Core Ontology for Biology and Biomedicine

Classes

action specification
agent role
assay
atom
atomic nucleus
biological process
cell
cell in vitro
cell nucleus
cellular membrane
cellular organism
characteristic
charge
collection of organisms
completely executed planned process
complex of molecular entities
conclusion based on data
data item
data transformation
device
directive information entity
disease course
disease diagnosis
disposition
document
drug product
ecosystem
electron
environmental process
evaluant role
exposure of organism
failed planned process
function
gene product
gene product or complex activity
geographical location
geophysical entity
gross anatomical part
immaterial anatomical entity
immaterial entity
information
information representation
investigation
mass
material entity
material processing
measurement datum
molecular entity
monoatomic ion
native cell
neutron
objective specification
obsolete macromolecular entity
obsolete_elementary charge
organism
organization
phenotypic finding
physical information carrier
physico-chemical process
plan
plan specification
planned process
process
processed material entity
protein
protein-containing macromolecular complex
proton
realizable
role
site
subatomic particle
subcellular structure
uncharged atom

action specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000077

has super-classes: directive information entity^c; has part^op some action specification^c; has part^op some objective specification^c

agent role^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SEPIO_0000048

has super-classes: role^c

assay^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000070

has super-classes: completely executed planned process^c; has specified input^op some material entity^c and (has characteristic^op some evaluant role^c); has specified output^op some measurement datum^c and (is about^op some material entity^c and (has characteristic^op some evaluant role^c))

atom^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000011

This atom is closely related to ChEBI's atom, but not exactly equivalent to.

is equivalent to: has number of atomic nuclei^dp value 1
has super-classes: material entity^c; has part^op some atomic nucleus^c
has sub-classes: monoatomic ion^c, uncharged atom^c
is in domain of: has atomic number^dp
is disjoint with: molecular entity^c

atomic nucleus^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33252

Some people may be uncomfortable calling every proton an atomic nucleus

has super-classes: subatomic particle^c

biological process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0008150

A biological process is an evolved process

has super-classes: process^c; (occurs in^op some organism^c) or (has participant^op some organism^c) or (has participant^op some part of^op some organism^c); has part^op some gene product or complex activity^c
is disjoint with: environmental process^c, gene product or complex activity^c, physico-chemical process^c

cell^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000000

CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.

has super-classes: material entity^c
has sub-classes: cell in vitro^c, native cell^c

cell in vitro^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0001034

has super-classes: cell^c

cell nucleus^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0005634

has super-classes: subcellular structure^c

cellular membrane^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000116

has super-classes: subcellular structure^c

cellular organism^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CARO_0010004

has super-classes: organism^c

characteristic^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000020

has super-classes: thing^c; inverse has characteristic^op some thing^c; has part^op only characteristic^c
has sub-classes: charge^c, information representation^c, mass^c, realizable^c
is in domain of: has quantity^dp
is in range of: has characteristic^op

charge^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0002193

has super-classes: characteristic^c; characteristic of^op some material entity^c

collection of organisms^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PCO_0000000

has super-classes: material entity^c

completely executed planned process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000011

has super-classes: planned process^c; realizes^op some plan^c
has sub-classes: assay^c, data transformation^c, investigation^c, material processing^c
is in domain of: has specified input^op, has specified output^op
is disjoint with: failed planned process^c

complex of molecular entities^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000080

has super-classes: material entity^c; has part^op some molecular entity^c
has sub-classes: protein-containing macromolecular complex^c
is disjoint with: molecular entity^c

conclusion based on data^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001909

has super-classes: information^c

data item^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000027

has super-classes: information^c
has sub-classes: measurement datum^c

data transformation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200000

has super-classes: completely executed planned process^c

device^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0001300

Date :: 24T16:04:27+00:00/03/2023

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.

has super-classes: processed material entity^c; is specified output of^op some material processing^c; has characteristic^op some function^c

directive information entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000033

has super-classes: information^c
has sub-classes: action specification^c, objective specification^c, plan specification^c

disease course^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OGMS_0000063

has super-classes: process^c

disease diagnosis^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OGMS_0000073

has super-classes: information^c

disposition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000016

has super-classes: realizable^c
has sub-classes: function^c

document^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000310

has super-classes: information^c

drug product^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DRON_0000005

has super-classes: processed material entity^c

ecosystem^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001110

has super-classes: material entity^c

electron^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_10545

has super-classes: subatomic particle^c; molecular entity^c; has number of atomic nuclei^dp value 0

environmental process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ENVO_02500000

has super-classes: process^c
is disjoint with: gene product or complex activity^c, biological process^c, physico-chemical process^c

evaluant role^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000119

has super-classes: role^c

exposure of organism^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0001000

has super-classes: process^c

failed planned process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000083

has super-classes: planned process^c
is disjoint with: completely executed planned process^c

function^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000034

has super-classes: disposition^c

gene product^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000073

has super-classes: molecular entity^c

gene product or complex activity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0003674

This is the same as GO molecular function

has super-classes: process^c; enabled by^op some gene product^c or protein-containing macromolecular complex^c
is disjoint with: environmental process^c, biological process^c, physico-chemical process^c

geographical location^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000032

has super-classes: immaterial entity^c

geophysical entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01000813

has super-classes: material entity^c

gross anatomical part^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CARO_0001008

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.

has super-classes: material entity^c

immaterial anatomical entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000056

has super-classes: immaterial entity^c

immaterial entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000141

has super-classes: thing^c
has sub-classes: geographical location^c, immaterial anatomical entity^c, site^c

information^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000030

Pier: 'data, information or knowledge'. OR 'representation

has super-classes: thing^c; is about^op some thing^c; inverse concretizes^op some information representation^c
has sub-classes: conclusion based on data^c, data item^c, directive information entity^c, disease diagnosis^c, document^c, phenotypic finding^c

information representation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000120

Pier 'representational entity'

is equivalent to: concretizes^op some information^c
has super-classes: characteristic^c
has sub-classes: plan^c

investigation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000066

has super-classes: completely executed planned process^c

mass^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000125

has super-classes: characteristic^c; characteristic of^op some material entity^c

material entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000040

has super-classes: thing^c
has sub-classes: atom^c, cell^c, collection of organisms^c, complex of molecular entities^c, ecosystem^c, geophysical entity^c, gross anatomical part^c, molecular entity^c, organism^c, organization^c, physical information carrier^c, processed material entity^c, subatomic particle^c, subcellular structure^c
is in domain of: has number of atomic nuclei^dp

material processing^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000094

has super-classes: completely executed planned process^c

measurement datum^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000121

has super-classes: data item^c

molecular entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000013

This molecular entity is different than ChEBI's 'molecular entity'.

has super-classes: material entity^c; has part^op some atom^c
has sub-classes: electron^c, gene product^c, protein^c
is disjoint with: atom^c, complex of molecular entities^c

monoatomic ion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_24867

has super-classes: atom^c
is disjoint with: uncharged atom^c

native cell^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000003

has super-classes: cell^c

neutron^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_30222

has super-classes: subatomic particle^c

objective specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000005

has super-classes: directive information entity^c

obsolete macromolecular entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000014

Terms moved to 'molecular entity', see https://github.com/OBOFoundry/Experimental-OBO-Core/issues/33

has super-classes: thing^c

obsolete_elementary charge^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000005

has super-classes: thing^c

organism^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CARO_0001010

"Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'.

has super-classes: material entity^c
has sub-classes: cellular organism^c

organization^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000245

Should revisit if we can place outside of material entity - a collection of roles.

has super-classes: material entity^c

phenotypic finding^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OGMS_0000014

has super-classes: information^c

physical information carrier^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000122

is equivalent to: has characteristic^op some concretizes^op some information^c
has super-classes: material entity^c

physico-chemical process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MOP_0000543

This is meant to capture processes that are more fundamental than macromolecular activities

has super-classes: process^c
is disjoint with: environmental process^c, gene product or complex activity^c, biological process^c

plan^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000260

has super-classes: realizable^c; information representation^c; concretizes^op some plan specification^c; inverse realizes^op only planned process^c

plan specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000104

has super-classes: directive information entity^c; has part^op some action specification^c; has part^op some objective specification^c

planned process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000082

has super-classes: process^c; intended to realize^op some plan^c; realizes^op some agent role^c
has sub-classes: completely executed planned process^c, failed planned process^c

process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000015

has super-classes: thing^c; part of^op only process^c
has sub-classes: biological process^c, disease course^c, environmental process^c, exposure of organism^c, gene product or complex activity^c, physico-chemical process^c, planned process^c
is in domain of: has participant^op, occurs in^op, realizes^op

processed material entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000047

has super-classes: material entity^c
has sub-classes: device^c, drug product^c

protein^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PR_000000001

has super-classes: molecular entity^c

protein-containing macromolecular complex^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032991

This is not covalently bonded, which conflicts with changes to the parent definition.

has super-classes: complex of molecular entities^c; has part^op some gene product^c

proton^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_24636

has super-classes: subatomic particle^c

realizable^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000017

has super-classes: characteristic^c
has sub-classes: disposition^c, plan^c, role^c
is in range of: realizes^op

role^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000023

has super-classes: realizable^c
has sub-classes: agent role^c, evaluant role^c

site^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000029

has super-classes: immaterial entity^c

subatomic particle^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_36342

has super-classes: material entity^c
has sub-classes: atomic nucleus^c, electron^c, neutron^c, proton^c

subcellular structure^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000020

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.

has super-classes: material entity^c; has part^op some molecular entity^c
has sub-classes: cell nucleus^c, cellular membrane^c

uncharged atom^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33250

has super-classes: atom^c
is disjoint with: monoatomic ion^c

Object Properties

characteristic of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000052

is inverse of: has characteristic^op

concretizes^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/COB_0000078

is inverse of: is concretized as^op

contains process^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000067

is inverse of: occurs in^op

enabled by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002333

has super-properties: has participant^op

executed by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/COB_0000016

is inverse of: executes^op

executes^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000102

is inverse of: executed by^op
has sub-property chains: realizes^op o concretizes^op

has characteristic^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000053

has characteristics : inverse functional

has domain: thing^c
has range: characteristic^c
is inverse of: characteristic of^op

has part^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000051

is inverse of: part of^op

has participant^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000057

has sub-properties: enabled by^op, has specified input^op, has specified output^op
has domain: process^c
is inverse of: participates in^op

has plan^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/COB_0000084

has specified input^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000293

has super-properties: has participant^op
has domain: completely executed planned process^c
is inverse of: is specified input of^op

has specified output^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000299

has super-properties: has participant^op
has domain: completely executed planned process^c
is inverse of: is specified output of^op

intended plan process type^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/COB_0000085

intended to realize^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/COB_0000081

is about^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000136

is concretized as^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000058

is inverse of: concretizes^op

is specified input of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000295

has super-properties: participates in^op
is inverse of: has specified input^op

is specified output of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000312

has super-properties: participates in^op
is inverse of: has specified output^op

occurs in^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000066

has domain: process^c
is inverse of: contains process^op

part of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000050

has characteristics : transitive

is inverse of: has part^op

participates in^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000056

has sub-properties: is specified input of^op, is specified output of^op
is inverse of: has participant^op

realized in^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000054

is inverse of: realizes^op

realizes^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/COB_0000087

has domain: process^c
has range: realizable^c
is inverse of: realized in^op

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni .

Core Ontology for Biology and Biomedicine

Abstract

Table of Content

Introduction

Classes

action specificationc back to ToC or Class ToC

agent rolec back to ToC or Class ToC

assayc back to ToC or Class ToC

atomc back to ToC or Class ToC

atomic nucleusc back to ToC or Class ToC

biological processc back to ToC or Class ToC

cellc back to ToC or Class ToC

cell in vitroc back to ToC or Class ToC

cell nucleusc back to ToC or Class ToC

cellular membranec back to ToC or Class ToC

cellular organismc back to ToC or Class ToC

characteristicc back to ToC or Class ToC

chargec back to ToC or Class ToC

collection of organismsc back to ToC or Class ToC

completely executed planned processc back to ToC or Class ToC

complex of molecular entitiesc back to ToC or Class ToC

conclusion based on datac back to ToC or Class ToC

data itemc back to ToC or Class ToC

data transformationc back to ToC or Class ToC

devicec back to ToC or Class ToC

directive information entityc back to ToC or Class ToC

disease coursec back to ToC or Class ToC

disease diagnosisc back to ToC or Class ToC

dispositionc back to ToC or Class ToC

documentc back to ToC or Class ToC

drug productc back to ToC or Class ToC

ecosystemc back to ToC or Class ToC

electronc back to ToC or Class ToC

environmental processc back to ToC or Class ToC

evaluant rolec back to ToC or Class ToC

exposure of organismc back to ToC or Class ToC

failed planned processc back to ToC or Class ToC

functionc back to ToC or Class ToC

gene productc back to ToC or Class ToC

gene product or complex activityc back to ToC or Class ToC

geographical locationc back to ToC or Class ToC

geophysical entityc back to ToC or Class ToC

gross anatomical partc back to ToC or Class ToC

immaterial anatomical entityc back to ToC or Class ToC

immaterial entityc back to ToC or Class ToC

informationc back to ToC or Class ToC

information representationc back to ToC or Class ToC

investigationc back to ToC or Class ToC

massc back to ToC or Class ToC

material entityc back to ToC or Class ToC

material processingc back to ToC or Class ToC

measurement datumc back to ToC or Class ToC

molecular entityc back to ToC or Class ToC

monoatomic ionc back to ToC or Class ToC

native cellc back to ToC or Class ToC

neutronc back to ToC or Class ToC

objective specificationc back to ToC or Class ToC

obsolete macromolecular entityc back to ToC or Class ToC

obsolete_elementary chargec back to ToC or Class ToC

organismc back to ToC or Class ToC

organizationc back to ToC or Class ToC

phenotypic findingc back to ToC or Class ToC

physical information carrierc back to ToC or Class ToC

physico-chemical processc back to ToC or Class ToC

planc back to ToC or Class ToC

plan specificationc back to ToC or Class ToC

planned processc back to ToC or Class ToC

processc back to ToC or Class ToC

processed material entityc back to ToC or Class ToC

proteinc back to ToC or Class ToC

protein-containing macromolecular complexc back to ToC or Class ToC

protonc back to ToC or Class ToC

realizablec back to ToC or Class ToC

rolec back to ToC or Class ToC

sitec back to ToC or Class ToC

subatomic particlec back to ToC or Class ToC

subcellular structurec back to ToC or Class ToC

uncharged atomc back to ToC or Class ToC