#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#" # owl: "http://www.w3.org/2002/07/owl#" # BFO: "http://purl.obolibrary.org/obo/BFO_" # CARO: "http://purl.obolibrary.org/obo/CARO_" # CHEBI: "http://purl.obolibrary.org/obo/CHEBI_" # CL: "http://purl.obolibrary.org/obo/CL_" # COB: "http://purl.obolibrary.org/obo/COB_" # ENVO: "http://purl.obolibrary.org/obo/ENVO_" # GEO: "http://purl.obolibrary.org/obo/GEO_" # GO: "http://purl.obolibrary.org/obo/GO_" # IAO: "http://purl.obolibrary.org/obo/IAO_" # MOP: "http://purl.obolibrary.org/obo/MOP_" # NCBITaxon: "http://purl.obolibrary.org/obo/NCBITaxon_" # OBI: "http://purl.obolibrary.org/obo/OBI_" # OGMS: "http://purl.obolibrary.org/obo/OGMS_" # PATO: "http://purl.obolibrary.org/obo/PATO_" # PCO: "http://purl.obolibrary.org/obo/PCO_" # PO: "http://purl.obolibrary.org/obo/PO_" # PR: "http://purl.obolibrary.org/obo/PR_" # SO: "http://purl.obolibrary.org/obo/SO_" # RO: "http://purl.obolibrary.org/obo/RO_" # UBERON: "http://purl.obolibrary.org/obo/UBERON_" # XAO: "http://purl.obolibrary.org/obo/XAO_" # ZFA: "http://purl.obolibrary.org/obo/ZFA_" # 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 mapping_justification COB:0000003 mass owl:equivalentClass PATO:0000125 mass . semapv:ManualMappingCuration COB:0000004 charge owl:equivalentClass PATO:0002193 electric . semapv:ManualMappingCuration COB:0000005 elementary charge rdfs:subClassOf owl:Thing owl:Thing Making ticket in PATO tracker semapv:ManualMappingCuration COB:0000006 material entity owl:equivalentClass BFO:0000040 material entity . semapv:ManualMappingCuration COB:0000006 material entity sssom:superClassOf SO:0000110 sequence_feature . semapv:ManualMappingCuration COB:0000006 material entity sssom:superClassOf SO:0001060 sequence_variant . semapv:ManualMappingCuration COB:0000006 material entity sssom:superClassOf SO:0001260 sequence_collection . semapv:ManualMappingCuration COB:0000007 subatomic particle owl:equivalentClass CHEBI:36342 subatomic particle . semapv:ManualMappingCuration COB:0000008 proton owl:equivalentClass CHEBI:24636 proton . semapv:ManualMappingCuration COB:0000009 neutron owl:equivalentClass CHEBI:30222 neutron . semapv:ManualMappingCuration COB:0000010 electron owl:equivalentClass CHEBI:10545 electron . semapv:ManualMappingCuration COB:0000011 atom skos:closeMatch CHEBI:33250 atom . semapv:ManualMappingCuration COB:0000012 atomic nucleus owl:equivalentClass CHEBI:33252 atomic nucleus . semapv:ManualMappingCuration COB:0000013 molecular entity skos:closeMatch CHEBI:23367 molecular entity No exact match in CHEBI semapv:ManualMappingCuration 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 semapv:ManualMappingCuration COB:0000015 protein owl:equivalentClass CHEBI:16541 protein polypeptide chain . semapv:ManualMappingCuration COB:0000015 protein owl:equivalentClass PR:000000001 protein . semapv:ManualMappingCuration COB:0000017 cell owl:equivalentClass CL:0000000 cell . semapv:ManualMappingCuration COB:0000017 cell sssom:superClassOf PO:0009002 plant cell . semapv:ManualMappingCuration COB:0000018 native cell owl:equivalentClass CL:0000003 native cell . semapv:ManualMappingCuration COB:0000018 native cell sssom:superClassOf XAO:0003012 xenopus cell . semapv:ManualMappingCuration COB:0000018 native cell sssom:superClassOf ZFA:0009000 zebrafish cell . semapv:ManualMappingCuration COB:0000018 native cell sssom:superClassOf PO:0025606 native plant cell . semapv:ManualMappingCuration COB:0000019 cell in vitro owl:equivalentClass CL:0001034 cell in vitro . semapv:ManualMappingCuration COB:0000020 subcellular structure rdfs:subClassOf owl:Thing owl:Thing Chris will follow up semapv:ManualMappingCuration COB:0000021 gross anatomical part owl:equivalentClass CARO:0001008 gross anatomical part . semapv:ManualMappingCuration COB:0000021 gross anatomical part sssom:superClassOf UBERON:0010000 multicellular anatomical structure . semapv:ManualMappingCuration COB:0000022 organism sssom:superClassOf NCBITaxon:10239 Viruses . semapv:ManualMappingCuration COB:0000022 organism sssom:superClassOf NCBITaxon:131567 cellular organisms . semapv:ManualMappingCuration COB:0000022 organism owl:equivalentClass OBI:0100026 organism . semapv:ManualMappingCuration COB:0000022 organism owl:equivalentClass CARO:0001010 organism or virus or viroid . semapv:ManualMappingCuration COB:0000025 organization owl:equivalentClass OBI:0000245 organization . semapv:ManualMappingCuration COB:0000026 processed material entity owl:equivalentClass OBI:0000047 processed material . semapv:ManualMappingCuration COB:0000031 immaterial entity owl:equivalentClass BFO:0000141 immaterial entity . semapv:ManualMappingCuration COB:0000032 geographical location rdfs:subClassOf owl:Thing owl:Thing semapv:ManualMappingCuration COB:0000033 realizable owl:equivalentClass BFO:0000017 realizable entity . semapv:ManualMappingCuration COB:0000034 process owl:equivalentClass BFO:0000015 process . semapv:ManualMappingCuration COB:0000035 planned process owl:equivalentClass OBI:0000011 planned process . semapv:ManualMappingCuration COB:0000037 biological process owl:equivalentClass GO:0008150 biological process . semapv:ManualMappingCuration COB:0000038 gene product or complex activity owl:equivalentClass GO:0003674 molecular function . semapv:ManualMappingCuration COB:0000042 monoatomic ion owl:equivalentClass CHEBI:24867 monoatomic ion . semapv:ManualMappingCuration COB:0000043 uncharged atom owl:equivalentClass CHEBI:33250 atom "we think our uncharged atom is actually chebi:atom, to be discussed with CHEBI people" semapv:ManualMappingCuration COB:0000049 nucleic acid polymer owl:equivalentClass CHEBI:33696 nucleic acid follow up with CHEBI on nomenclature semapv:ManualMappingCuration COB:0000055 collection of organisms owl:equivalentClass PCO:0000000 collection of organisms . semapv:ManualMappingCuration COB:0000056 immaterial anatomical entity sssom:superClassOf UBERON:0000466 immaterial anatomical entity . semapv:ManualMappingCuration COB:0000056 immaterial anatomical entity sssom:superClassOf PO:0025117 plant anatomical space . semapv:ManualMappingCuration COB:0000057 site owl:equivalentClass BFO:0000029 site . semapv:ManualMappingCuration COB:0000058 conclusion based on data owl:equivalentClass OBI:0001909 conclusion based on data . semapv:ManualMappingCuration COB:0000061 information owl:equivalentClass IAO:0000030 information content entity . semapv:ManualMappingCuration COB:0000062 disease diagnosis owl:equivalentClass OGMS:0000073 diagnosis . semapv:ManualMappingCuration COB:0000063 phenotypic finding owl:equivalentClass OGMS:0000014 clinical finding . semapv:ManualMappingCuration COB:0000064 disease course owl:equivalentClass OGMS:0000063 disease course . semapv:ManualMappingCuration COB:0000065 environmental process owl:equivalentClass ENVO:02500000 environmental system process . semapv:ManualMappingCuration 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" semapv:ManualMappingCuration COB:0000067 ecosystem owl:equivalentClass ENVO:01001110 ecosystem . semapv:ManualMappingCuration COB:0000068 geophysical entity owl:equivalentClass ENVO:01000813 astronomical body part . semapv:ManualMappingCuration COB:0000068 geophysical entity sssom:superClassOf GEO:000000370 geographical entity See https://github.com/OBOFoundry/COB/issues/91 semapv:ManualMappingCuration COB:0000069 directive information entity owl:equivalentClass IAO:0000033 directive information entity . semapv:ManualMappingCuration COB:0000073 gene product rdfs:subClassOf owl:Thing owl:Thing semapv:ManualMappingCuration COB:0000075 protein-containing macromolecular complex owl:equivalentClass GO:0032991 protein-containing complex . semapv:ManualMappingCuration COB:0000076 objective specification owl:equivalentClass IAO:0000005 objective specification . semapv:ManualMappingCuration COB:0000079 plan specification owl:equivalentClass IAO:0000104 plan specification . semapv:ManualMappingCuration COB:0000080 complex of molecular entities rdfs:subClassOf owl:Thing owl:Thing semapv:ManualMappingCuration COB:0000088 drug product owl:equivalentClass DRON:0000005 drug product we currently use a different text definition but we believe they do not contradict semapv:ManualMappingCuration 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. semapv:ManualMappingCuration COB:0000101 document owl:equivalentClass IAO:0000310 document . semapv:ManualMappingCuration COB:0000102 data item owl:equivalentClass IAO:0000027 data item . semapv:ManualMappingCuration COB:0000103 cell nucleus owl:equivalentClass GO:0005634 nucleus . semapv:ManualMappingCuration COB:0000107 assay owl:equivalentClass OBI:0000070 assay . semapv:ManualMappingCuration COB:0000108 data transformation owl:equivalentClass OBI:0200000 data transformation . semapv:ManualMappingCuration COB:0000109 investigation owl:equivalentClass OBI:0000066 investigation . semapv:ManualMappingCuration COB:0000110 material processing owl:equivalentClass OBI:0000094 material processing . semapv:ManualMappingCuration COB:0000111 disposition owl:equivalentClass BFO:0000016 disposition . semapv:ManualMappingCuration COB:0000112 function owl:equivalentClass BFO:0000034 function . semapv:ManualMappingCuration COB:0000113 plan owl:equivalentClass OBI:0000260 plan . semapv:ManualMappingCuration COB:0000114 role owl:equivalentClass BFO:0000023 role . semapv:ManualMappingCuration 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 semapv:ManualMappingCuration COB:0000116 cellular membrane rdfs:subClassOf owl:Thing owl:Thing semapv:ManualMappingCuration COB:0000118 cellular organism owl:equivalentClass NCBITaxon:131567 cellular organisms . semapv:ManualMappingCuration COB:0000118 cellular organism owl:equivalentClass CARO:0010004 cellular organism . semapv:ManualMappingCuration COB:0000118 cellular organism sssom:superClassOf UBERON:0000468 multicellular organism . semapv:ManualMappingCuration COB:0000118 cellular organism sssom:superClassOf PO:0000003 whole plant . semapv:ManualMappingCuration COB:0000036 contains process owl:equivalentProperty BFO:0000067 contains process . semapv:ManualMappingCuration COB:0000047 has part owl:equivalentProperty BFO:0000051 has part . semapv:ManualMappingCuration COB:0000070 has participant owl:equivalentProperty RO:0000057 has participant . semapv:ManualMappingCuration COB:0000071 occurs in owl:equivalentProperty BFO:0000066 occurs in . semapv:ManualMappingCuration COB:0000072 part of owl:equivalentProperty BFO:0000050 part of . semapv:ManualMappingCuration COB:0000074 enabled by owl:equivalentProperty RO:0002333 enabled by . semapv:ManualMappingCuration COB:0000502 characteristic owl:equivalentClass PATO:0000001 quality https://github.com/OBOFoundry/COB/issues/124 semapv:ManualMappingCuration COB:0000502 characteristic owl:equivalentClass BFO:0000020 specifically dependent continuant may be revised to be narrower semapv:ManualMappingCuration COB:0000502 characteristic sssom:superClassOf SO:0000400 sequence_attribute . semapv:ManualMappingCuration COB:0000511 has quantity rdfs:subPropertyOf owl:topDataProperty topDataProperty . semapv:ManualMappingCuration COB:0000512 has characteristic owl:equivalentProperty RO:0000053 bearer of . semapv:ManualMappingCuration COB:0000002 is concretized as owl:equivalentProperty RO:0000058 is concretized as . semapv:ManualMappingCuration COB:0000078 concretizes owl:equivalentProperty RO:0000059 concretizes . semapv:ManualMappingCuration COB:0000086 executes owl:equivalentProperty STATO:0000102 executes . semapv:ManualMappingCuration COB:0000016 executed by rdfs:subPropertyOf owl:topObjectProperty topObjectProperty "There is no inverse for 'executes' STATO, only in COB." semapv:ManualMappingCuration COB:0000023 characteristic of owl:equivalentProperty RO:0000052 inheres in "In RO, 'inheres in' is the inverse of 'bearer of'." semapv:ManualMappingCuration COB:0000024 participates in owl:equivalentProperty RO:0000056 participates in . semapv:ManualMappingCuration COB:0000027 is specified input of owl:equivalentProperty OBI:0000295 is_specified_input_of . semapv:ManualMappingCuration COB:0000028 is specified output of owl:equivalentProperty OBI:0000312 is_specified_output_of . semapv:ManualMappingCuration COB:0000039 has specified input owl:equivalentProperty OBI:0000293 has_specified_input . semapv:ManualMappingCuration COB:0000040 has specified output owl:equivalentProperty OBI:0000299 has_specified_output . semapv:ManualMappingCuration COB:0000087 realizes owl:equivalentProperty BFO:0000055 realizes . semapv:ManualMappingCuration COB:0000029 realized in owl:equivalentProperty BFO:0000054 realized in . semapv:ManualMappingCuration COB:0000513 is about owl:equivalentProperty IAO:0000136 is about There is no inverse for 'is about' in IAO. semapv:ManualMappingCuration COB:0000123 agent role owl:equivalentClass SEPIO:0000048 agent role semapv:ManualMappingCuration COB:0000123 agent role sssom:superClassOf OBI:0000202 investigation agent role semapv:ManualMappingCuration