Meaning of left and right values in json and value errors

[Cori Bushman]

I am trying to query wiki pathways for protein interactions given a protein name and in the json tree, the meaning of the values in the left and right fields are unclear. Some of these values are null strings or have a new line in them (such as “Oxidative \nstress”). I have noticed that the majority of the time these values are genes but sometimes they are categories or drugs like “Apoptosis”, “Group object”, or “Tamoxifen”. I wanted to bring these errors to your attention and I am curious to know the meaning of the values in these left and right fields so I can parse the json response body to only get desired gene interactions. Thank you.

[Alex Pico]

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:

https://www.wikipathways.org/index.php/Help:WikiPathways_Sparql_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.

http://sparql.wikipathways.org/?default-graph-uri=&query=SELECT+DISTINCT+%3Fpathway+%3Finteraction+%3Fparticipants+%3FDataNodeLabel%0D%0AWHERE+%7B%0D%0A%0D%0A+++%3Fpathway+a+wp%3APathway+.%0D%0A+++%3Fpathway+dc%3Aidentifier+%3Chttp%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP554%3E+.%0D%0A+++%3Finteraction+dcterms%3AisPartOf+%3Fpathway+.+%0D%0A+++%3Finteraction+a+wp%3AInteraction+.%0D%0A+++%3Finteraction+wp%3Aparticipants+%3Fparticipants+.%0D%0A+++%3Fparticipants+a+wp%3ADataNode+.%0D%0A+++%3Fparticipants+rdfs%3Alabel+%3FDataNodeLabel+.++%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on

 - Alex