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

•  Cytoscape (Keichiro Ono)
•  CellDesigner (Akira Funahashi, Keio Univ. & SBI)
• ... (please add yourself)

Existing Web Services

IntAct Web service

• IntAct already provides a very simple SOAP based web service ( http://www.ebi.ac.uk/~intact/devsite/remote/binarysearch_ws.html)
• NCBI Entrez Gene has meta-database of interactions (MINT, BioGrid, and BIND), but access to these dataset is hard due to API design.

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?)

Day 3

Client Side Topics

• Client (Cytoscape) code modifed to accept PSI-MI EntrySet object. This is based on existing PSI-MI reader in Cytoscape.
• PSI-MI Reader should be modifed to read more details in the object. (Currently, some of the details are skipped.)
• Need to add a switch to import minimal dataset (graph information only. No attributes) or full detail.