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As Protein Data Standards Initiative Rolls Ahead, HUPO Calls for Community Support

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Leaders of the Human Proteome Organization Proteomics Standards Initiative (PSI) are working to engage the wider proteomics world in their effort to create standards for mass spec data, protein interaction data, and general proteomics experimental information.

“This is not a process that we can dare to go any further with on our own — we need the participation of the community,” said Sandra Orchard, a scientist at the European Bioinformatics Institute and one of PSI’s coordinators, following a lecture during a session on the initiative at the HUPO Congress Oct. 9.

BioInform’s sister publication ProteoMonitor reported last week that PSI chair Rolf Apweiler, also of the EBI, kicked off the HUPO session by announcing that a paper describing the first version of the XML-based PSI Molecular Interaction format (PSI-MI XML), had been submitted to a major journal and that the group was currently working through the reviewers’ comments. Henning Hermjakob, sequence database group coordinator at the EBI and leader of the protein interactions workgroup within the initiative, said he hoped the paper would be published in early 2004.

Publication in a journal may be all the more important given the emphasis that the PSI organizers are placing on the participation of journals in enforcing a future standard. Several journals now require scientists submitting microarray-based papers to comply with the MIAME (minimum information about a microarray experiment) guidelines, but the lack of such a requirement for proteomics makes data impossible to collect, Hermjakob said. “The current motto for proteomics data still seems to be ‘publish and vanish,’” he told ProteoMonitor. Hermjakob acknowledged that the effort to create such a requirement was garnering some resistance, but said that “overall the scientific community is well aware of the long-term benefits of such requirements.”

This awareness of long-term benefits in the midst of short-term sacrifices is what Weimin Zhu, leader of the mass spec PSI workgroup, is counting on as he continues to try to entice vendors into participating in the effort. Zhu is currently working with Bruker Daltonics, Waters, and Ciphergen to create a draft XML-based schema and a standard peaklist output format. He is also working with Waters and Matrix Science to implement standards and format them in their search engines, and he said Protagen, Thermo Finnigan, and Shimadzu have contributed to the project as well.

Chris Taylor, another PSI leader based at EBI, said that organizers hope to eventually establish an official PSI-sponsored ontology, but added that this will only work if scientists are willing to take the time to enter their data in the ontological format. Taylor has already taken several steps toward the development of a related standardization effort: MIAPE (minimum information about a proteomics experiment), modeled along the lines of MIAME.

Taylor said that PSI wants to collaborate with the microarray standards efforts to “afford us a common handle for the various ‘omics’ experiments.” Currently, Taylor said, the project is still in the proof-of-concept stage, but “we intend over the next year to get a standard to recommend to the community.” In between now and then, Taylor is seeking as much input from proteomics and microarray experts as he can get in order to optimize the model.

The next PSI meeting is scheduled for January 2004.

— KAM

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