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Core Ontology for Biology and Biomedicine

Metadata

URI
http://purl.obolibrary.org/obo/cob.owl
Version Information
2021-02-21
License
https://creativecommons.org/publicdomain/zero/1.0/
Ontology RDF
RDF (turtle)

Description

COB brings together key terms from a wide range of OBO projects to improve interoperability.

Table of Contents

  1. Classes
  2. Object Properties
  3. Datatype Properties
  4. Annotation Properties
  5. Namespaces
  6. Legend

Overview

Pictures say 1,000 words
Figure 1: Ontology overview

Classes ↑

qualityc # Classes

URI http://purl.obolibrary.org/obo/COB_0000001
Super-classes obo:COB_0000502c
Sub-classes obo:COB_0000004c
obo:COB_0000003c
In range of obo:COB_0000041op

massc # Classes

URI http://purl.obolibrary.org/obo/COB_0000003
Super-classes obo:COB_0000001c

chargec # Classes

URI http://purl.obolibrary.org/obo/COB_0000004
Super-classes obo:COB_0000001c

obsolete_elementary chargec # Classes

URI http://purl.obolibrary.org/obo/COB_0000005
Super-classes owl:Thingc

material entityc # Classes

URI http://purl.obolibrary.org/obo/COB_0000006
Super-classes owl:Thingc
Sub-classes obo:COB_0000007c
obo:COB_0000013c
obo:COB_0000122c
obo:COB_0000022c
obo:COB_0000017c
obo:COB_0000020c
obo:COB_0000067c
obo:COB_0000011c
obo:COB_0000055c
obo:COB_0000025c
obo:COB_0000026c
obo:COB_0000021c
obo:COB_0000080c
obo:COB_0000068c
In domain of obo:COB_0000801dp

subatomic particlec # Classes

URI http://purl.obolibrary.org/obo/COB_0000007
Super-classes obo:COB_0000006c
Sub-classes obo:COB_0000008c
obo:COB_0000009c
obo:COB_0000010c
obo:COB_0000012c

protonc # Classes

URI http://purl.obolibrary.org/obo/COB_0000008
Super-classes obo:COB_0000007c

neutronc # Classes

URI http://purl.obolibrary.org/obo/COB_0000009
Super-classes obo:COB_0000007c

electronc # Classes

URI http://purl.obolibrary.org/obo/COB_0000010
Super-classes obo:COB_0000007c
Restrictions obo:COB_0000801dp value 0c

atomc # Classes

URI http://purl.obolibrary.org/obo/COB_0000011
Description

This atom is closely related to ChEBI's atom, but not exactly equivalent to.
Super-classes obo:COB_0000006c
Restrictions obo:COB_0000047op some obo:COB_0000012c
Sub-classes obo:COB_0000042c
obo:COB_0000043c
In domain of obo:COB_0000800dp

atomic nucleusc # Classes

URI http://purl.obolibrary.org/obo/COB_0000012
Description

This is equivalent to CHEBI:33252
Super-classes obo:COB_0000007c

molecular entityc # Classes

URI http://purl.obolibrary.org/obo/COB_0000013
Description

We would like to have cardinality restrictions on the logic, but there are some technical limitations.
Super-classes obo:COB_0000006c
Restrictions obo:COB_0000047op some obo:COB_0000011c
Sub-classes obo:COB_0000049c
obo:COB_0000015c
obo:COB_0000073c

obsolete macromolecular entityc # Classes

URI http://purl.obolibrary.org/obo/COB_0000014
Description

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

proteinc # Classes

URI http://purl.obolibrary.org/obo/COB_0000015
Super-classes obo:COB_0000013c

cellc # Classes

URI http://purl.obolibrary.org/obo/COB_0000017
Description

CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
Super-classes obo:COB_0000006c
Sub-classes obo:COB_0000019c
obo:COB_0000018c

native cellc # Classes

URI http://purl.obolibrary.org/obo/COB_0000018
Super-classes obo:COB_0000017c

cell in vitroc # Classes

URI http://purl.obolibrary.org/obo/COB_0000019
Super-classes obo:COB_0000017c

subcellular structurec # Classes

URI http://purl.obolibrary.org/obo/COB_0000020
Description

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.
Super-classes obo:COB_0000006c
Restrictions obo:COB_0000047op some obo:COB_0000013c
Sub-classes obo:COB_0000103c
obo:COB_0000116c

gross anatomical partc # Classes

URI http://purl.obolibrary.org/obo/COB_0000021
Description

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.
Super-classes obo:COB_0000006c

organismc # Classes

URI http://purl.obolibrary.org/obo/COB_0000022
Description

"Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'.
Super-classes obo:COB_0000006c
Sub-classes obo:COB_0000118c

organizationc # Classes

URI http://purl.obolibrary.org/obo/COB_0000025
Description

Should revisit if we can place outside of material entity - a collection of roles.
Super-classes obo:COB_0000006c

processed material entityc # Classes

URI http://purl.obolibrary.org/obo/COB_0000026
Super-classes obo:COB_0000006c
Sub-classes obo:COB_0000088c

immaterial entityc # Classes

URI http://purl.obolibrary.org/obo/COB_0000031
Super-classes owl:Thingc
Sub-classes obo:COB_0000057c
obo:COB_0000032c
obo:COB_0000056c

geographical locationc # Classes

URI http://purl.obolibrary.org/obo/COB_0000032
Super-classes obo:COB_0000031c

realizablec # Classes

URI http://purl.obolibrary.org/obo/COB_0000033
Super-classes obo:COB_0000502c
Sub-classes obo:COB_0000035c
obo:COB_0000113c
obo:COB_0000114c
obo:COB_0000111c
In domain of obo:COB_0000087op

processc # Classes

URI http://purl.obolibrary.org/obo/COB_0000034
Super-classes owl:Thingc
Restrictions obo:COB_0000072op only obo:COB_0000034c
Sub-classes obo:COB_0000082c
obo:COB_0000065c
obo:COB_0000066c
obo:COB_0000037c
obo:COB_0000038c
obo:COB_0000064c
In domain of obo:COB_0000070op
obo:COB_0000071op
In range of obo:COB_0000087op

completely executed planned processc # Classes

URI http://purl.obolibrary.org/obo/COB_0000035
Super-classes obo:COB_0000033c
obo:COB_0000082c
Restrictions obo:COB_0000087op some obo:COB_0000113c
Sub-classes obo:COB_0000110c
obo:COB_0000107c
obo:COB_0000109c
obo:COB_0000108c
In domain of obo:COB_0000040op
obo:COB_0000039op

biological processc # Classes

URI http://purl.obolibrary.org/obo/COB_0000037
Description

A biological process is an evolved process
Super-classes obo:COB_0000034c
(ub361bL256C22c or ub361bL261C13c or ub361bL270C13c)
Restrictions obo:COB_0000047op some obo:COB_0000038c

gene product or complex activityc # Classes

URI http://purl.obolibrary.org/obo/COB_0000038
Description

This is the same as GO molecular function
Super-classes obo:COB_0000034c
Restrictions obo:COB_0000074op some (obo:COB_0000073c or obo:COB_0000075c)

monoatomic ionc # Classes

URI http://purl.obolibrary.org/obo/COB_0000042
Super-classes obo:COB_0000011c

uncharged atomc # Classes

URI http://purl.obolibrary.org/obo/COB_0000043
Super-classes obo:COB_0000011c

nucleic acid polymerc # Classes

URI http://purl.obolibrary.org/obo/COB_0000049
Super-classes obo:COB_0000013c

collection of organismsc # Classes

URI http://purl.obolibrary.org/obo/COB_0000055
Super-classes obo:COB_0000006c

immaterial anatomical entityc # Classes

URI http://purl.obolibrary.org/obo/COB_0000056
Super-classes obo:COB_0000031c

sitec # Classes

URI http://purl.obolibrary.org/obo/COB_0000057
Super-classes obo:COB_0000031c

conclusion based on datac # Classes

URI http://purl.obolibrary.org/obo/COB_0000058
Super-classes obo:COB_0000061c

informationc # Classes

URI http://purl.obolibrary.org/obo/COB_0000061
Description

Pier: 'data, information or knowledge'. OR 'representation
Super-classes owl:Thingc
Restrictions ub361bL391C24 some obo:COB_0000120c
obo:COB_0000513op some owl:Thingc
Sub-classes obo:COB_0000062c
obo:COB_0000102c
obo:COB_0000063c
obo:COB_0000069c
obo:COB_0000101c
obo:COB_0000058c

disease diagnosisc # Classes

URI http://purl.obolibrary.org/obo/COB_0000062
Super-classes obo:COB_0000061c

phenotypic findingc # Classes

URI http://purl.obolibrary.org/obo/COB_0000063
Super-classes obo:COB_0000061c

disease coursec # Classes

URI http://purl.obolibrary.org/obo/COB_0000064
Super-classes obo:COB_0000034c

environmental processc # Classes

URI http://purl.obolibrary.org/obo/COB_0000065
Super-classes obo:COB_0000034c

physico-chemical processc # Classes

URI http://purl.obolibrary.org/obo/COB_0000066
Description

This is meant to capture processes that are more fundamental than macromolecular activities
Super-classes obo:COB_0000034c

ecosystemc # Classes

URI http://purl.obolibrary.org/obo/COB_0000067
Super-classes obo:COB_0000006c

geophysical entityc # Classes

URI http://purl.obolibrary.org/obo/COB_0000068
Super-classes obo:COB_0000006c

directive information entityc # Classes

URI http://purl.obolibrary.org/obo/COB_0000069
Super-classes obo:COB_0000061c
Sub-classes obo:COB_0000079c
obo:COB_0000076c
obo:COB_0000077c

gene productc # Classes

URI http://purl.obolibrary.org/obo/COB_0000073
Super-classes obo:COB_0000013c

protein-containing macromolecular complexc # Classes

URI http://purl.obolibrary.org/obo/COB_0000075
Description

This is not covalently bonded, which conflicts with changes to the parent definition.
Super-classes obo:COB_0000080c
Restrictions obo:COB_0000047op some obo:COB_0000073c

objective specificationc # Classes

URI http://purl.obolibrary.org/obo/COB_0000076
Super-classes obo:COB_0000069c

action specificationc # Classes

URI http://purl.obolibrary.org/obo/COB_0000077
Super-classes obo:COB_0000069c
Restrictions obo:COB_0000047op some obo:COB_0000077c
obo:COB_0000047op some obo:COB_0000076c

plan specificationc # Classes

URI http://purl.obolibrary.org/obo/COB_0000079
Super-classes obo:COB_0000069c
Restrictions obo:COB_0000047op some obo:COB_0000077c
obo:COB_0000047op some obo:COB_0000076c

complex of molecular entitiesc # Classes

URI http://purl.obolibrary.org/obo/COB_0000080
Super-classes obo:COB_0000006c
Restrictions obo:COB_0000047op some obo:COB_0000013c
Sub-classes obo:COB_0000075c

planned processc # Classes

URI http://purl.obolibrary.org/obo/COB_0000082
Description

Should we create agent?
Super-classes obo:COB_0000034c
Restrictions obo:COB_0000081op some obo:COB_0000113c
Sub-classes obo:COB_0000035c
obo:COB_0000083c

failed planned processc # Classes

URI http://purl.obolibrary.org/obo/COB_0000083
Super-classes obo:COB_0000082c

drug productc # Classes

URI http://purl.obolibrary.org/obo/COB_0000088
Super-classes obo:COB_0000026c

documentc # Classes

URI http://purl.obolibrary.org/obo/COB_0000101
Super-classes obo:COB_0000061c

data itemc # Classes

URI http://purl.obolibrary.org/obo/COB_0000102
Super-classes obo:COB_0000061c
Sub-classes obo:COB_0000121c

cell nucleusc # Classes

URI http://purl.obolibrary.org/obo/COB_0000103
Super-classes obo:COB_0000020c

assayc # Classes

URI http://purl.obolibrary.org/obo/COB_0000107
Super-classes obo:COB_0000035c
Restrictions obo:COB_0000040op some (obo:COB_0000121c and ub361bL603C17c and obo:COB_0000006c and ub361bL590C17c)
obo:COB_0000039op some (obo:COB_0000121c and ub361bL603C17c and obo:COB_0000006c and ub361bL590C17c)

data transformationc # Classes

URI http://purl.obolibrary.org/obo/COB_0000108
Super-classes obo:COB_0000035c

investigationc # Classes

URI http://purl.obolibrary.org/obo/COB_0000109
Super-classes obo:COB_0000035c

material processingc # Classes

URI http://purl.obolibrary.org/obo/COB_0000110
Super-classes obo:COB_0000035c

dispositionc # Classes

URI http://purl.obolibrary.org/obo/COB_0000111
Super-classes obo:COB_0000033c
Sub-classes obo:COB_0000112c

functionc # Classes

URI http://purl.obolibrary.org/obo/COB_0000112
Super-classes obo:COB_0000111c

planc # Classes

URI http://purl.obolibrary.org/obo/COB_0000113
Super-classes obo:COB_0000120c
obo:COB_0000033c
Restrictions obo:COB_0000078op some obo:COB_0000079c
ub361bL656C24 only obo:COB_0000082c

rolec # Classes

URI http://purl.obolibrary.org/obo/COB_0000114
Super-classes obo:COB_0000033c
Sub-classes obo:COB_0000119c

cellular membranec # Classes

URI http://purl.obolibrary.org/obo/COB_0000116
Super-classes obo:COB_0000020c

cellular organismc # Classes

URI http://purl.obolibrary.org/obo/COB_0000118
Super-classes obo:COB_0000022c

evaluant rolec # Classes

URI http://purl.obolibrary.org/obo/COB_0000119
Super-classes obo:COB_0000114c

information representationc # Classes

URI http://purl.obolibrary.org/obo/COB_0000120
Description

Pier 'representational entity'
Super-classes obo:COB_0000502c
Sub-classes obo:COB_0000113c

measurement datumc # Classes

URI http://purl.obolibrary.org/obo/COB_0000121
Super-classes obo:COB_0000102c

physical information carrierc # Classes

URI http://purl.obolibrary.org/obo/COB_0000122
Super-classes obo:COB_0000006c

characteristicc # Classes

URI http://purl.obolibrary.org/obo/COB_0000502
Super-classes owl:Thingc
Restrictions ub361bL720C24 some owl:Thingc
obo:COB_0000047op only obo:COB_0000502c
Sub-classes obo:COB_0000120c
obo:COB_0000033c
obo:COB_0000001c
In domain of obo:COB_0000511dp
In range of obo:COB_0000512op

Object Properties ↑

is concretized asop # OPs

URI http://purl.obolibrary.org/obo/COB_0000002
Inverse properties obo:COB_0000078op

executed byop # OPs

URI http://purl.obolibrary.org/obo/COB_0000016
Inverse properties obo:COB_0000086op

characteristic ofop # OPs

URI http://purl.obolibrary.org/obo/COB_0000023
Inverse properties obo:COB_0000512op

participates inop # OPs

URI http://purl.obolibrary.org/obo/COB_0000024
Inverse properties obo:COB_0000070op

is specified input ofop # OPs

URI http://purl.obolibrary.org/obo/COB_0000027
Super-properties obo:COB_0000024op
Inverse properties obo:COB_0000039op

is specified output ofop # OPs

URI http://purl.obolibrary.org/obo/COB_0000028
Super-properties obo:COB_0000024op
Inverse properties obo:COB_0000040op

realized inop # OPs

URI http://purl.obolibrary.org/obo/COB_0000029
Inverse properties obo:COB_0000087op

quality ofop # OPs

URI http://purl.obolibrary.org/obo/COB_0000030
Inverse properties obo:COB_0000041op

contains processop # OPs

URI http://purl.obolibrary.org/obo/COB_0000036
Inverse properties obo:COB_0000071op

has specified inputop # OPs

URI http://purl.obolibrary.org/obo/COB_0000039
Super-properties obo:COB_0000070op
Domain(s) obo:COB_0000035c

has specified outputop # OPs

URI http://purl.obolibrary.org/obo/COB_0000040
Super-properties obo:COB_0000070op
Domain(s) obo:COB_0000035c

has qualityop # OPs

URI http://purl.obolibrary.org/obo/COB_0000041
Description

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
Range(s) obo:COB_0000001c

has partop # OPs

URI http://purl.obolibrary.org/obo/COB_0000047
Inverse properties obo:COB_0000072op

has participantop # OPs

URI http://purl.obolibrary.org/obo/COB_0000070
Domain(s) obo:COB_0000034c

occurs inop # OPs

URI http://purl.obolibrary.org/obo/COB_0000071
Domain(s) obo:COB_0000034c

part ofop # OPs

URI http://purl.obolibrary.org/obo/COB_0000072

enabled byop # OPs

URI http://purl.obolibrary.org/obo/COB_0000074
Super-properties obo:COB_0000070op

concretizesop # OPs

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

intended to realizeop # OPs

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

has planop # OPs

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

intended plan process typeop # OPs

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

executesop # OPs

URI http://purl.obolibrary.org/obo/COB_0000086

realizesop # OPs

URI http://purl.obolibrary.org/obo/COB_0000087
Domain(s) obo:COB_0000033c
Range(s) obo:COB_0000034c

has characteristicop # OPs

URI http://purl.obolibrary.org/obo/COB_0000512
Domain(s) owl:Thingc
Range(s) obo:COB_0000502c

is aboutop # OPs

URI http://purl.obolibrary.org/obo/COB_0000513

Datatype Properties ↑

has quantitydp # DPs

URI http://purl.obolibrary.org/obo/COB_0000511
Description

The range of this property should be a user-defined unit datatype, e.g 182^:cm
Domain(s) obo:COB_0000502c

has atomic numberdp # DPs

URI http://purl.obolibrary.org/obo/COB_0000800
Description

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
Domain(s) obo:COB_0000011c
Range(s) xsd:nonNegativeIntegerc

has number of atomic nucleidp # DPs

URI http://purl.obolibrary.org/obo/COB_0000801
Domain(s) obo:COB_0000006c
Range(s) xsd:nonNegativeIntegerc

has inchi stringdp # DPs

URI http://purl.obolibrary.org/obo/COB_0000803
Super-properties owl:topDataProperty

Annotation Properties ↑

COB_based_onap # APs

URI http://purl.obolibrary.org/obo/COB_based_on

definitionap # APs

URI http://purl.obolibrary.org/obo/IAO_0000115

IAO_0000116ap # APs

URI http://purl.obolibrary.org/obo/IAO_0000116

descriptionap # APs

URI http://purl.org/dc/elements/1.1/description

titleap # APs

URI http://purl.org/dc/elements/1.1/title

licenseap # APs

URI http://purl.org/dc/terms/license

exactMatchap # APs

URI http://www.w3.org/2004/02/skos/core#exactMatch

Namespaces ↑

default (:)
http://purl.obolibrary.org/obo/cob.owl
dc
http://purl.org/dc/elements/1.1/
obo
http://purl.obolibrary.org/obo/
owl
http://www.w3.org/2002/07/owl#
prov
http://www.w3.org/ns/prov#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
sdo
https://schema.org/
skos
http://www.w3.org/2004/02/skos/core#
terms
http://purl.org/dc/terms/
xsd
http://www.w3.org/2001/XMLSchema#

Legend

cClasses
opObject Properties
fpFunctional Properties
dpData Properties
dpAnnotation Properties
pProperties
niNamed Individuals