Finding shortest path between any two genes/proteins

[Abel Jansma]

I am trying to find the shortest path between any two genes/proteins by querying the API, but am confused about the PATHSFROMTO field. What exactly does this return? For example: FOXP1 and FOXP2 have a binding reaction (https://apps.pathwaycommons.org/interactions?source=FOXP1%2CFOXP2), but the following query return an empty string:

https://www.pathwaycommons.org/pc2/graph?source=FOXP1&target=FOXP2&kind=PATHSFROMTO&format=SIF

Should I be using another field to find the shortest path between two genes/proteins? The GRAPH field is described in the docs as being able to find "the shortest path between two proteins" (https://www.pathwaycommons.org/pc2/#graph) 

Thanks!

[Özgün Babur]

Hi Abel, 

The paths-from-to query is the directed version of paths-between query. It takes a source set and a target set, and it traverses directed edges. The "interacts-with" edge is undirected, hence it is not traversed by this query. 

Ozgun

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[Abel Jansma]

Thanks for your response, Ozgun, that makes sense. Still, the query https://www.pathwaycommons.org/pc2/graph?source=FOXP1&target=FOXP2&kind=PATHSBETWEEN&format=SIF also returns an empty string. What would be the correct query to find the shortest path between these two proteins?

Abel

[Özgün Babur]

Oh, this is because you used the wrong API. The API at https://www.pathwaycommons.org/pc2/graph works on BioPAX graphs, then the results are converted to SIF format. The querying framework here is specifically designed to traverse over directed relationships in BioPAX. It does not traverse the MolecularInteraction objects which encode the most protein-protein interactions.

It may make more sense for you to use the API at https://www.pathwaycommons.org/sifgraph/v1 because that skips BioPAX and directly searches the SIF graphs. The below query brings the interaction that you are looking for.

https://www.pathwaycommons.org/sifgraph/v1/pathsbetween?directed=false&limit=1&source=FOXP1&source=FOXP2&pattern=INTERACTS_WITH

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[Abel Jansma]

Ahhh ok right, thanks! I'll have a look at that one. Thanks for your help!

Abel