Core Ontology for Biology and Biomedicine

Classes

action specification
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
directive information entity
disease course
disease diagnosis
disposition
document
drug product
ecosystem
electron
environmental process
evaluant role
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
nucleic acid polymer
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
quality
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

assay^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000107

has super-classes: completely executed planned process^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)); has specified input^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/COB_0000012

This is equivalent to CHEBI:33252

has super-classes: subatomic particle^c

biological process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000037

A biological process is an evolved process

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

cell^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000017

We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.

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/COB_0000019

has super-classes: cell^c

cell nucleus^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000103

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/COB_0000118

has super-classes: organism^c

characteristic^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000502

has super-classes: thing^c; inverse has characteristic^op some thing^c; has part^op only characteristic^c
has sub-classes: information representation^c, quality^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/COB_0000004

has super-classes: quality^c

collection of organisms^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000055

has super-classes: material entity^c

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

IRI: http://purl.obolibrary.org/obo/COB_0000035

has super-classes: realizable^c; 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

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

IRI: http://purl.obolibrary.org/obo/COB_0000058

has super-classes: information^c

data item^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000102

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/COB_0000108

has super-classes: completely executed planned process^c

directive information entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000069

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/COB_0000064

has super-classes: process^c

disease diagnosis^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000062

has super-classes: information^c

disposition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000111

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

document^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000101

has super-classes: information^c

drug product^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000088

has super-classes: processed material entity^c

ecosystem^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000067

has super-classes: material entity^c

electron^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000010

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

environmental process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000065

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

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/COB_0000112

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/COB_0000038

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: biological process^c, environmental 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/COB_0000068

has super-classes: material entity^c

gross anatomical part^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000021

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/COB_0000031

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/COB_0000061

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

has super-classes: thing^c; inverse concretizes^op some information representation^c; is about^op some thing^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

This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc

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/COB_0000109

has super-classes: completely executed planned process^c

mass^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000003

has super-classes: quality^c

material entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000006

is equivalent to: has quality^op some mass^c
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/COB_0000110

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: gene product^c, nucleic acid polymer^c, protein^c
is disjoint with: atom^c

monoatomic ion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000042

is equivalent to: atom^c and (has quality^op some charge^c)
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/COB_0000018

has super-classes: cell^c

neutron^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000009

has super-classes: subatomic particle^c

nucleic acid polymer^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000049

has super-classes: molecular entity^c

objective specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000076

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/COB_0000022

Includes virus - we will later have a class for cellular organisms.

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/COB_0000025

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/COB_0000063

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/COB_0000066

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

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

plan^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000113

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/COB_0000079

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

planned process^c back to ToC or Class ToC

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

Should we create agent?

has super-classes: process^c; intended to realize^op some plan^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/COB_0000034

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

processed material entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000026

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

protein^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000015

has super-classes: molecular entity^c

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

IRI: http://purl.obolibrary.org/obo/COB_0000075

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/COB_0000008

has super-classes: subatomic particle^c

quality^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000001

has super-classes: characteristic^c
has sub-classes: charge^c, mass^c
is in range of: has quality^op

realizable^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000033

has super-classes: characteristic^c
has sub-classes: completely executed planned process^c, disposition^c, plan^c, role^c
is in domain of: realizes^op

role^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000114

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

site^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000057

has super-classes: immaterial entity^c

subatomic particle^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/COB_0000007

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/COB_0000043

is equivalent to: atom^c and (not (has quality^op some charge^c))
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/COB_0000023

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/COB_0000036

is inverse of: occurs in^op

enabled by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/COB_0000074

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/COB_0000086

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/COB_0000512

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/COB_0000047

is inverse of: part of^op

has participant^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/COB_0000070

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 quality^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/COB_0000041

Note: this will end up being a subproperty of has-characteristic when we add it, TBD depends on discussion of whether has-characteristic is functional

has range: quality^c
is inverse of: quality of^op

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

IRI: http://purl.obolibrary.org/obo/COB_0000039

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/COB_0000040

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/COB_0000513

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

IRI: http://purl.obolibrary.org/obo/COB_0000002

is inverse of: concretizes^op

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

IRI: http://purl.obolibrary.org/obo/COB_0000027

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/COB_0000028

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/COB_0000071

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/COB_0000072

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/COB_0000024

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

quality of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/COB_0000030

is inverse of: has quality^op

realized in^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/COB_0000029

is inverse of: realizes^op

realizes^op back to ToC or Object Property ToC

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

has domain: realizable^c
has range: process^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

Table of Content

Introduction

Classes

action specificationc 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

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

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

nucleic acid polymerc 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

qualityc 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