A question about rBiopaxParser

Question

[sedaghat.nafiseh]

Hi all,

Who knows what is the difference between the outputs of 'listPathwayComponents' and 'pathway2Geneset' in rBiopaxParser?

It seems that the 'listPathwayComponents' returns all interactions which are available in the corresponding pathway and 'pathwayGeneset' returns physical entities and 'BiochemicalReactions' in the corresponding pathway, as well.

When I use both of them for a given pathway id, BiochemicalReactions in the output of both instructions are different and just some of them are common.

Can anyone tell me why 'BiochemicalReactions' for a given pathway are different in these two instructions?

Thanks

Nafiseh

Answer 1

[emekdemir]

Hi Nafiseh,

If you can post the owl files I might guess what the problem might be. I am suspecting nested pathways. But I don't develop/use rBioPAXParser so they would be at best guesses.

I also want to point out that there is another R library for acessing Pathways in BioPAX form - it is called PaxtoolsR, is in active development and it is based on the widely used Paxtools java library. You can find it here.

Best,
ED

[sedaghat.nafiseh]

Yes, you're right. It is because of nested pathways.

Thanks for introducing the 'paxtoolsr'. It is helpful.