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Editorial

Global Ocean Sampling Collection

  • Hemai Parthasarathy mail,

    To whom correspondence should be addressed. E-mail:hemai@plos.org

    X
  • Emma Hill,
  • Catriona MacCallum
  • Published: March 13, 2007
  • DOI: 10.1371/journal.pbio.0050083
  • Published in PLOS Biology

Today, PLoS Biology publishes landmark metagenomics papers from the J. Craig Venter Institute's Global Ocean Sampling expedition [1–3]. These papers describe the initial analyses of several gigabasepairs' worth of sequence data from oceanic microbes collected during the Sorcerer II expedition, as the ship made her way down from Canada, through the Panama Canal, and finally out beyond the Galapagos Islands well into the tropical Pacific and the South Pacific Gyre. Results from the first foray of this research mission into the Sargasso Sea were published three years ago [4]. As described in the accompanying Synopsis [5], the new voyage has added information from multiple biomes and several-fold more data.

Analysis of these data poses not only scientific challenges [6], but also significant legal hurdles. Craig Venter is no stranger to issues of intellectual property—his previous incarnation as the president of Celera saw him embroiled in controversy over the decision to “privatize” aspects of his company's work in sequencing the human genome. Now, at the head of the Global Ocean Sampling project, Venter finds himself on the side of greater accessibility, negotiating the claims of individual governments on the genomic wealth within their waters. In particular, as of this writing, there is an active negotiation with the Ecuadorian government (which has seen more than one change of power since the expedition began) over restricting commercial reuse of these data. Henry Nicholls describes this tangled legal landscape in an accompanying Feature [7].

Although extensive in scope, the papers presented here only touch the surface of the wealth of information to be gleaned from these data, which are freely available for all to explore from their desktops: the trace reads and processed data have been deposited in the National Center for Biotechnology Information's Trace Archive (http://www.ncbi.nlm.nih.gov/Traces) (with the exception of that fraction of the trace data acquired from Ecuadorian coastal waters), annotated with extensive geographical and physicochemical metadata. The assemblies and associated annotated peptides will be delivered to GenBank (http://www.ncbi.nlm.nih.gov/Genbank) around the time of publication, and will become available after GenBank has processed them. More immediately, and potentially more usefully, these data are also freely available through a specially built database, CAMERA—Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (http://camera.calit2.net)—which provides greater annotation and analysis capabilities [8]. (CAMERA was funded by the Gordon and Betty Moore Foundation, which also supports PLoS.)

The proponents of open-access publishing, ourselves included, often cite as an inspiration the power that open access to DNA sequence databases has had in transforming scientific discovery. As our founders noted in the inaugural issue of PLoS Biology, “With great foresight, it was decided in the early 1980s that published DNA sequences should be deposited in a central repository, in a common format, where they could be freely accessed and used by anyone. Simply giving scientists free and unrestricted access to the raw sequences led them to develop the powerful methods, tools, and resources that have made the whole much greater than the sum of the individual sequences…. Now imagine the possibilities if the same creative explosion that was fueled by open access to DNA sequences were to occur for the much larger body of published scientific results.” [9]

But the publishing reality in genomics research has been less inspiring. Although sequence data are publicly available and free to be reused by the community, the same creative license has not yet been awarded to the key papers resulting from the major genome projects, which are commonly published in subscription-based journals. Many of these genomics papers are “freely” available from publisher Web sites, but their use remains restricted, and to claim that freedom to read an article is the main benefit of open access is to miss the promise inspired by DNA sequence databases.

While we and other open-access journals have both enjoyed and been grateful for strong support from the genomics community, we are also disappointed that authors of landmark genomics papers, who adamantly support open access to sequence data, have not taken the opportunity to provide further leadership for their community by promoting open access to the scientific literature. We encourage all researchers to apply the same standards to their papers as they would to their data, regardless of the publisher. As Jensen et al. stated in a recent review about the benefits of text mining for the scientific community, “It is the restricted access to the full text of papers…that is currently the greatest limitation…” [10].

Acknowledgments

PLoS Biology relies on the support of our academic editors and reviewers in selecting and improving manuscripts for publication. We would like to extend particular thanks to our editorial board members Sean Eddy, Jonathan Eisen, and Nancy Moran, our guest editors Simon Levin and Tony Pawson, and our anonymous peer reviewers for their contributions to this collection of articles.

References

  1. 1. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Gobal Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77. doi:10.1371/journal.pbio.0050077.
  2. 2. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families. PLoS Biol 5: e16. doi:10.1371/journal.pbio.0050016.
  3. 3. Kannan N, Taylor SS, Zhai Y, Venter JC, Manning G (2006) Structural and functional diversity of the microbial kinome. PLoS Biol 5: e17. doi:10.1371/journal.pbio.0050017.
  4. 4. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 58–60.
  5. 5. Gross L (2007) Untapped bounty: Sampling the seas to survey microbial biodiversity. PLoS Biol 5: e85. doi:10.1371/journal.pbio.0050085.
  6. 6. Eisen JA (2007) Environmental shotgun sequencing: The potential and challenges of random and fragmented sampling of the hidden world of microbes. PLoS Biol 5: e82. doi:10.1371/journal.pbio.0050082.
  7. 7. Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M (2007) CAMERA: A community resource for metagenomics. PLoS Biol 5: e75. doi:10.1371/journal.pbio.0050075.
  8. 8. Nicholls H (2007) Sorcerer II: The search for microbial diversity roils the waters. PLoS Biol 5: e74. doi:10.1371/journal.pbio.0050074.
  9. 9. Brown PO, Eisen MB, Varmus HE (2003) Why PLoS became a publisher. PLoS Biol 1: e36. doi:10.1371/journal.pbio.0000036.
  10. 10. Jensen LJ, Saric J, Bork P (2006) Literature mining for the biologist: From information retrieval to biological discovery. Nat Rev Genet 7: 119–129.