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ebi-chebi / ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
https://www.ebi.ac.uk/chebi
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Add additional predicates #3429

Open cthoyt opened 6 years ago

cthoyt commented 6 years ago

By their name, it's possible to infer that ChEBI entries like nicotinic acetylcholine receptor agonist have a relation to some sort of external protein or class of proteins. In this case, the relation to the InterPro entry, Nicotinic acetylcholine receptor), might be encoded as

CHEBI:47958 agonizes INTERPRO:IPR002394

As another example the ChEBI entry, EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor, has two separate relations to the ExPASy entries 1.1.1.34 and 1.1.1.88 that might be encoded as

CHEBI:35664 inhibits EC:1.1.1.34
CHEBI:35664 inhibits EC:1.1.1.88

I'm not sent on any particular predicates, but is it within scope to include this information in the ChEBI ontology?

As a motivation for these changes: my recent project https://github.com/bio2bel/chebi has been aimed towards converting portions of the ChEBI ontology to Biological Expression Language, where these sort of statements are incredibly useful for reasoning over biological systems. I can imagine building a set of rules that could generate these automatically, but that's not as nice as having them as structured information. Perhaps that system could assist in extending the ChEBI ontology if you agree that this is relevant.

cthoyt commented 4 years ago

Hi @jannahastings, I think this got lost in the pile of issues.

I've come back to this recently and begun curating and storing some of these in a repository at https://github.com/chemical-roles/chemical-roles. Let me know if you have any thoughts