Stop by the British Library booth to find out more about Dryad’s expansion under the new JISC grant involving Oxford University and BL.

Meeting topics include:

• How is the web changing the way we conduct, communicate, share, and evaluate research? How can we employ these trends for the greater good?
• How is the internet changing the way we work with data?
• How are blogs and social networking facilitating scientific discussion? What challenges do we face?
• What challenges and opportunities are there when engaging with the public?

In particular, these sessions on Friday may be of interest to those involved in data sharing:

• Breakout 1: Publishing primary research data
• Breakout 8: Connecting scientific resources

Follow the conference on Twitter @soloconf (comment with hashtag #solo10).

Mass Spectrometer, photo from U.S. Department of Energy Genome Programs

Now “authors who publish a manuscript containing mass spectrometry data in Molecular and Cellular Proteomics (MCP) must submit the raw data to a publicly accessible site.”   The journal Proteomics also requires data deposit in a public archive.

There are several specialized data repositories in the field, and several are working together as ProteomExchange “to provide a single point of submission to proteomics repositories, and encourage the data exchange and sharing of identifiers between the repositories so that the community may easily find datasets in the participating repositories.”

Five of the Dryad team will be there:

• Hilmar Lapp, NESCent Asst. Director for Informatics
• Heather Piwowar, DataONE postdoc with NESCent and Dryad
• Peggy Schaeffer, Communications Coordinator
• Ryan Scherle, Data Repository Architect
• Todd Vision, Project Director

Come talk to us, learn about what’s up with Dryad, see a quick demo of the data deposit process, ask questions, anytime!  Find us at Booth #6 in the exhibit hall, from Friday through Tuesday.

The policy on data sets reads:

A condition of publication in a Nature journal is that authors are required to make materials, data and associated protocols promptly available to others without preconditions.

Data sets must be made freely available to readers from the date of publication, and must be provided to editors and peer-reviewers at submission, for the purposes of evaluating the manuscript.

For the following types of data set, submission to a community-endorsed, public repository is mandatory. Accession numbers must be provided in the paper. Examples of appropriate public repositories are listed below.

Try it out:

1. From this PANGAEA record, follow the DOI to the article in ScienceDirect (citations and abstracts only, unless you or your institution have subscription access)
2. The PANGAEA link is to the right of the article with Supplementary Data beside it

This valuable two-way connectivity between data and article is most easily achieved when the data are captured at the time of article submission.  See this previous post for more on Dryad’s approach to this problem, which is designed to work across multiple publishers.

Similar to the appearance of the PANGAEA logo in the online version of the article, we are toying with the idea of calling attention to the link in the opposite direction by placing  journal cover images next to article DOIs in the Dryad display.  We’d like to hear your thoughts on that.  Is it helpful signage?  Or distracting eye candy?

The creators recommend “adopting and acting on the following principles:”

1. When publishing data make an explicit and robust statement of your wishes.
2. Use a recognized waiver or license that is appropriate for data.
3. If you want your data to be effectively used and added to by others it should be open as defined by the Open Knowledge/Data Definition – in particular non-commercial and other restrictive clauses should not be used.
4. Explicit dedication of data underlying published science into the public domain via PDDL or CCZero is strongly recommended and ensures compliance with both the Science Commons Protocol for Implementing Open Access Data and the Open Knowledge/Data Definition.

These principles were written by Peter Murray-Rust, Cameron Neylon, Rufus Pollock and John Wilbanks at the Panton Arms in Cambridge, UK, and then refined by the Open Knowledge Foundation Working Group on Open Data in Science. There are open data web buttons available, and individuals and organizations can endorse the principles here.

What do you think are the barriers to data sharing?

Data from: Thompson S, Daniels K. 2010. A porous convection model for small-scale grass patterns. American Naturalist 175: E10-E15. Dryad Digital Repository. http://hdl.handle.net/10255/dryad.857

The need for archiving data in evolutionary biology.  Allen J. Moore, Mark A. McPeek, Mark D. Rausher, Loren Rieseberg, Michael C. Whitlock.  Journal of Evolutionary Biology 2010.
Published Online: Feb 9 2010
DOI: 10.1111/j.1420-9101.2010.01937.x

The editorial says

Data that are properly archived are saved for posterity, and the archives also function to preserve data in a useable form for the original authors. Moreover, if datasets are put into a readily interpretable format while the methods and structure of the data are foremost in the scientists’ minds, that data can be used later more easily by those scientists and others.

When fully in place, the policy will require authors to archive the data required to support the conclusions in their published paper, along with sufficient details that a third party can reasonably interpret those data correctly.

To be implemented next year, the policy is parallel to those already announced by two other prominent journals, also Dryad partners:

• Whitlock, M. C., M. A. McPeek, M. D. Rausher, L. Rieseberg, and A. J. Moore. 2010. Data Archiving. American Naturalist. 175:145-146, doi:10.1086/650340
• Rieseberg, L., T. Vines, and N. Kane. Editorial and retrospective 2010. Molecular Ecology. 19:1-22, doi:10.1111/j.1365-294X.2009.04450.x

“By putting together pieces of prior research, it is possible to transform how you do science and open the doors to findings that previously were unattainable,” said Brian Sidlauskas, a fish biologist from Oregon State University and lead author on the Evolution article. “But such an approach runs counter to the way science traditionally has been conducted, so pursuing synthetic science is somewhat risky.”

“We need to reduce the risk, remove the barriers, and encourage more pursuit of synthesis because the potential,” he added, “is staggering.”

Sidlauskas cites access to actionable data as one of the major obstacles. “When you’re looking to synthesize data from several hundred individual studies, data formatting, storage and accessibility become huge issues,” he said.   He says that  “…the vast majority of data supporting previous studies are unavailable, often because the data are lost or preserved in inaccessible forms (notebooks, floppy disks).”

The article refers to Dryad as

… working to alleviate the problem of data availability by providing an open-access home for ecological and evolutionary data that does not fit into more specialized repositories. Dryad actively works with a coalition of journals and scientific societies to make deposition of all data a normal part of the research workflow. As more journals require data deposition as part of the manuscript publication process, the opportunities for potential syntheses linking such data will increase substantially.

Sidlauskas adds, “It’s kind of an open-source approach to science,” he added. “Data archives may require some kind of proprietary protection for a few months or years, but after a certain amount of time, they should become public domain. Only by saving the data that underlie today’s science will we allow future scientists to use those data in ways that may far exceed what the original researchers envisioned.”

Other authors on the commentary piece include Ganeshkumar Ganapathy, of the National Evolutionary Synthesis Center (NESCent); Einat Hazkani-Covo, Duke University Medical Center; Kristin P. Jenkins, NESCent; Hilmar Lapp, NESCent; Lauren W. McCall, NESCent; Samantha Price, University of California-Davis; Ryan Scherle, NESCent; Paula A. Spaeth, Northland College; and David M. Kidd, NERC Centre for Population Biology, Imperial College London.

CITATION: Sidlauskas, B., G. Ganapathy, et al. (2010). “Linking big: The continuing promise of evolutionary synthesis.” Evolution doi: 10.1111/j.1558-5646.2009.00892.x.