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Core Ontology for Biology and Biomedicine

Metadata

URI
http://purl.obolibrary.org/obo/cob.owl
Version Information
2021-09-11
Version URI
http://purl.obolibrary.org/obo/cob/releases/2021-09-11/cob-native.owl
License
https://creativecommons.org/publicdomain/zero/1.0/
Ontology RDF
RDF (turtle)

Description

This version of COB includes native OBO URIs, only using COB IRIs where equivalent natives could not be found. To see the edition that includes native IRIs, consult cob-edit.owl.

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 ↑

processc # Classes

URI http://purl.obolibrary.org/obo/BFO_0000015
Super-classes owl:Thingc
Restrictions obo:BFO_0000050op only obo:BFO_0000015c
Sub-classes obo:GO_0008150c
obo:ENVO_02500000c
obo:MOP_0000543c
obo:OGMS_0000063c
obo:GO_0003674c
obo:COB_0000082c
In domain of obo:BFO_0000066op
obo:RO_0000057op
In range of obo:COB_0000087op

dispositionc # Classes

URI http://purl.obolibrary.org/obo/BFO_0000016
Super-classes obo:BFO_0000017c
Sub-classes obo:BFO_0000034c

realizablec # Classes

URI http://purl.obolibrary.org/obo/BFO_0000017
Super-classes obo:PATO_0000001c
Sub-classes obo:COB_0000082c
obo:BFO_0000023c
obo:OBI_0000260c
obo:BFO_0000016c
In domain of obo:COB_0000087op

rolec # Classes

URI http://purl.obolibrary.org/obo/BFO_0000023
Super-classes obo:BFO_0000017c
Sub-classes obo:COB_0000119c
obo:SEPIO_0000048c

sitec # Classes

URI http://purl.obolibrary.org/obo/BFO_0000029
Super-classes obo:BFO_0000041c

functionc # Classes

URI http://purl.obolibrary.org/obo/BFO_0000034
Super-classes obo:BFO_0000016c

material entityc # Classes

URI http://purl.obolibrary.org/obo/BFO_0000040
Super-classes owl:Thingc
Sub-classes obo:COB_0000011c
obo:NCBITaxon_1c
obo:CHEBI_36342c
obo:PCO_0000000c
obo:COB_0000122c
obo:COB_0000020c
obo:COB_0000080c
obo:OBI_0000047c
obo:OBI_0000245c
obo:COB_0000013c
obo:CL_0000000c
obo:ENVO_01001110c
obo:CARO_0001008c
obo:ENVO_01000813c
In domain of obo:COB_0000801dp

immaterial entityc # Classes

URI http://purl.obolibrary.org/obo/BFO_0000041
Super-classes owl:Thingc
Sub-classes obo:COB_0000056c
obo:BFO_0000029c
obo:COB_0000032c

gross anatomical partc # Classes

URI http://purl.obolibrary.org/obo/CARO_0001008
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:BFO_0000040c

nucleic acid polymerc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_10545
Super-classes obo:CHEBI_36342c
obo:COB_0000013c
Restrictions obo:COB_0000801dp value 0c

protonc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_24636
Super-classes obo:CHEBI_36342c

monoatomic ionc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_24867
Super-classes obo:COB_0000011c

neutronc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_30222
Super-classes obo:CHEBI_36342c

uncharged atomc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_33250
Super-classes obo:COB_0000011c

atomic nucleusc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_33252
Description

This is equivalent to CHEBI:33252
Super-classes obo:CHEBI_36342c

subatomic particlec # Classes

URI http://purl.obolibrary.org/obo/CHEBI_36342
Super-classes obo:BFO_0000040c
Sub-classes obo:CHEBI_30222c
obo:CHEBI_24636c
obo:CHEBI_10545c
obo:CHEBI_33252c

cellc # Classes

URI http://purl.obolibrary.org/obo/CL_0000000
Description

CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
Super-classes obo:BFO_0000040c
Sub-classes obo:CL_0001034c
obo:CL_0000003c

native cellc # Classes

URI http://purl.obolibrary.org/obo/CL_0000003
Super-classes obo:CL_0000000c

cell in vitroc # Classes

URI http://purl.obolibrary.org/obo/CL_0001034
Super-classes obo:CL_0000000c

obsolete_elementary chargec # Classes

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

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:BFO_0000040c
Restrictions obo:BFO_0000051op some obo:CHEBI_33252c
Sub-classes obo:CHEBI_33250c
obo:CHEBI_24867c
In domain of obo:COB_0000800dp

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:BFO_0000040c
Restrictions obo:BFO_0000051op some obo:COB_0000011c
Sub-classes obo:COB_0000073c
obo:PR_000000001c
obo:CHEBI_10545c

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

subcellular structurec # Classes

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

Overlaps with some cellular components from GO
Super-classes obo:BFO_0000040c
Restrictions obo:BFO_0000051op some obo:COB_0000013c
Sub-classes obo:COB_0000116c
obo:GO_0005634c

geographical locationc # Classes

URI http://purl.obolibrary.org/obo/COB_0000032
Super-classes obo:BFO_0000041c

immaterial anatomical entityc # Classes

URI http://purl.obolibrary.org/obo/COB_0000056
Super-classes obo:BFO_0000041c

gene productc # Classes

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

action specificationc # Classes

URI http://purl.obolibrary.org/obo/COB_0000077
Super-classes obo:IAO_0000033c
Restrictions obo:BFO_0000051op some obo:IAO_0000005c
obo:BFO_0000051op some obo:COB_0000077c

complex of molecular entitiesc # Classes

URI http://purl.obolibrary.org/obo/COB_0000080
Super-classes obo:BFO_0000040c
Restrictions obo:BFO_0000051op some obo:COB_0000013c
Sub-classes obo:GO_0032991c

planned processc # Classes

URI http://purl.obolibrary.org/obo/COB_0000082
Super-classes obo:BFO_0000017c
obo:BFO_0000015c
Restrictions obo:COB_0000087op some obo:SEPIO_0000048c
obo:COB_0000081op some obo:OBI_0000260c
Sub-classes obo:OBI_0000011c
obo:COB_0000083c

failed planned processc # Classes

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

cellular membranec # Classes

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

evaluant rolec # Classes

URI http://purl.obolibrary.org/obo/COB_0000119
Super-classes obo:BFO_0000023c

information representationc # Classes

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

This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc
Super-classes obo:PATO_0000001c
Sub-classes obo:OBI_0000260c

measurement datumc # Classes

URI http://purl.obolibrary.org/obo/COB_0000121
Super-classes obo:IAO_0000027c

physical information carrierc # Classes

URI http://purl.obolibrary.org/obo/COB_0000122
Super-classes obo:BFO_0000040c

drug productc # Classes

URI http://purl.obolibrary.org/obo/DRON_0000005
Super-classes obo:OBI_0000047c

geophysical entityc # Classes

URI http://purl.obolibrary.org/obo/ENVO_01000813
Super-classes obo:BFO_0000040c

ecosystemc # Classes

URI http://purl.obolibrary.org/obo/ENVO_01001110
Super-classes obo:BFO_0000040c

environmental processc # Classes

URI http://purl.obolibrary.org/obo/ENVO_02500000
Super-classes obo:BFO_0000015c

gene product or complex activityc # Classes

URI http://purl.obolibrary.org/obo/GO_0003674
Description

This is the same as GO molecular function
Super-classes obo:BFO_0000015c
Restrictions obo:RO_0002333op some (obo:COB_0000073c or obo:GO_0032991c)

cell nucleusc # Classes

URI http://purl.obolibrary.org/obo/GO_0005634
Super-classes obo:COB_0000020c

biological processc # Classes

URI http://purl.obolibrary.org/obo/GO_0008150
Description

A biological process is an evolved process
Super-classes obo:BFO_0000015c
(n0aee60f08c364bb9b6b4bd3ec77f1ef7b20c or n0aee60f08c364bb9b6b4bd3ec77f1ef7b21c or n0aee60f08c364bb9b6b4bd3ec77f1ef7b22c)
Restrictions obo:BFO_0000051op some obo:GO_0003674c

protein-containing macromolecular complexc # Classes

URI http://purl.obolibrary.org/obo/GO_0032991
Description

This is not covalently bonded, which conflicts with changes to the parent definition.
Super-classes obo:COB_0000080c
Restrictions obo:BFO_0000051op some obo:COB_0000073c

objective specificationc # Classes

URI http://purl.obolibrary.org/obo/IAO_0000005
Super-classes obo:IAO_0000033c

data itemc # Classes

URI http://purl.obolibrary.org/obo/IAO_0000027
Super-classes obo:IAO_0000030c
Sub-classes obo:COB_0000121c

informationc # Classes

URI http://purl.obolibrary.org/obo/IAO_0000030
Description

Pier: 'data, information or knowledge'. OR 'representation
Super-classes owl:Thingc
Restrictions n0aee60f08c364bb9b6b4bd3ec77f1ef7b31 some obo:COB_0000120c
obo:IAO_0000136op some owl:Thingc
Sub-classes obo:IAO_0000310c
obo:IAO_0000027c
obo:IAO_0000033c
obo:OGMS_0000014c
obo:OGMS_0000073c
obo:OBI_0001909c

directive information entityc # Classes

URI http://purl.obolibrary.org/obo/IAO_0000033
Super-classes obo:IAO_0000030c
Sub-classes obo:IAO_0000005c
obo:COB_0000077c
obo:IAO_0000104c

plan specificationc # Classes

URI http://purl.obolibrary.org/obo/IAO_0000104
Super-classes obo:IAO_0000033c
Restrictions obo:BFO_0000051op some obo:COB_0000077c
obo:BFO_0000051op some obo:IAO_0000005c

documentc # Classes

URI http://purl.obolibrary.org/obo/IAO_0000310
Super-classes obo:IAO_0000030c

physico-chemical processc # Classes

URI http://purl.obolibrary.org/obo/MOP_0000543
Description

This is meant to capture processes that are more fundamental than macromolecular activities
Super-classes obo:BFO_0000015c

organismc # Classes

URI http://purl.obolibrary.org/obo/NCBITaxon_1
Description

"Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'.
Super-classes obo:BFO_0000040c
Sub-classes obo:NCBITaxon_131567c

cellular organismc # Classes

URI http://purl.obolibrary.org/obo/NCBITaxon_131567
Super-classes obo:NCBITaxon_1c

completely executed planned processc # Classes

URI http://purl.obolibrary.org/obo/OBI_0000011
Super-classes obo:COB_0000082c
Restrictions obo:COB_0000087op some obo:OBI_0000260c
Sub-classes obo:OBI_0000070c
obo:OBI_0200000c
obo:OBI_0000066c
obo:OBI_0000094c
In domain of obo:OBI_0000293op
obo:OBI_0000299op

processed material entityc # Classes

URI http://purl.obolibrary.org/obo/OBI_0000047
Super-classes obo:BFO_0000040c
Sub-classes obo:DRON_0000005c

investigationc # Classes

URI http://purl.obolibrary.org/obo/OBI_0000066
Super-classes obo:OBI_0000011c

assayc # Classes

URI http://purl.obolibrary.org/obo/OBI_0000070
Super-classes obo:OBI_0000011c
Restrictions obo:OBI_0000299op some (obo:BFO_0000040c and n0aee60f08c364bb9b6b4bd3ec77f1ef7b37c and obo:COB_0000121c and n0aee60f08c364bb9b6b4bd3ec77f1ef7b42c)
obo:OBI_0000293op some (obo:BFO_0000040c and n0aee60f08c364bb9b6b4bd3ec77f1ef7b37c and obo:COB_0000121c and n0aee60f08c364bb9b6b4bd3ec77f1ef7b42c)

material processingc # Classes

URI http://purl.obolibrary.org/obo/OBI_0000094
Super-classes obo:OBI_0000011c

organizationc # Classes

URI http://purl.obolibrary.org/obo/OBI_0000245
Description

Should revisit if we can place outside of material entity - a collection of roles.
Super-classes obo:BFO_0000040c

planc # Classes

URI http://purl.obolibrary.org/obo/OBI_0000260
Super-classes obo:COB_0000120c
obo:BFO_0000017c
Restrictions obo:COB_0000078op some obo:IAO_0000104c
n0aee60f08c364bb9b6b4bd3ec77f1ef7b51 only obo:COB_0000082c

conclusion based on datac # Classes

URI http://purl.obolibrary.org/obo/OBI_0001909
Super-classes obo:IAO_0000030c

data transformationc # Classes

URI http://purl.obolibrary.org/obo/OBI_0200000
Super-classes obo:OBI_0000011c

phenotypic findingc # Classes

URI http://purl.obolibrary.org/obo/OGMS_0000014
Super-classes obo:IAO_0000030c

disease coursec # Classes

URI http://purl.obolibrary.org/obo/OGMS_0000063
Super-classes obo:BFO_0000015c

disease diagnosisc # Classes

URI http://purl.obolibrary.org/obo/OGMS_0000073
Super-classes obo:IAO_0000030c

characteristicc # Classes

URI http://purl.obolibrary.org/obo/PATO_0000001
Super-classes owl:Thingc
Restrictions obo:BFO_0000051op only obo:PATO_0000001c
n0aee60f08c364bb9b6b4bd3ec77f1ef7b53 some owl:Thingc
Sub-classes obo:COB_0000120c
obo:BFO_0000017c
obo:PATO_0002193c
obo:PATO_0000125c
In domain of obo:COB_0000511dp
In range of obo:RO_0000053op

massc # Classes

URI http://purl.obolibrary.org/obo/PATO_0000125
Super-classes obo:PATO_0000001c
Restrictions obo:RO_0000052op some obo:BFO_0000040c

chargec # Classes

URI http://purl.obolibrary.org/obo/PATO_0002193
Super-classes obo:PATO_0000001c
Restrictions obo:RO_0000052op some obo:BFO_0000040c

collection of organismsc # Classes

URI http://purl.obolibrary.org/obo/PCO_0000000
Super-classes obo:BFO_0000040c

proteinc # Classes

URI http://purl.obolibrary.org/obo/PR_000000001
Super-classes obo:COB_0000013c

agent rolec # Classes

URI http://purl.obolibrary.org/obo/SEPIO_0000048
Super-classes obo:BFO_0000023c

Object Properties ↑

part ofop # OPs

URI http://purl.obolibrary.org/obo/BFO_0000050
Inverse properties obo:BFO_0000051op

has partop # OPs

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

realized inop # OPs

URI http://purl.obolibrary.org/obo/BFO_0000054
Inverse properties obo:COB_0000087op

occurs inop # OPs

URI http://purl.obolibrary.org/obo/BFO_0000066
Inverse properties obo:BFO_0000067op
Domain(s) obo:BFO_0000015c

contains processop # OPs

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

executed byop # OPs

URI http://purl.obolibrary.org/obo/COB_0000016
Inverse properties obo:STATO_0000102op

concretizesop # OPs

URI http://purl.obolibrary.org/obo/COB_0000078
Inverse properties obo:RO_0000058op

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

realizesop # OPs

URI http://purl.obolibrary.org/obo/COB_0000087
Domain(s) obo:BFO_0000017c
Range(s) obo:BFO_0000015c

is aboutop # OPs

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

has specified inputop # OPs

URI http://purl.obolibrary.org/obo/OBI_0000293
Super-properties obo:RO_0000057op
Inverse properties obo:OBI_0000295op
Domain(s) obo:OBI_0000011c

is specified input ofop # OPs

URI http://purl.obolibrary.org/obo/OBI_0000295
Super-properties obo:RO_0000056op

has specified outputop # OPs

URI http://purl.obolibrary.org/obo/OBI_0000299
Super-properties obo:RO_0000057op
Inverse properties obo:OBI_0000312op
Domain(s) obo:OBI_0000011c

is specified output ofop # OPs

URI http://purl.obolibrary.org/obo/OBI_0000312
Super-properties obo:RO_0000056op

characteristic ofop # OPs

URI http://purl.obolibrary.org/obo/RO_0000052
Inverse properties obo:RO_0000053op

has characteristicop # OPs

URI http://purl.obolibrary.org/obo/RO_0000053
Domain(s) owl:Thingc
Range(s) obo:PATO_0000001c

participates inop # OPs

URI http://purl.obolibrary.org/obo/RO_0000056
Inverse properties obo:RO_0000057op

has participantop # OPs

URI http://purl.obolibrary.org/obo/RO_0000057
Domain(s) obo:BFO_0000015c

is concretized asop # OPs

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

enabled byop # OPs

URI http://purl.obolibrary.org/obo/RO_0002333
Super-properties obo:RO_0000057op

executesop # OPs

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

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:PATO_0000001c

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:BFO_0000040c
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
http://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