:17942485 PMID:17999079 PMID:18063755 PMID:18063757 PMID:18202849 PMID:18287199 PMID:19048075 PMID:19174194 PMID:19211673 PMID:19247960 PMID:19766622 PMID:20215344 PMID:20422023 PMID:20844018 PMID:20967238 PMID:21179478 PMID:21282632 PMID:21295481 PMID:21458439 PMID:21566195 PMID:21806978 PMID:22074376 PMID:22125640 PMID:22339734 PMID:22411224 PMID:22445864 PMID:22451003 PMID:22549959 PMID:23235145 PMID:23297191 PMID:23318635 PMID:23318641 PMID:23405188 PMID:23652002 PMID:24131630 PMID:24173799 PMID:24238224 PMID:24415944 PMID:24950970 PMID:25254346 PMID:25278423 PMID:25356635 PMID:25404302 PMID:25725068 PMID:25772472 PMID:25956527 PMID:26017970 PMID:26884331 PMID:27013241 PMID:27074666 PMID:27163480 PMID:27612382 PMID:27612384 PMID:27800171 PMID:28072387 PMID:28126842 PMID:28216315 PMID:28287248 PMID:29291974 PMID:29291981 PMID:29547123 PMID:29674431 PMID:30194301 PMID:30237141 UBERON:0000955 https://doi.org/10.1101/279364 bi-lobed brain bi-lobed cephalic ganglia brain cerebral ganglia Planarian_Anatomy cephalic ganglia Body wall muscle fibers arrayed around the dorsoventral axis. Upon regeneration, these are thought to be produced de novo in the blastema. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md circular muscle fiber Planarian_Anatomy circular muscle cell 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 Image is an electron micrograph depicting the body wall musculature beneath the dorsal epidermis. The first layer of muscle cells beneath the basal lamina (BL), circular muscle, have been colored and labeled with arrowheads. Circular muscle = magenta; longitudinal muscle = green; diagonal muscle = red. Scale bar is 2um. 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:16344473 PMID:19247960 PMID:20215344 PMID:21566185 PMID:21852957 PMID:21937596 PMID:22318224 PMID:22385657 PMID:22411224 PMID:22543868 PMID:22549959 PMID:22884275 PMID:22899852 PMID:23079596 PMID:23297191 PMID:23318641 PMID:23652002 PMID:23954785 PMID:24040508 PMID:24120894 PMID:24173799 PMID:25017721 PMID:25254346 PMID:25356635 PMID:26711341 PMID:27063937 PMID:27074666 PMID:27149082 PMID:27150006 PMID:27502555 PMID:27523733 PMID:27551436 PMID:28434803 PMID:29357350 PMID:29674431 PMID:29674432 PMID:29906446 PMID:30962434 adult pluripotent stem cell cNeoblast clonogenic stem cell pluripotent stem cell Planarian_Anatomy clonogenic neoblast 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:26057828 PMID:27068018 PMID:29674431 UBERON:0001232 collection duct Planarian_Anatomy collecting duct Non-ciliated tubules associated with the distal tubules, which cross the basement membrane and terminate in the dorsal epidermis. PMID:26057828 Image is an electron micrograph depicting a collecting duct (arrowheads) passing through the basal lamina (BL). Dorsal is up and the scale bar is 5 um. Body wall muscle fibers arrayed diagonally along the anteroposterior axis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:23903188 PMID:26904543 PMID:27068018 PMID:28461239 PMID:28807897 PMID:30471994 diagonal fiber diagonal muscle diagonal muscle fiber Planarian_Anatomy diagonal muscle cell Body wall muscle fibers arrayed diagonally along the anteroposterior axis. PMID:26904543 Image is an electron micrograph depicting the body wall musculature beneath the dorsal epidermis. The third layer of cells beneath the basement membrane, diagonal muscle cells, have been colored and labeled with arrowheads. Circular muscle = magenta; longitudinal muscle = green; diagonal muscle = red. Scale bar is 2um. Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:15866156 PMID:16311336 PMID:16344473 PMID:17390146 PMID:17553481 PMID:17905225 PMID:18063757 PMID:18287199 PMID:19048075 PMID:19247960 PMID:19766622 PMID:19933103 PMID:20040488 PMID:20215344 PMID:20707997 PMID:21356107 PMID:21664348 PMID:21806978 PMID:22451003 PMID:22479207 PMID:23079596 PMID:24737865 PMID:24922054 PMID:25254346 PMID:25558068 PMID:26556349 PMID:27068018 PMID:27501047 PMID:29357350 UBERON:0001007 gastrointestinal system gastrovascular system Planarian_Anatomy digestive system 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 removing all processes. may bring back if PLANA expanded to cover processes. obsolete direct development true removing all processes. may bring back if PLANA expanded to cover processes. obsolete dispersed cleavage true Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21828097 PMID:27068018 UBERON:0004135 Planarian_Anatomy distal tubule Sinusoidal, non-ciliated tubules connected to proximal tubules within the parenchyma. Tubules are formed via intercellular junctions between two epithelial cells. PMID:21828097 Depicted by field contains a diagram representing the protonephrida unit (top) as well as a 3D rendering of confocal data depicting the same. In the diagram, terminal flame cells and their corresponding cilia are in blues, the proximal tubule is in reds, the distal tubule is in greens while thecollecting duct is in purple. In the 3D rendering below the cilia (AcTub) are in blue, portions of the proximal tubule (slc6a-13) are in red while the distal tubule (slc6a-12) is in green. Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe. dorsal epithelium dorsal region of epidermis Planarian_Anatomy PLANA:0000054 dorsal region of the epidermis Single cell layer of dorsal, post-mitotic, epithelial cells containing the dorsal stripe. ISBN:9780070316607 PMID:17942485 PMID:19048075 PMID:19852954 PMID:20599901 PMID:20844018 PMID:22385657 PMID:22479207 PMID:26457503 PMID:27612382 PMID:28292427 Image is an electron micrograph depicting the dorsal epidermis (arrowheads). Also visible in this micrograph, immediately deep to the epidermis is the basal lamina and beneath that is a photoreceptor. Scale bar is 10 um. Ciliated epithelial cells along the dorsal midline. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:17553481 racing stripe Planarian_Anatomy dorsal stripe Ciliated epithelial cells along the dorsal midline. PMID:17553481 Image is an electron micrograph showing the dorsal side of the head of an adult worm. Arrowheads mark where the ciliated cells of the dorsal stripe can be seen. Anterior is up and scale bar is 100um. 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:22074376 PMID:27149082 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000002.md Planarian_Anatomy ectolecithal embryo 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 removing all processes. may bring back if PLANA expanded to cover processes. obsolete embryonic cleavage true A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 UBERON:6001842 Planarian_Anatomy embryonic digestive system A cryptic digestive system in Stage 3-6 embryos comprised of temporary embryonic cell types and organs, including the 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Planarian_Anatomy embryonic gut cell 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 PMID:12888018 PMID:28072387 Planarian_Anatomy embryonic wall The parenchymal space between the gut cavity and the primitive ectoderm containing undifferentiated blastomeres in Stage 3-5 embryos. OCLC:16809160 PMID:12888018 Depicted by field contains hematoxylin and eosin staining section of a stage 5 embryo with anatomical feature noted with black indicators. Visceral muscle surrounding the gut. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21664348 PMID:22411224 PMID:23079596 PMID:26904543 PMID:30471994 PMID:30962434 UBERON:2001324 enteric muscle intestinal muscle Planarian_Anatomy enteric musculature Image is an electron micrograph depicting the enteric musculature (arrowheads) surrounding the gut, which extends across the top of the image. These cells are very small compared to the layer of medial muscle underneath them. Scale bar is 1um. Attachment between the triclad gut and the proximal end of the pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:18063757 PMID:20707997 PMID:21806978 PMID:24737865 PMID:27063937 PMID:29674431 PMID:30485821 UBERON:0001043 gut pharynx intersection pharynx root root of pharynx Planarian_Anatomy esophagus A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 UBERON:0000478 Planarian_Anatomy extraembryonic structure 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 Terminal structure of protonephridia unit; consists of flame cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21828097 PMID:26057828 Planarian_Anatomy flame bulb Image is an electron micrograph depicting a flame cell (outlined), which is a part of the flame bulb. "N" marks this cell's nucleus and the cilia are noted by an arrowhead. Scale bar is 1um. Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the filtration weir‚ or filtration diaphragm, 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:17670787 PMID:19247960 PMID:19852954 PMID:21828097 PMID:21937596 PMID:24523458 PMID:26057828 PMID:26711341 PMID:27068018 PMID:27542689 PMID:29674431 PMID:29674432 Planarian_Anatomy flame cell Terminal structure of the protonephridia unit, capping the proximal tubules. Flame cells are defined by the filtration weir‚ or filtration diaphragm, 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 Image is an electron micrograph depicting a flame cell (outlined), which is a part of the flame bulb. "N" marks this cell's nucleus and the cilia are noted by an arrowhead. Scale bar is 1um. The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0000509 ISBN:9780070316607 PMID:21282632 PMID:21664348 PMID:24120894 PMID:25558068 PMID:27441386 PMID:27501047 PMID:28287248 PMID:30608231 gut epithelia gut epithelium intestinal epithelium Planarian_Anatomy gastrodermis The single cell layer columnar epithelial lining of the intestine. The gastrodermis is surrounded by a basal lamina and enteric muscle. PMID:3490491 Secretory cells that release digestive enzymes into the lumen of the intestine. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0001540 PMID:20865784 PMID:21664348 PMID:23079596 PMID:27501047 PMID:28137894 PMID:28287248 PMID:29674431 PMID:29674432 Planarian_Anatomy goblet cell Secretory cells that release digestive enzymes into the lumen of the intestine. PMID:3490491 Image is an electron micrograph showing part of the gastrodermis. A goblet cell, a type of gastrodermal cell is labeled with arrowheads. Note the large, dark mucus granules contained in the cell body. The lumen of the gut can be seen on the right side of the image and has been labeled with "L." Scale bar is 1 um. Cavity encompassed by the embryonic digestive tract, prior to formation of the branched defintive gut. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Planarian_Anatomy embryonic gut cavity Cavity encompassed by the 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:26904543 PMID:30962434 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000003.md inner longitudinal muscle fiber inner longitudinal muscle layer Planarian_Anatomy inner longitudinal muscle cell 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:19933103 PMID:21664348 PMID:23079596 PMID:27542689 PMID:28072387 PMID:29674431 PMID:29674432 enterocyte gut enterocyte gut phagocyte intestinal epithelial cell Planarian_Anatomy intestinal phagocyte Absorptive digestive cells that engulf food particles for intracellular digestion. PMID:3490491 Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers.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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:23903188 PMID:26904543 PMID:27551436 PMID:28461239 PMID:28807897 PMID:30471994 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md BW longitudinal fiber body wall longitudinal fiber longitudinal fiber longitudinal muscle longitudinal muscle cell longitudinal muscle fiber Planarian_Anatomy longitudinal muscle cell Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers.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-0000005.md Image is an electron micrograph depicting the body wall musculature beneath the dorsal epidermis. The longitudinal muscle cells (arrowheads) sit behind both the circular muscle and the diagonal muscle. Circular muscle = magenta; longitudinal muscle = green; diagonal muscle = red. Scale bar is 2um. 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 pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:17251262 PMID:17905225 PMID:18287199 PMID:19174194 PMID:19211673 PMID:20707997 PMID:21295481 PMID:21458439 PMID:21806978 PMID:23954785 PMID:26457503 PMID:26556349 PMID:27034770 PMID:27063937 PMID:27074666 PMID:27122174 PMID:28807897 PMID:29674431 PMID:30399335 PMID:30471994 PMID:30485821 UBERON:0000165 anus manus Planarian_Anatomy mouth The sole point of entry and exit for the Triclad planarian flatworm gut. The mouth is connected to the pharyngeal pouch to allow for exit and re-entry of the pharynx on the ventral side of the animal. The mouth contains several cell types, including epithelial cells, muscle, and secretory cells. OCLC:16809160 Image is an electron micrograph of the mouth (arrowheads), which is located on the ventral side of the animal. Note the heavily ciliated pharynx that is peeking out. Scale bar is 10um. A female germ cell that has entered meiosis. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000023 PMID:25278423 PMID:27149082 PMID:27163480 PMID:27304889 PMID:27330085 PMID:27501047 PMID:28072387 PMID:28434803 PMID:28812561 egg female gamete ovum Planarian_Anatomy oocyte A female germ cell that has entered meiosis. CL:0000023 A portion of the eye containing pigment cells and dendritic projections from photoreceptor neurons. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:15866156 PMID:20707997 PMID:20865784 PMID:21458439 PMID:21828097 PMID:21852957 PMID:22411224 PMID:22427692 PMID:22445864 PMID:22549959 PMID:22884275 PMID:25493551 PMID:26017970 PMID:26618653 PMID:27068018 PMID:27240733 PMID:27542689 PMID:27606067 PMID:27800171 PMID:28495872 PMID:29547123 PMID:30143032 PMID:30194301 UBERON:0003072 eye cup photoreceptor pigment cup photoreceptor pigmentation pigment cup pigmented cell cup pigmented optic cup Planarian_Anatomy optic cup 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 embryonic pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Planarian_Anatomy oral hemisphere Stage 3-5 embryo hemisphere centered around the embryonic pharynx. PMID:28072387 Illustration of the oral hemispshere (in green). Body wall muscle fibers arrayed along the anteroposterior axis. Upon regeneration, these muscles are thought to be established from truncated pre-existing fibers. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:26904543 https://github.com/obophenotype/planaria-ontology/blob/master/metadata/planarefs/planaref-0000005.md outer longitudinal muscle layer Planarian_Anatomy outer longitudinal muscle cell 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 Muscles that are present through the mesenchyme, inclusing dorsal-ventral muscles, intestinal muscles and pharynx muscles. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 OCLC:16809160 PMID:30962434 dorsoventral muscle fibers parenchymal muscle Planarian_Anatomy parenchymal musculature Muscles that are present through the mesenchyme, inclusing dorsal-ventral muscles, intestinal muscles and pharynx muscles. OCLC:16809160 Image is an electron micrograph of the parenchyma. Three muscle cells have been notated with an arrowhead. Scale bar is 2 um. 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:20967238 PMID:22339734 PMID:23903188 PMID:26017970 PMID:26884331 PMID:27150006 PMID:27612382 PMID:29674431 UBERON:0000010 Planarian_Anatomy peripheral nervous system 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 An epithelial structure housing the pharynx, connected to the esophagus and mouth. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 pharyngeal pocket pharyngeal pouch Planarian_Anatomy pharynx pouch An epithelial structure housing the pharynx, connected to the esophagus and mouth. OCLC:16809160 racing stripe is now a synonym of PLANA:0000055 dorsal stripe obsolete racing stripe true The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21664348 PMID:23318641 PMID:24063805 major posterior gut branch primary posterior intestinal branch Planarian_Anatomy posterior primary gut branch The primary gut branches of the triclad gut lateral and posterior to the pharynx and pharyngeal pouch. PMID:3490491 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 A phagocytic cell closely associated with the embryonic pharynx. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:28072387 Planarian_Anatomy primitive gut cell A phagocytic cell closely associated with the embryonic pharynx. PMID:28072387 removing all processes. may bring back if PLANA expanded to cover processes. obsolete protosphere true 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21828097 PMID:21937596 PMID:26057828 PMID:27068018 UBERON:0004134 Planarian_Anatomy proximal tubule 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 Image is an electron micrograph depicting a proximal tubule (arrowheads) of the protonephridia structure. Note the cilia and the characteristic way the cell membrane connects with other proximal tubule epithelial cells. Scale bar is 2um. 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 ISBN:9780070316607 PMID:17670787 PMID:19048075 PMID:19247960 PMID:19852954 PMID:20707997 PMID:21828097 PMID:21937596 PMID:22427692 PMID:23079596 PMID:23235145 PMID:23903188 PMID:24173799 PMID:24523458 PMID:24737865 PMID:25254346 PMID:26057828 PMID:26711341 PMID:27068018 PMID:27542689 PMID:28461239 PMID:29674431 PMID:30297872 UBERON:0001008 excretory system protonephridial system Planarian_Anatomy renal system 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 Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21664348 PMID:27122174 PMID:28287248 PMID:30471994 Planarian_Anatomy secondary gut branch Gut branches, originating from and connected to the primary gut branches, that extend laterally towards the body edge. PMID:3490491 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 A mature male germ cell that develops from a spermatid. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000019 PMID:17390146 PMID:20844018 PMID:22074376 PMID:25278423 PMID:27149082 PMID:27163480 PMID:27304889 PMID:28072387 PMID:29095551 https://doi.org/10.1101/279364 mature sperm spermatozoa Planarian_Anatomy sperm A mature male germ cell that develops from a spermatid. CL:0000019 removing all processes. may bring back if PLANA expanded to cover processes. obsolete sphere formation true Fused yolk cells surrounding blastomeres undergoing dispersed cleavage during Stages 1 and 2. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:15599763 syncytial yolk cell Planarian_Anatomy yolk syncytium 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21664348 PMID:23250205 PMID:27122174 PMID:28137894 PMID:28287248 PMID:30194301 PMID:30471994 tertiary branch tertiary intestinal branch Planarian_Anatomy tertiary gut branch Gut branches originating from and connected to the secondary gut branches. PMID:3490491 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 removing all processes. may bring back if PLANA expanded to cover processes. obsolete tissue morphogenesis true 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:21852957 PMID:22884275 PMID:23250205 PMID:24040508 PMID:27606067 PMID:28072387 PMID:28245923 PMID:29674431 PMID:30485821 eye progenitor eye progenitor cell ovo+ eye progenitor Planarian_Anatomy trail cell 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 cilated ventral epidermis ciliated ventral epithelium ventral epidermin ventral epithelia ventral epithelium ventral region of epidermis Planarian_Anatomy PLANA:0000096 ventral epidermis Single cell layer of ventral, post-mitotic, heavily ciliated epithelial cells ISBN:9780070316607 PMID:15866156 PMID:17942485 PMID:19852954 PMID:20599901 PMID:21282632 PMID:23144623 PMID:23903188 PMID:24523458 PMID:25017721 PMID:26457503 PMID:26912790 PMID:27068018 PMID:28292427 PMID:29100657 PMID:30383829 PMID:30962434 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]. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0002328 EFO:0000896 FBbt:00001102 ISBN:9780070316607 MAT:0000339 MIAA:0000339 PMID:16033796 PMID:16890156 PMID:17251262 PMID:17390146 PMID:17553481 PMID:17905225 PMID:18063755 PMID:18063757 PMID:18202849 PMID:18287199 PMID:19174194 PMID:19211673 PMID:19247960 PMID:20215344 PMID:20223763 PMID:20422023 PMID:20599901 PMID:20707997 PMID:20967238 PMID:21179478 PMID:21282632 PMID:21566185 PMID:21806978 PMID:21828097 PMID:22074376 PMID:22125640 PMID:22339734 PMID:22479207 PMID:23250205 PMID:23297191 PMID:23318635 PMID:23954785 PMID:24063805 PMID:24120894 PMID:24131630 PMID:24173799 PMID:24950970 PMID:25254346 PMID:25356635 PMID:25558068 PMID:25772472 PMID:25956527 PMID:26017970 PMID:26062938 PMID:26457503 PMID:26556349 PMID:27013241 PMID:27034770 PMID:27150006 PMID:27163480 PMID:27612382 PMID:28072387 PMID:28126842 PMID:28245923 PMID:28807897 PMID:29291974 PMID:29674431 PMID:30143032 PMID:30471994 UBERON:0000934 WBbt:0005829 http://en.wikipedia.org/wiki/Ventral:nerve:cord nlx:146329 VNC nerve cord ventral cord Planarian_Anatomy ventral nerve cord 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]. UBERON:0000934 Diploid cell resulting from the fusion of male and female gametes at fertilization. [The_Dictionary_of_Cell_and_Molecular_Biology:Third_Edition ]. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0000854 CL:0000365 PMID:28812561 UBERON:0000106 Planarian_Anatomy zygote Diploid cell resulting from the fusion of male and female gametes at fertilization. [The_Dictionary_of_Cell_and_Molecular_Biology:Third_Edition ]. CL:0000365 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BTO:0000938 CL:0000540 NCIT:C12623 PMID:16033796 PMID:16890156 PMID:17553481 PMID:17905225 PMID:18202849 PMID:18287199 PMID:19048075 PMID:19174194 PMID:19211673 PMID:20215344 PMID:21566185 PMID:22411224 PMID:22439894 PMID:22479207 PMID:22549959 PMID:23297191 PMID:23903188 PMID:23954785 PMID:24040508 PMID:24131630 PMID:24173799 PMID:24737865 PMID:24922054 PMID:24950970 PMID:25254346 PMID:25356635 PMID:25558068 PMID:26457503 PMID:26525673 PMID:27013241 PMID:27063937 PMID:27150006 PMID:27163480 PMID:27542689 PMID:27612382 PMID:27612384 PMID:27864883 PMID:28072387 PMID:28126842 PMID:28137894 PMID:28245923 PMID:28292427 PMID:28461239 PMID:28807897 PMID:29100657 PMID:29184198 PMID:29291974 PMID:29291981 PMID:29357350 PMID:29674432 PMID:30143032 PMID:30399335 WBbt:0003679 differentiated neuron nerve cell neural cell neuronal cell Planarian_Anatomy neuron The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. CL:0000540 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000066 PMID:18202849 PMID:19048075 PMID:20865784 PMID:22479207 PMID:24737865 PMID:26114597 PMID:28072387 PMID:28461239 epidermis cell Planarian_Anatomy epithelial cell 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 A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000187 PMID:15972844 PMID:18202849 PMID:19174194 PMID:20422023 PMID:20511647 PMID:21458439 PMID:21828097 PMID:22252539 PMID:22479207 PMID:23318641 PMID:23405188 PMID:23954785 PMID:24415944 PMID:24737865 PMID:25254346 PMID:25558068 PMID:26062938 PMID:27063937 PMID:27523733 PMID:28216315 PMID:28287248 PMID:28292427 PMID:28461239 PMID:28686611 PMID:28807897 PMID:28893948 PMID:30471994 PMID:30962434 muscle fiber myocyte Planarian_Anatomy muscle cell A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. CL:0000187 Image is an electron micrograph depicting a muscle cell (arrowheads) cut in a transverse orientation with respect to the fiber length. Note the texture of the cytoplasm that comes from the organization of myofibrils. Scale bar is 1um. A subdivision of an anatomical compartment. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 BSPO:0000070 PMID:28292427 PMID:29547123 body region Planarian_Anatomy anatomical region 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 PMID:16033796 PMID:16344473 PMID:16890156 PMID:17251262 PMID:17553481 PMID:17670787 PMID:17905225 PMID:17942485 PMID:18063757 PMID:18202849 PMID:18287199 PMID:19174194 PMID:19247960 PMID:19933103 PMID:20865784 PMID:20967238 PMID:21282632 PMID:21295481 PMID:21458439 PMID:21664348 PMID:21806978 PMID:21828097 PMID:22125640 PMID:22252539 PMID:22339734 PMID:22385657 PMID:22411224 PMID:22427692 PMID:22439894 PMID:22445864 PMID:23297191 PMID:23318635 PMID:23318641 PMID:23903188 PMID:24063805 PMID:24173799 PMID:24367277 PMID:24704339 PMID:24737865 PMID:24922054 PMID:24950970 PMID:25356635 PMID:25493551 PMID:25772472 PMID:25956527 PMID:26017970 PMID:26459857 PMID:26711341 PMID:26884331 PMID:27013241 PMID:27063937 PMID:27068018 PMID:27074666 PMID:27150006 PMID:27163480 PMID:27240733 PMID:27523733 PMID:27542689 PMID:27612382 PMID:27612384 PMID:27800171 PMID:27864883 PMID:28126842 PMID:28434803 PMID:28461239 PMID:28807897 PMID:28976975 PMID:29273738 PMID:29291981 PMID:30399335 PMID:30471994 PMID:30729158 PMID:30962434 UBERON:0001017 https://doi.org/10.1101/279364 CNS head-restricted nervous system Planarian_Anatomy central nervous system 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 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. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 OCLC:16809160 Planarian_Anatomy rhabdite 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 Image is an electron micrograph depicting the epidermis. Inside of the epidermal cells, rhabdites (arrowheads) can be seen in various stages of expansion. Scale bar is 5 um. A cell that specializes in controlled release of one or more substances. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000151 NCIT:C13055 Planarian_Anatomy secretory cell A cell that specializes in controlled release of one or more substances. CL:0000151 Image is an electron micrograph of a viscid gland cell (arrowheads) passing across the basal lamina (BL). This cell secretes a specialized type of mucus. The secretory duct transports mucus to the outside of the animal, through the secretory pore. Ventral is down and scale bar is 5um. An epithelial cell that has cilia. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000067 PMID:24737865 PMID:28461239 PMID:28807897 ciliated epidermal cell Planarian_Anatomy ciliated epithelial cell An epithelial cell that has cilia. CL:0000067 An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo. https://orcid.org/0000-0003-2569-1939 | https://orcid.org/0000-0002-7535-4407 CL:0000428 ISBN:9780070316607 PMID:22074376 PMID:27149082 PMID:28072387 PMID:28434803 PMID:29674431 vitellocyte Planarian_Anatomy yolk cell An extraembryonic cell, produced by somatic vitellogenic glands in adult hermaphrodites, that provides nutrition to the developing embryo. PMID:27149082 extra layer of complexity not needed upon further examination obsolete anatomical compartment subdivision feature