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Pandey's Human Proteinpedia is for Entire Community

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While large-scale genomics research continues to hog much of the spotlight these days, the field of proteomics might finally be catching up to its more photogenic sibling. With the launch of a Wikipedia-like portal for the massive quantities of proteomic data generated around the world, Johns Hopkins University professor Akhilesh Pandey hopes to build a community of not just proteomic data, but one of proteomic researchers who are willing to freely share their data for the benefit of moving both their and others’ research forward.

"We need to get the entire proteomics community involved," Pandey says. “We want this initiative to be so widespread that investigators will be conspicuous by their absence of participation."

Pandey began work on the Human Proteinpedia, modeled after Wikipedia, three years ago; he and his team published their results, a description of the website, and instructions for how to use it in Nature Biotechnology this February. Though other protein databases exist, none is as comprehensive as this one, claims Pandey. It’s also unique in that researchers can log on to the site and submit and annotate their data, just like in Wikipedia entries. Distinguishing it from the online encyclopedia, however, is that only the original contributor can edit the data.

"What we wanted to do was to correlate a lot of experimental data, and we also wanted a broad range of data related to protein features," Pandey says. “It provides for the first time most of the features that the protein researcher needs — and honestly, it’s not [just] what the protein researcher needs, it’s what the biologist needs." To date, the database includes more than 15,000 human proteins and almost 205,000 annotations. In addition to being able to upload data from a variety of different platforms — such as mass spec, protein arrays, western blots, and others — users can annotate their data for a range of features including post-translational modifications, tissue and cell-line expression, cellular localization, enzyme substrates, and protein-protein interactions.

More than 70 researchers have contributed their data to the Human Proteinpedia so far, including scientists at the Ludwig Institute for Cancer Research, the Fred Hutchinson Cancer Research Center, and others. Pandey believes this is just a first step for the proteomics community. Describing his efforts as a bottom-up, or grassroots, approach to assembling proteomic data, he says he thinks the community is ready to open up to the kind of large-scale, collaborative research that’s common these days in the world of genomics research.

"I would say that this is the first paper with so many groups involved in the field of proteomics," he says. In genomics, the co-authoring of papers, especially when it comes to sequencing genomes, is common enough to be expected; in proteomics, the standard has been that “people agree to disagree," he says. However, in efforts to seed the Proteinpedia, getting people to share their data was relatively easy. "We may have had a few non-responders to our request, but pretty much I don’t recall anyone saying, no, we don’t want to contribute the data,' Pandey says.

Pandey hopes the wiki nature of the database will promote not only data sharing, but also collaborative editing. Unpublished data can, of course, be submitted; he will leave it to the proteomics community to decide which data are most valuable. In the end, it is up to the proteomics scientists to open up their labs, so to speak. As for the original authors on the paper, Pandey says, "We think of them as founding members, and without them this initiative definitely would not have been possible. We really are serious about getting the community involved and to keep it up and going."

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