Question: How does Reactome format pathways in BioPAX?
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gravatar for tim.gallengor
3.9 years ago by
United States
tim.gallengor10 wrote:

I am new to bioInformatics, and am trying to build some molecular pathways. I would like to make pathways that can merge with those in Reactome. I have been importing Reactome BioPAX networks into Cytoscape and I am confused as to how they format nodes and edges. For example, a single edge may be just a simple activation between two nodes or an entire chemical reaction that involves more than 2 nodes.

I have been reading about BioPAX, and also slowly going through its documentation (http://www.biopax.org/release/biopax-level3-documentation.pdf). I am still not sure how to create my own pathways that could work with Reactome BioPAX networks, as I don't really understand how they format the nodes and edges. Does Reactome BioPAX not use a simple node/edge network?

I know that I can export any network from Cytoscape in BioPAX format, but there seems to be many different ways to represent the same pathway in BioPAX. How does Reactome go about representing their pathways in BioPAX?

Any advice or pointers in the right direction would be greatly appreciated. Thanks in advance.

biopax reactome pathway • 1.4k views
ADD COMMENTlink modified 3.8 years ago by Biostar ♦♦ 20 • written 3.9 years ago by tim.gallengor10
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