I'm working on bacterial sulfur metabolism and I would like to be able to extract as much information as I can from the different pathways linked to this metabolism (at least all the biochemical reactions and the enzymes that catalyze these reactions and if possible, the genes coding for these enzymes). Here is what I've done so far:
I've obtained a free license to download the MetaCyc database in Biopax level 2 and 3 format so I try to extract the information from these files.
I've used the R package rBiopaxParser to read and import the Biopax in R but now I'm quite stuck because I don't really know how I can proceed to extract a pathway ( by pathway I mean the pathway level but also all the lower levels of information like nested pathways, reactions, molecules and proteins interactions,...).
My aim would be to get these pathways as individual Biopax files and the covert them in sif format thanks to the R package paxtoolsr and then visualise my pathways as a network and manipulate it with graphiz or RCytoscape packages.
I don't know if it's the best strategy to be able to visualise and manipulate the whole metabolic pathways but since I don't have any knowledge in XML like langages I try to use R to get rid of this format^^. What could I do to be able to extract the needed information to get my metabolic pathways networks (all the biochemical reactions and the enzymes that catalyze these reactions)?