Using BioPAX & associated tools

Question

[EOX123]

Hi Everyone!

I am currently trying to recreate a gene network using BioPAX in R. I am very new to BioPAX and I would like to know if anyone here could please help me understand a few things:

-What is the best way to automatically import BioPAX data for specific pathways from databases (ie. Reactome, KEGG... etc)? I have paxtoolsr and RBiopaxParser.

-Would you recommend using Paxtools in Java or in R? Or is this irrelevant?

-I would like to use BioASF (to generate executable pathway models).... has anyone here used it by any chance and could help me wrap my head around it?

Thank you in advance for your help!

Answer 1

[cannin]

• Databases like KEGG and Reactome already exist in Pathway Commons, so you might not need to import anything: http://www.pathwaycommons.org/pc2/ If you need to do custom imports, take a look at this repository, it might help: https://bitbucket.org/armish/gsoc14/

• paxtoolsr uses the Java Paxtools underneath, but it only makes a some capabilities available. Custom imports would likely need Java, but extracting some types of data from existing BioPAX files might not (especially if they are already in Pathway Commons). Tutorial for paxtoolsr: https://www.bioconductor.org/packages/release/bioc/vignettes/paxtoolsr/inst/doc/using_paxtoolsr.html

• Unfortunately, I have no experience with BioASF.