Version 1 (modified by baranda, 10 years ago)

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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)
  • ... (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)

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
  • 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 - we have agreed that the acronym is horrible :)
  •  http://lucene.apache.org Lucene based searches over PSI-MI tab files - 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.

Implementation of an Interaction DAS Server

Nothing specific has been said about this, but it was in the original agenda.

Important reminder

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

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