Common Anatomy Reference Ontology (CARO)
An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species.
Tag: CARO
acellular anatomical structure [CARO_0000040]
An anatomical structure that has no cells or cell parts as a part. Example. Insect cuticle, eggshell, hair.
anatomical boundary [CARO_0000010]
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. 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.
anatomical entity [CARO_0000000]
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. Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.
anatomical space [CARO_0000005]
An Immaterial anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes and that is bounded by an anatomical surface. 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.
biological entity [CARO_0030000]
Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them. Important for alignment with Darwin Core class “Organism”.
cell [CARO_0000013]
An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. deprecate and replace with CL or GO term?
cell part [CARO_0000014]
Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher. 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.
cell space [CARO_0000062]
Anatomical space that is part of a cell.
cellular anatomical structure [CARO_0020003]
An anatomical structure consisting of one or more cells.
cellular organism [CARO_0010004]
An individual member of a clade of cellular organisms. 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. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. 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.
connected anatomical structure [CARO_0000003]
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism’s own genome. 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.
connected anatomical system [CARO_0000011]
[connected anatomical system; multicellular anatomical structure]
disconnected anatomical group [CARO_0020000]
Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.
expression pattern [CARO_0030002]
[confocal microscopy; VDRC_VT048834_LexAGAD_attP40_2; VDRC_VT911043_GAL4_attP2_4; JRC2018Unisex; expression pattern; VDRC_VT039576_LexAGAD_attP40_1; adult brain template JFRC2; anatomical entity]
extraembryonic structure [CARO_0000042]
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. 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?
gross anatomical part [CARO_0001008]
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.
immaterial anatomical entity [CARO_0000007]
Anatomical entity that has no mass.
material anatomical entity [CARO_0000006]
An anatomical entity that has mass.
multi-cell-part structure [CARO_0001000]
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. 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.
multicellular anatomical structure [CARO_0010000]
An anatomical structure that has more than one cell as a part.
multicellular organism [CARO_0000012]
Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell. 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. 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. MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities.
neuron projection bundle [CARO_0001001]
[neuron projection bundle; dorsal prothoracic nerve on adult VNS template, Court2018; prothoracic leg nerve on adult VNS template, Court2018; adult VNS template - Court2018; accessory prothoracic nerve on adult VNS template, Court2018; accessory mesothoracic nerve on adult VNS template, Court2018; computer graphic; multi-cell-part structure; ventral prothoracic nerve on adult VNS template, Court2018]
organism or virus or viroid [CARO_0001010]
Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
organism subdivision [CARO_0000032]
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.
organism substance [CARO_0000004]
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. Note - CARO explicitly declares organisms substances to be part of (some) organism.