Reactome integration
For looking at the small molecules currently released in Reactome, you can look at this page:
http://www.reactome.org/content/schema/objects/ReferenceMolecule
The vast majority of our small molecules use ChEBI as a reference although we do occasionally reference COMPOUND, PubChem.
At the moment, all our information regarding which of our proteins/genes are targetable and the subset of our small molecules that target something comes from cross-references to ZINC. You can see the ZINC cross-references to small molecules here:
http://www.reactome.org/cgi-bin/instancebrowser?DB=gk_current&ID=9642001&
and the ZINC cross-references to protein targets here:
http://www.reactome.org/cgi-bin/instancebrowser?DB=gk_current&ID=9643251&
Antonio and the guys at EBI have also been working on making a graph database version of Reactome available for direct querying:
http://www.reactome.org/pages/documentation/developer-guide/graph-database/
Unfortunately, we don’t have direct target associations between small molecules and genes in Reactome, but in some cases it may be possible to pull information from looking at reactions that involve them.