Make use of CHEBi "applications" and "biological role" relations - CHIRO?

[ppavlidis]

Assuming these are in the OWL file, they might be more useful for grouping chemicals than just the part-of/is-a relations.

There are use cases for this:

1. For downstream applications where we want to aggregate studies based on chemicals, doing it by role or application would be sensible.
2. For searches, it would enable searches for these roles or applications to get all relevant compounds -> associated experiments.

Example: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:5931 (Insulin) has biological role "hormone" and application "hypoglycemic agent", both of which are ontology terms

Role = CHEBI:24432 Application=CHEBI:33232

Before we do that we should see how many such annotations there are - if it's very incomplete it might not be that useful in practice.

Here's a term that has multiple roles and applications https://www.ebi.ac.uk/chebi/chebiOntology.do?treeView=true&chebiId=CHEBI:16796

It's possible that other ontologies have relations like this that would be needed, so a general mechanism for customizing the propagation factors might be good.

[ppavlidis]

I'm not sure but CHIRO might be what we want https://github.com/obophenotype/chiro

However:

• Hasn't been updated in at least 3 years; last release was 8 years ago
• Uses DO not MONDO
• A competing effort is apparently https://github.com/chemical-roles/chemical-roles and there was some discussion to merge the efforts? But they seem stuck.

[ppavlidis]

It looks like we could use CHEBI to do some additional inference we aren't via the has_role relations like:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_10362">
...
<rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_22586"/>
            </owl:Restriction>
        </rdfs:subClassOf>

CHEBI_10362=β-Cryptoxanthin RO_0000087=has role CHEBI_22586=antioxidant