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.