Extract directionality from Reactome

Question

[Nikolas]

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

Answer 1

[NancyTLi]

Nikolas,

Have you tried using the Reactome graph database? I would suggest you reach out to the Reactome HelpDesk to get further assistance from the team directly.

[Nikolas]

Thanks for the input and sorry for taking so long to answering. I had a look at the Reactome graph database but I should actually reach their Help Desk.