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Locating solid, experimental data about protein interactions

Date:
March 28, 2012
Source:
European Molecular Biology Laboratory - European Bioinformatics Institute
Summary:
A new service makes it simple to find solid, experimental data about protein interactions. A new non-redundant experimental dataset will make it much easier for researchers to understand the complex set of protein interactions in cells.

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.
Credit: Image courtesy of European Molecular Biology Laboratory - European Bioinformatics Institute

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.

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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.

"There are over 100 interaction databases available, but none of them holds enough information to describe the interactome of any organism," explains Sandra Orchard of the EMBL-European Bioinformatics Institute (EMBL-EBI) in the UK. "In addition to the problem of repeated data entries in these databases, only around 1% of the 151 million binary pairs available are reliable data from published experimental work." The remaining data are theoretical, or the product of text mining; as such, they are far less dependable.

"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."


Story Source:

The above story is based on materials provided by European Molecular Biology Laboratory - European Bioinformatics Institute. Note: Materials may be edited for content and length.


Journal Reference:

  1. Sandra Orchard, Samuel Kerrien, Sara Abbani, Bruno Aranda, Jignesh Bhate, Shelby Bidwell, Alan Bridge, Leonardo Briganti, Fiona Brinkman, Gianni Cesareni, Andrew Chatr-aryamontri, Emilie Chautard, Carol Chen, Marine Dumousseau, Johannes Goll, Robert Hancock, Linda I Hannick, Igor Jurisica, Jyoti Khadake, David J Lynn, Usha Mahadevan, Livia Perfetto, Arathi Raghunath, Sylvie Ricard-Blum, Bernd Roechert, Lukasz Salwinski, Volker Stόmpflen, Mike Tyers, Peter Uetz, Ioannis Xenarios, Henning Hermjakob. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nature Methods, 2012; 9 (4): 345 DOI: 10.1038/nmeth.1931

Cite This Page:

European Molecular Biology Laboratory - European Bioinformatics Institute. "Locating solid, experimental data about protein interactions." ScienceDaily. ScienceDaily, 28 March 2012. <www.sciencedaily.com/releases/2012/03/120328104326.htm>.
European Molecular Biology Laboratory - European Bioinformatics Institute. (2012, March 28). Locating solid, experimental data about protein interactions. ScienceDaily. Retrieved November 23, 2014 from www.sciencedaily.com/releases/2012/03/120328104326.htm
European Molecular Biology Laboratory - European Bioinformatics Institute. "Locating solid, experimental data about protein interactions." ScienceDaily. www.sciencedaily.com/releases/2012/03/120328104326.htm (accessed November 23, 2014).

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