Hi Cori,
There are many ways to query WikiPathways, each tailored to different workflows and questions. In WikiPathways folks draw models they find useful in their research, that sometimes include interactions/relationships between proteins and other things.
The web service query for ‘findInteractions’ simply returns every interaction draw by researchers, including connections to groups, object and free text.
If you want to focus on only protein-protein interactions, then you’ll probably want to perform a query against our RDF modeled content, which has already taken in account the participant type. Wow provide a SPARQL endpoint for such queries. Here are a bunch of example queries:
This query, for example, gives the interactions and participants for a particular pathway and you can see whether a participant is a small molecule or protein.
- Alex