Compound roles from ChEBI ontology

[rafael-alcantara]

ChEBI includes manually curated information about enzyme inhibitors and reactivators.

Though these entities are high level, and ChEBI does not store the concrete target of the concrete entities, these concrete entities (ex. cyclooxygenase inhibitor) have names ("cyclooxygenase inhibitor") and synonyms ("COX inhibitor") taken from the enzyme name.

Currently, activators and inhibitors are extracted from the "Enzyme regulation" sections of UniProt, using regular expressions. This is far from perfect and we end up missing many compounds. Using the ChEBI ontology we may retrieve some high-quality information which might be missing. The queries should be:

• "{enzyme name} inhibitor"
• "{enzyme name} inhibitors"
• "{enzyme synonym} inhibitor"
• "{enzyme synonym} inhibitors"

and then gather all of the leaf children of the matching entities.

[computingfacts]

query chEBI ("{enzyme name} inhibitor" and "{enzyme synonym} inhibitors") while building the mega mapper. populate the mega mapper with ChEBI small molecules that are classified as "enzyme inhibitor".

1. query ChEBI using ("{enzyme name} inhibitor/(s)" and "{enzyme synonym} inhibitor/(s)")
2. above query will return a ChEBI id. make a webservice call getAllOntologyChildrenInPath
3. the webservice call will return a list of ChEBI ids, make another webservice call (getCompleteEntityByList) to return the compound name.