I'm new to drug discovery, and I have a question from a colleague about using Broad's Connectivity Map (CMAP) for drug repurposing. They're wondering if it's possible to characterize drugs/molecules in CMAP with the functional category they up- or down-regulate, using annotations from Gene Ontology, Reactome, whatever.

I can imagine how I might go about this (make decisions about how to combine cell lines/dosages/etc., then run a gene-set enrichment for every drug in CMAP), but I'm new and CMAP is big, so I'm wary about coding something from scratch. Does an off the shelf tool exist for this?? For clarity, I'd like to label all drugs in CMAP with all GO terms that are significantly up-/down-regulated for that drug.

I see an old paper that does something similar but their online tool is dead, and an R package that does something similar but not identical (cogena).