caro-simple.obo

format-version: 1.2
data-version: caro/releases/2023-03-15/caro-simple.owl
subsetdef: core "CARO2 core class"
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam ""
subsetdef: olfactory_system_draft "adult olfactory system model"
subsetdef: plus "CARO2 plus class"
subsetdef: ro-eco ""
synonymtypedef: InChIKey ""
synonymtypedef: systematic_synonym "" EXACT
remark: Based on CARO 1.0, with modifications and additions by David Osumi-Sutherland, Chris Mungall, Ramona Walls and Melissa Haendel.
ontology: caro/caro-simple
property_value: dc-description "The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies." xsd:string
property_value: dc-title "Common Anatomy Reference Ontology" xsd:string
property_value: dcterms-license https://creativecommons.org/licenses/by/4.0/
property_value: owl:versionInfo "2023-03-15" xsd:string

[Term]
id: CARO:0000000
name: anatomical entity
def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex.  Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [CAROC:Brownsville2014]
comment: Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach).  The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.
is_a: CARO:0030000 ! biological entity

[Term]
id: CARO:0000003
name: connected anatomical structure
def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." []
comment: Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development.
subset: core
is_a: CARO:0000006 ! material anatomical entity
disjoint_from: CARO:0000004 ! organism substance

[Term]
id: CARO:0000004
name: organism substance
def: "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome." []
comment: Note - CARO explicitly declares organisms substances to be part of (some) organism.
synonym: "portion of organism substance" EXACT []
is_a: CARO:0001008 ! gross anatomical part
property_value: example_of_usage "Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid.  This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle." xsd:string

[Term]
id: CARO:0000005
name: anatomical space
def: "An Immaterial anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes and that is bounded by an anatomical surface." []
comment: Original definition: "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures."  The last clause. "contains one or more organism substances or anatomical structures" was dropped from the definition because it was an unnecessary restriction.
is_a: CARO:0000007 ! immaterial anatomical entity
disjoint_from: CARO:0000008 ! anatomical line
disjoint_from: CARO:0000009 ! anatomical point
disjoint_from: CARO:0001002 ! anatomical surface
relationship: part_of CARO:0001010 ! organism

[Term]
id: CARO:0000006
name: material anatomical entity
def: "An anatomical entity that has mass." []
subset: core
is_a: CARO:0000000 ! anatomical entity
disjoint_from: CARO:0000007 ! immaterial anatomical entity

[Term]
id: CARO:0000007
name: immaterial anatomical entity
def: "Anatomical entity that has no mass." []
subset: core
is_a: CARO:0000000 ! anatomical entity

[Term]
id: CARO:0000008
name: anatomical line
def: "A one dimensional, immaterial anatomical entity." []
is_a: CARO:0000007 ! immaterial anatomical entity
disjoint_from: CARO:0000009 ! anatomical point
disjoint_from: CARO:0001002 ! anatomical surface
property_value: example_of_usage "A line between two points where these are typically used to measure some aspect of morphology, such as the distance between the eyes or the length of a leg. " xsd:string

[Term]
id: CARO:0000009
name: anatomical point
def: "Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface." []
is_a: CARO:0000007 ! immaterial anatomical entity
disjoint_from: CARO:0001002 ! anatomical surface
property_value: example_of_usage "The tip of the nose or other material anatomical entity, or the end of an anatomical line. " xsd:string

[Term]
id: CARO:0000010
name: anatomical boundary
def: "A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures." []
comment: Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection.  For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension.  Note that boundaries are 2D structures.  They have no thickness - and so can not be sites of gene expression or gene product localisation.  For this, use boundary region terms.
is_a: CARO:0000007 ! immaterial anatomical entity

[Term]
id: CARO:0000011
name: connected anatomical system
def: "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function." []
is_a: CARO:0010000 ! multicellular anatomical structure
disjoint_from: CARO:0000032 ! organism subdivision

[Term]
id: CARO:0000012
name: multicellular organism
def: "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." []
comment: MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. \n\nMH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities.
is_a: CARO:0010004 ! cellular organism
disjoint_from: CARO:0000024 ! compound organ
disjoint_from: CARO:0010001 ! cell cluster organ
disjoint_from: CARO:0010002 ! compound cell cluster organ

[Term]
id: CARO:0000013
name: cell
def: "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." []
comment: deprecate and replace with CL or GO term?
xref: CL:0000000
xref: GO:0005623
is_a: CARO:0000003 ! connected anatomical structure
is_a: CARO:0020003 ! cellular anatomical structure
disjoint_from: CARO:0000014 ! cell part
disjoint_from: CARO:0000040 ! acellular anatomical structure
disjoint_from: CARO:0000042 ! extraembryonic structure
disjoint_from: CARO:0001000 ! multi-cell-part structure
disjoint_from: CARO:0010000 ! multicellular anatomical structure

[Term]
id: CARO:0000014
name: cell part
def: "Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher." []
comment: This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class.
is_a: CARO:0000003 ! connected anatomical structure
disjoint_from: CARO:0000040 ! acellular anatomical structure
disjoint_from: CARO:0000042 ! extraembryonic structure
disjoint_from: CARO:0001000 ! multi-cell-part structure
disjoint_from: CARO:0010000 ! multicellular anatomical structure
relationship: part_of CARO:0000013 ! cell
property_value: IAO:0000118 "cell component" xsd:string

[Term]
id: CARO:0000019
name: compound organ component
def: "Multi-tissue structure that is part of a compound organ." []
is_a: CARO:0000055 ! multi-tissue structure
relationship: part_of CARO:0000024 ! compound organ

[Term]
id: CARO:0000021
name: simple organ
def: "An organ that consists of a single multi-tissue structure." []
is_a: CARO:0020004 ! organ
relationship: has_component CARO:0000055 ! multi-tissue structure

[Term]
id: CARO:0000024
name: compound organ
def: "An organ consisting of multiple, distinct multi-tissue structures." []
is_a: CARO:0000055 ! multi-tissue structure
is_a: CARO:0020004 ! organ
disjoint_from: CARO:0010001 ! cell cluster organ
disjoint_from: CARO:0010002 ! compound cell cluster organ
relationship: has_component CARO:0000055 ! multi-tissue structure

[Term]
id: CARO:0000027
name: male organism
def: "Gonochoristic organism that can produce male gametes." []
is_a: CARO:0000048 ! gonochoristic organism

[Term]
id: CARO:0000028
name: female organism
def: "Gonochoristic organism that can produce female gametes." []
is_a: CARO:0000048 ! gonochoristic organism

[Term]
id: CARO:0000029
name: hermaphroditic organism
def: "Multi-cellular organism that can produce both male and female gametes." []
is_a: CARO:0000012 ! multicellular organism
property_value: IAO:0000118 "dioecious organism" xsd:string {http://purl.obolibrary.org/obo/IAO_scope="RELATED"}

[Term]
id: CARO:0000030
name: asexual multi-cellular organism
def: "Multi-cellular organism that does not produce gametes." []
is_a: CARO:0000012 ! multicellular organism

[Term]
id: CARO:0000032
name: organism subdivision
def: "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." []
subset: core
is_a: CARO:0010000 ! multicellular anatomical structure
property_value: editor_note "Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism." xsd:string

[Term]
id: CARO:0000040
name: acellular anatomical structure
def: "An anatomical structure that has no cells or cell parts as a part." []
comment: Example.  Insect cuticle, eggshell, hair.
is_a: CARO:0000003 ! connected anatomical structure
is_a: CARO:0001008 ! gross anatomical part
disjoint_from: CARO:0000042 ! extraembryonic structure
disjoint_from: CARO:0001000 ! multi-cell-part structure
disjoint_from: CARO:0010000 ! multicellular anatomical structure

[Term]
id: CARO:0000041
name: anatomical cluster
def: "Anatomical group that has its parts adjacent to one another." [FMA:49443, https://orcid.org/0000-0001-9114-8737]
subset: plus
is_obsolete: true
replaced_by: CARO:0020001

[Term]
id: CARO:0000042
name: extraembryonic structure
def: "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." []
comment: MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures.  Old def: "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.".  One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids?\n
subset: plus
is_a: CARO:0000003 ! connected anatomical structure
is_a: CARO:0001008 ! gross anatomical part
disjoint_from: CARO:0001000 ! multi-cell-part structure
disjoint_from: CARO:0010000 ! multicellular anatomical structure

[Term]
id: CARO:0000043
name: tissue
def: "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." []
is_a: CARO:0010000 ! multicellular anatomical structure
property_value: editor_note "relabel 'tissue'?" xsd:string
property_value: IAO:0000118 "portion of tissue" xsd:string

[Term]
id: CARO:0000045
name: sequential hermaphroditic organism
def: "Hermaphroditic organism that produces gametes first of one sex, and then later of the other sex." []
is_a: CARO:0000029 ! hermaphroditic organism
property_value: IAO:0000118 "consecutive hermaphroditic organism" xsd:string {http://purl.obolibrary.org/obo/IAO_scope="RELATED"}

[Term]
id: CARO:0000046
name: synchronous hermaphroditic organism
def: "Hermaphroditic organism that produces both male and female gametes at the same time." []
is_a: CARO:0000029 ! hermaphroditic organism
property_value: IAO:0000118 "serially hermaphroditic organism" xsd:string {http://purl.obolibrary.org/obo/IAO_scope="RELATED"}

[Term]
id: CARO:0000048
name: gonochoristic organism
def: "Multi-cellular organism that has male and female sexes." []
is_a: CARO:0000012 ! multicellular organism
property_value: IAO:0000118 "monoecious organism" xsd:string {http://purl.obolibrary.org/obo/IAO_scope="RELATED"}

[Term]
id: CARO:0000049
name: protandrous hermaphroditic organism
def: "Sequential hermaphroditic organism that produces\\ngametes first of the male sex, and then later of the\\nfemale sex." []
is_a: CARO:0000045 ! sequential hermaphroditic organism

[Term]
id: CARO:0000050
name: protogynous hermaphroditic organism
def: "Sequential hermaphroditic organism that produces\\ngametes first of the female sex, and then later of the\\nmale sex." []
is_a: CARO:0000045 ! sequential hermaphroditic organism

[Term]
id: CARO:0000054
name: anatomical group
def: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.\n" [https://orcid.org/0000-0001-9114-8737]
comment: Obsoleted because the definition is too opaque.  Also because this class was a subclass of 'anatomical structure' (CARO_0000003), but a similarly named class in the refactored caro (CARO_0020000) is a sibling of 'anatomical structure'.
subset: core
is_obsolete: true
consider: CARO:0020000

[Term]
id: CARO:0000055
name: multi-tissue structure
def: "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types." []
is_a: CARO:0010000 ! multicellular anatomical structure
relationship: has_component CARO:0000043 {minCardinality="2"} ! tissue

[Term]
id: CARO:0000062
name: cell space
def: "Anatomical space that is part of a cell." []
is_a: CARO:0000005 ! anatomical space
relationship: part_of CARO:0000013 ! cell

[Term]
id: CARO:0000063
name: portion of cell substance
def: "Portion of organism substance located within a cell." []
comment: Deprecate this as better to leave it up to GO to define?
is_a: CARO:0000004 ! organism substance

[Term]
id: CARO:0000064
name: unicellular organism
def: "Organism that consists of a single cell for all of its life-cycle." []
is_a: CARO:0010004 ! cellular organism
relationship: has_component CARO:0000013 {cardinality="1"} ! cell
relationship: has_component CARO:0000013 {all_only="true"} ! cell
property_value: IAO:0000118 "single-cell organism" xsd:string

[Term]
id: CARO:0000065
name: basal lamina
def: "Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue." []
is_obsolete: true

[Term]
id: CARO:0000066
name: epithelium
def: "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina." []
is_a: CARO:0000043 ! tissue

[Term]
id: CARO:0000067
name: simple cuboidal epithelium
def: "Unilaminar epithelium that consists of a single layer of cuboidal cells." []
is_a: CARO:0000073 ! unilaminar epithelium

[Term]
id: CARO:0000068
name: simple columnar epithlium
def: "Unilaminar epithelium that consists of a single layer of columnar cells." []
is_a: CARO:0000073 ! unilaminar epithelium

[Term]
id: CARO:0000069
name: multilaminar epithelium
def: "Epithelium that consists of more than one layer of epithelial cells." []
is_a: CARO:0000066 ! epithelium
disjoint_from: CARO:0000071 ! atypical epithelium
disjoint_from: CARO:0000073 ! unilaminar epithelium

[Term]
id: CARO:0000070
name: simple squamous epithelium
def: "Unilaminar epithelium that consists of a single layer of squamous cells." []
is_a: CARO:0000073 ! unilaminar epithelium

[Term]
id: CARO:0000071
name: atypical epithelium
def: "Epithelium that consists of epithelial cells not arranged in one ore more layers." []
is_a: CARO:0000066 ! epithelium
disjoint_from: CARO:0000073 ! unilaminar epithelium

[Term]
id: CARO:0000072
name: cavitated compound organ
def: "Compound organ that contains one or more macroscopic anatomical spaces." []
is_a: CARO:0000024 ! compound organ

[Term]
id: CARO:0000073
name: unilaminar epithelium
def: "Epithelium that consists of a single layer of epithelial cells." []
is_a: CARO:0000066 ! epithelium

[Term]
id: CARO:0000074
name: solid compound organ
def: "Compound organ that does not contain macroscopic anatomical spaces." []
is_a: CARO:0000024 ! compound organ

[Term]
id: CARO:0000077
name: epithelial cell
def: "Cell which has as its part a cytoskeleton that allows for tight cell to cell contact and which has apical-basal cell polarity." []
is_obsolete: true

[Term]
id: CARO:0000081
name: circulating fluid
def: "A fluid that is circulated around a multicellular organism carrying nutrients and carrying away waste products." []
comment: Examples: blood, lymph, hemolymph
is_a: CARO:0000004 ! organism substance

[Term]
id: CARO:0000133
name: paired appendage
def: "An appendage that is one of a bilateral pair." []
is_a: CARO:0010003 ! appendage
disjoint_from: CARO:0000134 ! unpaired appendage

[Term]
id: CARO:0000134
name: unpaired appendage
is_a: CARO:0010003 ! appendage

[Term]
id: CARO:0001000
name: multi-cell-part structure
def: "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." []
comment: Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain.
subset: core
is_a: CARO:0001008 ! gross anatomical part
disjoint_from: CARO:0010000 ! multicellular anatomical structure
property_value: IAO:0000118 "multi-cell-component structure" xsd:string

[Term]
id: CARO:0001001
name: neuron projection bundle
def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." []
is_a: CARO:0001000 ! multi-cell-part structure
property_value: IAO:0000118 "nerve fiber bundle" xsd:string {http://purl.obolibrary.org/obo/IAO_scope="EXACT"}

[Term]
id: CARO:0001002
name: anatomical surface
def: "A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment.  Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.\n" []
comment: Old definition: "Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures."  Note, in the new definition, the space referred to is not necessarily an anatomical space.  It may be the outside of an organism.
is_a: CARO:0001007 ! morphological boundary

[Term]
id: CARO:0001003
name: fiat anatomical boundary
def: "A  two dimensional anatomical entity that does not correspond to any physical discontinuity." []
comment: Fiat anatomical boundaries are generally defined using external physical criteria as landmarks.  One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity.  This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)
is_a: CARO:0000010 ! anatomical boundary

[Term]
id: CARO:0001004
name: bona-fide anatomical boundary
def: "An anatomical boundary that corresponds to some physical discontinuity." []
comment: One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity.  This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)
is_a: CARO:0000010 ! anatomical boundary

[Term]
id: CARO:0001005
name: gene expression boundary
def: "A two dimensional anatomical entity that is the boundary of a domain of  expression of some gene." []
is_a: CARO:0001004 ! bona-fide anatomical boundary

[Term]
id: CARO:0001006
name: developmental compartment boundary
def: "A two dimensional anatomical entity that is not a morphological boundary and that cells do not cross during development." []
is_a: CARO:0001004 ! bona-fide anatomical boundary

[Term]
id: CARO:0001007
name: morphological boundary
def: "A two dimensional anatomical structure that corresponds to some structural discontinuity." []
is_a: CARO:0001004 ! bona-fide anatomical boundary

[Term]
id: CARO:0001008
name: gross anatomical part
def: "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell.  Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. " []
subset: plus
is_a: CARO:0000006 ! material anatomical entity
relationship: part_of CARO:0000012 ! multicellular organism
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "10.7.2011" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737

[Term]
id: CARO:0001009
name: obsolete anatomical chamber
def: "Anatomical structure that surrounds an immaterial anatomical entity." []
comment: See CARO tracker #6, but essentially Chamber has connotations of space, rather than wall: see http://en.wiktionary.org/wiki/chamber\n\nThis term is extremely abstract as a genus - it specifies no granularity at all. It could refer to a chamber in a protein complex in a membrane as easily as some big multi-tissue structure like a segment of gut.
subset: plus
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "10.10.2011" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737
is_obsolete: true

[Term]
id: CARO:0001010
name: organism
def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." []
synonym: "organism or virus or viroid" EXACT []
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string
property_value: IAO:0000117 "Melissa Haendel" xsd:string

[Term]
id: CARO:0001013
name: anatomical plane
comment: All anatomical planes are fiat anatomical boundaries - no morphological boundary could ever be a perfect plane.
is_a: CARO:0001003 ! fiat anatomical boundary

[Term]
id: CARO:0001500
name: neuron projection bundle segment
def: "A fiber-shaped subdivision of a neuron projection along its long axis." [] {http://purl.obolibrary.org/obo/IAO_0000117="https://orcid.org/0000-0002-7073-9172"}
is_a: CARO:0001000 ! multi-cell-part structure
relationship: part_of CARO:0001001 ! neuron projection bundle

[Term]
id: CARO:0001501
name: neuron projection bundle subsegment
def: "A subdivision of a neuron projection along its long axis that is as long as it is wide (and so does not qualify as fiber-shaped)." [] {http://purl.obolibrary.org/obo/IAO_0000117="https://orcid.org/0000-0002-7073-9172"}
comment: This term was added in order to define fasciculation relations.  It seems unlikely that it will be used directly in curation.
is_a: CARO:0001000 ! multi-cell-part structure
relationship: part_of CARO:0001001 ! neuron projection bundle

[Term]
id: CARO:0002000
name: epidermis
def: "Epithelium of the integumentary system." []
is_a: CARO:0000066 ! epithelium
relationship: part_of CARO:0002001 ! integumentary system

[Term]
id: CARO:0002001
name: integumentary system
def: "Connected anatomical system that forms a barrier between an animal and its environment - generally consisting of an epidermis, which may be covered by some acellular structure." []
is_a: CARO:0000011 ! connected anatomical system

[Term]
id: CARO:0002002
name: aligned anatomical group
def: "An anatomical group whose members are arranged in a line." []
comment: Examples include the rows of sense organs commonly found in the cuticles of insects.
is_a: CARO:0020000 ! disconnected anatomical group

[Term]
id: CARO:0002003
name: clustered anatomical group
def: "Anatomical group whose parts are close together, forming a cluster." [https://orcid.org/0000-0002-7073-9172]
comment: Not to be confused with anatomical cluster, in the FMA sense.  FMA anatomical structures are connected structures made up of heterologous parts.  For example, joints are anatomical clusters in the FMA.  The FMA definition on anatomical cluster, and the CARO1 definition that was based on it, are defined largely by exclusion.
is_a: CARO:0020000 ! disconnected anatomical group

[Term]
id: CARO:0002004
name: segment body
def: "One of a set of semi-repetitive organism subdivisions serially arranged along the anterior-posterior axis of an organism and excluding appendages if present." []
is_a: CARO:0000032 ! organism subdivision

[Term]
id: CARO:0002005
name: appendage subdivision
def: "A subdivision of an appendage along its proximal-distal axis, consisting consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." []
is_a: CARO:0000032 ! organism subdivision

[Term]
id: CARO:0002006
name: obsolete body cavity
def: "A major anatomical space of an organism in which major organs are located." []
property_value: example_of_usage "Ceolom, cranial cavity, mammalian thoracic and abdominal body cavities, arthropod hemoceol." xsd:string
is_obsolete: true

[Term]
id: CARO:0002100
name: anatomical system
def: "An anatomical structure consisting of multiple cells, organs, tissues, distributed throught an organism, that act together to perform some physiological function." []
comment: Examples include connected systems such as the circulatory system - whose elements function together to perform the function or blood circulation - and disconected systems such as the immune system. {xref="https://orcid.org/0000-0002-7073-9172"}
is_a: CARO:0000000 ! anatomical entity

[Term]
id: CARO:0002101
name: disconnected anatomical system
def: "An anatomical system consisting of multiple disconnected parts." [https://orcid.org/0000-0002-7073-9172]
comment: Examples include the immune system and the endocrine system.
is_a: CARO:0002100 ! anatomical system
relationship: has_component CARO:0000003 ! connected anatomical structure

[Term]
id: CARO:0010000
name: multicellular anatomical structure
def: "An anatomical structure that has more than one cell as a part." []
subset: core
is_a: CARO:0000003 ! connected anatomical structure
is_a: CARO:0001008 ! gross anatomical part
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Sun Feb 27 10:53:00 GMT 2011" xsd:string
property_value: IAO:0000117 "djs93" xsd:string

[Term]
id: CARO:0010001
name: cell cluster organ
def: "A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function." []
comment: Examples include arthropod sensilla.
is_a: CARO:0020002 ! cell cluster
is_a: CARO:0020004 ! organ
disjoint_from: CARO:0010002 ! compound cell cluster organ
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Sun Feb 27 11:00:35 GMT 2011" xsd:string
property_value: IAO:0000117 "djs93" xsd:string

[Term]
id: CARO:0010002
name: compound cell cluster organ
def: "An anatomical structure consisting of multiple cell cluster organs, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function." []
comment: Examples: compound eye; Johnston's organ.
is_a: CARO:0020004 ! organ
relationship: has_component CARO:0010001 {minCardinality="2"} ! cell cluster organ
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Sun Feb 27 11:13:17 GMT 2011" xsd:string
property_value: IAO:0000117 "djs93" xsd:string

[Term]
id: CARO:0010003
name: appendage
def: "An organism subdivision that protrudes from the body." []
is_a: CARO:0000032 ! organism subdivision
disjoint_from: CARO:0010005 ! segment
disjoint_from: CARO:0010006 ! tagma
disjoint_from: CARO:0010007 ! appendage segment
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Fri Mar 04 07:09:17 GMT 2011" xsd:string
property_value: IAO:0000117 "djs93" xsd:string

[Term]
id: CARO:0010004
name: cellular organism
def: "An individual member of a clade of cellular organisms." []
comment: A general term for organism that is agnostic about single cell vs multi-cellular.  Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. 
is_a: CARO:0000003 ! connected anatomical structure
is_a: CARO:0001010 ! organism
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737

[Term]
id: CARO:0010005
name: segment
def: "One of a set of semi-repetitive organism subdivisions serially arranged along the anterior-posterior axis of an organism, including appendages if present." [https://orcid.org/0000-0002-7073-9172]
synonym: "metamere" EXACT []
is_a: CARO:0000032 ! organism subdivision
disjoint_from: CARO:0010006 ! tagma
disjoint_from: CARO:0010007 ! appendage segment
relationship: has_part CARO:0010006 ! tagma
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Fri Mar 04 07:13:46 GMT 2011" xsd:string
property_value: IAO:0000117 "djs93" xsd:string

[Term]
id: CARO:0010006
name: tagma
def: "A subdivision of the organism along the anterior-posterior axis that consists of multiple adjacent segments that are either fused, and/or share more structure with each other than with segments in adjacent tagmata." []
is_a: CARO:0000032 ! organism subdivision
disjoint_from: CARO:0010007 ! appendage segment
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Fri Mar 04 07:14:57 GMT 2011" xsd:string
property_value: IAO:0000117 "djs93" xsd:string

[Term]
id: CARO:0010007
name: appendage segment
def: "One of a set of semi-repetitive organism subdivisions serially arranged along the proximal-distal axis of an appendage" []
is_a: CARO:0002005 ! appendage subdivision
relationship: part_of CARO:0010003 ! appendage
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Fri Mar 04 07:16:21 GMT 2011" xsd:string
property_value: IAO:0000117 "djs93" xsd:string

[Term]
id: CARO:0010009
name: epithelial tube
def: "An epithelium that is rolled into a tube." []
is_a: CARO:0000066 ! epithelium
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Wed Mar 09 06:22:07 GMT 2011" xsd:string
property_value: IAO:0000117 "djs93" xsd:string

[Term]
id: CARO:0010010
name: epithelial sac
is_a: CARO:0000066 ! epithelium
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Wed Mar 09 08:02:50 GMT 2011" xsd:string
property_value: IAO:0000117 "djs93" xsd:string

[Term]
id: CARO:0020000
name: disconnected anatomical group
def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." []
subset: core
is_a: CARO:0000006 ! material anatomical entity
relationship: has_component CARO:0000003 ! connected anatomical structure

[Term]
id: CARO:0020001
name: multi organ part structure
def: "A multicellular anatomical structure that has subparts of\nmultiple organs as a part." []
comment: Examples include joints of the vertebrate musculoskeletal system (each has (fiat) parts of multiple bone organs as a part).
subset: plus
synonym: "anatomical cluster" RELATED []
is_a: CARO:0010000 ! multicellular anatomical structure

[Term]
id: CARO:0020002
name: cell cluster
def: "A cluster of cells, largely surrounded by a morphological boundary." [] {comment="https://orcid.org/0000-0002-7073-9172"}
is_a: CARO:0010000 ! multicellular anatomical structure

[Term]
id: CARO:0020003
name: cellular anatomical structure
def: "An anatomical structure consisting of one or more cells." []
is_a: CARO:0000006 ! material anatomical entity
created_by: https://orcid.org/0000-0002-7073-9172
creation_date: 2018-09-28T14:20:19Z

[Term]
id: CARO:0020004
name: organ
def: "A multicellular anatomical structure largely delimited by a morphological boundary whose components work together to make the whole structure capable of a specific function." []
is_a: CARO:0010000 ! multicellular anatomical structure

[Term]
id: CARO:0020005
name: single tissue organ
def: "An single tissue, largely surrounded by a morpholigical boundary, whose cells work together to make the whole structure capable of a specific function." []
is_a: CARO:0000043 ! tissue
is_a: CARO:0020004 ! organ
relationship: has_component CARO:0000043 ! tissue

[Term]
id: CARO:0030000
name: biological entity
def: "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them." []
comment: Important for alignment with Darwin Core class "Organism".

[Term]
id: CARO:0030002
name: expression pattern
def: "The mereological sum of all cells in a single organism in which expression of some specified gene occurs." []
is_a: CARO:0020003 ! cellular anatomical structure
relationship: has_part CARO:0000013 ! cell

[Typedef]
id: bearer_of
name: bearer of
name: has characteristic
namespace: external
def: "Inverse of characteristic_of" []
xref: RO:0000053
property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string
property_value: example_of_usage "this apple is bearer of this red color" xsd:string
property_value: example_of_usage "this vase is bearer of this fragility" xsd:string
property_value: IAO:0000111 "bearer of" xsd:string
property_value: IAO:0000118 "bearer_of" xsd:string
property_value: IAO:0000118 "is bearer of" xsd:string
property_value: RO:0001900 RO:0001901
is_inverse_functional: true

[Typedef]
id: dc-creator
name: creator
namespace: uberon
xref: http://purl.org/dc/elements/1.1/creator
is_metadata_tag: true

[Typedef]
id: dc-description
name: description
namespace: uberon
xref: http://purl.org/dc/elements/1.1/description
is_metadata_tag: true

[Typedef]
id: dc-title
name: title
namespace: uberon
xref: http://purl.org/dc/elements/1.1/title
is_metadata_tag: true

[Typedef]
id: dcterms-license
name: license
namespace: uberon
xref: http://purl.org/dc/terms/license
is_metadata_tag: true

[Typedef]
id: editor_note
name: editor note
namespace: uberon
xref: IAO:0000116
is_metadata_tag: true

[Typedef]
id: example_of_usage
name: example of usage
namespace: uberon
xref: IAO:0000112
is_metadata_tag: true

[Typedef]
id: has_boundary
name: has 2D boundary
name: has_boundary
namespace: uberon
def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" []
xref: RO:0002002
property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string
property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string
property_value: example_of_usage "my body has 2D boundary the surface of my skin" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
property_value: IAO:0000118 "has boundary" xsd:string
property_value: IAO:0000118 "has_2D_boundary" xsd:string
property_value: RO:0001900 RO:0001901
domain: CARO:0000003 ! connected anatomical structure
range: CARO:0000010 ! anatomical boundary

[Typedef]
id: has_component
name: has component
namespace: external
namespace: uberon
def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." []
subset: ro-eco
xref: RO:0002180
property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency
is_a: has_part ! has part

[Typedef]
id: has_part
name: has part
name: has_part
namespace: external
namespace: quality
namespace: uberon
def: "a core relation that holds between a whole and its part" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
xref: BFO:0000051
property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string
property_value: 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/" xsd:string
property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string
property_value: example_of_usage "my body has part my brain (continuant parthood, two material entities)" xsd:string
property_value: example_of_usage "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string
property_value: example_of_usage "this year has part this day (occurrent parthood)" xsd:string
property_value: IAO:0000111 "has part" xsd:string
property_value: IAO:0000118 "has_part" xsd:string
property_value: RO:0001900 RO:0001901
is_transitive: true

[Typedef]
id: part_of
name: part of
name: part_of
namespace: external
namespace: quality
namespace: uberon
def: "a core relation that holds between a part and its whole" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
xref: BFO:0000050
property_value: 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." xsd:string
property_value: 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/" xsd:string
property_value: 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.)\n\nA 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'." xsd:string
property_value: example_of_usage "my brain is part of my body (continuant parthood, two material entities)" xsd:string
property_value: example_of_usage "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
property_value: example_of_usage "this day is part of this year (occurrent parthood)" xsd:string
property_value: IAO:0000111 "is part of" xsd:string
property_value: IAO:0000118 "part_of" xsd:string
property_value: RO:0001900 RO:0001901
property_value: RO:0040042 BFO:0000002
property_value: RO:0040042 BFO:0000003
property_value: RO:0040042 BFO:0000004
property_value: RO:0040042 BFO:0000017
property_value: RO:0040042 BFO:0000019
property_value: RO:0040042 BFO:0000020
property_value: RO:0040042 BFO:0000031
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string
is_transitive: true
inverse_of: has_part ! has part