diff --git a/src/ontology/cob.Makefile b/src/ontology/cob.Makefile index c0cf854..981c20c 100644 --- a/src/ontology/cob.Makefile +++ b/src/ontology/cob.Makefile @@ -81,7 +81,7 @@ cob.tsv: cob.owl # this is a really hacky way to do this, replace with robot report? .PHONY: sssom sssom: - pip install sssom + pip install sssom pandasql pip install --upgrade --no-deps --force-reinstall sssom==0.3.2 $(TMPDIR)/cob-to-external.sssom.owl: $(COMPONENTSDIR)/cob-to-external.tsv | sssom diff --git a/src/ontology/components/cob-to-external.tsv b/src/ontology/components/cob-to-external.tsv index 0de3cd2..018bc45 100644 --- a/src/ontology/components/cob-to-external.tsv +++ b/src/ontology/components/cob-to-external.tsv @@ -92,6 +92,7 @@ COB:0000076 objective specification owl:equivalentClass IAO:0000005 objective sp 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 . @@ -103,6 +104,7 @@ 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 .