Version 7 (modified by baranda, 7 years ago)

--

Overview

Exchange format

It already exists an standard exchange format: PSI-MI. Two possibilities:

  •  PSI-MI XML
  • PSI-MI TAB (tabulated)
    •  Standard
    • Expanded (IntAct) - Additional columns to the standard, containing information like bait-prey, types, cross-references...

Service Providers

Service providers at the Hackathon

  •  IntAct (Bruno Aranda, EBI)
  •  DIP (Lukasz Salwinski, UCLA)
  •  STRING (Michael Kuhn)
  • ... (please add yourself)

Service consumers

Existing Web Services

IntAct Web service

Existing Clients

  • Please visit  this page for Cytoscape clients and its visualizations.

Objectives

Improve the existing IntAct web service

Note: the IntAct web service is in fact a web service that searches on a PSI-MI TAB file that contains all the interactions present at IntAct. All the (java) code generated at IntAct is open-source and licensed under the Apache Commons License 2.0. It means that this web service implementation could be used over any PSI-MI TAB file (not just the IntAct ones).

  • Taverna client
  • BioMoby
  • Check use-cases:
    • Get interaction or partners not only using Uniprot IDs (the primary identifiers for interactors used in IntAct)

Define a common Interaction Query Language

It would be useful to have a common query language for interactions. Options:

  • PSICQUIC - attempt to create a REST-based query language.
  •  http://lucene.apache.org Lucene based searches over PSI-MI tab files - this is what is currently used in IntAct.
    • This option seems to be the simplest according to the participants in the group, and could be a starting point.

Define specific use-cases

Cytoscape, as active consumer, has a bunch of use cases that can be a starting point to discuss how interaction data could be mined/queried.

Interaction DAS Server

Possibility:  http://www.dasregistry.org/extension_interaction.jsp

Problems: it does not comply neither with the PSI-MI specification nor with the DAS one.

Other Resources

 The minimum information required for reporting a molecular interaction experiment (MIMIx)

Important reminder

This is a wiki. Please, participate with your thoughts/additions/comments! :)

Progress

Day 2

  • Trying to define a web service with common interface for all the Interaction Service Providers.
    • The methods should be in the default exchange format (PSI-MI XML).
    • Problem: This means dealing with potentially huge files (about 30 Mb for 2000 interactions, and databases such as IntAct? contain 100000+ and increasing exponentially).
      • Solution: unknown (using URIs?)

Attachments