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hubmapconsortium / ontology-api

The HuBMAP Ontology Service
MIT License
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Ontology: obtain relationship information for edge IRIs that are not in Relations Ontology #167

Closed AlanSimmons closed 1 year ago

AlanSimmons commented 1 year ago

Long-term enhancement.

Issue

Ontologies that are published as OWL files use IRIs to describe edges/relationships. The PheKnowLator script adds these IRIs to the predicate field of the edgelist file.

Although most of the edges from OWL files use IRIs that point to the Relations Ontology, some use IRIs from other ontologies. Example from the OBI OWL: http://purl.obolibrary.org/obo/OBI_0000417.

If the OWL file does not store a label for the relation in the relations.txt file, the ontology generation script cannot resolve a non-RO IRI to either the label for the relationship or that of the relationship's inverse. For example, the relationship property for OBI_0000417 in OBI is "achieves_planned_objective", for which the inverse is "objective_achieved_by". Because the relationship is not in RO, the generation framework can only derive the "pseudo-inverse" of "inverse_achieves_planned_objective".

Solution

Expand relationship property resolution to ontologies other than Relations Ontology. This might entail querying a source such as OntoBee, perhaps via SPARQL.

AlanSimmons commented 1 year ago

This will be moved to the new UBKG repo.

AlanSimmons commented 1 year ago

Moved.