Core Ontology for Biology and Biomedicine
type: Ontology
version IRI: cob.owl
description: COB brings together key terms from a wide range of OBO projects to improve interoperability.
license: https://creativecommons.org/publicdomain/zero/1.0/
comment: This version of COB includes native OBO URIs, only using COB IRIs where equivalent natives could not be found. To see the edition that includes native IRIs, consult cob-edit.owl.
version info: 2023-05-12

definition
type: AnnotationProperty

part of
type: ObjectProperty
inverse of: has part
type: TransitiveProperty

has part
type: ObjectProperty

realized in
type: ObjectProperty
inverse of: realizes

occurs in
type: ObjectProperty
inverse of: contains process
domain: process

contains process
type: ObjectProperty

executed by
type: ObjectProperty
inverse of: executes

concretizes
type: ObjectProperty
inverse of: is concretized as

intended to realize
type: ObjectProperty

has plan
type: ObjectProperty

intended plan process type
type: ObjectProperty

realizes
type: ObjectProperty
domain: process
range: realizable

is about
type: ObjectProperty

has specified input
type: ObjectProperty
sub property of: has participant
inverse of: is specified input of
domain: completely executed planned process

is specified input of
type: ObjectProperty
sub property of: participates in

has specified output
type: ObjectProperty
sub property of: has participant
inverse of: is specified output of
domain: completely executed planned process

is specified output of
type: ObjectProperty
sub property of: participates in

characteristic of
type: ObjectProperty
inverse of: has characteristic

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
domain: Thing
range: characteristic

Axiom
annotated source: has characteristic
annotated property: domain
annotated target: Thing
comment: Anything can have a characteristic

participates in
type: ObjectProperty
inverse of: has participant

has participant
type: ObjectProperty
domain: process

is concretized as
type: ObjectProperty

enabled by
type: ObjectProperty
sub property of: has participant

executes
type: ObjectProperty
property chain axiom: realizes
property chain axiom: concretizes

has quantity
type: DatatypeProperty
domain: characteristic
comment: The range of this property should be a user-defined unit datatype, e.g 182^:cm

has atomic number
type: DatatypeProperty
domain: atom
range: nonNegativeInteger
definition: Number of protons in an atomic nucleus
comment: We are undecided as to whether to ultimately model this as a data property of object property + cardinality, but for now we are using DPs as these are faster for reasoning

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

has inchi string
type: DatatypeProperty
sub property of: topDataProperty

process
type: Class
subclass of: Thing
subclass of: Restriction
  on property: part of
  all values from: process

disposition
type: Class
subclass of: realizable

realizable
type: Class
subclass of: characteristic

characteristic
type: Class
subclass of: Thing
subclass of: Restriction
subclass of: Restriction
  on property: has part
  all values from: characteristic

Axiom
annotated source: characteristic
annotated property: subClassOf
annotated target: Restriction
comment: We should name the inverse in COB and avoid the confusing inverse(..) construct

role
type: Class
subclass of: realizable

site
type: Class
subclass of: immaterial entity

function
type: Class
subclass of: disposition

material entity
type: Class
subclass of: Thing

immaterial entity
type: Class
subclass of: Thing

gross anatomical part
type: Class
subclass of: material entity
definition: A part of a multicellular organism that is a collection of cell components that are not all contained in one cell.
comment: Bodily fluids, such as urine, are currently defined as anatomical entities in UBERON. We should make sure there is a proper home for these here.

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

cellular organism
type: Class
subclass of: organism

nucleic acid polymer
type: Class
subclass of: subatomic particle
subclass of: molecular entity
subclass of: Restriction
  on property: has number of atomic nuclei
  has value: 0
label: electron

proton
type: Class
subclass of: subatomic particle

monoatomic ion
type: Class
subclass of: atom
disjoint with: uncharged atom

neutron
type: Class
subclass of: subatomic particle

uncharged atom
type: Class
subclass of: atom

atomic nucleus
type: Class
subclass of: subatomic particle
comment: Some people may be uncomfortable calling every proton an atomic nucleus
comment: This is equivalent to CHEBI:33252

subatomic particle
type: Class
subclass of: material entity

cell
type: Class
subclass of: material entity
definition: A material entity that has a plasma membrane and results from cellular division.
comment: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
comment: We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.

native cell
type: Class
subclass of: cell

cell in vitro
type: Class
subclass of: cell

obsolete_elementary charge
type: Class
subclass of: Thing
IAO_0000116: no longer needed
deprecated: true

atom
type: Class
equivalent class: Restriction
  on property: has number of atomic nuclei
  has value: 1
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: atomic nucleus
disjoint with: molecular entity
definition: A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.
comment: This atom is closely related to ChEBI's atom, but not exactly equivalent to.

molecular entity
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: atom
disjoint with: complex of molecular entities
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.
comment: This molecular entity is different than ChEBI's 'molecular entity'.
comment: We would like to have cardinality restrictions on the logic, but there are some technical limitations.

obsolete macromolecular entity
type: Class
subclass of: Thing
definition: A material entity consisting of multiple atoms that are completely connected by covalent bonds and structured in subunits, and where the most determinate class identity of the macromolecule is not necessarily changed when there is an addition or subtraction of atoms or bonds.
comment: Terms moved to 'molecular entity', see https://github.com/OBOFoundry/Experimental-OBO-Core/issues/33
deprecated: true

subcellular structure
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: molecular entity
definition: A material entity consisting of at least two macromolecular entities derived from a cell as parts, and that has a function for the cell.
comment: 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.
comment: Overlaps with some cellular components from GO

geographical location
type: Class
subclass of: immaterial entity

immaterial anatomical entity
type: Class
subclass of: immaterial entity

gene product
type: Class
subclass of: molecular entity

action specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: action specification
subclass of: Restriction
  on property: has part
  some values from: objective specification

complex of molecular entities
type: Class
subclass of: material entity
subclass of: Restriction
definition: A complex of two or more molecular entities that are not covalently bound.

Axiom
annotated source: complex of molecular entities
annotated property: subClassOf
annotated target: Restriction
comment: >=2 parts (not we cannot use cardinality with transitive properties)

planned process
type: Class
subclass of: process
subclass of: Restriction
  on property: intended to realize
  some values from: plan
subclass of: Restriction
  on property: realizes
  some values from: agent role
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
disjoint with: completely executed planned process

cellular membrane
type: Class
subclass of: subcellular structure

evaluant role
type: Class
subclass of: role
COB based on: OBI:0000067

information representation
type: Class
equivalent class: Restriction
  on property: concretizes
  some values from: information
subclass of: characteristic
COB based on: http://purl.obolibrary.org/obo/IAO_0000015
comment: Pier 'representational entity'
comment: This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc

measurement datum
type: Class
subclass of: data item
COB based on: http://purl.obolibrary.org/obo/IAO_0000109

physical information carrier
type: Class
equivalent class: Restriction
  on property: has characteristic
  some values from: Restriction
    on property: concretizes
    some values from: information
subclass of: material entity

exposure of organism
type: Class
subclass of: process
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: is specified output of
  some values from: material processing
subclass of: Restriction
  on property: has characteristic
  some values from: function
definition: A processed material entity which is designed to perform a function.
IAO_0000117: https://orcid.org/0000-0002-8844-9165
date: 2023-03-24T16:04:27+00:00
comment: In this definition we assume devices are made of processed material, not natural artifacts, so we involve artifactual function rather than biological function, but align with a general BFO function sense where functions such as pumping, lifting can occur in both contexts. Thus we can compare a biological arm with a robotic arm device. We say "designed" to emphasize a device's primary function rather than all the other possible dispositions a device may have that may also be useful. E.g. one can use a hammer for a paper weight. Regarding usage then, we don't say a naturally formed rock is a hammering device - it wasn't designed to bear a hammering function per se. However, a given rock may still happen to have the disposition to bear a hammering function, and so we could say it is a hammering "tool", which does not necessarily convey intentional design. Example of use: A whole device like an engine; a component like a bolt is also a device.

drug product
type: Class
subclass of: processed material entity
COB based on: DRON_00000005
definition: A processed material entity created to be administered to an individual with the intent to improve health.

geophysical entity
type: Class
subclass of: material entity

ecosystem
type: Class
subclass of: material entity

environmental process
type: Class
subclass of: process
disjoint with: gene product or complex activity
disjoint with: biological process
disjoint with: physico-chemical process

gene product or complex activity
type: Class
subclass of: process
subclass of: Restriction
  on property: enabled by
  some values from: Class
    union of: gene product
    union of: protein-containing macromolecular complex
disjoint with: biological process
disjoint with: physico-chemical process
comment: This is the same as GO molecular function

cell nucleus
type: Class
subclass of: subcellular structure

biological process
type: Class
subclass of: process
subclass of: Class
  union of: Restriction
    on property: occurs in
    some values from: organism
  union of: Restriction
    on property: has participant
    some values from: organism
  union of: Restriction
    on property: has participant
    some values from: Restriction
      on property: part of
      some values from: organism
subclass of: Restriction
  on property: has part
  some values from: gene product or complex activity
disjoint with: physico-chemical process
definition: A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
comment: A biological process is an evolved process

protein-containing macromolecular complex
type: Class
subclass of: complex of molecular entities
subclass of: Restriction
  on property: has part
  some values from: gene product
comment: This is not covalently bonded, which conflicts with changes to the parent definition.

objective specification
type: Class
subclass of: directive information entity

data item
type: Class
subclass of: information

information
type: Class
subclass of: Thing
subclass of: Restriction
  on property: is about
  some values from: Thing
subclass of: Restriction
  on property:
    inverse of: concretizes
  some values from: information representation
comment: Pier: 'data, information or knowledge'. OR 'representation

directive information entity
type: Class
subclass of: information

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: action specification
subclass of: Restriction
  on property: has part
  some values from: objective specification

document
type: Class
subclass of: information

physico-chemical process
type: Class
subclass of: process
comment: This is meant to capture processes that are more fundamental than macromolecular activities

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

processed material entity
type: Class
subclass of: material entity
definition: A material entity processed by human activity with an intent to produce

investigation
type: Class
subclass of: completely executed planned process

assay
type: Class
subclass of: completely executed planned process
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has characteristic
      some values from: evaluant role
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction

material processing
type: Class
subclass of: completely executed planned process

organization
type: Class
subclass of: material entity
comment: Should revisit if we can place outside of material entity - a collection of roles.

plan
type: Class
subclass of: realizable
subclass of: information representation
subclass of: Restriction
  on property: concretizes
  some values from: plan specification
subclass of: Restriction
  on property:
    inverse of: realizes
  all values from: planned process

conclusion based on data
type: Class
subclass of: information

data transformation
type: Class
subclass of: completely executed planned process

phenotypic finding
type: Class
subclass of: information

disease course
type: Class
subclass of: process

disease diagnosis
type: Class
subclass of: information

mass
type: Class
subclass of: characteristic
subclass of: Restriction
  on property: characteristic of
  some values from: material entity

charge
type: Class
subclass of: characteristic
subclass of: Restriction
  on property: characteristic of
  some values from: material entity

collection of organisms
type: Class
subclass of: material entity

protein
type: Class
subclass of: molecular entity

agent role
type: Class
subclass of: role
IAO_0000116: A role realized by a participant in a process such that the participant causes the process.