EBIInformationNewsPress Releases
Major networking opportunity: IMEx Consortium brings interactomes to lightDownload a PDF of this release 27 March 2012
Like people bustling around busy cities, the thousands of molecules inside our cells are constantly interacting with each other: turning each other on or off, working together, splitting up and networking. Understanding the countless ways in which they do so is a major challenge in biology, but it is fundamental to understanding life. Scientists at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) and colleagues in the International Molecular Exchange (IMEx) consortium are rising to the challenge by offering researchers a freely available set of experimental interaction data that can be queried from a single interface. Reporting in Nature Methods, IMEx partners describe the advantages of their service and invite others to join the effort. To make it easier to create a picture of an organism’s ‘interactome’ – the interactions between all of its molecules – IMEx partners have been working since 2004 to create a one-stop-shop for interaction data. A single standard for curating protein interaction data now makes it much simpler for scientists to identify which protein interactions are supported by the strongest evidence.
“We’ve now made it easier to find information about proteins that interact with a given molecule, and to compare new experimental results with publicly available, curated experimental data,” says Gianni Cesareni of the University of Rome ‘Tor Vergata’ in Italy.
“IMEx web services now display curated, experimental data from several reputable resources so that a clearer picture of interactions between proteins can begin to emerge,” says Henning Hermjakob, head of Proteomics Services at EMBL-EBI. “We are in effect optimising the return on public investment in interaction databases by co-ordinating global annotation efforts. We are certainly looking forward to having more curated data resources join the consortium.”
IMEx partners currently include DIP (the Database of Interacting Proteins at UCLA in the US), I2D (at the Ontario Cancer Institute in Canada), InnateDB (Simon Fraser University and the University of British Columbia in Canada and the Teagasc Bioscience Department in Ireland), IntAct (at EMBL-EBI); MatrixDB (at CNRS / Lyon1 University in France), MINT; Molecular Connections (in Bangalore, India); MPIDB (at the J. Craig Venter Institute in the US); observer BioGRID (the Biological General Repository for Interaction Datasets) and the most recent member, the Swiss-Prot group from the SIB Swiss Institute of Bioinformatics, representing the UniProt consortium. IMEx is an outcome of PSIMEx, which is funded under the Health Theme of the European Commissions Seventh Framework Programme.
Publication Details
Caption: When you search IMEx for interaction data, the web service shows results from all of the partner databases. Specific, high-quality records in each database are identified as being part of the IMEx dataset. This ensures that you won’t see the same record twice in your results list. This diagram shows how the PSICQUIC service behind IMEx works. ContactAn e-mail to contactpress@ebi.ac.uk will reach everyone in the EMBL press office.
Mary Todd-Bergman, Outreach Programme Project Leader, Hinxton, UK, Tel: +44 1223 494665, www.ebi.ac.uk/information/news
Katrina Pavelin, EMBL-EBI Scientific Outreach Officer - Hinxton, UK, Tel: +44 1223 494452, www.ebi.ac.uk/information/news
Sonia Furtado Neves, EMBL Press Officer, Heidelberg, Germany, Tel: +49 6221 387 8263, www.embl.org About IMExThe IMEx consortium is an international collaboration between major public interaction data providers who have agreed to share curation efforts. Each IMEx partner produces a separate resource. These include all-encompassing molecular interaction databases (e.g. IntAct, MINT, DIP), organism-centric resources (e.g. BioGrid, I2D and MPIDB) and biological-domain-centric resources (e.g. MatrixDB). The partners are committed to sharing records of interactions that are curated to the IMEx standard, making them publicly available as a single, searchable, non-redundant set of curated publications. Whenever a participating database issues a new release, the dataset is updated. Data are made available in standards-compliant, tab-delineated and XML formats. This allows users to visualise the data in tools such as Cytoscape, NAViGaTOR and R Bioconductor. Data redundancy is managed by co-ordinating curation among all IMEx partners. Direct data depositions by authors as part of the publication process are very welcome. www.imexconsortium.org/about-imex
|