Hi everyone.

I am trying to extract some simple directionality for the Reactome pathways, i.e. simple information of the type: Protein A activates Protein B

I used paxtools and the human level3 biopax file to create a SIF file:

java -jar paxtools-6.0.0.jar toSIF --extended input output

and i get what I want e.g.

CHEBI:1294 reacts-with CHEBI:15378 .....

but the whole results contains only small molecules from ChEMBL.

Is there some other file that contains the information I want?

Any input is welcome