Organiser

Henning Hermjakob, EBI, Hinxton, Cambridge, UK

Introduction

Molecular interaction data is a key resource in modern biomedical research, and molecular interaction datasets are currently generated on a large scale, demonstrating from one to tens of thousands of interactions per experiment. These interaction data sets are represented in many different forms, from simple pairs of protein names to detailed textual descriptions, and are collected in various databases, each with their own database schema. In 2004, the HUPO Proteomics Standards Initiative developed and published the PSI-MI XML format for molecular interactions as a community format for the exchange of protein interaction data. This format had been jointly developed by major producers of protein interaction data and by data providers, among them BIND, DIP, IntAct, MINT, MIPS and Hybrigenics. The PSI-MI XML format is now widely implemented and supported by both software tool development and data providers.

However, practical implementation of the standard often differs from resource to resource, sometimes resulting in actually invalid XML, sometimes only resulting in minor discrepancies in the use of attributes. In addition, a number of additional conventions and protocols leveraging the PSI MI format are currently under development, in particular the PSI Common Scoring Framework (PSISCORE) and the PSI Common Query Interface (PSIQUIC). The aim of the workshop is to facilitate and co-ordinate the precise and efficient use and implementation of the PSI MI standard for molecular interactions, as well as related standards and protocols. The expected result is a harmonised provision of molecular interaction data through participating databases, both in the form of data files and computational services. These interfaces, in turn, will be used by analysis tools like interaction confidence scoring systems or Cytoscape*. The invited participants reflect this aim and include bioinformaticians from key molecular interaction databases and tool developers.

Preliminary Programme

Day 1
The PSI MI XML 2.5 standard – Samuel Kerrien, EBI , UK
The PSI validator – Arnaud Ceol, U Tor Vergata, Rome , Italy
The PSIQUIC interface – Bruno Aranda, EBI , UK
Hands-on software development training in small groups
Evening: Short status summary

Day 2
Cytoscape – Benno Schwikowski, Institut Pasteur , France
The PSIQUIC common query interface – Bruno Aranda, EBI , UK
The PSISCORE molecular interaction confidence scoring framework – Mario Albrecht, MPI, Germany
Definition of development targets and developer teams
Hands-on software development training in small groups
Evening: Short status summary

Day 3
Definition of development targets and developer teams
Hands-on software development training in small groups
Summay session: Results and further planning of development and dissemination

Invited Speakers

Ian Donaldson, U Oslo, Norway
Gary Bader, U Toronto, Canada
Volker Stuempflen, MIPS, Germany
Sylvie Ricard-Blum, U Lyon, France
Johannes Goll, Craig Venter Institute, US
Ioannis Xenarios, SIB, Switzerland
Lukasz Salvinski, UCLA , US
Jitao David Zhang, DKFZ, Germany
Andrew Winter, U Edinburgh , UK

Venue

The meeting will be located in the IT training room of the European Bioinformatics Institute.

Registration

Registration is open on the course website.