BFO:0000050 (part_of) missing

[spficklin]

Hi, it seems the BFO:0000050 (part_of) term is missing in the most recent version of the BFO. However, there are a large number of vocabularies that use it. We are working on a general parser for ontologies and we are using EBI's Ontology Lookup Service API to find terms. Unfortunately this term is not in EBIs OLS. So, we're a bit stuck on what to do when a vocabulary uses it but we can't find it in the current vocabulary. We're looking for clarification. Thanks.

[zhengj2007]

Due to debate on temporal relations, the BFO 2 only contains classes. The relations are kept in Relations ontology (RO).

The BFO:'part_of' IRI is solvable in RO:
http://purl.obolibrary.org/obo/BFO_0000050

[spficklin]

If the term was moved to the relationship ontology shouldn't it be renamed with an RO prefix? Our software is using the term prefix (e.g. BFO) to lookup the term and it makes it seem as though the term is still in the BFO even though it has moved.

[zhengj2007]

I know your concern. However, BFO_0000050 has been widely used. So the ID is preserved in RO.

[spficklin]

How are we supposed to know what vocabulary now owns a term? There's nothing in the current RO obo file that indicates the term belongs to the relationship ontology now: https://raw.githubusercontent.com/oborel/obo-relations/master/ro.obo

[zhengj2007]

It is under discussion. Someone has proposed to use property 'is_defined_by' to indicate which ontology own a term.

I will bring it up to OBO Foundry group for discussion.

[spficklin]

That would be helpful. Thank you. We are currently using the EBI Ontology Lookup Service to query for terms using their RESTful API. They have a flag that indicates if an ontology defines the term, but in the case of the BFO:0000050 they have no ontology listed that defines the term.

[zhengj2007]

May contact OLS group to see whether it is possible to add that tag to term BFO:0000050. Actually RO use few relations with BFO prefix (the relations defined in BFO pre-Graz version but not in BFO official release)

[spficklin]

Thanks, that would be very helpful.

[cmungall]

See https://github.com/oborel/obo-relations/wiki/ROAndBFO