Monthly Archives: February 2011

Archiving legacy data, or “Why is Dryad better than a floppy disk?”

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If you have recently published data in Dryad, chances are it was in the course of publishing an article at a partner journal that steered you our way.

But you may be aware that Dryad accepts data from any peer-reviewed article in biology or biomedicine.  That includes journals that are not (at least not yet) partners.  In fact, as of the the time of writing, Dryad has data associated with articles in 79 journals, approximately four times the number of partners.

Dryad even accepts data from articles that have already been published.  Now, why might you wish to go to the trouble of rummaging through those old files and putting your legacy data online?

Well, we noticed a while back that some individuals were beginning to do this systematically.  For example, there was a sudden influx of data packages with Frédéric Delsuc’s name on them a little while back.  Delsuc, of the French National Centre for Scientific Research (CNRS) and the Université Montpellier, is a member of an international team of collaborators (from France, Norway, Canada, Spain, Japan, Germany, Switzerland, and the United States) that has been using DNA sequence data to reconstruct the evolutionary history of a wide range of vertebrates and vertebrate relatives, from anteaters to sea squirts.

Giant Anteaters

Giant Anteaters (Myrmecophaga tridactyla). The pup clinging to his mother is Cyrano, who was born at the Smithsonian’s National Zoo in 2009. Photo credit: Mehgan Murphy, CC-BY-NC-ND, http://creativecommons.org/licenses/by-nc-nd/2.0/

So far, Delsuc and his team [1] have deposited data from 20 articles in Dryad. The articles are in partner journals such as Molecular Biology and Evolution, Molecular Phylogenetics and Evolution, Systematic Biology, as well as more general science journals such as Nature, Science, and the Proceedings of the National Academy of Sciences USA.

The articles stretch back to 2002, a time when most new desktop computers were still being outfitted with floppy drives. (Remember those?)

We asked Delsuc what he saw as the advantages to archiving his team’s heritage of legacy data?

We […] decided in our team to try to systematically submit our datasets to Dryad because we really think they are valuable. Dryad offers a very nice way of archiving the data ensuring their durability over time.

For Delsuc and his team, no more rummaging through old storage devices to find the files when they receive an email request.  No more worrying about the data when  lab or departmental websites move.  They just need to point their colleagues to Dryad.

It has been reported that the number one reason cited when scientists are asked why they have denied their colleagues’ requests for data in the past was the amount of effort required to dig them up [2].  Delsuc’s and his team intuitively understood that, and went back to archive their data before memories faded, storage devices failed, and graduate students moved on.

The downside to archiving legacy data in this way is that an article’s readers won’t immediately know about the existence of the Dryad data package, since the data DOI will not be published within the text. So, while archiving legacy data has its advantages, there is no substitute for depositing the data before the article is published, as Dryad does with the new articles appearing in its partner journals.

To give Delsuc the final word:

It would be great if more and more journals in the field decide to include data deposit in their publication policies.

[1] Equipe Phylogénie et Evolution Moléculaire” (Phylogeny and Molecular Evolution team) of the Institut des Sciences de l’Evolution (Institute of Evolutionary Sciences), part of the CNRS: Centre National de la Recherche Scientifique (French National Centre for Scientific Research) and the Université Montpellier 2 (University of Montpellier 2).

[2] Campbell EG et al. (2002) Data Withholding in Academic Genetics: Evidence From a National Survey. JAMA 287(4):473-480. doi:10.1001/jama.287.4.473

How can the Dryad repository help researchers’ data management plans?

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We encourage individuals and project teams seeking to comply with data management planning mandates to consider Dryad as the destination repository for published data from their research.  Dryad is not only a widely applicable, best-practice solution for research data management, it is also a quick and easy solution!

Research datasets associated with a publication in any biological or biomedical field are welcome in Dryad, regardless of file type. Archived data files may include spreadsheets or other tables, images or maps, alignments, character matrices, etc.

Data files deposited in Dryad are permanently preserved, publicly available with no legal restrictions on re-use, and uniquely identified for attribution.

Data submission is simple, quick, and easy. Data files may be uploaded to Dryad in any file format, with a short README and a few metadata terms.

Finally, using an established best-practice data repository like Dryad facilitates a simple description in a data management plan. For example, grant applicants can use language like this to describe their intention to archive data in Dryad:

We plan to use the Dryad public repository for the long-term preservation and dissemination of data underlying publications from this funded research project. Data submitted to Dryad is made publicly available upon online publication** of the associated article. All data in Dryad is released to the public domain without legal restrictions on reuse, through a Creative Commons Zero waiver. There is a (legally non-binding) expectation of attribution of the Dryad data record and associated article. A one-time data deposit charge is paid by the authors or the associated journals, which allows Dryad data to be available for download without cost to users.

**Researchers may instead choose to stipulate an embargo period of 1 year.

If your funding agency allows it, don’t forget to budget for data preservation (data submission to Dryad is free through 2011).

Data deposited in Dryad can help researchers meet these policies and expectations:

  • the (US) National Science Foundation requires that data management plans include provisions for data archiving and preservation, and access policies and provisions for secondary use
  • the Wellcome Trust “expects all of its funded researchers to maximise the availability of research data with as few restrictions as possible”
  • the (US) National Institutes of Health data sharing policies state that “Data sharing is essential for expedited translation of research results into knowledge, products and procedures to improve human health.”
  • the (UK) Medical Research Council policy on data sharing and preservation states: “Where possible, published results should include links to the associated data. Investigators must show how data will be preserved and their strategies for sharing, e.g. by depositing it in a community database.”

Summaries of funding agencies’ data policies can be found here:

Resources on data management & sharing:

Questions about the role of the Dryad repository in data management planning can be directed to the Dryad team.

Sample data file, Gilbert J and Manica A (2010) Data from: Parental care trade-offs and life history relationships in insects. Dryad Digital Repository. doi:10.5061/dryad.1451