Core Ontology for Biology and Biomedicine
type: Ontology
version IRI: cob.owl
contributor: https://orcid.org/0000-0001-5139-5557
contributor: https://orcid.org/0000-0001-5809-9523
contributor: https://orcid.org/0000-0001-8910-9851
contributor: https://orcid.org/0000-0001-9189-9661
contributor: https://orcid.org/0000-0001-9625-1899
contributor: https://orcid.org/0000-0001-9990-8331
contributor: https://orcid.org/0000-0002-1604-3078
contributor: https://orcid.org/0000-0002-2999-0103
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0002-7356-1779
contributor: https://orcid.org/0000-0002-8457-6693
contributor: https://orcid.org/0000-0002-8688-6599
contributor: https://orcid.org/0000-0002-8844-9165
contributor: https://orcid.org/0000-0003-1640-9989
contributor: https://orcid.org/0000-0003-4423-4370
contributor: https://orcid.org/0000-0003-4871-5569
contributor: https://orcid.org/0009-0009-4008-3801
description: COB brings together key terms from a wide range of OBO projects to improve interoperability.
license: https://creativecommons.org/publicdomain/zero/1.0/
version info: 2025-12-12

definition
type: AnnotationProperty

editor note
type: AnnotationProperty

term replaced by
type: AnnotationProperty

part of
type: ObjectProperty
definition: a core relation that holds between a part and its whole

has part
type: ObjectProperty
definition: a core relation that holds between a whole and its part

realizes
type: ObjectProperty
domain: process
range: realizable entity
definition: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

executed by
type: ObjectProperty

intended to realize
type: ObjectProperty

has plan
type: ObjectProperty

intended plan process type
type: ObjectProperty

is about
type: ObjectProperty
domain: information content entity

has specified input
type: ObjectProperty
domain: completely executed planned process
definition: The inverse property of is specified input of

is specified input of
type: ObjectProperty
range: completely executed planned process
definition: A relation between a completely executed planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.

has specified output
type: ObjectProperty
domain: completely executed planned process
definition: The inverse property of is specified output of

is specified output of
type: ObjectProperty
range: completely executed planned process
definition: A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.

characteristic of
type: ObjectProperty
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.

has characteristic
type: ObjectProperty
definition: Inverse of characteristic_of

participates in
type: ObjectProperty
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process

has participant
type: ObjectProperty
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process

is concretized as
type: ObjectProperty
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.

concretizes
type: ObjectProperty
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.

derives from
type: ObjectProperty
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity

location of
type: ObjectProperty
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location

located in
type: ObjectProperty
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location

capable of
type: ObjectProperty
range: process
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.

surrounded by
type: ObjectProperty
definition: x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x

surrounds
type: ObjectProperty
definition: inverse of surrounded by

has input
type: ObjectProperty
domain: process
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.

has output
type: ObjectProperty
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.

enabled by
type: ObjectProperty
definition: inverse of enables

has quantity
type: DatatypeProperty

has atomic number
type: DatatypeProperty
domain: atom
definition: Number of protons in an atomic nucleus

has number of atomic nuclei
type: DatatypeProperty
domain: material entity

has inchi string
type: DatatypeProperty

process
type: Class

disposition
type: Class
subclass of: realizable entity

realizable entity
type: Class
subclass of: characteristic

role
type: Class
subclass of: realizable entity

site
type: Class
subclass of: immaterial entity

function
type: Class
subclass of: disposition

material entity
type: Class
editor note: Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.

immaterial entity
type: Class

electron
type: Class
subclass of: subatomic particle
definition: Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.

proton
type: Class
subclass of: subatomic particle
definition: Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.

neutron
type: Class
subclass of: subatomic particle
definition: Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u.

atomic nucleus
type: Class
subclass of: subatomic particle
subclass of: Restriction
  on property: has part
  some values from: proton
definition: A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
editor note: Some people may be uncomfortable calling every proton an atomic nucleus
editor note: This is equivalent to CHEBI:33252

subatomic particle
type: Class
subclass of: material entity
disjoint with: atom
definition: A particle smaller than an atom.

cell
type: Class
subclass of: material anatomical entity
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
editor note: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
editor note: We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.

obsolete elementary charge
type: Class
deprecated: true

atom
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: atomic nucleus
disjoint with: molecule
definition: A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.
editor note: This atom is closely related to ChEBI's atom, but not exactly equivalent to.

molecule
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: atom
definition: A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom.
editor note: This molecular entity is different than ChEBI's 'molecular entity'.
editor note: We would like to have cardinality restrictions on the logic, but there are some technical limitations.

obsolete macromolecular entity
type: Class
deprecated: true

obsolete subcellular structure
type: Class
term replaced by: cellular anatomical entity
deprecated: true

gross anatomical part
type: Class
subclass of: material anatomical entity
definition: A part of a multicellular organism that is a collection of cell components that are not all contained in one cell.

organism
type: Class
subclass of: material anatomical entity
definition: A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome
editor note: 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'.
editor note: Includes virus - we will later have a class for cellular organisms.

processed material entity
type: Class
subclass of: material entity
subclass of: Restriction
  on property: is specified output of
  some values from: material processing
definition: A material entity processed by human activity with an intent to produce it.
editor note: In the COB 2024 workshop there was much disagreement about this label.

obsolete geographical location
type: Class
deprecated: true

completely executed planned process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: plan
disjoint with: failed planned process

nucleic acid chain
type: Class
subclass of: molecule
definition: A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds.

obsolete immaterial anatomical entity
type: Class
term replaced by: immaterial anatomical entity
deprecated: true

obsolete gene product
type: Class
deprecated: true

obsolete action specification
type: Class
term replaced by: action specification
deprecated: true

complex of molecules
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: molecule
definition: A complex of two or more molecules that are not covalently bound.

planned process
type: Class
subclass of: process
definition: A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification.

failed planned process
type: Class
subclass of: planned process

material processing
type: Class
subclass of: completely executed planned process
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: material entity
  intersection of: Restriction
    on property: has specified output
    some values from: material entity
definition: A completely executed planned process that intends to output material entities from input material entities

obsolete cellular membrane
type: Class
deprecated: true

obsolete physical information carrier
type: Class
deprecated: true

characteristic
type: Class

exposure of organism
type: Class
subclass of: process
subclass of: Restriction
  on property: has participant
  some values from: organism
definition: A process during which an organism comes into contact with another entity.

device
type: Class
subclass of: processed material entity
subclass of: Restriction
  on property: capable of
  some values from: process
definition: A processed material entity which is designed to be capable of a process.

geophysical entity
type: Class
subclass of: material entity
definition: A material part of an astronomical body.

ecosystem
type: Class
subclass of: material entity
definition: An environmental system which includes both living and non-living components.

environmental system process
type: Class
subclass of: process
definition: A process in which includes the components of an environmental system as participants.

gene product or complex activity
type: Class
subclass of: process
definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
editor note: This is the same as GO molecular function

cellular_component
type: Class
equivalent class: Class
  union of: protein-containing complex
  union of: virion component
  union of: cellular anatomical entity
subclass of: material entity
definition: A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).

biological process
type: Class
subclass of: process
subclass of: Restriction
  on property: has part
  some values from: gene product or complex activity
definition: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.

protein-containing complex
type: Class
subclass of: complex of molecules
subclass of: cellular_component
subclass of: Restriction
  on property: has part
  some values from: protein
definition: A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
editor note: This is not covalently bonded, which conflicts with changes to the parent definition.

virion component
type: Class
subclass of: cellular_component
definition: Any constituent part of a virion, a complete fully infectious extracellular virus particle.

cellular anatomical entity
type: Class
subclass of: cellular_component
subclass of: material anatomical entity
subclass of: Restriction
  on property: has part
  some values from: molecule
definition: 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 but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
editor note: Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes.
editor note: Overlaps with some cellular components from GO

objective specification
type: Class
subclass of: directive information entity
definition: A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.

action specification
type: Class
subclass of: directive information entity
definition: A directive information entity that describes an action the bearer will take.

data item
type: Class
subclass of: information content entity
definition: An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.

information content entity
type: Class
definition: A generically dependent continuant that is about some thing.
editor note: Pier: 'data, information or knowledge'. OR 'representation'

directive information entity
type: Class
subclass of: information content entity
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.

plan specification
type: Class
subclass of: directive information entity
definition: A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.

measurement datum
type: Class
subclass of: data item
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.

physico-chemical process
type: Class
subclass of: process
definition: A process in which at least one of the participants is a molecule.
editor note: This is meant to capture processes that are more fundamental than macromolecular activities

cellular organism
type: Class
subclass of: organism

investigation
type: Class
subclass of: completely executed planned process
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).

assay
type: Class
subclass of: completely executed planned process
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: material entity
  intersection of: Restriction
    on property: has specified output
    some values from: data item
definition: A planned process that has the objective to produce information about a material entity (the evaluant) by examining it.

plan
type: Class
subclass of: realizable entity
subclass of: Restriction
  on property: concretizes
  some values from: plan specification
definition: A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process.

data transformation
type: Class
subclass of: completely executed planned process
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: data item
  intersection of: Restriction
    on property: has specified output
    some values from: data item
definition: A completely executed planned process that produces output data from input data.

mass
type: Class
subclass of: characteristic
definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.

electric charge
type: Class
subclass of: characteristic
definition: A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons.

collection of organisms
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: organism
definition: A material entity that consists of two or more organisms, viruses, or viroids.

plant anatomical entity
type: Class
subclass of: material anatomical entity
definition: An anatomical entity that is or was part of a plant.

protein
type: Class
subclass of: amino acid chain
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.

amino acid chain
type: Class
subclass of: molecule
definition: An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.

material anatomical entity
type: Class
equivalent class: Class
  union of: cell
  union of: gross anatomical part
  union of: organism
  union of: cellular anatomical entity
subclass of: material entity
subclass of: anatomical entity
definition: Anatomical entity that has mass.

immaterial anatomical entity
type: Class
subclass of: immaterial entity
subclass of: anatomical entity
definition: Anatomical entity that has no mass.

anatomical entity
type: Class
equivalent class: Class
  union of: material anatomical entity
  union of: immaterial anatomical entity
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.