Development of standards-compliant tools for molecular interaction data management

 

 


 

The outcome of this meeting was published here.




Abstract

Molecular interaction data is a key resource in modern biomedical research, but interactions are often presented in different data formats and managed in different protocols. The HUPO Proteomics Standards Initiative has developed the PSI MI XML format, a community standard for molecular interactions that is now widely implemented. The aim of this workshop is to provide intensive hands-on training in the development of standards-compliant software for molecular interaction data management.

Organisational

The workshop will take place at the European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, Cambridgeshire, UK. Thanks to generous funding by the European Science Foundation, participation in the meeting if free, including accomodation. However, you will have to pay for your travel expenses. 

Signup for participation is now closed.

For travel information please see http://www.ebi.ac.uk/Information/Travel/travel.html 

Scientific Summary

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 harmonized 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, the list includes bioinformaticians from key molecular interaction databases and tool developers.

The meeting will be located in the IT training room of the European Bioinformatics Institute, the focus will be on actual collaborative software development, using concepts from the extreme programming paradigm.

 

Provisional Meeting Program

Sunday, November 16, 2008

13:00 Introduction – Henning Hermjakob, EBI, UK

13:20 The PSI MI XML 2.5 standard – Arnaud Ceol, U Tor Vergata, Rome, Italy

13:40 PSI tools: Java API, validator – Samuel Kerrien, EBI, UK

14:00 PSI tools: RpsiXML - Jitao David Zhang, DKFZ, Germany

14:20 The PSIQUIC common query interface – Bruno Aranda, EBI, UK

14:45 Coffee

15:00 Definition of development targets and developer teams

          Hands-on software specification/development in small groups

17:00 Short status summary

18:00 Hinxton Hall Bar open (self-funding)

19:00 Meeting dinner Hinxton Hall.

 

Monday, November 17, 2008

09:15 Cytoscape as a web services client - Keiichiro Ono, UCSD, US

10:00 The PSISCORE molecular interaction confidence scoring framework – Hagen Blankenburg, MPI, Germany

10:20 Definition of development targets and developer teams

          Hands-on software specification/development in small groups

12:30 Lunch

13:30 Hands-on software development in small groups

15:00 Coffee

17:00 Short status summary

19:00 Meeting dinner, Red Lion, Hinxton

Tuesday, November 18, 2008

09:15: Definition of development targets and developer teams

           Hands-on software development training in small groups

12:30 Lunch

13:30 Hands-on software development in small groups

15:00 Coffee

17:00 Short status summary

 

Wednesday, November 19, 2008

09:15: Definition of development targets and developer teams

           Hands-on software development training in small groups

12:30 Lunch

13:30 Summary session: Results and further planning of development and dissemination (publications, updates of http://www.psidev.info)

15:00 Meeting end

 

Aims

The optimum results at the end of the workshop would be:

  • The PSICQUIC protocol is formally defined and approved.
  • The participating databases have PSICQUIC implemented
  • Cytoscape can connect to all the databases simultaneously, query for a given list of proteins, and visualize the joint data contents of these databases
  • The PSISCORE protocol is formally defined and approved.
  • The participating resources have PSISCORE implemented.

Background material

Familiarity with the PSI MI 2.5 standard would be highly advantageous: 

Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A,
Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D,
Cesareni G, Apweiler R, Hermjakob H.: Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
BMC Biol. 2007 Oct 9;5:44. PMID: 17925023

Sponsorship

The workshop is generously funded by the European Science Foundation.