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Add superclass mapping from COB characteristic to ChEBI role #173

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merged 7 commits into from
Sep 14, 2021
Merged

Add superclass mapping from COB characteristic to ChEBI role #173

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9630a9e
Add equivalence from COB role to ChEBI role
cthoyt Sep 12, 2021
9714149
Fix space
cthoyt Sep 12, 2021
4149a78
Apply update from #177
cthoyt Sep 12, 2021
a5d29c2
Add equivalence between COB drug product and ChEBI drug
cthoyt Sep 12, 2021
8405385
Update cob-to-external.tsv
cthoyt Sep 12, 2021
e1e8c52
Update COB drug product - chebi drug relation and notes
cthoyt Sep 13, 2021
e52e163
Update cob-to-external.tsv
cthoyt Sep 13, 2021
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2 changes: 1 addition & 1 deletion src/ontology/cob.Makefile
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Expand Up @@ -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
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2 changes: 2 additions & 0 deletions src/ontology/components/cob-to-external.tsv
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Expand Up @@ -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.
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I like this. closeMatch is also not wrong, but I think seeAlso is good as it's even weaker. We should systematize this a bit more

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 .
Expand All @@ -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 .
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