Outcome of the Molecular Interaction ESF Workshop

  Development of standards-compliant tools for molecular interaction data management

 

The original workshop description is available here: http://www.psidev.info/index.php?q=esf-2008

 


 

Workshop Participants (by alphabetical order)

Name

Affiliation

working on

Use of the PSI-MI standards

Achuthan Premanand

European Bioinformatics Institute

IntAct [1]

Integration of PSI standards in the IntAct services.

Arnaud Ceol

University of Rome Tor Vergata

MINT database [2]

PSI-MI/XML and tab export/import (exchange), web-services

Bruno Aranda

European Bioinformatics Institute

IntAct [1]

Integration of PSI standards in the IntAct services.

Hagen Blankenburg

Max Planck Institute for Informatics

PSI Common Interaction Confidence Scoring System (PSISCORE)

 

Distributed Annotation System for Molecular Interactions (DASMI) [3]

PSISCORE uses PSI-MI XML and TAB files as the basis for a common confidence scoring system. Users/clients can send these files to distributed scoring servers, which perform calculations, store the resulting scores in the original files, and return them.

Henning Hermjakob

European Bioinformatics Institute

IntAct molecular interaction database
PSI-MI standard development [1]

IntAct data representation and dissemination
Data exchange with IMEx partner databases

Dr Ian Donaldson

Biotechnology Centre of Oslo, University of Oslo

iRefIndex [4]

We are using PSI-MI standards to consolidate and re-distribute interaction data

Dr Iskra Ventseslavova

IEMAM – BAS, Bulgaria

Differentiation of stem and progenitor cells from bone-marrow material and peripheral blood, in activated myeloid and lymphoid cells with anti-malignant properties

none

Dr Jan Wildenhain

Tyers Lab, The University of Edinburgh

Programmer on the BioGrid database [11]

 

Javier de Las Rivas

CancerResearchCenter(CIC-IBMCC, CSIC/USAL)

APID and APID2NET [5]
PSIMEx [6]

Using PSI-MI standards in APID

Jens Hansen

HelmholtzCenterMunich - GermanResearchCenter for Environmental Health

High-throughput interaction screen on disease-related proteins

planned to implement PSI-MI standards  in the project

Jitao David Zhang

DKFZ, Heidelberg

R PSI XML [7]

Statistical analysis of PPIN

Johannes Goll

J. Craig Venter Institute

MPIDB [8], Literature curation and analysis of interaction data

MPIDB download format

 

Jules Kessemakers

Radboud University Nijmegen

 IntAct interaction validation on basis of structural information (SIC - Structural Interaction Confirmation) [1]

none

Keiichiro Ono

University of California, San Diego(US)

Cytoscape [9]

PSI-MI 1.0 & 2.5 support in Cytoscape

Milan Simonovic

Institute of Molecular Biology, University of Zurich

STRING [10]

STRING has a web service API which exposes search results in PSI-MI XML format and STRING team is committed to implement PSICQUIC interface

Sabry Razick

Biotech Center of Oslo, Norway

IRefIndex [4]

 Use PSI-MI as a data source and as data export

Samuel Kerrien

European Bioinformatics Institute

IntAct [1]

Development of the PSI-MI standards and implementation in IntAct

 

[1] IntAct - http://www.ebi.ac.uk/intact

[2] MINT - http://mint.bio.uniroma2.it/mint/

[3] DASMI - http://dasmi.bioinf.mpi-inf.mpg.de/

[4] iRefIndex - http://irefindex.uio.no/wiki/iRefIndex

[5] APID and APID2NET - http://bioinfow.dep.usal.es/apid

[6] PSIMEx - http://imex.sourceforge.net/

[7] R PSI XML - http://www.bioconductor.org/packages/2.3/bioc/vignettes/RpsiXML/inst/doc/RpsiXML.pdf

[8] MPIDB - http://www.jcvi.org/mpidb

[9] Cytoscape - http://cytoscape.org/

[10] String - http://string-db.org

[11] BioGrid - http://www.thebiogrid.org/

 

Presentations

Sunday

Opening - Henning Hermjakob

The PSI MI XML 2.5 standard – Arnaud Ceol

PSI tools: Java API, validator – Samuel Kerrien

PSI tools: RpsiXML - Jitao David Zhang

The PSICQUIC common query interface – Bruno Aranda

Monday

Cytoscape as a web services client - Keiichiro Ono

The PSISCORE molecular interaction confidence scoring framework – Hagen Blankenburg

IRefIndex – Ian Donaldson

 

Outcome of the workshop

The goals that have been set for this workshop were essentially targeting 2 fronts:

1) PSICQUIC

A protocol definition was finalized and resulted in a final Web Service Definition (WSDL) and made available here: http://psidev.sourceforge.net/mi/psicquic/psicquic.wsdl

In order to be able to get a fully working Web Service, we have also had to re-engineer the PSI-MI XML 2.5 schema. It resulted in a version 2.5.4 of this schema that is not backward compatible with previous versions as the namespace was updated from net:sf:psidev:mi  to http://psi.hupo.org/mi/mif in order to be standard compliant and allow interoperability.
The resulting schema is available here: http://psidev.sourceforge.net/mi/rel25/src/MIF254.xsd

A sample Java project was put together to get people wishing to implement a PSIMITAB based PSICQUIC service started quickly.
Project home: http://psicquic.googlecode.com
More information in the WIKI pages: http://code.google.com/p/psicquic/w/list

A session was also held to discuss other features that are seen to be desirable in a version 2 of the PSICQUIC interface, namely, having a Molecular Interaction Query Language that would (like SQL is to databases) allow for flexible querying of interaction resources. The outcome of this session was summarized in this document: http://docs.google.com/Doc?id=dfzwcd95_69g997hqfk&invite=mdqfbt

At the term of this workshop, the participants have committed to delivers the following components:

Future PSICQUIC Data Providers

MINT

Aiming at a early January implementation of PSICQUIC

MPIDB

Aiming at a early January implementation of PSICQUIC. It will use the reference MITAB implementation code

IRefIndex

Trying to solve some technical issues. Will use existing MITAB open source tools

Proposes writing a MITAB validator

IntAct

Aiming at a early January implementation of PSICQUIC

String

Currently cannot commit due to licensing issues

GRID

Haven't committed to delivering a service yet

 

Future PSICQUIC Clients

Cytoscape

 

Creating a basic skeleton for a PSICQUIC client. Aiming at integrating it for release 2.6.2 (possibly early January)

 

R PSI-MI XML

RpsiXML package is able to digest WSDL on the server side, to output methods to distribute. There is still bugs/pitfalls to process WSDL file in R from a client side, I suppose it is resolved soon as the WSDL file gets updated .

For now we only support parsing XML files, so we hope to see PSICQUIC returns XML 2.5 soon.

Note: We aim to support MPIDB and IRefIndex as soon as the data is available in XML 2.5 version.

 

2) PSISCORE

 Once a WSDL has been drafted, it will been agreed upon, it will be made available here: http://psidev.sourceforge.net/mi/psiscore/

 A preliminary Web Service Definition was put together by Hagen Blankenburg: http://www.mpi-inf.mpg.de/~hagen/misc/PSISCORE.wsdl

 A summary of the outcome of this track is available in this document: http://docs.google.com/View?docid=dhbv9wv8_1gqbbd4gj

 At the term of this workshop, the participants have committed to delivers the following components:

DASMI

Aiming at an early January implementation of PSISCORE.

Hagen proposed to put together a list of controlled vocabulary terms reflecting:

a.      Classes of algorithm used to score molecular interactions.

b.      Known implementation of such algorithms

IntAct

Aiming at implementing a PSISCORE service based on protein docking algorithm as part of Jules Kessemakers’ traineeship which will end in March 2009.

 

Finally, a Shared spreadsheet has been put together in order to give the opportunity to any interested party to follow the progress of every participants. The document is available here:

http://spreadsheets.google.com/pub?key=pxVt172Ytud2lPIa7lfirIg

The PSI-MI mailing list (psidev-mi-dev@lists.sourceforge.net) should be the principal mean of communication between the participants after the workshop. Participant that weren’t registered prior to the meeting have also been invited onto this list.