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making rewired release version
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cmungall committed Sep 12, 2021
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566 changes: 449 additions & 117 deletions cob-base-reasoned.owl
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745 changes: 588 additions & 157 deletions cob-base.owl
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548 changes: 443 additions & 105 deletions cob-examples-reasoned.owl
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4 changes: 2 additions & 2 deletions cob-full.owl
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Expand Up @@ -11,11 +11,11 @@
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/cob-full.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2021-09-07/cob-full.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2021-09-11/cob-full.owl"/>
<dc:description xml:lang="en">COB brings together key terms from a wide range of OBO projects to improve interoperability.</dc:description>
<dc:title xml:lang="en">Core Ontology for Biology and Biomedicine</dc:title>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-09-07</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-09-11</owl:versionInfo>
</owl:Ontology>


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1,293 changes: 644 additions & 649 deletions cob.owl
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133 changes: 66 additions & 67 deletions cob.tsv
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ID ID [LABEL] definition subClassOf [ID NAMED] subClassOf [LABEL NAMED] subClassOf [ID ANON] subClassOf [LABEL ANON]
COB:0000003 mass COB:0000502 characteristic COB:0000023 some COB:0000006 characteristic of some material entity
COB:0000004 charge COB:0000502 characteristic COB:0000023 some COB:0000006 characteristic of some material entity
BFO:0000015 process BFO:0000050 only BFO:0000015 part of only process
BFO:0000016 disposition BFO:0000017 realizable
BFO:0000017 realizable PATO:0000001 characteristic
BFO:0000023 role BFO:0000017 realizable
BFO:0000029 site BFO:0000041 immaterial entity
BFO:0000034 function BFO:0000016 disposition
BFO:0000040 material entity
BFO:0000041 immaterial entity
CARO:0001008 gross anatomical part A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. BFO:0000040 material entity
CHEBI:10545 electron CHEBI:36342|COB:0000013 molecular entity|subatomic particle COB:0000801 value 0 has number of atomic nuclei value 0
CHEBI:24636 proton CHEBI:36342 subatomic particle
CHEBI:24867 monoatomic ion COB:0000011 atom
CHEBI:30222 neutron CHEBI:36342 subatomic particle
CHEBI:33250 uncharged atom COB:0000011 atom
CHEBI:33252 atomic nucleus CHEBI:36342 subatomic particle
CHEBI:36342 subatomic particle BFO:0000040 material entity
CL:0000000 cell A material entity that has a plasma membrane and results from cellular division. BFO:0000040 material entity
CL:0000003 native cell CL:0000000 cell
CL:0001034 cell in vitro CL:0000000 cell
COB:0000005 obsolete_elementary charge
COB:0000006 material entity
COB:0000007 subatomic particle COB:0000006 material entity
COB:0000008 proton COB:0000007 subatomic particle
COB:0000009 neutron COB:0000007 subatomic particle
COB:0000010 electron COB:0000007 subatomic particle COB:0000801 value 0 has number of atomic nuclei value 0
COB:0000011 atom A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. COB:0000006 material entity COB:0000047 some COB:0000012 has part some atomic nucleus
COB:0000012 atomic nucleus COB:0000007 subatomic particle
COB:0000013 molecular entity 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. COB:0000006 material entity COB:0000047 some COB:0000011 has part some atom
COB:0000011 atom A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. BFO:0000040 material entity BFO:0000051 some CHEBI:33252 has part some atomic nucleus
COB:0000013 molecular entity 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. BFO:0000040 material entity BFO:0000051 some COB:0000011 has part some atom
COB:0000014 obsolete macromolecular entity 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.
COB:0000015 protein COB:0000013 molecular entity
COB:0000017 cell A material entity that has a plasma membrane and results from cellular division. COB:0000006 material entity
COB:0000018 native cell COB:0000017 cell
COB:0000019 cell in vitro COB:0000017 cell
COB:0000020 subcellular structure A material entity consisting of at least two macromolecular entities derived from a cell as parts, and that has a function for the cell. COB:0000006 material entity COB:0000047 some COB:0000013 has part some molecular entity
COB:0000021 gross anatomical part A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. COB:0000006 material entity
COB:0000022 organism A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome. COB:0000006 material entity
COB:0000025 organization COB:0000006 material entity
COB:0000026 processed material entity A material entity processed by human activity with an intent to produce COB:0000006 material entity
COB:0000031 immaterial entity
COB:0000032 geographical location COB:0000031 immaterial entity
COB:0000033 realizable COB:0000502 characteristic
COB:0000034 process COB:0000072 only COB:0000034 part of only process
COB:0000035 completely executed planned process COB:0000082 planned process COB:0000087 some COB:0000113 realizes some plan
COB:0000037 biological process A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. COB:0000034 process (COB:0000070 some COB:0000022) or (COB:0000070 some (COB:0000072 some COB:0000022)) or (COB:0000071 some COB:0000022)|COB:0000047 some COB:0000038 (has participant some organism) or (has participant some (part of some organism)) or (occurs in some organism)|has part some gene product or complex activity
COB:0000038 gene product or complex activity COB:0000034 process COB:0000074 some (COB:0000073 or COB:0000075) enabled by some (gene product or protein-containing macromolecular complex)
COB:0000042 monoatomic ion COB:0000011 atom
COB:0000043 uncharged atom COB:0000011 atom
COB:0000049 nucleic acid polymer COB:0000013 molecular entity
COB:0000055 collection of organisms COB:0000006 material entity
COB:0000056 immaterial anatomical entity COB:0000031 immaterial entity
COB:0000057 site COB:0000031 immaterial entity
COB:0000058 conclusion based on data COB:0000061 information
COB:0000061 information inverse (COB:0000078) some COB:0000120|COB:0000513 some owl:Thing inverse (concretizes) some information representation|is about some
COB:0000062 disease diagnosis COB:0000061 information
COB:0000063 phenotypic finding COB:0000061 information
COB:0000064 disease course COB:0000034 process
COB:0000065 environmental process COB:0000034 process
COB:0000066 physico-chemical process COB:0000034 process
COB:0000067 ecosystem COB:0000006 material entity
COB:0000068 geophysical entity COB:0000006 material entity
COB:0000069 directive information entity COB:0000061 information
COB:0000020 subcellular structure A material entity consisting of at least two macromolecular entities derived from a cell as parts, and that has a function for the cell. BFO:0000040 material entity BFO:0000051 some COB:0000013 has part some molecular entity
COB:0000032 geographical location BFO:0000041 immaterial entity
COB:0000056 immaterial anatomical entity BFO:0000041 immaterial entity
COB:0000073 gene product COB:0000013 molecular entity
COB:0000075 protein-containing macromolecular complex COB:0000080 complex of molecular entities COB:0000047 some COB:0000073 has part some gene product
COB:0000076 objective specification COB:0000069 directive information entity
COB:0000077 action specification COB:0000069 directive information entity COB:0000047 some COB:0000076|COB:0000047 some COB:0000077 has part some action specification|has part some objective specification
COB:0000079 plan specification COB:0000069 directive information entity COB:0000047 some COB:0000076|COB:0000047 some COB:0000077 has part some action specification|has part some objective specification
COB:0000080 complex of molecular entities A complex of two or more molecular entities that are not covalently bound. COB:0000006 material entity COB:0000047 some COB:0000013 has part some molecular entity
COB:0000082 planned process 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. COB:0000033|COB:0000034 process|realizable COB:0000081 some COB:0000113|COB:0000087 some COB:0000123 intended to realize some plan|realizes some agent role
COB:0000077 action specification IAO:0000033 directive information entity BFO:0000051 some COB:0000077|BFO:0000051 some IAO:0000005 has part some action specification|has part some objective specification
COB:0000080 complex of molecular entities A complex of two or more molecular entities that are not covalently bound. BFO:0000040 material entity BFO:0000051 some COB:0000013 has part some molecular entity
COB:0000082 planned process 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. BFO:0000015|BFO:0000017 process|realizable COB:0000081 some OBI:0000260|COB:0000087 some SEPIO:0000048 intended to realize some plan|realizes some agent role
COB:0000083 failed planned process COB:0000082 planned process
COB:0000088 drug product A processed material entity created to be administered to an individual with the intent to improve health. COB:0000026 processed material entity
COB:0000101 document COB:0000061 information
COB:0000102 data item COB:0000061 information
COB:0000103 cell nucleus COB:0000020 subcellular structure
COB:0000107 assay COB:0000035 completely executed planned process COB:0000039 some (COB:0000006 and (COB:0000512 some COB:0000119))|COB:0000040 some (COB:0000121 and (COB:0000513 some (COB:0000006 and (COB:0000512 some COB:0000119)))) has specified input some (material entity and (has characteristic some evaluant role))|has specified output some (measurement datum and (is about some (material entity and (has characteristic some evaluant role))))
COB:0000108 data transformation COB:0000035 completely executed planned process
COB:0000109 investigation COB:0000035 completely executed planned process
COB:0000110 material processing COB:0000035 completely executed planned process
COB:0000111 disposition COB:0000033 realizable
COB:0000112 function COB:0000111 disposition
COB:0000113 plan COB:0000033|COB:0000120 information representation|realizable inverse (COB:0000087) only COB:0000082|COB:0000078 some COB:0000079 inverse (realizes) only planned process|concretizes some plan specification
COB:0000114 role COB:0000033 realizable
COB:0000116 cellular membrane COB:0000020 subcellular structure
COB:0000118 cellular organism COB:0000022 organism
COB:0000119 evaluant role COB:0000114 role
COB:0000120 information representation COB:0000502 characteristic
COB:0000121 measurement datum COB:0000102 data item
COB:0000122 physical information carrier COB:0000006 material entity
COB:0000123 agent role COB:0000114 role
COB:0000502 characteristic inverse (COB:0000512) some owl:Thing|COB:0000047 only COB:0000502 inverse (has characteristic) some |has part only characteristic
COB:0000119 evaluant role BFO:0000023 role
COB:0000120 information representation PATO:0000001 characteristic
COB:0000121 measurement datum IAO:0000027 data item
COB:0000122 physical information carrier BFO:0000040 material entity
DRON:0000005 drug product A processed material entity created to be administered to an individual with the intent to improve health. OBI:0000047 processed material entity
ENVO:01000813 geophysical entity BFO:0000040 material entity
ENVO:01001110 ecosystem BFO:0000040 material entity
ENVO:02500000 environmental process BFO:0000015 process
GO:0003674 gene product or complex activity BFO:0000015 process RO:0002333 some (COB:0000073 or GO:0032991) enabled by some (gene product or protein-containing macromolecular complex)
GO:0005634 cell nucleus COB:0000020 subcellular structure
GO:0008150 biological process A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. BFO:0000015 process (BFO:0000066 some NCBITaxon:1) or (RO:0000057 some NCBITaxon:1) or (RO:0000057 some (BFO:0000050 some NCBITaxon:1))|BFO:0000051 some GO:0003674 (occurs in some organism) or (has participant some organism) or (has participant some (part of some organism))|has part some gene product or complex activity
GO:0032991 protein-containing macromolecular complex COB:0000080 complex of molecular entities BFO:0000051 some COB:0000073 has part some gene product
IAO:0000005 objective specification IAO:0000033 directive information entity
IAO:0000027 data item IAO:0000030 information
IAO:0000030 information inverse (COB:0000078) some COB:0000120|IAO:0000136 some owl:Thing inverse (concretizes) some information representation|is about some
IAO:0000033 directive information entity IAO:0000030 information
IAO:0000104 plan specification IAO:0000033 directive information entity BFO:0000051 some COB:0000077|BFO:0000051 some IAO:0000005 has part some action specification|has part some objective specification
IAO:0000310 document IAO:0000030 information
MOP:0000543 physico-chemical process BFO:0000015 process
NCBITaxon:1 organism A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome. BFO:0000040 material entity
NCBITaxon:131567 cellular organism NCBITaxon:1 organism
OBI:0000011 completely executed planned process COB:0000082 planned process COB:0000087 some OBI:0000260 realizes some plan
OBI:0000047 processed material entity A material entity processed by human activity with an intent to produce BFO:0000040 material entity
OBI:0000066 investigation OBI:0000011 completely executed planned process
OBI:0000070 assay OBI:0000011 completely executed planned process OBI:0000293 some (BFO:0000040 and (RO:0000053 some COB:0000119))|OBI:0000299 some (COB:0000121 and (IAO:0000136 some (BFO:0000040 and (RO:0000053 some COB:0000119)))) has specified input some (material entity and (has characteristic some evaluant role))|has specified output some (measurement datum and (is about some (material entity and (has characteristic some evaluant role))))
OBI:0000094 material processing OBI:0000011 completely executed planned process
OBI:0000245 organization BFO:0000040 material entity
OBI:0000260 plan BFO:0000017|COB:0000120 information representation|realizable inverse (COB:0000087) only COB:0000082|COB:0000078 some IAO:0000104 inverse (realizes) only planned process|concretizes some plan specification
OBI:0001909 conclusion based on data IAO:0000030 information
OBI:0200000 data transformation OBI:0000011 completely executed planned process
OGMS:0000014 phenotypic finding IAO:0000030 information
OGMS:0000063 disease course BFO:0000015 process
OGMS:0000073 disease diagnosis IAO:0000030 information
PATO:0000001 characteristic inverse (RO:0000053) some owl:Thing|BFO:0000051 only PATO:0000001 inverse (has characteristic) some |has part only characteristic
PATO:0000125 mass PATO:0000001 characteristic RO:0000052 some BFO:0000040 characteristic of some material entity
PATO:0002193 charge PATO:0000001 characteristic RO:0000052 some BFO:0000040 characteristic of some material entity
PCO:0000000 collection of organisms BFO:0000040 material entity
PR:000000001 protein COB:0000013 molecular entity
SEPIO:0000048 agent role BFO:0000023 role
21 changes: 10 additions & 11 deletions src/ontology/cob.Makefile
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Expand Up @@ -38,14 +38,23 @@ $(TMPDIR)/robot.jar: | $(TMPDIR)
########################################

# build main release product
cob.owl: $(SRC)
REWIRE_PRECEDENCE = PR CHEBI
cob.ttl: components/cob-to-external.tsv cob-native.owl
sssom rewire -I xml -m $< $(patsubst %,--precedence %,$(REWIRE_PRECEDENCE)) cob-native.owl -o $@
cob.owl: cob.ttl
robot merge --include-annotations true -i $< -i ontology-metadata.owl \
annotate -O $(OBO)/$@ -o $@
.PRECIOUS: cob.owl

cob-native.owl: $(SRC)
$(ROBOT) remove --input $< \
--select imports \
reason --reasoner hermit \
annotate --ontology-iri $(OBO)/$@ \
$(ANNOTATE_ONTOLOGY_VERSION) \
--output $@


# base file is main cob plus linking axioms
cob-base.owl: cob.owl $(COB_TO_EXTERNAL)
$(ROBOT) merge $(patsubst %, -i %, $^) -o $@
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--annotation owl:versionInfo $(TODAY) \
--output $@

########################################
# -- REWIRING --
########################################

# NOTE: this code currently depends on sssom code not yet on pypi: https://github.com/mapping-commons/sssom-py/pull/119
REWIRE_PRECEDENCE = PR CHEBI
cob-rewired.ttl: components/cob-to-external.tsv cob.owl
sssom rewire -I xml -m $< $(patsubst %,--precedence %,$(REWIRE_PRECEDENCE)) cob.owl -o $@
cob-rewired.owl: cob-rewired.ttl
robot annotate -i $< -O $(OBO)/cob/$@ -o $@

########################################
# -- TESTING --
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18 changes: 18 additions & 0 deletions src/ontology/ontology-metadata.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/cob/cob-edit.owl#"
xml:base="http://purl.obolibrary.org/obo/cob/cob-edit.owl"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/ontology-metadata.owl">
<rdfs:comment xml:lang="en">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.</rdfs:comment>
</owl:Ontology>
</rdf:RDF>


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