ppavlidis
commented
6 months ago The more specific issue here is that we have been adding terms to ChEBI and the maintainers turn that around pretty quickly. Same with TGEMO of course. Adding terms to other ontologies is very difficult/impossible so the need to refresh them is less common.
But the more general issue is being able to refresh ontologies without restarting the application. Note that there is an admin tool for indexing that might be a reasonable place to add this functionality (and the backend for that might be relevant).
But in terms of ChEBI, another thing to look into is inference on the "has role" relation which is rendered as "application" (https://www.ebi.ac.uk/chebi/chebiOntology.do?chebiId=CHEBI:33232) and "biological role" (https://www.ebi.ac.uk/chebi/chebiOntology.do?chebiId=CHEBI:24432) on the chebi website. Example: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:45716
vorinostat (CHEBI:45716) has role antineoplastic agent (CHEBI:35610) vorinostat (CHEBI:45716) has role apoptosis inducer (CHEBI:68495) vorinostat (CHEBI:45716) has role EC 3.5.1.98 (histone deacetylase) inhibitor (CHEBI:61115)
A more direct use case from the other direction is to allow searches for things like "antidepressant"
For the Gemma Browser, showing annotations for compounds that have these types of relationships would be useful.
arteymix
ChEBI is a fast evolving ontology and having to wait until a restart can impede curation efforts.