Core Ontology for Biology and Biomedicine
type: Ontology
version IRI: cob-base.owl
description: COB brings together key terms from a wide range of OBO projects to improve interoperability.
type: IAO_8000001
license: https://creativecommons.org/publicdomain/zero/1.0/
version info: 2023-11-16

based on
type: AnnotationProperty

definition
type: AnnotationProperty

Axiom
annotated source: BFO_0000050
annotated property: equivalentProperty
annotated target: part of
mapping justification: ManualMappingCuration
object label: part of
subject label: part of

Axiom
annotated source: BFO_0000051
annotated property: equivalentProperty
annotated target: has part
mapping justification: ManualMappingCuration
object label: has part
subject label: has part

Axiom
annotated source: BFO_0000054
annotated property: equivalentProperty
annotated target: realized in
mapping justification: ManualMappingCuration
object label: realized in
subject label: realized in

Axiom
annotated source: BFO_0000066
annotated property: equivalentProperty
annotated target: occurs in
mapping justification: ManualMappingCuration
object label: occurs in
subject label: occurs in

Axiom
annotated source: BFO_0000067
annotated property: equivalentProperty
annotated target: contains process
mapping justification: ManualMappingCuration
object label: contains process
subject label: contains process

is concretized as
type: ObjectProperty
equivalent property: RO_0000058
inverse of: concretizes

Axiom
annotated source: is concretized as
annotated property: equivalentProperty
annotated target: RO_0000058
mapping justification: ManualMappingCuration
object label: is concretized as
subject label: is concretized as

executed by
type: ObjectProperty
sub property of: topObjectProperty
inverse of: executes

Axiom
annotated source: executed by
annotated property: subPropertyOf
annotated target: topObjectProperty
mapping justification: ManualMappingCuration
object label: topObjectProperty
subject label: executed by

characteristic of
type: ObjectProperty
equivalent property: RO_0000052
inverse of: has characteristic

Axiom
annotated source: characteristic of
annotated property: equivalentProperty
annotated target: RO_0000052
mapping justification: ManualMappingCuration
object label: inheres in
subject label: characteristic of

participates in
type: ObjectProperty
equivalent property: RO_0000056
inverse of: has participant

Axiom
annotated source: participates in
annotated property: equivalentProperty
annotated target: RO_0000056
mapping justification: ManualMappingCuration
object label: participates in
subject label: participates in

is specified input of
type: ObjectProperty
equivalent property: OBI_0000295
sub property of: participates in
inverse of: has specified input

Axiom
annotated source: is specified input of
annotated property: equivalentProperty
annotated target: OBI_0000295
mapping justification: ManualMappingCuration
object label: is_specified_input_of
subject label: is specified input of

is specified output of
type: ObjectProperty
equivalent property: OBI_0000312
sub property of: participates in
inverse of: has specified output

Axiom
annotated source: is specified output of
annotated property: equivalentProperty
annotated target: OBI_0000312
mapping justification: ManualMappingCuration
object label: is_specified_output_of
subject label: is specified output of

realized in
type: ObjectProperty
inverse of: realizes

contains process
type: ObjectProperty
inverse of: occurs in

has specified input
type: ObjectProperty
equivalent property: OBI_0000293
sub property of: has participant
domain: completely executed planned process

Axiom
annotated source: has specified input
annotated property: equivalentProperty
annotated target: OBI_0000293
mapping justification: ManualMappingCuration
object label: has_specified_input
subject label: has specified input

has specified output
type: ObjectProperty
equivalent property: OBI_0000299
sub property of: has participant
domain: completely executed planned process

Axiom
annotated source: has specified output
annotated property: equivalentProperty
annotated target: OBI_0000299
mapping justification: ManualMappingCuration
object label: has_specified_output
subject label: has specified output

has part
type: ObjectProperty
inverse of: part of

has participant
type: ObjectProperty
equivalent property: RO_0000057
domain: process

Axiom
annotated source: has participant
annotated property: equivalentProperty
annotated target: RO_0000057
mapping justification: ManualMappingCuration
object label: has participant
subject label: has participant

occurs in
type: ObjectProperty
domain: process

part of
type: ObjectProperty
type: TransitiveProperty

enabled by
type: ObjectProperty
equivalent property: RO_0002333
sub property of: has participant

Axiom
annotated source: enabled by
annotated property: equivalentProperty
annotated target: RO_0002333
mapping justification: ManualMappingCuration
object label: enabled by
subject label: enabled by

concretizes
type: ObjectProperty

intended to realize
type: ObjectProperty

has plan
type: ObjectProperty

intended plan process type
type: ObjectProperty

executes
type: ObjectProperty
equivalent property: STATO_0000102
property chain axiom: realizes
property chain axiom: concretizes

Axiom
annotated source: executes
annotated property: equivalentProperty
annotated target: STATO_0000102
mapping justification: ManualMappingCuration
object label: executes
subject label: executes

realizes
type: ObjectProperty
domain: process
range: realizable

has characteristic
type: ObjectProperty
equivalent property: RO_0000053
type: InverseFunctionalProperty
domain: Thing
range: characteristic

Axiom
annotated source: has characteristic
annotated property: equivalentProperty
annotated target: RO_0000053
mapping justification: ManualMappingCuration
object label: bearer of
subject label: has characteristic

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

is about
type: ObjectProperty
equivalent property: IAO_0000136
based on: http://purl.obolibrary.org/obo/IAO_0000136

Axiom
annotated source: is about
annotated property: equivalentProperty
annotated target: IAO_0000136
mapping justification: ManualMappingCuration
object label: is about
subject label: is about

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

Axiom
annotated source: has quantity
annotated property: subPropertyOf
annotated target: topDataProperty
mapping justification: ManualMappingCuration
object label: topDataProperty
subject label: has quantity

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

Axiom
annotated source: BFO_0000015
annotated property: equivalentClass
annotated target: process
mapping justification: ManualMappingCuration
object label: process
subject label: process

Axiom
annotated source: BFO_0000016
annotated property: equivalentClass
annotated target: disposition
mapping justification: ManualMappingCuration
object label: disposition
subject label: disposition

Axiom
annotated source: BFO_0000017
annotated property: equivalentClass
annotated target: realizable
mapping justification: ManualMappingCuration
object label: realizable entity
subject label: realizable

Axiom
annotated source: BFO_0000020
annotated property: equivalentClass
annotated target: characteristic
mapping justification: ManualMappingCuration
object label: specifically dependent continuant
subject label: characteristic

Axiom
annotated source: BFO_0000023
annotated property: equivalentClass
annotated target: role
mapping justification: ManualMappingCuration
object label: role
subject label: role

Axiom
annotated source: BFO_0000029
annotated property: equivalentClass
annotated target: site
mapping justification: ManualMappingCuration
object label: site
subject label: site

Axiom
annotated source: BFO_0000034
annotated property: equivalentClass
annotated target: function
mapping justification: ManualMappingCuration
object label: function
subject label: function

Axiom
annotated source: BFO_0000040
annotated property: equivalentClass
annotated target: material entity
mapping justification: ManualMappingCuration
object label: material entity
subject label: material entity

Axiom
annotated source: BFO_0000141
annotated property: equivalentClass
annotated target: immaterial entity
mapping justification: ManualMappingCuration
object label: immaterial entity
subject label: immaterial entity

Axiom
annotated source: CARO_0001008
annotated property: equivalentClass
annotated target: gross anatomical part
mapping justification: ManualMappingCuration
object label: gross anatomical part
subject label: gross anatomical part

Axiom
annotated source: CARO_0001010
annotated property: equivalentClass
annotated target: organism
mapping justification: ManualMappingCuration
object label: organism or virus or viroid
subject label: organism

Axiom
annotated source: CARO_0010004
annotated property: equivalentClass
annotated target: cellular organism
mapping justification: ManualMappingCuration
object label: cellular organism
subject label: cellular organism

Axiom
annotated source: CHEBI_10545
annotated property: equivalentClass
annotated target: electron
mapping justification: ManualMappingCuration
object label: electron
subject label: electron

Axiom
annotated source: CHEBI_16541
annotated property: equivalentClass
annotated target: protein
mapping justification: ManualMappingCuration
object label: protein polypeptide chain
subject label: protein

Axiom
annotated source: CHEBI_24636
annotated property: equivalentClass
annotated target: proton
mapping justification: ManualMappingCuration
object label: proton
subject label: proton

Axiom
annotated source: CHEBI_24867
annotated property: equivalentClass
annotated target: monoatomic ion
mapping justification: ManualMappingCuration
object label: monoatomic ion
subject label: monoatomic ion

Axiom
annotated source: CHEBI_30222
annotated property: equivalentClass
annotated target: neutron
mapping justification: ManualMappingCuration
object label: neutron
subject label: neutron

Axiom
annotated source: CHEBI_33250
annotated property: equivalentClass
annotated target: uncharged atom
mapping justification: ManualMappingCuration
object label: atom
subject label: uncharged atom

Axiom
annotated source: CHEBI_33252
annotated property: equivalentClass
annotated target: atomic nucleus
mapping justification: ManualMappingCuration
object label: atomic nucleus
subject label: atomic nucleus

Axiom
annotated source: CHEBI_33696
annotated property: equivalentClass
annotated target: nucleic acid polymer
mapping justification: ManualMappingCuration
object label: nucleic acid
subject label: nucleic acid polymer

Axiom
annotated source: CHEBI_36342
annotated property: equivalentClass
annotated target: subatomic particle
mapping justification: ManualMappingCuration
object label: subatomic particle
subject label: subatomic particle

Axiom
annotated source: CHEBI_50906
annotated property: subClassOf
annotated target: characteristic
mapping justification: ManualMappingCuration
object label: characteristic
subject label: role

Axiom
annotated source: CL_0000000
annotated property: equivalentClass
annotated target: cell
mapping justification: ManualMappingCuration
object label: cell
subject label: cell

Axiom
annotated source: CL_0000003
annotated property: equivalentClass
annotated target: native cell
mapping justification: ManualMappingCuration
object label: native cell
subject label: native cell

Axiom
annotated source: CL_0001034
annotated property: equivalentClass
annotated target: cell in vitro
mapping justification: ManualMappingCuration
object label: cell in vitro
subject label: cell in vitro

mass
type: Class
equivalent class: PATO_0000125
subclass of: characteristic
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
based on: http://purl.obolibrary.org/obo/PATO_0000125

Axiom
annotated source: mass
annotated property: equivalentClass
annotated target: PATO_0000125
mapping justification: ManualMappingCuration
object label: mass
subject label: mass

charge
type: Class
equivalent class: PATO_0002193
subclass of: characteristic
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
based on: http://purl.obolibrary.org/obo/PATO_0002193

Axiom
annotated source: charge
annotated property: equivalentClass
annotated target: PATO_0002193
mapping justification: ManualMappingCuration
object label: electric
subject label: charge

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

Axiom
annotated source: obsolete_elementary charge
annotated property: subClassOf
annotated target: Thing
mapping justification: ManualMappingCuration
object label: owl:Thing
subject label: elementary charge

material entity
type: Class
based on: http://purl.obolibrary.org/obo/BFO_0000040

subatomic particle
type: Class
subclass of: material entity
based on: http://purl.obolibrary.org/obo/CHEBI_36342

proton
type: Class
subclass of: subatomic particle
based on: http://purl.obolibrary.org/obo/CHEBI_24636

neutron
type: Class
subclass of: subatomic particle
based on: http://purl.obolibrary.org/obo/CHEBI_30222

electron
type: Class
subclass of: subatomic particle
subclass of: Restriction
  on property: has number of atomic nuclei
  has value: 0
based on: http://purl.obolibrary.org/obo/CHEBI_10545

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.

Axiom
annotated source: atom
annotated property: closeMatch
annotated target: CHEBI_33250
mapping justification: ManualMappingCuration
object label: atom
subject label: atom

atomic nucleus
type: Class
subclass of: subatomic particle
based on: http://purl.obolibrary.org/obo/CHEBI_33252
comment: Some people may be uncomfortable calling every proton an atomic nucleus
comment: This is equivalent to CHEBI:33252

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.

Axiom
annotated source: molecular entity
annotated property: closeMatch
annotated target: CHEBI_23367
mapping justification: ManualMappingCuration
object label: molecular entity
subject label: molecular entity

Axiom
annotated source: molecular entity
annotated property: closeMatch
annotated target: CHEBI_25367
mapping justification: ManualMappingCuration
object label: molecule
subject label: molecular entity

obsolete macromolecular entity
type: Class
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

protein
type: Class
equivalent class: PR_000000001
subclass of: molecular entity
based on: http://purl.obolibrary.org/obo/CHEBI_16541
based on: http://purl.obolibrary.org/obo/PR_000000001

Axiom
annotated source: protein
annotated property: equivalentClass
annotated target: PR_000000001
mapping justification: ManualMappingCuration
object label: protein
subject label: protein

cell
type: Class
subclass of: material entity
based on: http://purl.obolibrary.org/obo/CL_0000000
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
based on: http://purl.obolibrary.org/obo/CL_0000003

cell in vitro
type: Class
subclass of: cell
based on: http://purl.obolibrary.org/obo/CL_0001034

subcellular structure
type: Class
subclass of: material entity
subclass of: Thing
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

Axiom
annotated source: subcellular structure
annotated property: subClassOf
annotated target: Thing
mapping justification: ManualMappingCuration
object label: owl:Thing
subject label: subcellular structure

gross anatomical part
type: Class
subclass of: material entity
based on: http://purl.obolibrary.org/obo/CARO_0001008
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
equivalent class: OBI_0100026
subclass of: material entity
based on: http://purl.obolibrary.org/obo/CARO_0001010
based on: http://purl.obolibrary.org/obo/OBI_0100026
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.

Axiom
annotated source: organism
annotated property: equivalentClass
annotated target: OBI_0100026
mapping justification: ManualMappingCuration
object label: organism
subject label: organism

organization
type: Class
equivalent class: OBI_0000245
subclass of: material entity
based on: http://purl.obolibrary.org/obo/OBI_0000245
comment: Should revisit if we can place outside of material entity - a collection of roles.

Axiom
annotated source: organization
annotated property: equivalentClass
annotated target: OBI_0000245
mapping justification: ManualMappingCuration
object label: organization
subject label: organization

processed material entity
type: Class
equivalent class: OBI_0000047
subclass of: material entity
based on: http://purl.obolibrary.org/obo/OBI_0000047
definition: A material entity processed by human activity with an intent to produce

Axiom
annotated source: processed material entity
annotated property: equivalentClass
annotated target: OBI_0000047
mapping justification: ManualMappingCuration
object label: processed material
subject label: processed material entity

immaterial entity
type: Class
based on: http://purl.obolibrary.org/obo/BFO_0000141

geographical location
type: Class
subclass of: immaterial entity
subclass of: Thing

Axiom
annotated source: geographical location
annotated property: subClassOf
annotated target: Thing
mapping justification: ManualMappingCuration
object label: owl:Thing
subject label: geographical location

realizable
type: Class
subclass of: characteristic
based on: http://purl.obolibrary.org/obo/BFO_0000017

process
type: Class
subclass of: Restriction
  on property: part of
  all values from: process
based on: http://purl.obolibrary.org/obo/BFO_0000015

completely executed planned process
type: Class
equivalent class: OBI_0000011
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: plan
disjoint with: failed planned process
based on: http://purl.obolibrary.org/obo/OBI_0000011

Axiom
annotated source: completely executed planned process
annotated property: equivalentClass
annotated target: OBI_0000011
mapping justification: ManualMappingCuration
object label: planned process
subject label: planned process

biological process
type: Class
equivalent class: GO_0008150
subclass of: process
subclass of: Class
  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
  union of: Restriction
    on property: occurs in
    some values from: organism
subclass of: Restriction
  on property: has part
  some values from: gene product or complex activity
disjoint with: gene product or complex activity
disjoint with: environmental process
disjoint with: physico-chemical process
based on: http://purl.obolibrary.org/obo/GO_0008150
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

Axiom
annotated source: biological process
annotated property: equivalentClass
annotated target: GO_0008150
mapping justification: ManualMappingCuration
object label: biological process
subject label: biological process

gene product or complex activity
type: Class
equivalent class: GO_0003674
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: environmental process
disjoint with: physico-chemical process
based on: http://purl.obolibrary.org/obo/GO_0003674
comment: This is the same as GO molecular function

Axiom
annotated source: gene product or complex activity
annotated property: equivalentClass
annotated target: GO_0003674
mapping justification: ManualMappingCuration
object label: molecular function
subject label: gene product or complex activity

monoatomic ion
type: Class
subclass of: atom
disjoint with: uncharged atom
based on: http://purl.obolibrary.org/obo/CHEBI_24867

uncharged atom
type: Class
subclass of: atom
based on: http://purl.obolibrary.org/obo/CHEBI_33250

nucleic acid polymer
type: Class
subclass of: molecular entity
based on: http://purl.obolibrary.org/obo/CHEBI_33696

collection of organisms
type: Class
equivalent class: PCO_0000000
subclass of: material entity
based on: http://purl.obolibrary.org/obo/PCO_0000000

Axiom
annotated source: collection of organisms
annotated property: equivalentClass
annotated target: PCO_0000000
mapping justification: ManualMappingCuration
object label: collection of organisms
subject label: collection of organisms

immaterial anatomical entity
type: Class
subclass of: immaterial entity

site
type: Class
subclass of: immaterial entity
based on: http://purl.obolibrary.org/obo/BFO_0000029

conclusion based on data
type: Class
equivalent class: OBI_0001909
subclass of: information
based on: http://purl.obolibrary.org/obo/OBI_0001909

Axiom
annotated source: conclusion based on data
annotated property: equivalentClass
annotated target: OBI_0001909
mapping justification: ManualMappingCuration
object label: conclusion based on data
subject label: conclusion based on data

information
type: Class
equivalent class: IAO_0000030
subclass of: Restriction
  on property: is about
  some values from: Thing
subclass of: Restriction
  on property:
    inverse of: concretizes
  some values from: information representation
based on: http://purl.obolibrary.org/obo/IAO_0000030
comment: Pier: 'data, information or knowledge'. OR 'representation

Axiom
annotated source: information
annotated property: equivalentClass
annotated target: IAO_0000030
mapping justification: ManualMappingCuration
object label: information content entity
subject label: information

disease diagnosis
type: Class
equivalent class: OGMS_0000073
subclass of: information
based on: http://purl.obolibrary.org/obo/OGMS_0000073

Axiom
annotated source: disease diagnosis
annotated property: equivalentClass
annotated target: OGMS_0000073
mapping justification: ManualMappingCuration
object label: diagnosis
subject label: disease diagnosis

phenotypic finding
type: Class
equivalent class: OGMS_0000014
subclass of: information
based on: http://purl.obolibrary.org/obo/OGMS_0000014

Axiom
annotated source: phenotypic finding
annotated property: equivalentClass
annotated target: OGMS_0000014
mapping justification: ManualMappingCuration
object label: clinical finding
subject label: phenotypic finding

disease course
type: Class
equivalent class: OGMS_0000063
subclass of: process
based on: http://purl.obolibrary.org/obo/OGMS_0000063

Axiom
annotated source: disease course
annotated property: equivalentClass
annotated target: OGMS_0000063
mapping justification: ManualMappingCuration
object label: disease course
subject label: disease course

environmental process
type: Class
equivalent class: ENVO_02500000
subclass of: process
disjoint with: physico-chemical process
based on: http://purl.obolibrary.org/obo/ENVO_02500000

Axiom
annotated source: environmental process
annotated property: equivalentClass
annotated target: ENVO_02500000
mapping justification: ManualMappingCuration
object label: environmental system process
subject label: environmental process

physico-chemical process
type: Class
equivalent class: MOP_0000543
subclass of: process
based on: http://purl.obolibrary.org/obo/MOP_0000543
comment: This is meant to capture processes that are more fundamental than macromolecular activities

Axiom
annotated source: physico-chemical process
annotated property: equivalentClass
annotated target: MOP_0000543
mapping justification: ManualMappingCuration
object label: molecular process
subject label: physico-chemical process

ecosystem
type: Class
equivalent class: ENVO_01001110
subclass of: material entity
based on: http://purl.obolibrary.org/obo/ENVO_01001110

Axiom
annotated source: ecosystem
annotated property: equivalentClass
annotated target: ENVO_01001110
mapping justification: ManualMappingCuration
object label: ecosystem
subject label: ecosystem

geophysical entity
type: Class
equivalent class: ENVO_01000813
subclass of: material entity
based on: http://purl.obolibrary.org/obo/ENVO_01000813

Axiom
annotated source: geophysical entity
annotated property: equivalentClass
annotated target: ENVO_01000813
mapping justification: ManualMappingCuration
object label: astronomical body part
subject label: geophysical entity

directive information entity
type: Class
equivalent class: IAO_0000033
subclass of: information
based on: http://purl.obolibrary.org/obo/IAO_0000033

Axiom
annotated source: directive information entity
annotated property: equivalentClass
annotated target: IAO_0000033
mapping justification: ManualMappingCuration
object label: directive information entity
subject label: directive information entity

gene product
type: Class
subclass of: molecular entity
subclass of: Thing

Axiom
annotated source: gene product
annotated property: subClassOf
annotated target: Thing
mapping justification: ManualMappingCuration
object label: owl:Thing
subject label: gene product

protein-containing macromolecular complex
type: Class
equivalent class: GO_0032991
subclass of: complex of molecular entities
subclass of: Restriction
  on property: has part
  some values from: gene product
based on: http://purl.obolibrary.org/obo/GO_0032991
comment: This is not covalently bonded, which conflicts with changes to the parent definition.

Axiom
annotated source: protein-containing macromolecular complex
annotated property: equivalentClass
annotated target: GO_0032991
mapping justification: ManualMappingCuration
object label: protein-containing complex
subject label: protein-containing macromolecular complex

objective specification
type: Class
equivalent class: IAO_0000005
subclass of: directive information entity
based on: http://purl.obolibrary.org/obo/IAO_0000005

Axiom
annotated source: objective specification
annotated property: equivalentClass
annotated target: IAO_0000005
mapping justification: ManualMappingCuration
object label: objective specification
subject label: objective specification

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

plan specification
type: Class
equivalent class: IAO_0000104
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
based on: http://purl.obolibrary.org/obo/IAO_0000104

Axiom
annotated source: plan specification
annotated property: equivalentClass
annotated target: IAO_0000104
mapping justification: ManualMappingCuration
object label: plan specification
subject label: plan specification

complex of molecular entities
type: Class
subclass of: material entity
subclass of: Thing
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: Thing
mapping justification: ManualMappingCuration
object label: owl:Thing
subject label: complex of molecular entities

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

drug product
type: Class
equivalent class: DRON_0000005
subclass of: processed material entity
based on: DRON_00000005
based on: http://purl.obolibrary.org/obo/DRON_0000005
definition: A processed material entity created to be administered to an individual with the intent to improve health.

Axiom
annotated source: drug product
annotated property: equivalentClass
annotated target: DRON_0000005
mapping justification: ManualMappingCuration
object label: drug product
subject label: drug product

Axiom
annotated source: drug product
annotated property: seeAlso
annotated target: CHEBI_23888
mapping justification: ManualMappingCuration
object label: drug
subject label: drug product

document
type: Class
equivalent class: IAO_0000310
subclass of: information
based on: http://purl.obolibrary.org/obo/IAO_0000310

Axiom
annotated source: document
annotated property: equivalentClass
annotated target: IAO_0000310
mapping justification: ManualMappingCuration
object label: document
subject label: document

data item
type: Class
equivalent class: IAO_0000027
subclass of: information
based on: http://purl.obolibrary.org/obo/IAO_0000027

Axiom
annotated source: data item
annotated property: equivalentClass
annotated target: IAO_0000027
mapping justification: ManualMappingCuration
object label: data item
subject label: data item

cell nucleus
type: Class
equivalent class: GO_0005634
subclass of: subcellular structure
based on: http://purl.obolibrary.org/obo/GO_0005634

Axiom
annotated source: cell nucleus
annotated property: equivalentClass
annotated target: GO_0005634
mapping justification: ManualMappingCuration
object label: nucleus
subject label: cell nucleus

assay
type: Class
equivalent class: OBI_0000070
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
based on: http://purl.obolibrary.org/obo/OBI_0000070

Axiom
annotated source: assay
annotated property: equivalentClass
annotated target: OBI_0000070
mapping justification: ManualMappingCuration
object label: assay
subject label: assay

data transformation
type: Class
equivalent class: OBI_0200000
subclass of: completely executed planned process
based on: http://purl.obolibrary.org/obo/OBI_0200000

Axiom
annotated source: data transformation
annotated property: equivalentClass
annotated target: OBI_0200000
mapping justification: ManualMappingCuration
object label: data transformation
subject label: data transformation

investigation
type: Class
equivalent class: OBI_0000066
subclass of: completely executed planned process
based on: http://purl.obolibrary.org/obo/OBI_0000066

Axiom
annotated source: investigation
annotated property: equivalentClass
annotated target: OBI_0000066
mapping justification: ManualMappingCuration
object label: investigation
subject label: investigation

material processing
type: Class
equivalent class: OBI_0000094
subclass of: completely executed planned process
based on: http://purl.obolibrary.org/obo/OBI_0000094

Axiom
annotated source: material processing
annotated property: equivalentClass
annotated target: OBI_0000094
mapping justification: ManualMappingCuration
object label: material processing
subject label: material processing

disposition
type: Class
subclass of: realizable
based on: http://purl.obolibrary.org/obo/BFO_0000016

function
type: Class
subclass of: disposition
based on: http://purl.obolibrary.org/obo/BFO_0000034

plan
type: Class
equivalent class: OBI_0000260
subclass of: realizable
subclass of: Restriction
  on property: concretizes
  some values from: plan specification
subclass of: Restriction
  on property:
    inverse of: realizes
  all values from: planned process
based on: http://purl.obolibrary.org/obo/OBI_0000260

Axiom
annotated source: plan
annotated property: equivalentClass
annotated target: OBI_0000260
mapping justification: ManualMappingCuration
object label: plan
subject label: plan

role
type: Class
subclass of: realizable
based on: http://purl.obolibrary.org/obo/BFO_0000023

cellular membrane
type: Class
subclass of: subcellular structure
subclass of: Thing

Axiom
annotated source: cellular membrane
annotated property: subClassOf
annotated target: Thing
mapping justification: ManualMappingCuration
object label: owl:Thing
subject label: cellular membrane

cellular organism
type: Class
equivalent class: NCBITaxon_131567
subclass of: organism
based on: http://purl.obolibrary.org/obo/CARO_0010004
based on: http://purl.obolibrary.org/obo/NCBITaxon_131567

Axiom
annotated source: cellular organism
annotated property: equivalentClass
annotated target: NCBITaxon_131567
mapping justification: ManualMappingCuration
object label: cellular organisms
subject label: cellular organism

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

information representation
type: Class
equivalent class: Restriction
  on property: concretizes
  some values from: information
subclass of: characteristic
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
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

agent role
type: Class
equivalent class: SEPIO_0000048
subclass of: role
based on: http://purl.obolibrary.org/obo/SEPIO_0000048
IAO_0000116: A role realized by a participant in a process such that the participant causes the process.

Axiom
annotated source: agent role
annotated property: equivalentClass
annotated target: SEPIO_0000048
mapping justification: ManualMappingCuration
object label: agent role
subject label: agent role

characteristic
type: Class
equivalent class: PATO_0000001
subclass of: Restriction
subclass of: Restriction
  on property: has part
  all values from: characteristic
based on: http://purl.obolibrary.org/obo/BFO_0000020
based on: http://purl.obolibrary.org/obo/PATO_0000001

Axiom
annotated source: characteristic
annotated property: equivalentClass
annotated target: PATO_0000001
mapping justification: ManualMappingCuration
object label: quality
subject label: 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

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: 2023-03-24T16:04:27Z
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.

Axiom
annotated source: GEO_000000370
annotated property: subClassOf
annotated target: geophysical entity
mapping justification: ManualMappingCuration
object label: geophysical entity
subject label: geographical entity

Axiom
annotated source: NCBITaxon_10239
annotated property: subClassOf
annotated target: organism
mapping justification: ManualMappingCuration
object label: organism
subject label: Viruses

Axiom
annotated source: NCBITaxon_131567
annotated property: subClassOf
annotated target: organism
mapping justification: ManualMappingCuration
object label: organism
subject label: cellular organisms

Axiom
annotated source: OBI_0000202
annotated property: subClassOf
annotated target: agent role
mapping justification: ManualMappingCuration
object label: agent role
subject label: investigation agent role

Axiom
annotated source: PO_0000003
annotated property: subClassOf
annotated target: cellular organism
mapping justification: ManualMappingCuration
object label: cellular organism
subject label: whole plant

Axiom
annotated source: PO_0009002
annotated property: subClassOf
annotated target: cell
mapping justification: ManualMappingCuration
object label: cell
subject label: plant cell

Axiom
annotated source: PO_0025117
annotated property: subClassOf
annotated target: immaterial anatomical entity
mapping justification: ManualMappingCuration
object label: immaterial anatomical entity
subject label: plant anatomical space

Axiom
annotated source: PO_0025606
annotated property: subClassOf
annotated target: native cell
mapping justification: ManualMappingCuration
object label: native cell
subject label: native plant cell

Axiom
annotated source: SO_0000110
annotated property: subClassOf
annotated target: material entity
mapping justification: ManualMappingCuration
object label: material entity
subject label: sequence_feature

Axiom
annotated source: SO_0000400
annotated property: subClassOf
annotated target: characteristic
mapping justification: ManualMappingCuration
object label: characteristic
subject label: sequence_attribute

Axiom
annotated source: SO_0001060
annotated property: subClassOf
annotated target: material entity
mapping justification: ManualMappingCuration
object label: material entity
subject label: sequence_variant

Axiom
annotated source: SO_0001260
annotated property: subClassOf
annotated target: material entity
mapping justification: ManualMappingCuration
object label: material entity
subject label: sequence_collection

Axiom
annotated source: UBERON_0000466
annotated property: subClassOf
annotated target: immaterial anatomical entity
mapping justification: ManualMappingCuration
object label: immaterial anatomical entity
subject label: immaterial anatomical entity

Axiom
annotated source: UBERON_0000468
annotated property: subClassOf
annotated target: cellular organism
mapping justification: ManualMappingCuration
object label: cellular organism
subject label: multicellular organism

Axiom
annotated source: UBERON_0010000
annotated property: subClassOf
annotated target: gross anatomical part
mapping justification: ManualMappingCuration
object label: gross anatomical part
subject label: multicellular anatomical structure

Axiom
annotated source: XAO_0003012
annotated property: subClassOf
annotated target: native cell
mapping justification: ManualMappingCuration
object label: native cell
subject label: xenopus cell

Axiom
annotated source: ZFA_0009000
annotated property: subClassOf
annotated target: native cell
mapping justification: ManualMappingCuration
object label: native cell
subject label: zebrafish cell