Your Input

The GREEKC Action aims to foster close interaction of Knowledge Commons resource providers with computational biologists and software tool builders. This requires efforts both in gap analysis concerning data storage formats, exchange languages and web service protocols, and in producing an overview of specific wishes and uses of these resources in subsequent analysis, often in concert with other data and knowledge sources. We are keen to gain further insight in these interoperability needs, and we therefore request feedback from you in the form of specific use cases.

We will invite the person who sends in the most useful use case(s) to an upcoming GREEKC Workshop!

An example of a use case is the following:

Use Case entered by: Martin Kuiper

Definition of the aim and problem: I would like to add Transcription Factor interactions with known Target Genes to my network in Cytoscape, to build a gene regulatory network.

Details: I am using Cytoscape v. 3.2.0, and I want to apply the ‘import network from web service’ function for fetching interaction data in which at least one of the interacting partners is a Transcription Factor. I am interested in the data from the TRRUST resource, and the SIGNOR database.

Proposed solution: Make the information from TRRUST available through a web service, does this need to be PSICQUIC? Does PSICQUIC need to be refactored to be able to deliver causal information? Can data from TRRUST or SIGNOR be incorporated in a resource that is already accessible through a web service?