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Merge pull request #189 from OBOFoundry/adding-match-type-col
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Adding mapping_set_id and match_type to SSSOM file
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@cmungall
cmungall authored Dec 8, 2021
2 parents cde6759 + a4f785b commit a2f7141
Showing 1 changed file with 107 additions and 106 deletions.
213 changes: 107 additions & 106 deletions src/ontology/components/cob-to-external.tsv
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#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#mapping_set_id: "http://purl.obolibrary.org/obo/cob/components/cob-to-external.tsv"
#curie_map:
# rdfs: "http://www.w3.org/2000/01/rdf-schema#"
# skos: "http://www.w3.org/2004/02/skos/core#"
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# SEPIO: "http://purl.obolibrary.org/obo/SEPIO_"
# STATO: "http://purl.obolibrary.org/obo/STATO_"
# DRON: "http://purl.obolibrary.org/obo/DRON_"
subject_id subject_label predicate_id object_id object_label notes
COB:0000003 mass owl:equivalentClass PATO:0000125 mass .
COB:0000004 charge owl:equivalentClass PATO:0002193 electric .
COB:0000005 elementary charge rdfs:subClassOf owl:Thing owl:Thing Making ticket in PATO tracker
COB:0000006 material entity owl:equivalentClass BFO:0000040 material entity .
COB:0000006 material entity sssom:superClassOf SO:0000110 sequence_feature .
COB:0000006 material entity sssom:superClassOf SO:0001060 sequence_variant .
COB:0000006 material entity sssom:superClassOf SO:0001260 sequence_collection .
COB:0000007 subatomic particle owl:equivalentClass CHEBI:36342 subatomic particle .
COB:0000008 proton owl:equivalentClass CHEBI:24636 proton .
COB:0000009 neutron owl:equivalentClass CHEBI:30222 neutron .
COB:0000010 electron owl:equivalentClass CHEBI:10545 electron .
COB:0000011 atom skos:closeMatch CHEBI:33250 atom .
COB:0000012 atomic nucleus owl:equivalentClass CHEBI:33252 atomic nucleus .
COB:0000013 molecular entity skos:closeMatch CHEBI:23367 molecular entity No exact match in CHEBI
COB:0000013 molecular entity skos:closeMatch CHEBI:25367 molecule This is electrically neutral in CHEBI but in COB it is generic. We should make it union of molecule and polyatomic ion
COB:0000015 protein owl:equivalentClass CHEBI:16541 protein polypeptide chain .
COB:0000015 protein owl:equivalentClass PR:000000001 protein .
COB:0000017 cell owl:equivalentClass CL:0000000 cell .
COB:0000017 cell sssom:superClassOf PO:0009002 plant cell .
COB:0000018 native cell owl:equivalentClass CL:0000003 native cell .
COB:0000018 native cell sssom:superClassOf XAO:0003012 xenopus cell .
COB:0000018 native cell sssom:superClassOf ZFA:0009000 zebrafish cell .
COB:0000018 native cell sssom:superClassOf PO:0025606 native plant cell .
COB:0000019 cell in vitro owl:equivalentClass CL:0001034 cell in vitro .
COB:0000020 subcellular structure rdfs:subClassOf owl:Thing owl:Thing Chris will follow up
COB:0000021 gross anatomical part owl:equivalentClass CARO:0001008 gross anatomical part .
COB:0000021 gross anatomical part sssom:superClassOf UBERON:0010000 multicellular anatomical structure .
COB:0000022 organism owl:equivalentClass NCBITaxon:1 root .
COB:0000022 organism owl:equivalentClass OBI:0100026 organism .
COB:0000022 organism owl:equivalentClass CARO:0001010 organism or virus or viroid .
COB:0000025 organization owl:equivalentClass OBI:0000245 organization .
COB:0000026 processed material entity owl:equivalentClass OBI:0000047 processed material .
COB:0000031 immaterial entity owl:equivalentClass BFO:0000041 immaterial entity .
COB:0000032 geographical location rdfs:subClassOf owl:Thing owl:Thing
COB:0000033 realizable owl:equivalentClass BFO:0000017 realizable entity .
COB:0000034 process owl:equivalentClass BFO:0000015 process .
COB:0000035 planned process owl:equivalentClass OBI:0000011 planned process .
COB:0000037 biological process owl:equivalentClass GO:0008150 biological process .
COB:0000038 gene product or complex activity owl:equivalentClass GO:0003674 molecular function .
COB:0000042 monoatomic ion owl:equivalentClass CHEBI:24867 monoatomic ion .
COB:0000043 uncharged atom owl:equivalentClass CHEBI:33250 atom "we think our uncharged atom is actually chebi:atom, to be discussed with CHEBI people"
COB:0000049 nucleic acid polymer owl:equivalentClass CHEBI:10545 nucleic acid follow up with CHEBI on nomenclature
COB:0000055 collection of organisms owl:equivalentClass PCO:0000000 collection of organisms .
COB:0000056 immaterial anatomical entity sssom:superClassOf UBERON:0000466 immaterial anatomical entity .
COB:0000056 immaterial anatomical entity sssom:superClassOf PO:0025117 plant anatomical space .
COB:0000057 site owl:equivalentClass BFO:0000029 site .
COB:0000058 conclusion based on data owl:equivalentClass OBI:0001909 conclusion based on data .
COB:0000061 information owl:equivalentClass IAO:0000030 information content entity .
COB:0000062 disease diagnosis owl:equivalentClass OGMS:0000073 diagnosis .
COB:0000063 phenotypic finding owl:equivalentClass OGMS:0000014 clinical finding .
COB:0000064 disease course owl:equivalentClass OGMS:0000063 disease course .
COB:0000065 environmental process owl:equivalentClass ENVO:02500000 environmental system process .
COB:0000066 physico-chemical process owl:equivalentClass MOP:0000543 molecular process "we are not sure if these are equivalent, or if we even want to retain this. Follow up with Colin"
COB:0000067 ecosystem owl:equivalentClass ENVO:01001110 ecosystem .
COB:0000068 geophysical entity owl:equivalentClass ENVO:01000813 astronomical body part .
COB:0000068 geophysical entity sssom:superClassOf GEO:000000370 geographical entity See https://github.com/OBOFoundry/COB/issues/91
COB:0000069 directive information entity owl:equivalentClass IAO:0000033 directive information entity .
COB:0000073 gene product rdfs:subClassOf owl:Thing owl:Thing
COB:0000075 protein-containing macromolecular complex owl:equivalentClass GO:0032991 protein-containing complex .
COB:0000076 objective specification owl:equivalentClass IAO:0000005 objective specification .
COB:0000079 plan specification owl:equivalentClass IAO:0000104 plan specification .
COB:0000080 complex of molecular entities rdfs:subClassOf owl:Thing owl:Thing
COB:0000088 drug product owl:equivalentClass DRON:0000005 drug product we currently use a different text definition but we believe they do not contradict
COB:0000088 drug product rdfs:seeAlso CHEBI:23888 drug These can't be equivalent because COB drug product is a material entity, and ChEBI's drug is a role. See issue #140 for more information.
COB:0000101 document owl:equivalentClass IAO:0000310 document .
COB:0000102 data item owl:equivalentClass IAO:0000027 data item .
COB:0000103 cell nucleus owl:equivalentClass GO:0005634 nucleus .
COB:0000107 assay owl:equivalentClass OBI:0000070 assay .
COB:0000108 data transformation owl:equivalentClass OBI:0200000 data transformation .
COB:0000109 investigation owl:equivalentClass OBI:0000066 investigation .
COB:0000110 material processing owl:equivalentClass OBI:0000094 material processing .
COB:0000111 disposition owl:equivalentClass BFO:0000016 disposition .
COB:0000112 function owl:equivalentClass BFO:0000034 function .
COB:0000113 plan owl:equivalentClass OBI:0000260 plan .
COB:0000114 role owl:equivalentClass BFO:0000023 role .
COB:0000502 characteristic sssom:superClassOf CHEBI:50906 role The ChEBI notion of a role doesn't strictly follow the BFO sense of either being a role or disposition, meaning that it's hard, if not impossible, to impose BFO order to this branch of ChEBI. See issue #173
COB:0000116 cellular membrane rdfs:subClassOf owl:Thing owl:Thing
COB:0000118 cellular organism owl:equivalentClass NCBITaxon:131567 cellular organisms .
COB:0000118 cellular organism owl:equivalentClass CARO:0010004 cellular organism .
COB:0000118 cellular organism sssom:superClassOf UBERON:0000468 multicellular organism .
COB:0000118 cellular organism sssom:superClassOf PO:0000003 whole plant .
COB:0000036 contains process owl:equivalentProperty BFO:0000067 contains process .
COB:0000047 has part owl:equivalentProperty BFO:0000051 has part .
COB:0000070 has participant owl:equivalentProperty RO:0000057 has participant .
COB:0000071 occurs in owl:equivalentProperty BFO:0000066 occurs in .
COB:0000072 part of owl:equivalentProperty BFO:0000050 part of .
COB:0000074 enabled by owl:equivalentProperty RO:0002333 enabled by .
COB:0000502 characteristic owl:equivalentClass PATO:0000001 quality https://github.com/OBOFoundry/COB/issues/124
COB:0000502 characteristic owl:equivalentClass BFO:0000020 specifically dependent continuant may be revised to be narrower
COB:0000502 characteristic sssom:superClassOf SO:0000400 sequence_attribute .
COB:0000511 has quantity rdfs:subPropertyOf owl:topObjectProperty topObjectProperty .
COB:0000512 has characteristic owl:equivalentProperty RO:0000053 bearer of .
COB:0000002 is concretized as owl:equivalentProperty RO:0000058 is concretized as .
COB:0000086 executes owl:equivalentProperty STATO:0000102 executes .
COB:0000016 executed by rdfs:subPropertyOf owl:topObjectProperty topObjectProperty "There is no inverse for 'executes' STATO, only in COB."
COB:0000023 characteristic of owl:equivalentProperty RO:0000052 inheres in "In RO, 'inheres in' is the inverse of 'bearer of'."
COB:0000024 participates in owl:equivalentProperty RO:0000056 participates in .
COB:0000027 is specified input of owl:equivalentProperty OBI:0000295 is_specified_input_of .
COB:0000028 is specified output of owl:equivalentProperty OBI:0000312 is_specified_output_of .
COB:0000039 has specified input owl:equivalentProperty OBI:0000293 has_specified_input .
COB:0000040 has specified output owl:equivalentProperty OBI:0000299 has_specified_output .
COB:0000029 realized in owl:equivalentProperty BFO:0000054 realized in .
COB:0000513 is about owl:equivalentProperty IAO:0000136 is about There is no inverse for 'is about' in IAO.
COB:0000123 agent role owl:equivalentClass SEPIO:0000048 agent role
COB:0000123 agent role sssom:superClassOf OBI:0000202 investigation agent role
subject_id subject_label predicate_id object_id object_label notes match_type
COB:0000003 mass owl:equivalentClass PATO:0000125 mass . HumanCurated
COB:0000004 charge owl:equivalentClass PATO:0002193 electric . HumanCurated
COB:0000005 elementary charge rdfs:subClassOf owl:Thing owl:Thing Making ticket in PATO tracker HumanCurated
COB:0000006 material entity owl:equivalentClass BFO:0000040 material entity . HumanCurated
COB:0000006 material entity sssom:superClassOf SO:0000110 sequence_feature . HumanCurated
COB:0000006 material entity sssom:superClassOf SO:0001060 sequence_variant . HumanCurated
COB:0000006 material entity sssom:superClassOf SO:0001260 sequence_collection . HumanCurated
COB:0000007 subatomic particle owl:equivalentClass CHEBI:36342 subatomic particle . HumanCurated
COB:0000008 proton owl:equivalentClass CHEBI:24636 proton . HumanCurated
COB:0000009 neutron owl:equivalentClass CHEBI:30222 neutron . HumanCurated
COB:0000010 electron owl:equivalentClass CHEBI:10545 electron . HumanCurated
COB:0000011 atom skos:closeMatch CHEBI:33250 atom . HumanCurated
COB:0000012 atomic nucleus owl:equivalentClass CHEBI:33252 atomic nucleus . HumanCurated
COB:0000013 molecular entity skos:closeMatch CHEBI:23367 molecular entity No exact match in CHEBI HumanCurated
COB:0000013 molecular entity skos:closeMatch CHEBI:25367 molecule This is electrically neutral in CHEBI but in COB it is generic. We should make it union of molecule and polyatomic ion HumanCurated
COB:0000015 protein owl:equivalentClass CHEBI:16541 protein polypeptide chain . HumanCurated
COB:0000015 protein owl:equivalentClass PR:000000001 protein . HumanCurated
COB:0000017 cell owl:equivalentClass CL:0000000 cell . HumanCurated
COB:0000017 cell sssom:superClassOf PO:0009002 plant cell . HumanCurated
COB:0000018 native cell owl:equivalentClass CL:0000003 native cell . HumanCurated
COB:0000018 native cell sssom:superClassOf XAO:0003012 xenopus cell . HumanCurated
COB:0000018 native cell sssom:superClassOf ZFA:0009000 zebrafish cell . HumanCurated
COB:0000018 native cell sssom:superClassOf PO:0025606 native plant cell . HumanCurated
COB:0000019 cell in vitro owl:equivalentClass CL:0001034 cell in vitro . HumanCurated
COB:0000020 subcellular structure rdfs:subClassOf owl:Thing owl:Thing Chris will follow up HumanCurated
COB:0000021 gross anatomical part owl:equivalentClass CARO:0001008 gross anatomical part . HumanCurated
COB:0000021 gross anatomical part sssom:superClassOf UBERON:0010000 multicellular anatomical structure . HumanCurated
COB:0000022 organism owl:equivalentClass NCBITaxon:1 root . HumanCurated
COB:0000022 organism owl:equivalentClass OBI:0100026 organism . HumanCurated
COB:0000022 organism owl:equivalentClass CARO:0001010 organism or virus or viroid . HumanCurated
COB:0000025 organization owl:equivalentClass OBI:0000245 organization . HumanCurated
COB:0000026 processed material entity owl:equivalentClass OBI:0000047 processed material . HumanCurated
COB:0000031 immaterial entity owl:equivalentClass BFO:0000041 immaterial entity . HumanCurated
COB:0000032 geographical location rdfs:subClassOf owl:Thing owl:Thing HumanCurated
COB:0000033 realizable owl:equivalentClass BFO:0000017 realizable entity . HumanCurated
COB:0000034 process owl:equivalentClass BFO:0000015 process . HumanCurated
COB:0000035 planned process owl:equivalentClass OBI:0000011 planned process . HumanCurated
COB:0000037 biological process owl:equivalentClass GO:0008150 biological process . HumanCurated
COB:0000038 gene product or complex activity owl:equivalentClass GO:0003674 molecular function . HumanCurated
COB:0000042 monoatomic ion owl:equivalentClass CHEBI:24867 monoatomic ion . HumanCurated
COB:0000043 uncharged atom owl:equivalentClass CHEBI:33250 atom "we think our uncharged atom is actually chebi:atom, to be discussed with CHEBI people" HumanCurated
COB:0000049 nucleic acid polymer owl:equivalentClass CHEBI:10545 nucleic acid follow up with CHEBI on nomenclature HumanCurated
COB:0000055 collection of organisms owl:equivalentClass PCO:0000000 collection of organisms . HumanCurated
COB:0000056 immaterial anatomical entity sssom:superClassOf UBERON:0000466 immaterial anatomical entity . HumanCurated
COB:0000056 immaterial anatomical entity sssom:superClassOf PO:0025117 plant anatomical space . HumanCurated
COB:0000057 site owl:equivalentClass BFO:0000029 site . HumanCurated
COB:0000058 conclusion based on data owl:equivalentClass OBI:0001909 conclusion based on data . HumanCurated
COB:0000061 information owl:equivalentClass IAO:0000030 information content entity . HumanCurated
COB:0000062 disease diagnosis owl:equivalentClass OGMS:0000073 diagnosis . HumanCurated
COB:0000063 phenotypic finding owl:equivalentClass OGMS:0000014 clinical finding . HumanCurated
COB:0000064 disease course owl:equivalentClass OGMS:0000063 disease course . HumanCurated
COB:0000065 environmental process owl:equivalentClass ENVO:02500000 environmental system process . HumanCurated
COB:0000066 physico-chemical process owl:equivalentClass MOP:0000543 molecular process "we are not sure if these are equivalent, or if we even want to retain this. Follow up with Colin" HumanCurated
COB:0000067 ecosystem owl:equivalentClass ENVO:01001110 ecosystem . HumanCurated
COB:0000068 geophysical entity owl:equivalentClass ENVO:01000813 astronomical body part . HumanCurated
COB:0000068 geophysical entity sssom:superClassOf GEO:000000370 geographical entity See https://github.com/OBOFoundry/COB/issues/91 HumanCurated
COB:0000069 directive information entity owl:equivalentClass IAO:0000033 directive information entity . HumanCurated
COB:0000073 gene product rdfs:subClassOf owl:Thing owl:Thing HumanCurated
COB:0000075 protein-containing macromolecular complex owl:equivalentClass GO:0032991 protein-containing complex . HumanCurated
COB:0000076 objective specification owl:equivalentClass IAO:0000005 objective specification . HumanCurated
COB:0000079 plan specification owl:equivalentClass IAO:0000104 plan specification . HumanCurated
COB:0000080 complex of molecular entities rdfs:subClassOf owl:Thing owl:Thing HumanCurated
COB:0000088 drug product owl:equivalentClass DRON:0000005 drug product we currently use a different text definition but we believe they do not contradict HumanCurated
COB:0000088 drug product rdfs:seeAlso CHEBI:23888 drug These can't be equivalent because COB drug product is a material entity, and ChEBI's drug is a role. See issue #140 for more information. HumanCurated
COB:0000101 document owl:equivalentClass IAO:0000310 document . HumanCurated
COB:0000102 data item owl:equivalentClass IAO:0000027 data item . HumanCurated
COB:0000103 cell nucleus owl:equivalentClass GO:0005634 nucleus . HumanCurated
COB:0000107 assay owl:equivalentClass OBI:0000070 assay . HumanCurated
COB:0000108 data transformation owl:equivalentClass OBI:0200000 data transformation . HumanCurated
COB:0000109 investigation owl:equivalentClass OBI:0000066 investigation . HumanCurated
COB:0000110 material processing owl:equivalentClass OBI:0000094 material processing . HumanCurated
COB:0000111 disposition owl:equivalentClass BFO:0000016 disposition . HumanCurated
COB:0000112 function owl:equivalentClass BFO:0000034 function . HumanCurated
COB:0000113 plan owl:equivalentClass OBI:0000260 plan . HumanCurated
COB:0000114 role owl:equivalentClass BFO:0000023 role . HumanCurated
COB:0000502 characteristic sssom:superClassOf CHEBI:50906 role The ChEBI notion of a role doesn't strictly follow the BFO sense of either being a role or disposition, meaning that it's hard, if not impossible, to impose BFO order to this branch of ChEBI. See issue #173 HumanCurated
COB:0000116 cellular membrane rdfs:subClassOf owl:Thing owl:Thing HumanCurated
COB:0000118 cellular organism owl:equivalentClass NCBITaxon:131567 cellular organisms . HumanCurated
COB:0000118 cellular organism owl:equivalentClass CARO:0010004 cellular organism . HumanCurated
COB:0000118 cellular organism sssom:superClassOf UBERON:0000468 multicellular organism . HumanCurated
COB:0000118 cellular organism sssom:superClassOf PO:0000003 whole plant . HumanCurated
COB:0000036 contains process owl:equivalentProperty BFO:0000067 contains process . HumanCurated
COB:0000047 has part owl:equivalentProperty BFO:0000051 has part . HumanCurated
COB:0000070 has participant owl:equivalentProperty RO:0000057 has participant . HumanCurated
COB:0000071 occurs in owl:equivalentProperty BFO:0000066 occurs in . HumanCurated
COB:0000072 part of owl:equivalentProperty BFO:0000050 part of . HumanCurated
COB:0000074 enabled by owl:equivalentProperty RO:0002333 enabled by . HumanCurated
COB:0000502 characteristic owl:equivalentClass PATO:0000001 quality https://github.com/OBOFoundry/COB/issues/124 HumanCurated
COB:0000502 characteristic owl:equivalentClass BFO:0000020 specifically dependent continuant may be revised to be narrower HumanCurated
COB:0000502 characteristic sssom:superClassOf SO:0000400 sequence_attribute . HumanCurated
COB:0000511 has quantity rdfs:subPropertyOf owl:topObjectProperty topObjectProperty . HumanCurated
COB:0000512 has characteristic owl:equivalentProperty RO:0000053 bearer of . HumanCurated
COB:0000002 is concretized as owl:equivalentProperty RO:0000058 is concretized as . HumanCurated
COB:0000086 executes owl:equivalentProperty STATO:0000102 executes . HumanCurated
COB:0000016 executed by rdfs:subPropertyOf owl:topObjectProperty topObjectProperty "There is no inverse for 'executes' STATO, only in COB." HumanCurated
COB:0000023 characteristic of owl:equivalentProperty RO:0000052 inheres in "In RO, 'inheres in' is the inverse of 'bearer of'." HumanCurated
COB:0000024 participates in owl:equivalentProperty RO:0000056 participates in . HumanCurated
COB:0000027 is specified input of owl:equivalentProperty OBI:0000295 is_specified_input_of . HumanCurated
COB:0000028 is specified output of owl:equivalentProperty OBI:0000312 is_specified_output_of . HumanCurated
COB:0000039 has specified input owl:equivalentProperty OBI:0000293 has_specified_input . HumanCurated
COB:0000040 has specified output owl:equivalentProperty OBI:0000299 has_specified_output . HumanCurated
COB:0000029 realized in owl:equivalentProperty BFO:0000054 realized in . HumanCurated
COB:0000513 is about owl:equivalentProperty IAO:0000136 is about There is no inverse for 'is about' in IAO. HumanCurated
COB:0000123 agent role owl:equivalentClass SEPIO:0000048 agent role HumanCurated
COB:0000123 agent role sssom:superClassOf OBI:0000202 investigation agent role HumanCurated

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