Pathways by compound missing & illegible results

[leeharland]

[USC Feedback]
see mabel document for info

[askjaer]

There is a problem with the RDF schema of the WikiPathways data that is used for this query. Andra is looking at remodelling the RDF to make it better so until we have that RDF in the LDC we should not do more on the GUI side. I am reassigning this to Andra

[leeharland]

At TTF was agreed that the workflow would be :

• devise examples
• work with andra to make sure wikipathways + chembl/pdsp supports these
• work with antonis to get the queries done
• sune can then look at visualising, either in wikipathways widget or just a basic table for now

[leeharland]

Some notes on the actual query:

Which pathways are influced by compound X
So, we need example of compound X which hits multiple proteins (e.g. a dirty kinase inhibitor) where those proteins are members of pathways in wiki pathways

&

For a pathway, what are all the small molecules that hit proteins in these pathways
Here, we need to find a wikipathway pathway and then for each protein, find compounds that hit it; giving us an idea of which nodes are druggable etc

Of course, there was the option of creating a new pathway in WP if there wasnt a suitable one

and if there are alternative questions that everyone thinks might be better etc, i am more than flexible, as manuel said, what we want is some queries which show interesting and useful stuff for integrated data