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To Researchers Surprise, Protein Interaction Data Standards Emerge from EBI Meeting


Potentially paving the way for a universal standard in how researchers submit and compare data from protein-protein interaction experiments, a group of researchers and database curators who gathered for a weekend conference at the European Bioinformatics Institute (EBI) have agreed upon a basic XML framework for exchanging protein interaction data.

Describing the event as a “big step forward,” EBI researcher and meeting organizer Henning Hermjakob said the 50-odd participants in the “Proteomics Standards Initiative Meeting,” held October 19-20 on the EBI’s campus in Hinxton, UK, agreed on a multi-level data exchange standard, with the first level covering “all the common denominators.” A multi-level format, Henning said, would help create a system where researchers have several options for how to submit their protein interaction information to a database. In addition, Henning and others hope they can convince a journal to adopt the standard, which would apply to any papers accepted for publication.

Specifically, the participants reached agreement on the general form of a “requirements document” mandating that the interchange format should include multiple levels of detail depending on the user’s requirements, represent pair-wise interactions and complexes but not small-molecule pathways, and that it should be able to describe posttranslational modifications, said Chris Hogue, a bioinformaticist at the University of Toronto and developer of the BIND database. In addition, the document states that the format should accommodate multiple experiments from a single paper in a record, and that the database curators should work together to create a standard vocabulary for representing their data, Hogue said.

The interchange format also allows for users to attach some form of quality measurement with their interaction data, primarily through describing the type of experiment used to generate the results, said Ioannis Xenarios, a former DIP curator at the University of California, Los Angeles, who now works as a bioinformatics researcher at Serono in Switzerland.

Although the meeting participants, acting at the behest of HUPO to create a standard, deferred deciding on its final form until after the HUPO Congress in Versailles next month, the first version will allow users and curators to compare protein complex and interaction data collected from yeast two-hybrid and mass spec “pull-down” experiments, as well as more detailed analysis based on, for example, site-directed mutagenesis experiments, said Hogue.

The first version of the data exchange standard does not include fields for additional interaction information, such as protein-DNA or protein-RNA interactions, but the representatives from the various protein interaction databases who attended the meeting agreed that the second and third iterations or levels of the data exchange standard would include mechanisms for sharing these types of data as well.

“The consensus we agreed on is remarkable,” said Hogue. Some attendees said they were initially worried there would be some bickering over which database the standard should most closely resemble, but in the end the meeting “was one of the more successful meetings of its kind,” he added.

In addition to protein-protein interaction data standards, meeting attendees also discussed the potential for establishing standards for exchanging and creating a common repository for mass spectrometry data. The goal of the discussions, according to Hermjakob, was to establish the purposes of such a repository, and to determine what information would be necessary to include in a repository of mass spec data to make it useful. “A simple collection of of peak lists without context would be useless,” he said.

Working groups will meet during the HUPO Congress next month to discuss taking further action with respect to mass spectrometry data standards, Hermjakob said. “It’s at a much earlier stage [compared to protein interaction data standards],” he said. “In [Versailles] we’re going to involve a lot more people and a lot more of the proteomics community.”


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