example of usage
type: AnnotationProperty
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
database_cross_reference: IAO:0000112
has_obo_namespace: uberon
id: example_of_usage
is metadata tag: true
shorthand: example_of_usage

definition
type: AnnotationProperty
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 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.

editor note
type: AnnotationProperty
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
database_cross_reference: IAO:0000116
has_obo_namespace: uberon
id: editor_note
is metadata tag: true
shorthand: editor_note

has obsolescence reason
type: AnnotationProperty
definition: Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.

curator note
type: AnnotationProperty
definition: An administrative note of use for a curator but of no use for a user
database_cross_reference: IAO:0000232
has_obo_namespace: uberon
id: curator_notes
is metadata tag: true
shorthand: curator_notes
label: curator notes

term tracker item
type: AnnotationProperty
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
definition: An IRI or similar locator for a request or discussion of an ontology term.
database_cross_reference: IAO:0000233
has_obo_namespace: uberon
id: term_tracker_item
is metadata tag: true
shorthand: term_tracker_item
comment: The 'tracker item' can associate a tracker with a specific ontology term.

expand assertion to
type: AnnotationProperty
example of usage: ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.

has ontology root term
type: AnnotationProperty
definition: Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
database_cross_reference: IAO:0000700
has_obo_namespace: uberon
id: has_ontology_root_term
is metadata tag: true
shorthand: has_ontology_root_term
label: preferred_root

scheduled for obsoletion on or after
type: AnnotationProperty
definition: Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
term tracker item: https://github.com/geneontology/go-ontology/issues/15532
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/32
database_cross_reference: IAO:0006012
has_obo_namespace: uberon
id: scheduled_for_obsoletion_on_or_after
is metadata tag: true
shorthand: scheduled_for_obsoletion_on_or_after

term replaced by
type: AnnotationProperty
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
comment: Add as annotation triples in the granting ontology

abbreviation
type: AnnotationProperty
example of usage: CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
definition: A synonym type for describing abbreviations or initalisms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
sub property of: synonym_type_property

dubious synonym
type: AnnotationProperty
definition: A synonym type for describing dubious synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
sub property of: synonym_type_property

plural form
type: AnnotationProperty
example of usage: CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
definition: A synonym type for describing pluralization synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
sub property of: synonym_type_property

latin term
type: AnnotationProperty
example of usage: nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis
definition: A synonym type for describing Latin term synonyms.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/146
contributor: https://orcid.org/0000-0002-1773-2692
sub property of: synonym_type_property

never in taxon
type: AnnotationProperty
example of usage: tooth SubClassOf 'never in taxon' value 'Aves'
definition: S never_in_taxon T iff: S SubClassOf in_taxon only not T.
definition: x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y)
expand assertion to: Class: ?X DisjointWith: RO_0002162 some ?Y
database_cross_reference: RO:0002161
has_obo_namespace: uberon
id: never_in_taxon
is class level: true
is metadata tag: true
shorthand: never_in_taxon
label: never_in_taxon

Axiom
annotated source: never in taxon
annotated property: definition
annotated target: S never_in_taxon T iff: S SubClassOf in_taxon only not T.
database_cross_reference: PMID:20973947

mutually_spatially_disjoint_with
type: AnnotationProperty
definition: A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
database_cross_reference: RO:0002171
has_obo_namespace: uberon
id: mutually_spatially_disjoint_with
is class level: true
is metadata tag: true
shorthand: mutually_spatially_disjoint_with
label: mutually spatially disjoint with

ambiguous_for_taxon
type: AnnotationProperty
definition: S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage.
definition: S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]
database_cross_reference: RO:0002173
has_obo_namespace: uberon
id: ambiguous_for_taxon
is class level: true
is metadata tag: true
shorthand: ambiguous_for_taxon
label: ambiguous for taxon

Axiom
annotated source: ambiguous_for_taxon
annotated property: definition
annotated target: S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage.
database_cross_reference: PHENOSCPAE:asilomar_mtg

dubious_for_taxon
type: AnnotationProperty
definition: S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
database_cross_reference: RO:0002174
has_obo_namespace: uberon
id: dubious_for_taxon
is class level: true
is metadata tag: true
shorthand: dubious_for_taxon
comment: This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost
comment: this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost
label: dubious for taxon

Axiom
annotated source: dubious_for_taxon
annotated property: definition
annotated target: S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

present_in_taxon
type: AnnotationProperty
definition: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
definition: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S.
database_cross_reference: RO:0002175
has_exact_synonym: applicable for taxon
has_obo_namespace: uberon
id: present_in_taxon
is class level: true
is metadata tag: true
shorthand: present_in_taxon
comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.
label: present in taxon

Axiom
annotated source: present_in_taxon
annotated property: definition
annotated target: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

has no connections with
type: AnnotationProperty
example of usage: 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
definition: A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
database_cross_reference: RO:0002475
has_obo_namespace: uberon
id: has_no_connections_with
is class level: true
is metadata tag: true
shorthand: has_no_connections_with
label: has_no_connections_with

Axiom
annotated source: has no connections with
annotated property: definition
annotated target: A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

external_definition
type: AnnotationProperty
definition: 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.
database_cross_reference: UBPROP:0000001
has_obo_namespace: uberon
id: external_definition
is metadata tag: true
shorthand: external_definition
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO

Axiom
annotated source: external_definition
annotated property: definition
annotated target: 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.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

axiom_lost_from_external_ontology
type: AnnotationProperty
definition: A textual description of an axiom loss in this ontology compared to an external ontology.
database_cross_reference: UBPROP:0000002
has_obo_namespace: uberon
id: axiom_lost_from_external_ontology
is metadata tag: true
shorthand: axiom_lost_from_external_ontology
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO

Axiom
annotated source: axiom_lost_from_external_ontology
annotated property: definition
annotated target: A textual description of an axiom loss in this ontology compared to an external ontology.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

homology_notes
type: AnnotationProperty
definition: Notes on the homology status of this class.
database_cross_reference: UBPROP:0000003
has_obo_namespace: uberon
id: homology_notes
is metadata tag: true
shorthand: homology_notes
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO

Axiom
annotated source: homology_notes
annotated property: definition
annotated target: Notes on the homology status of this class.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

provenance_notes
type: AnnotationProperty
database_cross_reference: UBPROP:0000004
has_obo_namespace: uberon
id: provenance_notes
is metadata tag: true
shorthand: provenance_notes

external_comment
type: AnnotationProperty
definition: An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info.
database_cross_reference: UBPROP:0000005
has_obo_namespace: uberon
id: external_comment
is metadata tag: true
shorthand: external_comment
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO

Axiom
annotated source: external_comment
annotated property: definition
annotated target: An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

implements_design_pattern
type: AnnotationProperty
database_cross_reference: UBPROP:0000006
has_obo_namespace: uberon
id: implements_design_pattern
is metadata tag: true
shorthand: implements_design_pattern

has_relational_adjective
type: AnnotationProperty
curator note: Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
database_cross_reference: UBPROP:0000007
has_obo_namespace: uberon
id: has_relational_adjective
is metadata tag: true
shorthand: has_relational_adjective

taxon_notes
type: AnnotationProperty
definition: Notes on the how instances of this class vary across species.
database_cross_reference: UBPROP:0000008
has_obo_namespace: uberon
id: taxon_notes
is metadata tag: true
shorthand: taxon_notes

Axiom
annotated source: taxon_notes
annotated property: definition
annotated target: Notes on the how instances of this class vary across species.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

function_notes
type: AnnotationProperty
definition: Notes on the evolved function of instances of this class.
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000009
has_obo_namespace: uberon
id: function_notes
is metadata tag: true
shorthand: function_notes

Axiom
annotated source: function_notes
annotated property: definition
annotated target: Notes on the evolved function of instances of this class.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

structure_notes
type: AnnotationProperty
definition: Notes on the structure, composition or histology of instances of this class.
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000010
has_obo_namespace: uberon
id: structure_notes
is metadata tag: true
shorthand: structure_notes

Axiom
annotated source: structure_notes
annotated property: definition
annotated target: Notes on the structure, composition or histology of instances of this class.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

development_notes
type: AnnotationProperty
definition: Notes on the ontogenic development of instances of this class.
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000011
has_obo_namespace: uberon
id: development_notes
is metadata tag: true
shorthand: development_notes

Axiom
annotated source: development_notes
annotated property: definition
annotated target: Notes on the ontogenic development of instances of this class.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

external_ontology_notes
type: AnnotationProperty
definition: Notes on how similar or equivalent classes are represented in other ontologies.
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000012
has_obo_namespace: uberon
id: external_ontology_notes
is metadata tag: true
shorthand: external_ontology_notes

Axiom
annotated source: external_ontology_notes
annotated property: definition
annotated target: Notes on how similar or equivalent classes are represented in other ontologies.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

terminology_notes
type: AnnotationProperty
definition: Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000013
has_obo_namespace: uberon
id: terminology_notes
is metadata tag: true
shorthand: terminology_notes

Axiom
annotated source: terminology_notes
annotated property: definition
annotated target: Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

actions_notes
type: AnnotationProperty
definition: Notes on how instances of this class functon biomechanically.
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000014
has_obo_namespace: uberon
id: action_notes
is metadata tag: true
shorthand: action_notes

Axiom
annotated source: actions_notes
annotated property: definition
annotated target: Notes on how instances of this class functon biomechanically.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

location_notes
type: AnnotationProperty
definition: Notes on the location, position or part-parents of instances of this class.
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000015
has_obo_namespace: uberon
id: location_notes
is metadata tag: true
shorthand: location_notes

Axiom
annotated source: location_notes
annotated property: definition
annotated target: Notes on the location, position or part-parents of instances of this class.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

is count of
type: AnnotationProperty
database_cross_reference: UBPROP:0000100
has_obo_namespace: uberon
id: is_count_of
is metadata tag: true
shorthand: is_count_of

preceding element is
type: AnnotationProperty
definition: A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates).
database_cross_reference: UBPROP:0000101
has_obo_namespace: uberon
id: preceding_element_is
is metadata tag: true
shorthand: preceding_element_is

Axiom
annotated source: preceding element is
annotated property: definition
annotated target: A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates).
database_cross_reference: https://orcid.org/0000-0002-6601-2165

repeated element number
type: AnnotationProperty
definition: A property used to indicate the position of an element where that element is of a type that is serially repeated linearly along some axis for which a total ordering exists. The ordering may represent an ancestral condition.
database_cross_reference: UBPROP:0000102
has_obo_namespace: uberon
id: repeated_element_number
is metadata tag: true
shorthand: repeated_element_number
comment: The range is currently non-negative integer

Axiom
annotated source: repeated element number
annotated property: definition
annotated target: A property used to indicate the position of an element where that element is of a type that is serially repeated linearly along some axis for which a total ordering exists. The ordering may represent an ancestral condition.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

pharyngeal arch number
type: AnnotationProperty
definition: x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch.
terminology_notes: gill arch N = PA N-2. the term branchial_arch is ambiguous.
is count of: UBERON_0002539
database_cross_reference: UBPROP:0000103
has_obo_namespace: uberon
id: pharyngeal_arch_number
is metadata tag: true
shorthand: pharyngeal_arch_number

Axiom
annotated source: pharyngeal arch number
annotated property: definition
annotated target: x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

ray number
type: AnnotationProperty
definition: x ray_number N if and only if (i) x is a ray, and (ii) x is ancestrally associated with ray number N in a series of phalanges repeated along a radio-ulnar or equivalent axis, with ray_number 1 being the anteriormost ray.
is count of: UBERON_0002544
database_cross_reference: UBPROP:0000104
has_obo_namespace: uberon
id: ray_number
is metadata tag: true
shorthand: ray_number
comment: The correct terminology is yet to be established; in tetrapods 'ray' might mean the mereological sum of the phalanges of a manual digit plus a metatarsal bone (or equivalent for hindlimb)

Axiom
annotated source: ray number
annotated property: definition
annotated target: x ray_number N if and only if (i) x is a ray, and (ii) x is ancestrally associated with ray number N in a series of phalanges repeated along a radio-ulnar or equivalent axis, with ray_number 1 being the anteriormost ray.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

phalanx number
type: AnnotationProperty
definition: x phalanx_number N if and only if (i) x is a phalanx, and (ii) x is phalanx number N in a series of phalanges repeated along an prixomo-distal axis, with phalanx_number 1 being the proximalmost phalanx. Note that in humans, the distalmost phalanx has phlanax_number 3, except in ray_number 1, where the distalmost has phalanx_number 2.
is count of: UBERON_0003221
database_cross_reference: UBPROP:0000105
has_obo_namespace: uberon
id: phalanx_number
is metadata tag: true
shorthand: phalanx_number
comment: Most land mammals including humans have a 2-3-3-3-3 formula in both the hands (or paws) and feet. Primitive reptiles typically had the formula 2-3-4-4-5, and this pattern, with some modification, remained in many later reptiles and in the mammal-like reptiles. The phalangeal formula in the flippers of cetaceans (marine mammals) is 2-12-8-1

Axiom
annotated source: phalanx number
annotated property: definition
annotated target: x phalanx_number N if and only if (i) x is a phalanx, and (ii) x is phalanx number N in a series of phalanges repeated along an prixomo-distal axis, with phalanx_number 1 being the proximalmost phalanx. Note that in humans, the distalmost phalanx has phlanax_number 3, except in ray_number 1, where the distalmost has phalanx_number 2.
database_cross_reference: Wikipedia:Phalanx_bone#Phalangeal_formula
database_cross_reference: https://orcid.org/0000-0002-6601-2165

rib number
type: AnnotationProperty
definition: x rib_number N if and only if (i) x is a rib, and (ii) x is rib number N in a series of ribs repeated along an anterior-posterior axis, with rib_number 1 being the anteriormost rib. Note that this property counts ribs, *not* the adjoining vertebrae.
taxon_notes: In the early tetrapods, every vertebra bore a pair of ribs, although those on the thoracic vertebrae are typically the longest. In most subsequent forms, many of these early ribs have been lost, and in living amphibians and reptiles, there is great variation in rib structure and number. For example, turtles have only eight pairs of ribs, which are developed into a bony or cartilagenous carapace and plastron, while snakes have numerous ribs running along the full length of their trunk. Frogs typically have no ribs, aside from a sacral pair, which form part of the pelvis. Mammals usually also only have distinct ribs on the thoracic vertebra, although fixed cervical ribs are also present in monotremes. In marsupials and placental mammals, the cervical and lumbar ribs are found only as tiny remnants fused to the vertebrae, where they are referred to as transverse processes. In general, the structure and number of the true ribs in humans is similar to that in other mammals. Unlike reptiles, caudal ribs are never found in mammals.
external_ontology_notes: Note that in TAO, ribs are numbered by *vertebrae*
is count of: UBERON_0002228
database_cross_reference: UBPROP:0000106
has_obo_namespace: uberon
id: rib_number
is metadata tag: true
shorthand: rib_number

Axiom
annotated source: rib number
annotated property: definition
annotated target: x rib_number N if and only if (i) x is a rib, and (ii) x is rib number N in a series of ribs repeated along an anterior-posterior axis, with rib_number 1 being the anteriormost rib. Note that this property counts ribs, *not* the adjoining vertebrae.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: rib number
annotated property: external_ontology_notes
annotated target: Note that in TAO, ribs are numbered by *vertebrae*
external ontology: TAO

vertebra number
type: AnnotationProperty
definition: x vertebra_number N if and only if (i) x is a vertebra, and (ii) x is vertebra number N in a series of vertebras repeated along an anterior-posterior axis, with vertebra_number 1 being the anteriormost vertebra (also known as the atlas).
is count of: UBERON_0002412
database_cross_reference: UBPROP:0000107
has_obo_namespace: uberon
id: vertebra_number
is metadata tag: true
shorthand: vertebra_number

Axiom
annotated source: vertebra number
annotated property: definition
annotated target: x vertebra_number N if and only if (i) x is a vertebra, and (ii) x is vertebra number N in a series of vertebras repeated along an anterior-posterior axis, with vertebra_number 1 being the anteriormost vertebra (also known as the atlas).
database_cross_reference: https://orcid.org/0000-0002-6601-2165

somite number
type: AnnotationProperty
definition: x somite_number N if and only if (i) x is a somite, and (ii) x is somite number N in a series of somites repeated along an anterior-posterior axis, with somite_number 1 being the anteriormost somite.
is count of: UBERON_0002329
database_cross_reference: UBPROP:0000108
has_obo_namespace: uberon
id: somite_number
is metadata tag: true
shorthand: somite_number

Axiom
annotated source: somite number
annotated property: definition
annotated target: x somite_number N if and only if (i) x is a somite, and (ii) x is somite number N in a series of somites repeated along an anterior-posterior axis, with somite_number 1 being the anteriormost somite.
database_cross_reference: https://github.com/obophenotype/uberon/issues/100
database_cross_reference: https://orcid.org/0000-0002-6601-2165

paired_appendage number
type: AnnotationProperty
definition: x paired_appendage_number N if and only if (i) x is a paired_appendage, and (ii) x is paired_appendage number N in a series of paired_appendages repeated along an anterior-posterior axis, with paired_appendage_number 1 being the anteriormost paired_appendage. In vertebrates, this is the pectoral appendage.
is count of: UBERON_0000026
database_cross_reference: UBPROP:0000109
has_obo_namespace: uberon
id: paired_appendage_number
is metadata tag: true
shorthand: paired_appendage_number

Axiom
annotated source: paired_appendage number
annotated property: definition
annotated target: x paired_appendage_number N if and only if (i) x is a paired_appendage, and (ii) x is paired_appendage number N in a series of paired_appendages repeated along an anterior-posterior axis, with paired_appendage_number 1 being the anteriormost paired_appendage. In vertebrates, this is the pectoral appendage.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

appendage segment number
type: AnnotationProperty
definition: x appendage_segment_number N if and only if (i) x is a appendage_segment, and (ii) x is appendage_segment number N in a series of appendage_segments repeated along an proximo-distal axis, with appendage_segment_number 1 being the proximalmost appendage_segment (in tetrapods this would be the stylopod, as we do not classify girdles as appendage segments).
is count of: UBERON_0010758
database_cross_reference: UBPROP:0000110
has_obo_namespace: uberon
id: appendage_segment_number
is metadata tag: true
shorthand: appendage_segment_number
comment: Examples: in dropsphila coxa=1, trochanter=2, femur=3, tibia=4, tarsal segments 1-5=5-9, pretarsus=10

Axiom
annotated source: appendage segment number
annotated property: definition
annotated target: x appendage_segment_number N if and only if (i) x is a appendage_segment, and (ii) x is appendage_segment number N in a series of appendage_segments repeated along an proximo-distal axis, with appendage_segment_number 1 being the proximalmost appendage_segment (in tetrapods this would be the stylopod, as we do not classify girdles as appendage segments).
database_cross_reference: https://orcid.org/0000-0002-6601-2165

rhombomere number
type: AnnotationProperty
definition: x rhombomere_number N if and only if (i) x is a rhombomere, and (ii) x is rhombomere number N in a series of rhombomeres repeated along an anterior-posterior axis, with rhombomere_number 1 being the anteriormost rhombomere.
is count of: UBERON_0001892
database_cross_reference: UBPROP:0000111
has_obo_namespace: uberon
id: rhombomere_number
is metadata tag: true
shorthand: rhombomere_number

Axiom
annotated source: rhombomere number
annotated property: definition
annotated target: x rhombomere_number N if and only if (i) x is a rhombomere, and (ii) x is rhombomere number N in a series of rhombomeres repeated along an anterior-posterior axis, with rhombomere_number 1 being the anteriormost rhombomere.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

tooth number
type: AnnotationProperty
definition: x tooth_number N if and only if (i) x is a tooth, and (ii) x is ancestrally tooth number N in a series of teeth repeated along an anterior-posterior axis, typically on the lateral side of a structure such as a jaw, with tooth_number 1 being the anteriormost. Note that this count refers to the total number of teeth starting from the first, regardless of the type of tooth. If sub-systems are required for numbering within a series of teeth of the same type, consider a subproperty. For example, in a human, maxillary canine = tooth 3 of upper jaw = canine_tooth 1 of upper jaw.
is count of: UBERON_0001091
database_cross_reference: UBPROP:0000112
has_obo_namespace: uberon
id: tooth_number
is metadata tag: true
shorthand: tooth_number

dental formula
type: AnnotationProperty
definition: Syntax: upper/lower = I.C.P.M / I.C.P.M. When used with generic tooth class applies to both deciduous and primary. Should also be used with a taxon property.
database_cross_reference: UBPROP:0000113
has_obo_namespace: uberon
id: dental_formula
is metadata tag: true
shorthand: dental_formula

Axiom
annotated source: dental formula
annotated property: definition
annotated target: Syntax: upper/lower = I.C.P.M / I.C.P.M. When used with generic tooth class applies to both deciduous and primary. Should also be used with a taxon property.
database_cross_reference: Wikipedia:Dentition#Dental_formula

source atlas
type: AnnotationProperty
database_cross_reference: UBPROP:0000201
has_obo_namespace: uberon
id: source_atlas
is metadata tag: true
shorthand: source_atlas

fma_set_term
type: AnnotationProperty
external_ontology_notes: FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term
database_cross_reference: UBPROP:0000202
has_obo_namespace: uberon
id: fma_set_term
is metadata tag: true
shorthand: fma_set_term

Axiom
annotated source: fma_set_term
annotated property: external_ontology_notes
annotated target: FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term
external ontology: FMA

brain name abbreviations (drosophila)
type: AnnotationProperty
sub property of: synonym_type_property

preferred term in the context of comparative anatomy
type: AnnotationProperty
sub property of: synonym_type_property

A historic synonym, no longer encouraged
type: AnnotationProperty
sub property of: synonym_type_property

developmental term
type: AnnotationProperty
sub property of: synonym_type_property

a synonym made on the basis of a possibly homologous structure in another species
type: AnnotationProperty
sub property of: synonym_type_property

preferred term when talking about an instance of this class in Homo sapiens
type: AnnotationProperty
sub property of: synonym_type_property

indicates that a synonym is used in an inconsistent or confusing way, typically between species
type: AnnotationProperty
sub property of: synonym_type_property

a mis-spelling that is in common use and thus recorded
type: AnnotationProperty
sub property of: synonym_type_property

synonym that is inappropriate for amniotes
type: AnnotationProperty
sub property of: synonym_type_property

synonym that is inappropriate for mammals
type: AnnotationProperty
sub property of: synonym_type_property

expert consultation and attribution required
type: AnnotationProperty
sub property of: synonym_type_property

taxonomic disambiguation
type: AnnotationProperty
sub property of: synonym_type_property

a systematic synonym used as the base name for design patterns
type: AnnotationProperty
sub property of: synonym_type_property

added for HCA
type: AnnotationProperty
comment: Classes tagged with this subset property were added upon request from the Human Cell Atlas (HCA).
sub property of: subset_property

common anatomy
type: AnnotationProperty
comment: Terms applicable across life, not restricted to Metazoa
sub property of: subset_property

cumbo
type: AnnotationProperty
comment: CUMBO
sub property of: subset_property

cyclostome subset
type: AnnotationProperty
comment: cyclostome structures
sub property of: subset_property

defined by cytoarchitecture
type: AnnotationProperty
comment: brain region defined by cyto-architecture
sub property of: subset_property

defined by ordinal series
type: AnnotationProperty
comment: classes that are defined by relative position counting from first in a series of elements along an axis in an individual organism rather than by strict homology
sub property of: subset_property

developmental classification
type: AnnotationProperty
comment: developmental_classification
sub property of: subset_property

dubious grouping
type: AnnotationProperty
comment: Indicates that subclasses in AOs may be inappropriately linked
sub property of: subset_property

early development
type: AnnotationProperty
comment: A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.
sub property of: subset_property

efo slim
type: AnnotationProperty
comment: EFO slim
sub property of: subset_property

emapa ehdaa2
type: AnnotationProperty
comment: derived from the union of EHDAA2 and EMAPA - still to be checked
sub property of: subset_property

feed aligned
type: AnnotationProperty
comment: subset of classes that have logical defs text defs and synonyms aligned with FEED
sub property of: subset_property

functional classification
type: AnnotationProperty
comment: functional_classification
sub property of: subset_property

grouping class
type: AnnotationProperty
comment: Subset consisting of classes creating for grouping purposes
sub property of: subset_property

homologous_in
type: AnnotationProperty
has_obo_namespace: uberon
id: homologous_in
is metadata tag: true
comment: Status: experimental

homology grouping
type: AnnotationProperty
comment: A grouping class that depends on an assumption of homology between subclasses
sub property of: subset_property

inconsistent with fma
type: AnnotationProperty
comment: classes that have some inconsistency with FMA
sub property of: subset_property

major organ
type: AnnotationProperty
comment: somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads
sub property of: subset_property

metazoa core
type: AnnotationProperty
comment: core classes typically found across metazoa. one purpose is to create a rough set of terms that could be used to start a new metazoan AO. Note this subset is not yet fully fleshed out
sub property of: subset_property

non informative
type: AnnotationProperty
comment: abstract class brought in to group ontology classes but not informative
sub property of: subset_property

organ slim
type: AnnotationProperty
comment: organs, excluding individual muscles and skeletal elements
sub property of: subset_property

pheno slim
type: AnnotationProperty
comment: Phenotype slim
sub property of: subset_property

phenotype rcn
type: AnnotationProperty
comment: A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA
sub property of: subset_property

uberon slim
type: AnnotationProperty
comment: Uberon slim - subset that excludes obscure terms and deep compositional terms
sub property of: subset_property

unverified taxonomic grouping
type: AnnotationProperty
comment: Indicates that the class encompasses classes from other AOs that have not been verified
sub property of: subset_property

upper level
type: AnnotationProperty
comment: abstract upper-level terms not directly useful for analysis
sub property of: subset_property

vertebrate core
type: AnnotationProperty
comment: core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO
sub property of: subset_property

creator
type: AnnotationProperty
has_obo_namespace: uberon
id: dc-creator
is metadata tag: true
shorthand: dc-creator

description
type: AnnotationProperty
has_obo_namespace: uberon
id: dc-description
is metadata tag: true
shorthand: dc-description

publisher
type: AnnotationProperty
has_obo_namespace: uberon
id: dc-publisher
is metadata tag: true
shorthand: dc-publisher

derived from resource
type: AnnotationProperty
has_obo_namespace: uberon
id: dc-source
is metadata tag: true
shorthand: dc-source

title
type: AnnotationProperty
has_obo_namespace: uberon
id: dc-title
is metadata tag: true
shorthand: dc-title

contributor
type: AnnotationProperty
has_obo_namespace: uberon
id: dc-contributor
is metadata tag: true
shorthand: dc-contributor

date
type: AnnotationProperty
has_obo_namespace: uberon
id: dcterms-date
is metadata tag: true
shorthand: dcterms-date

is referenced by
type: AnnotationProperty
has_obo_namespace: uberon
id: dcterms-isReferencedBy
is metadata tag: true
shorthand: dcterms-isReferencedBy

license
type: AnnotationProperty
has_obo_namespace: uberon
id: dcterms-license
is metadata tag: true
shorthand: dcterms-license

Git repository
type: AnnotationProperty
has_obo_namespace: uberon
id: doap-GitRepository
is metadata tag: true
shorthand: doap-GitRepository

SVN repository
type: AnnotationProperty
has_obo_namespace: uberon
id: doap-SVNRepository
is metadata tag: true
shorthand: doap-SVNRepository

bug database
type: AnnotationProperty
has_obo_namespace: uberon
id: doap-bug-database
is metadata tag: true
shorthand: doap-bug-database

mailing list
type: AnnotationProperty
has_obo_namespace: uberon
id: doap-mailing-list
is metadata tag: true
shorthand: doap-mailing-list

wiki
type: AnnotationProperty
has_obo_namespace: uberon
id: doap-wiki
is metadata tag: true
shorthand: doap-wiki

subset_property
type: AnnotationProperty

synonym_type_property
type: AnnotationProperty

consider
type: AnnotationProperty

created by
type: AnnotationProperty

creation date
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/18
label: has broad synonym

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
label: has exact synonym

has_narrow_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/19
label: has narrow synonym

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty
definition: 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.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
label: has related synonym

has_scope
type: AnnotationProperty

has_synonym_type
type: AnnotationProperty

id
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

treat-xrefs-as-equivalent
type: AnnotationProperty

treat-xrefs-as-has-subclass
type: AnnotationProperty

treat-xrefs-as-is_a
type: AnnotationProperty

treat-xrefs-as-reverse-genus-differentia
type: AnnotationProperty

see also
type: AnnotationProperty
has_obo_namespace: spatial
has_obo_namespace: uberon
id: seeAlso
is metadata tag: true
shorthand: seeAlso

depiction
type: AnnotationProperty
has_obo_namespace: uberon
id: depiction
is metadata tag: true
shorthand: depiction

homepage
type: AnnotationProperty
has_obo_namespace: uberon
id: foaf-homepage
is metadata tag: true
shorthand: foaf-homepage

page
type: AnnotationProperty
has_obo_namespace: uberon
id: foaf-page
is metadata tag: true
shorthand: foaf-page

part of
type: ObjectProperty
type: TransitiveProperty
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: 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.
editor note: 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/
editor note: 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'.
database_cross_reference: BFO:0000050
has_obo_namespace: quality
has_obo_namespace: spatial
has_obo_namespace: uberon
id: part_of
in_subset: valid for go annotation extension
in_subset: valid for go gp2term
in_subset: valid for go ontology
in_subset: valid for gocam
shorthand: part_of
label: part_of

develops from
type: ObjectProperty
type: TransitiveProperty
property chain axiom: part of
definition: 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
database_cross_reference: RO:0002202
has_obo_namespace: uberon
id: develops_from
shorthand: develops_from
comment: This is the transitive form of the develops from relation

transformation of
type: ObjectProperty
sub property of: develops from
type: TransitiveProperty
definition: x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
database_cross_reference: RO:0002494
has_obo_namespace: uberon
id: transformation_of
shorthand: transformation_of

immediate transformation of
type: ObjectProperty
sub property of: develops from
sub property of: transformation of
definition: x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
database_cross_reference: RO:0002495
has_obo_namespace: uberon
id: immediate_transformation_of
shorthand: immediate_transformation_of

peripheral nervous system
type: Class
subclass of: Restriction
  on property: part of
  some values from: nervous system
definition: 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.
present_in_taxon: NCBITaxon 9606
external_definition: Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
external_definition: Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
external_definition: The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
homology_notes: (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
has_broad_synonym: PNS
database_cross_reference: AAO:0000429
database_cross_reference: BAMS:PNS
database_cross_reference: BILA:0000081
database_cross_reference: BIRNLEX:1111
database_cross_reference: BTO:0001028
database_cross_reference: CALOHA:TS-0808
database_cross_reference: EFO:0000891
database_cross_reference: EHDAA2:0001445
database_cross_reference: EHDAA:2893
database_cross_reference: EMAPA:16665
database_cross_reference: EV:0100335
database_cross_reference: FBbt:00005098
database_cross_reference: FMA:9903
database_cross_reference: GAID:715
database_cross_reference: MA:0000218
database_cross_reference: MAT:0000338
database_cross_reference: MESH:D017933
database_cross_reference: MIAA:0000338
database_cross_reference: NCIT:C12465
database_cross_reference: SCTID:362292005
database_cross_reference: TAO:0000142
database_cross_reference: UMLS:C0206417
database_cross_reference: UMLS:C1305921
database_cross_reference: VHOG:0000399
database_cross_reference: Wikipedia:Peripheral_nervous_system
database_cross_reference: XAO:0000178
database_cross_reference: ZFA:0000142
database_cross_reference: neuronames:3232
has_exact_synonym: pars peripherica
has_exact_synonym: systema nervosum periphericum
has_obo_namespace: uberon
id: UBERON:0000010
in_subset: cumbo
in_subset: efo slim
in_subset: human reference atlas
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core

Axiom
annotated source: peripheral nervous system
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0007422

Axiom
annotated source: peripheral nervous system
annotated property: external_definition
annotated target: Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000142
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: peripheral nervous system
annotated property: external_definition
annotated target: Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000429
ontology: AAO
source: AAO:BJB

Axiom
annotated source: peripheral nervous system
annotated property: external_definition
annotated target: The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
source: http://neurolex.org/wiki/Cumbo_terms

Axiom
annotated source: peripheral nervous system
annotated property: homology_notes
annotated target: (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000399
ontology: VHOG
source: DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)
source: http://bgee.unil.ch/

Axiom
annotated source: peripheral nervous system
annotated property: has_broad_synonym
annotated target: PNS
has_synonym_type: abbreviation

Axiom
annotated source: peripheral nervous system
annotated property: database_cross_reference
annotated target: FBbt:00005098
mapping justification: ManualMappingCuration

Axiom
annotated source: peripheral nervous system
annotated property: database_cross_reference
annotated target: UMLS:C0206417
source: BIRNLEX:1111
source: ncithesaurus:Peripheral_Nervous_System

Axiom
annotated source: peripheral nervous system
annotated property: database_cross_reference
annotated target: UMLS:C1305921
source: BIRNLEX:1111

Axiom
annotated source: peripheral nervous system
annotated property: has_exact_synonym
annotated target: pars peripherica
database_cross_reference: FMA:9903
database_cross_reference: FMA:TA
database_cross_reference: Wikipedia:Peripheral_nervous_system
has_synonym_type: latin term

Axiom
annotated source: peripheral nervous system
annotated property: has_exact_synonym
annotated target: systema nervosum periphericum
database_cross_reference: FMA:9903
database_cross_reference: FMA:TA
database_cross_reference: Wikipedia:Peripheral_nervous_system
has_synonym_type: latin term

neural nucleus
type: Class
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO).
external_definition: Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021].
external_ontology_notes: Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate.
has_broad_synonym: nucleus
database_cross_reference: AEO:0000136
database_cross_reference: FMA:83686
database_cross_reference: NCIT:C13197
database_cross_reference: NLX:28443
database_cross_reference: Wikipedia:Nucleus_(neuroanatomy)
has_exact_synonym: nervous system nucleus
has_exact_synonym: neuraxis nucleus
has_exact_synonym: neuronal nucleus
has_exact_synonym: nucleus of CNS
has_obo_namespace: uberon
has_related_synonym: nucleus of neuraxis
id: UBERON:0000125
in_subset: cumbo

Axiom
annotated source: neural nucleus
annotated property: definition
annotated target: A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO).
database_cross_reference: NLX:28443

Axiom
annotated source: neural nucleus
annotated property: external_definition
annotated target: Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021].
source: GO_REF:0000021

Axiom
annotated source: neural nucleus
annotated property: has_exact_synonym
annotated target: neuraxis nucleus
database_cross_reference: FMA:83686

Axiom
annotated source: neural nucleus
annotated property: has_exact_synonym
annotated target: neuronal nucleus
database_cross_reference: AEO:0000136

Axiom
annotated source: neural nucleus
annotated property: has_exact_synonym
annotated target: nucleus of CNS
database_cross_reference: NLX:28443

brain
type: Class
subclass of: Restriction
  on property: part of
  some values from: central nervous system
subclass of: Restriction
  on property: part of
  some values from: central nervous system
subclass of: Restriction
  on property: immediate transformation of
  some values from: future brain
subclass of: Restriction
  on property: immediate transformation of
  some values from: future brain
definition: The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
editor note: requires review for applicability to invertebrate structures, e.g. synganglion
present_in_taxon: NCBITaxon 9606
external_definition: Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
external_definition: Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
external_definition: The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
homology_notes: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
database_cross_reference: AAO:0010478
database_cross_reference: ABA:Brain
database_cross_reference: BAMS:Br
database_cross_reference: BAMS:Brain
database_cross_reference: BILA:0000135
database_cross_reference: BIRNLEX:796
database_cross_reference: BTO:0000142
database_cross_reference: CALOHA:TS-0095
database_cross_reference: DHBA:10155
database_cross_reference: EFO:0000302
database_cross_reference: EHDAA2:0000183
database_cross_reference: EHDAA:2641
database_cross_reference: EHDAA:6485
database_cross_reference: EMAPA:16894
database_cross_reference: EV:0100164
database_cross_reference: FBbt:00005095
database_cross_reference: FMA:50801
database_cross_reference: GAID:571
database_cross_reference: HBA:4005
database_cross_reference: MA:0000168
database_cross_reference: MAT:0000098
database_cross_reference: MBA:8
database_cross_reference: MBA:997
database_cross_reference: MESH:D001921
database_cross_reference: MIAA:0000098
database_cross_reference: NCIT:C12439
database_cross_reference: PBA:3999
database_cross_reference: SCTID:258335003
database_cross_reference: TAO:0000008
database_cross_reference: UMLS:C0006104
database_cross_reference: UMLS:C1269537
database_cross_reference: VHOG:0000157
database_cross_reference: Wikipedia:Brain
database_cross_reference: XAO:0000010
database_cross_reference: ZFA:0000008
database_cross_reference: galen:Brain
database_cross_reference: neuronames:21
has_obo_namespace: uberon
has_related_synonym: encephalon
has_related_synonym: suprasegmental levels of nervous system
has_related_synonym: suprasegmental structures
has_related_synonym: synganglion
has_related_synonym: the brain
id: UBERON:0000955
in_subset: cumbo
in_subset: efo slim
in_subset: human reference atlas
in_subset: major organ
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core

Axiom
annotated source: brain
annotated property: subClassOf
annotated target: Restriction
  on property: part of
  some values from: central nervous system
source: FMA

Axiom
annotated source: brain
annotated property: subClassOf
annotated target: Restriction
  on property: immediate transformation of
  some values from: future brain
source: Bgee:AN

Axiom
annotated source: brain
annotated property: definition
annotated target: The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
database_cross_reference: Wikipedia:Brain
database_cross_reference: https://github.com/obophenotype/uberon/issues/300

Axiom
annotated source: brain
annotated property: external_definition
annotated target: Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000008
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: brain
annotated property: external_definition
annotated target: Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010478
ontology: AAO
source: AAO:BJB

Axiom
annotated source: brain
annotated property: external_definition
annotated target: The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
source: http://neurolex.org/wiki/Cumbo_terms

Axiom
annotated source: brain
annotated property: homology_notes
annotated target: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000157
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
source: http://bgee.unil.ch/

Axiom
annotated source: brain
annotated property: database_cross_reference
annotated target: FBbt:00005095
mapping justification: ManualMappingCuration

Axiom
annotated source: brain
annotated property: database_cross_reference
annotated target: UMLS:C0006104
source: BIRNLEX:796
source: ncithesaurus:Brain

Axiom
annotated source: brain
annotated property: database_cross_reference
annotated target: UMLS:C1269537
source: BIRNLEX:796

Axiom
annotated source: brain
annotated property: database_cross_reference
annotated target: neuronames:21
source: BIRNLEX:796

Axiom
annotated source: brain
annotated property: has_related_synonym
annotated target: encephalon
database_cross_reference: BTO:0000142

Axiom
annotated source: brain
annotated property: has_related_synonym
annotated target: suprasegmental levels of nervous system
database_cross_reference: NeuroNames:21

Axiom
annotated source: brain
annotated property: has_related_synonym
annotated target: suprasegmental structures
database_cross_reference: NeuroNames:21

Axiom
annotated source: brain
annotated property: has_related_synonym
annotated target: the brain
database_cross_reference: NeuroNames:21

nervous system
type: Class
definition: The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, 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].
never in taxon: NCBITaxon 6040
present_in_taxon: NCBITaxon 9606
external_definition: A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
external_definition: Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
homology_notes: Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
has_relational_adjective: nervous
has_relational_adjective: neural
database_cross_reference: AAO:0000324
database_cross_reference: BILA:0000079
database_cross_reference: BIRNLEX:844
database_cross_reference: BTO:0001484
database_cross_reference: CALOHA:TS-1313
database_cross_reference: EFO:0000802
database_cross_reference: EHDAA2:0001246
database_cross_reference: EHDAA:826
database_cross_reference: EMAPA:16469
database_cross_reference: EV:0100162
database_cross_reference: FBbt:00005093
database_cross_reference: FMA:7157
database_cross_reference: GAID:466
database_cross_reference: MA:0000016
database_cross_reference: MAT:0000026
database_cross_reference: MESH:D009420
database_cross_reference: MIAA:0000026
database_cross_reference: NCIT:C12755
database_cross_reference: SCTID:278196006
database_cross_reference: TAO:0000396
database_cross_reference: UMLS:C0027763
database_cross_reference: VHOG:0000402
database_cross_reference: WBbt:0005735
database_cross_reference: Wikipedia:Nervous_system
database_cross_reference: XAO:0000177
database_cross_reference: ZFA:0000396
database_cross_reference: neuronames:3236
has_exact_synonym: neurological system
has_narrow_synonym: nerve net
has_obo_namespace: uberon
has_related_synonym: systema nervosum
id: UBERON:0001016
in_subset: cumbo
in_subset: efo slim
in_subset: human reference atlas
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core

Axiom
annotated source: nervous system
annotated property: definition
annotated target: The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, 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].
database_cross_reference: BIRNLEX:844
database_cross_reference: ISBN:0-14-051288-8
database_cross_reference: ISBN:3110148986
database_cross_reference: NLM:nervous+system
database_cross_reference: WB:rynl
database_cross_reference: Wikipedia:Nervous_system
database_cross_reference: ZFIN:curator

Axiom
annotated source: nervous system
annotated property: external_definition
annotated target: A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
date retrieved: 2012-08-14
external class: TAO:0000396
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: nervous system
annotated property: external_definition
annotated target: Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000324
ontology: AAO
source: AAO:BJB

Axiom
annotated source: nervous system
annotated property: homology_notes
annotated target: Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000402
ontology: VHOG
source: ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117
source: http://bgee.unil.ch/

Axiom
annotated source: nervous system
annotated property: database_cross_reference
annotated target: FBbt:00005093
mapping justification: ManualMappingCuration

Axiom
annotated source: nervous system
annotated property: database_cross_reference
annotated target: UMLS:C0027763
source: ncithesaurus:Nervous_System

Axiom
annotated source: nervous system
annotated property: has_exact_synonym
annotated target: neurological system
database_cross_reference: GO:0050877

Axiom
annotated source: nervous system
annotated property: has_narrow_synonym
annotated target: nerve net
database_cross_reference: Wikipedia:Nerve_net

Axiom
annotated source: nervous system
annotated property: has_related_synonym
annotated target: systema nervosum
database_cross_reference: Wikipedia:Nervous_system
has_synonym_type: latin term

central nervous system
type: Class
subclass of: Restriction
  on property: part of
  some values from: nervous system
definition: 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.
never in taxon: NCBITaxon_147099
present_in_taxon: NCBITaxon 9606
external_definition: Part of the nervous system which includes the brain and spinal cord.[AAO]
external_definition: The brain and spinal cord. Kimmel et al, 1995.[TAO]
external_definition: The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
homology_notes: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
database_cross_reference: AAO:0000090
database_cross_reference: BAMS:CNS
database_cross_reference: BILA:0000080
database_cross_reference: BIRNLEX:1099
database_cross_reference: BTO:0000227
database_cross_reference: CALOHA:TS-0150
database_cross_reference: EFO:0000908
database_cross_reference: EHDAA2:0000225
database_cross_reference: EHDAA:828
database_cross_reference: EMAPA:16470
database_cross_reference: EMAPA:16754
database_cross_reference: EV:0100163
database_cross_reference: FBbt:00005094
database_cross_reference: FMA:55675
database_cross_reference: GAID:570
database_cross_reference: MA:0000167
database_cross_reference: MAT:0000457
database_cross_reference: MESH:D002490
database_cross_reference: NCIT:C12438
database_cross_reference: SCTID:278199004
database_cross_reference: TAO:0000012
database_cross_reference: UMLS:C0927232
database_cross_reference: VHOG:0000293
database_cross_reference: Wikipedia:Central_nervous_system
database_cross_reference: XAO:0000215
database_cross_reference: ZFA:0000012
database_cross_reference: neuronames:854
has_exact_synonym: CNS
has_exact_synonym: systema nervosum centrale
has_narrow_synonym: cerebrospinal axis
has_obo_namespace: uberon
has_related_synonym: neuraxis
id: UBERON:0001017
in_subset: cumbo
in_subset: efo slim
in_subset: human reference atlas
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core

Axiom
annotated source: central nervous system
annotated property: definition
annotated target: 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.
database_cross_reference: GO:0021551
database_cross_reference: http://www.frontiersinzoology.com/content/7/1/29
database_cross_reference: https://sourceforge.net/p/geneontology/ontology-requests/11422/

Axiom
annotated source: central nervous system
annotated property: never in taxon
annotated target: NCBITaxon_147099
source: Wikipedia:Acoelomorpha

Axiom
annotated source: central nervous system
annotated property: external_definition
annotated target: Part of the nervous system which includes the brain and spinal cord.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000090
ontology: AAO
source: AAO:BJB

Axiom
annotated source: central nervous system
annotated property: external_definition
annotated target: The brain and spinal cord. Kimmel et al, 1995.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000012
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: central nervous system
annotated property: external_definition
annotated target: The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
source: BIRNLEX:1099

Axiom
annotated source: central nervous system
annotated property: homology_notes
annotated target: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000293
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)
source: http://bgee.unil.ch/

Axiom
annotated source: central nervous system
annotated property: database_cross_reference
annotated target: FBbt:00005094
mapping justification: ManualMappingCuration

Axiom
annotated source: central nervous system
annotated property: database_cross_reference
annotated target: UMLS:C0927232
source: BIRNLEX:1099
source: ncithesaurus:Central_Nervous_System

Axiom
annotated source: central nervous system
annotated property: has_exact_synonym
annotated target: CNS
has_synonym_type: abbreviation

Axiom
annotated source: central nervous system
annotated property: has_exact_synonym
annotated target: systema nervosum centrale
database_cross_reference: FMA:55675
database_cross_reference: FMA:TA
has_synonym_type: latin term

Axiom
annotated source: central nervous system
annotated property: has_narrow_synonym
annotated target: cerebrospinal axis
database_cross_reference: FMA:55675

Axiom
annotated source: central nervous system
annotated property: has_related_synonym
annotated target: neuraxis
database_cross_reference: FMA:55675

axon tract
type: Class
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: A group of axons linking two or more neuropils and having a common origin, termination[FBbt].
external_definition: White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)
database_cross_reference: BIRNLEX:1649
database_cross_reference: EV:0100304
database_cross_reference: FBbt:00005100
database_cross_reference: FMA:83847
database_cross_reference: NLX:147822
has_exact_synonym: axonal tract
has_exact_synonym: neuraxis tract
has_exact_synonym: tract of neuraxis
has_narrow_synonym: nerve tract
has_obo_namespace: uberon
has_related_synonym: nerve tract
has_related_synonym: tract
id: UBERON:0001018
in_subset: cumbo
in_subset: pheno slim
comment: WP says this is the analog of peripheral nerves in CNS.

Axiom
annotated source: axon tract
annotated property: has_exact_synonym
annotated target: tract of neuraxis
database_cross_reference: FMA:83847

Axiom
annotated source: axon tract
annotated property: has_narrow_synonym
annotated target: nerve tract
database_cross_reference: BIRNLEX:1649

Axiom
annotated source: axon tract
annotated property: definition
annotated target: A group of axons linking two or more neuropils and having a common origin, termination[FBbt].
database_cross_reference: http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html
database_cross_reference: https://github.com/obophenotype/uberon/issues/286

Axiom
annotated source: axon tract
annotated property: external_definition
annotated target: White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)
source: http://neurolex.org/wiki/Cumbo_terms

Axiom
annotated source: axon tract
annotated property: database_cross_reference
annotated target: FBbt:00005100
mapping justification: ManualMappingCuration

Axiom
annotated source: axon tract
annotated property: has_exact_synonym
annotated target: neuraxis tract
database_cross_reference: FMA:83847

nervous system commissure
type: Class
subclass of: axon tract
definition: Axon tract that crosses the midline of the central nervous system[NIF, modified]. In the context of Drosophila refers to a broad band of axons connecting equivalent neuropils each side of the brain[FBbt].
external_definition: White matter fiber bundle that crosses the midline of the brain or spinal cord, that connects similar structures on both sides. (CUMBO; Heimer, L. The Human Brain, 2nd ed., 1995, pg 6)
has_relational_adjective: commissural
has_broad_synonym: commissure
database_cross_reference: FMA:83906
database_cross_reference: NCIT:C32349
database_cross_reference: NLX:110
database_cross_reference: NLXANAT:20090513
database_cross_reference: TADS:0000201
database_cross_reference: UMLS:C1185742
database_cross_reference: Wikipedia:Commissure
has_exact_synonym: commissure of neuraxis
has_exact_synonym: neuraxis commissure
has_narrow_synonym: white matter commissure
has_obo_namespace: uberon
id: UBERON:0001020
in_subset: cumbo
in_subset: uberon slim
comment: *not* the same as FMA:76741 Commissure

Axiom
annotated source: nervous system commissure
annotated property: definition
annotated target: Axon tract that crosses the midline of the central nervous system[NIF, modified]. In the context of Drosophila refers to a broad band of axons connecting equivalent neuropils each side of the brain[FBbt].
database_cross_reference: NLXANAT:20090513
database_cross_reference: https://github.com/obophenotype/uberon/issues/300
database_cross_reference: https://github.com/obophenotype/uberon/issues/325

Axiom
annotated source: nervous system commissure
annotated property: external_definition
annotated target: White matter fiber bundle that crosses the midline of the brain or spinal cord, that connects similar structures on both sides. (CUMBO; Heimer, L. The Human Brain, 2nd ed., 1995, pg 6)
source: http://neurolex.org/wiki/Cumbo_terms

Axiom
annotated source: nervous system commissure
annotated property: database_cross_reference
annotated target: UMLS:C1185742
source: ncithesaurus:Commissure

Axiom
annotated source: nervous system commissure
annotated property: has_exact_synonym
annotated target: commissure of neuraxis
database_cross_reference: FMA:83906

Axiom
annotated source: nervous system commissure
annotated property: has_exact_synonym
annotated target: neuraxis commissure
database_cross_reference: FMA:83906

Axiom
annotated source: nervous system commissure
annotated property: has_narrow_synonym
annotated target: white matter commissure
database_cross_reference: CUMBO:CUMBO

spinal cord
type: Class
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO).
editor note: TODO - add superclass to unify with VNC?
mutually_spatially_disjoint_with: brain
present_in_taxon: NCBITaxon 9606
external_definition: Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
homology_notes: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
database_cross_reference: AAO:0010151
database_cross_reference: BAMS:SP
database_cross_reference: BAMS:Spinal
database_cross_reference: BIRNLEX:1709
database_cross_reference: BM:SpC
database_cross_reference: BTO:0001279
database_cross_reference: CALOHA:TS-0953
database_cross_reference: DHBA:12890
database_cross_reference: DMBA:17651
database_cross_reference: EFO:0000110
database_cross_reference: EHDAA2:0001255
database_cross_reference: EHDAA:2863
database_cross_reference: EMAPA:17577
database_cross_reference: EV:0100316
database_cross_reference: FMA:7647
database_cross_reference: GAID:695
database_cross_reference: MA:0000216
database_cross_reference: MAT:0000183
database_cross_reference: MESH:D013116
database_cross_reference: MIAA:0000183
database_cross_reference: NCIT:C12464
database_cross_reference: SCTID:180959008
database_cross_reference: TAO:0000075
database_cross_reference: UMLS:C0037925
database_cross_reference: VHOG:0000601
database_cross_reference: Wikipedia:Spinal_cord
database_cross_reference: XAO:0000020
database_cross_reference: ZFA:0000075
database_cross_reference: neuronames:22
has_obo_namespace: uberon
has_related_synonym: SpC
has_related_synonym: cerebro-cerebellar fissure
has_related_synonym: cerebrocerebellar fissure
has_related_synonym: fissura cerebro-cerebellaris
has_related_synonym: fissura cerebrocerebellaris
has_related_synonym: medulla spinalis
has_related_synonym: spinal cord structure
has_related_synonym: spinal medulla
id: UBERON:0002240
in_subset: cumbo
in_subset: efo slim
in_subset: human reference atlas
in_subset: major organ
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core

Axiom
annotated source: spinal cord
annotated property: definition
annotated target: Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO).
database_cross_reference: BIRNLEX:1709

Axiom
annotated source: spinal cord
annotated property: mutually_spatially_disjoint_with
annotated target: brain
exceptions: ZFA
source: https://github.com/obophenotype/uberon/issues/378
status: pending

Axiom
annotated source: spinal cord
annotated property: external_definition
annotated target: Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010151
ontology: AAO
source: AAO:BJB

Axiom
annotated source: spinal cord
annotated property: homology_notes
annotated target: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000601
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
source: http://bgee.unil.ch/

Axiom
annotated source: spinal cord
annotated property: database_cross_reference
annotated target: UMLS:C0037925
source: BIRNLEX:1709
source: ncithesaurus:Spinal_Cord

Axiom
annotated source: spinal cord
annotated property: database_cross_reference
annotated target: neuronames:22
source: BIRNLEX:1709

Axiom
annotated source: spinal cord
annotated property: has_related_synonym
annotated target: SpC
has_synonym_type: abbreviation

Axiom
annotated source: spinal cord
annotated property: has_related_synonym
annotated target: cerebro-cerebellar fissure
database_cross_reference: NeuroNames:22

Axiom
annotated source: spinal cord
annotated property: has_related_synonym
annotated target: cerebrocerebellar fissure
database_cross_reference: NeuroNames:22

Axiom
annotated source: spinal cord
annotated property: has_related_synonym
annotated target: fissura cerebro-cerebellaris
database_cross_reference: NeuroNames:22
has_synonym_type: latin term

Axiom
annotated source: spinal cord
annotated property: has_related_synonym
annotated target: fissura cerebrocerebellaris
database_cross_reference: NeuroNames:22
has_synonym_type: latin term

Axiom
annotated source: spinal cord
annotated property: has_related_synonym
annotated target: medulla spinalis
database_cross_reference: BTO:0001279
database_cross_reference: Wikipedia:Spinal_cord
has_synonym_type: latin term

Axiom
annotated source: spinal cord
annotated property: has_related_synonym
annotated target: spinal cord structure
database_cross_reference: ZFA:0000075

Axiom
annotated source: spinal cord
annotated property: has_related_synonym
annotated target: spinal medulla
database_cross_reference: BTO:0001279

ganglion of peripheral nervous system
type: Class
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
definition: A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO).
external_ontology_notes: we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS
database_cross_reference: BIRNLEX:2548
database_cross_reference: BTO:0001123
database_cross_reference: EMAPA:32814
database_cross_reference: MA:0001161
has_exact_synonym: peripheral nervous system ganglion
has_obo_namespace: uberon
id: UBERON:0003338
in_subset: cumbo

Axiom
annotated source: ganglion of peripheral nervous system
annotated property: definition
annotated target: A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO).
database_cross_reference: BIRNLEX:2548

Axiom
annotated source: ganglion of peripheral nervous system
annotated property: external_ontology_notes
annotated target: we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS
external ontology: MA

Axiom
annotated source: ganglion of peripheral nervous system
annotated property: has_exact_synonym
annotated target: peripheral nervous system ganglion
database_cross_reference: OBOL:automatic

future brain
type: Class
definition: The embryonic precursor of the brain.
external_definition: The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)
database_cross_reference: BAMS:Enc
database_cross_reference: BTO:0004726
database_cross_reference: EFO:0003431
database_cross_reference: EHDAA:300
database_cross_reference: EHDAA:830
database_cross_reference: EMAPA:16089
database_cross_reference: FMA:312967
database_cross_reference: RETIRED_EHDAA2:0000591
database_cross_reference: TAO:0000146
database_cross_reference: ZFA:0000146
has_exact_synonym: brain rudiment
has_exact_synonym: presumptive brain
has_narrow_synonym: encephalon
has_obo_namespace: uberon
has_related_synonym: embryonic brain
id: UBERON:0006238
in_subset: cumbo
in_subset: efo slim
in_subset: emapa ehdaa2
in_subset: vertebrate core

Axiom
annotated source: future brain
annotated property: definition
annotated target: The embryonic precursor of the brain.
database_cross_reference: NLX:94995

Axiom
annotated source: future brain
annotated property: external_definition
annotated target: The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)
source: http://neurolex.org/wiki/Cumbo_terms

Axiom
annotated source: future brain
annotated property: has_exact_synonym
annotated target: brain rudiment
database_cross_reference: TAO:0000146

Axiom
annotated source: future brain
annotated property: has_exact_synonym
annotated target: presumptive brain
database_cross_reference: ZFA:0000146

Axiom
annotated source: future brain
annotated property: has_narrow_synonym
annotated target: encephalon
database_cross_reference: NLX:94995

Axiom
annotated source: future brain
annotated property: has_related_synonym
annotated target: embryonic brain
database_cross_reference: BTO:0004726

neural decussation
type: Class
subclass of: Restriction
  on property: part of
  some values from: central nervous system
definition: Nerve fibers crossing the midline of the neuraxis relative to their point of origin, on a course to from one level of the nervous system to another. (CUMBO, Heimer, L. The Human Brain, 2nd ed., 1995, pg 6).
has_broad_synonym: chiasm
has_broad_synonym: chiasma
has_broad_synonym: decussation
database_cross_reference: FMA:83858
database_cross_reference: NCIT:C28351
database_cross_reference: NLX:144064
has_exact_synonym: decussation of neuraxis
has_exact_synonym: neuraxis chiasm
has_exact_synonym: neuraxis chiasma
has_exact_synonym: neuraxis decussation
has_obo_namespace: uberon
id: UBERON:0007418
in_subset: cumbo

Axiom
annotated source: neural decussation
annotated property: definition
annotated target: Nerve fibers crossing the midline of the neuraxis relative to their point of origin, on a course to from one level of the nervous system to another. (CUMBO, Heimer, L. The Human Brain, 2nd ed., 1995, pg 6).
database_cross_reference: NLX:144064

Axiom
annotated source: neural decussation
annotated property: has_exact_synonym
annotated target: decussation of neuraxis
database_cross_reference: FMA:83858

Axiom
annotated source: neural decussation
annotated property: has_exact_synonym
annotated target: neuraxis decussation
database_cross_reference: FMA:83858

sulcus of brain
type: Class
subclass of: Restriction
  on property: part of
  some values from: brain
definition: A depression or fissure in the surface of the brain. It surrounds the gyri, creating the characteristic appearance of the brain in humans and other large mammals.
editor note: sulci are considered absent from lissencephalic mammals such as mice, but they may possess fissures. For example, the Allen mouse brain Atlas includes hippocampal, rhinal and choroid fissure. For this reason we do not place a taxon constraint on this class
dubious_for_taxon: NCBITaxon_10088
external_definition: Indentation on the surface of the brain or spinal cord that forms a recognizable landmark, e.g., central sulcus, sulcus limitans (CUMBO)
has_broad_synonym: sulci & spaces
has_broad_synonym: sulcus
database_cross_reference: DHBA:10610
database_cross_reference: HBA:9352
database_cross_reference: NCIT:C32292
database_cross_reference: SCTID:279337001
database_cross_reference: Wikipedia:Sulcus_(neuroanatomy)
database_cross_reference: neuronames:1208
has_exact_synonym: cerebral sulci
has_narrow_synonym: fissure of brain
has_obo_namespace: uberon
has_related_synonym: cerebral sulci
has_related_synonym: cerebral sulcus
id: UBERON:0013118
in_subset: cumbo

Axiom
annotated source: sulcus of brain
annotated property: definition
annotated target: A depression or fissure in the surface of the brain. It surrounds the gyri, creating the characteristic appearance of the brain in humans and other large mammals.
database_cross_reference: Wikipedia:Sulcus_(neuroanatomy)
database_cross_reference: https://github.com/obophenotype/uberon/issues/315

Axiom
annotated source: sulcus of brain
annotated property: external_definition
annotated target: Indentation on the surface of the brain or spinal cord that forms a recognizable landmark, e.g., central sulcus, sulcus limitans (CUMBO)
source: http://neurolex.org/wiki/Cumbo_terms

Axiom
annotated source: sulcus of brain
annotated property: has_broad_synonym
annotated target: sulci & spaces
database_cross_reference: HBA:9352
has_synonym_type: plural form

Axiom
annotated source: sulcus of brain
annotated property: has_broad_synonym
annotated target: sulcus
database_cross_reference: NLX:144078

Axiom
annotated source: sulcus of brain
annotated property: has_exact_synonym
annotated target: cerebral sulci
database_cross_reference: DHBA:10610
has_synonym_type: plural form

Axiom
annotated source: sulcus of brain
annotated property: has_narrow_synonym
annotated target: fissure of brain
database_cross_reference: Wikipedia:Sulcus_(neuroanatomy)

Axiom
annotated source: sulcus of brain
annotated property: has_related_synonym
annotated target: cerebral sulci
database_cross_reference: NeuroNames:1208

Axiom
annotated source: sulcus of brain
annotated property: has_related_synonym
annotated target: cerebral sulcus
database_cross_reference: NeuroNames:1208

cell group
type: Class
definition: A group of cells that may not be contained within macroscopic anatomical boundaries, e.g., A9 dopaminergic cell group; massa intercalata of the amygdala (CUMBO).
editor note: consider adding to CARO.
has_exact_synonym: group of cells
has_obo_namespace: uberon
id: UBERON:0014778
in_subset: cumbo
in_subset: upper level

Axiom
annotated source: cell group
annotated property: definition
annotated target: A group of cells that may not be contained within macroscopic anatomical boundaries, e.g., A9 dopaminergic cell group; massa intercalata of the amygdala (CUMBO).
database_cross_reference: NLX:532

nervous system cell part layer
type: Class
subclass of: Restriction
  on property: part of
  some values from: nervous system
definition: Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].
editor note: this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer
has_broad_synonym: lamina
has_broad_synonym: layer
database_cross_reference: NLX:149357
has_obo_namespace: uberon
id: UBERON:0022303
in_subset: cumbo

Axiom
annotated source: nervous system cell part layer
annotated property: definition
annotated target: Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].
database_cross_reference: NLX:149357

Axiom
annotated source: nervous system cell part layer
annotated property: has_broad_synonym
annotated target: lamina
database_cross_reference: CUMBO:CUMBO

Axiom
annotated source: nervous system cell part layer
annotated property: has_broad_synonym
annotated target: layer
database_cross_reference: CUMBO:CUMBO