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EBISPOT / ols4

Version 4 of the EMBL-EBI Ontology Lookup Service (OLS)
http://www.ebi.ac.uk/ols4/
Apache License 2.0
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BFO:0000050 #371

Open jamesamcl opened 1 year ago

jamesamcl commented 1 year ago

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.

serjoshua commented 1 year ago
Screen Shot 2023-06-06 at 1 49 29 PM

(maybe related, short form or name is truncated)

henrietteharmse commented 11 months ago

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.

matentzn commented 11 months ago

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

henrietteharmse commented 11 months ago

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.

jamesamcl commented 11 months ago

We do consider rdfs:isDefinedBy I think

jamesamcl commented 11 months ago

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

serjoshua commented 11 months ago

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