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Published 20 hours ago • verified publisher icon EBISPOT

BFO:0000050

Open jamesamcl opened this issue 2 years ago • 7 comments
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When I search for BFO:0000050 I get this

Screenshot 2023-05-26 at 02 00 07

it's defined by RO but RO is nowhere to be seen. This is because it's defined by RO but uses the BFO prefix.

jamesamcl avatar May 26 '23 01:05 jamesamcl

Screen Shot 2023-06-06 at 1 49 29 PM

(maybe related, short form or name is truncated)

serjoshua avatar Jun 06 '23 12:06 serjoshua

It is not immediately clear how to address this without causing a lot of noise for various ontologies since many of our ontologies do not use owl:imports.

henrietteharmse avatar Aug 03 '23 09:08 henrietteharmse

Is there no rdfs:isDefinedBy property for these terms in RO? If not, I can request it

matentzn avatar Aug 03 '23 09:08 matentzn

No, not for BFO_0000050. For BFO_0000054, BFO_0000066 and BFO_0000067 it has <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/> and for BFO_0000055 it has <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>

It will be helpful in RO for BFO terms that are intended to be defined in RO to have <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>. Currently we assume IsDefiningOntology=true only when prefix of ontology matches prefix of term. Then we can extend this to consider rdfs:isDefinedBy.

henrietteharmse avatar Aug 03 '23 10:08 henrietteharmse

We do consider rdfs:isDefinedBy I think

jamesamcl avatar Aug 03 '23 11:08 jamesamcl

We are using the wrong predicate. This should be changed to isDefinedBy rather than definedBy:

https://github.com/EBISPOT/ols4/blob/dev/dataload/linker/src/main/java/LinkerPass1.java#L238C34-L238C34

jamesamcl avatar Aug 03 '23 11:08 jamesamcl

@udp should we just change that line? Will there be any dependencies we need to be aware of and check?

serjoshua avatar Aug 04 '23 13:08 serjoshua