We believe this validates one of the premises on which Dryad was founded, that a non-specialist data repository can serve as shared infrastructure for a large and diverse set of journals.  As a group, they have little in common, serving authors and readers from many different research communities, nationalities, types of institutional affiliation, etc., and working with many different kinds of data.  Some are owned by societies, some by commercial publishers, some by not-for-profits.  Some are Open Access, many are not.  Some have specialized disciplinary or taxonomic scope (e.g. including journals that publish on birds, herps, insects, mammals, plants, protists, viruses, etc.) while some publish findings from all corners of science (Nature, PNAS, Science).

Interestingly, this set of 100 is roughly five times the number of journals that have integrated manuscript submission with Dryad in order to facilitate authors’ data archiving.  While the integrated journals still account for the majority of new data submissions, we are pleased to continue receiving data volunteered by authors publishing in outlets new to Dryad.

The journals that have integrated their manuscript processing with Dryad to date are mostly, though not exclusively, from the fields of evolutionary biology and ecology:

• The American Naturalist
• Biological Journal of the Linnean Society
• BMJ Open (an important first step in that it is our first integrated biomedical journal)
• Ecological Monographs
• Evolution
• Evolutionary Applications
• Heredity
• Journal of Evolutionary Biology
• Journal of Heredity
• Molecular Ecology and Molecular Ecology Resources
• Paleobiology
• Pensoft Publishers – 8 different journals
• Systematic Biology

But Dryad’s broadening disciplinary coverage is best illustrated by listing some of the journals with content in the repository that have not, at least not yet, implemented integrated submission:

• Animal Behaviour
• Bioinformatics
• Biotropica
• Conservation Genetics
• Environmental Microbiology
• Evolution and Development
• Frontiers in Psychology
• Genome Biology and Evolution
• Human Genomics
• Integrative and Comparative Biology
• Journal of Biogeography
• Journal of Fish and Wildlife Management
• The Journal of Parasitology
• Limnology and Oceanography
• The Plant Cell
• PLoS Pathogens
• Symbiosis
• Toxicon

And we are particularly pleased by the irony of hosting data from Genesis

If you are an editor, publisher, or just a passionate reader of a journal that currently has content in Dryad (you can find out for yourself here), and you would like to talk about how manuscript submission integration could strengthen the service that Dryad provides to your journal, then please contact us.

Obviously, one of the primary purposes of archiving data in Dryad is to enable its reuse by others.  Having clear and open terms of reuse helps realize that goal.  (Along with having well-organized data, good documentation, persistent file-formats, etc.)

CC0 was crafted specifically to reduce any legal and technical impediments, be they intentional and unintentional, to the reuse of data.   In most cases, CC0 does not actually affect the legal status of the data, since facts in and of themselves are not eligible for copyright in most countries (e.g. see this commentary from Bitlaw regarding U.S. copyright law).  But where they are, CC0 waives copyright and related rights to the extent permitted by law.

Importantly, CC0 does not exempt those who reuse the data from following community norms for scholarly communication.  It does not exempt researchers from reusing the data in a way that is mindful of its limitations.  Nor does it exempt researchers from the obligation of citing the original data authors.  However, like other scientific norms, these expectations are best articulated and enforced by the community itself through processes such as peer review.

In fact, by removing un-enforcable legal barriers, CC0 facilitates the discovery, re-use, and citation of that data.

“Community norms can be a much more effective way of encouraging positive behaviour, such as citation, than applying licenses. A well functioning community supports its members in their application of norms, whereas licences can only be enforced through court action and thus invite people to ignore them when they are confident that this is unlikely.” (Panton Principles FAQ)

Dryad’s policy ultimately follows the recommendations of Science Commons, which discourage researchers from presuming copyright and using licenses that include “attribution” and “share-alike” conditions for scientific data.

Both of these conditions can put legitimate users in awkward positions.  First, specifying how “attribution” must be carried out may put a user at odds with accepted citation practice:

“when you federate a query from 50,000 databases (not now, perhaps, but definitely within the 70-year duration of copyright!) will you be liable to a lawsuit if you don’t formally attribute all 50,000 owners?” Science Commons Database Protocol FAQ)

While “share-alike” conditions create their own unnecessary legal tangle:

“ ‘share-alike’ licenses typically impose the condition that some or all derivative products be identically licensed. Such conditions have been known to create significant “license compatibility” problems under existing license schemes that employ them. In the context of data, license compatibility problems will likely create significant barriers for data integration and reuse for both providers and users of data.” (Science Commons Database Protocol FAQ)

Thus,

“… given the potential for significantly negative unintended consequences of using copyright, the size of the public domain, and the power of norms inside science, we believe that copyright licenses and contractual restrictions are simply the wrong tool [for data], even if those licenses and contracts are used with the best of intentions.” (Science Commons Database Protocol FAQ)

Furthermore, Dryad’s use of CC0 to make the terms of reuse explicit has some important advantages:

• interoperability: Since CC0 is both human and machine-readable, other people and indexing services will automatically be able to determine the terms of use.
• universality: CC0 is a single mechanism that is both global and universal, covering all data and all countries.  It is also widely recognized.
• simplicity: there is no need for humans to make, and respond to, individual data requests, and no need for click-through agreements.  This allows more scientists to spend their time doing science.

It is important to note that if you have data that, due to pre-existing agreements, cannot be released under the terms of CC0, please do not deposit that data to Dryad.  Journals that require data archiving in Dryad as a condition of publication can make exceptions for such special cases.

Footnote:  Interestingly, the repository had originally applied CC-BY to all its contents.  The very deliberate decision to use CC0 instead, made by Dryad’s Board in May of 2009, required us to obtain permission from all the early contributors to change the terms of reuse of their content.   And today, there are still a few items in Dryad under CC-BY for which permission was not granted.

Section 4 of the report (para 189) concludes:

…If reviewers and editors are to assess whether authors of manuscripts are providing sufficient accompanying data, it is essential that they are given confidential access to relevant data associated with the work during the peer-review process. This can be problematical in the case of the large and complex datasets which are becoming increasingly common. The Dryad project is an initiative seeking to address this. If it proves successful, funding should be sought to expand it to other disciplines. Alternatively, we recommend that funders of research and publishers work together to develop similar repositories for other disciplines.

The Science and Technology Committee concludes that in order to allow others to repeat and build on experiments, researchers should aim for the gold standard of making their data fully disclosed and made publicly available:

Access to data is fundamental if researchers are to reproduce, verify and build on results that are reported in the literature. We welcome the Government’s recognition of the importance of openness and transparency. The presumption must be that, unless there is a strong reason otherwise, data should be fully disclosed and made publicly available. In line with this principle, where possible, data associated with all publicly funded research should be made widely and freely available. Funders of research must coordinate with publishers to ensure that researchers disclose their data in a timely manner. The work of researchers who expend time and effort adding value to their data, to make it usable by others, should be acknowledged as a valuable part of their role. Research funders and publishers should explore how researchers could be encouraged to add this value.

H.M.S.O. Science and Technology  Committee. Eighth Report: Peer review in scientific publications. Published 28 July 2011  Available at: http://www.publications.parliament.uk/pa/cm201012/cmselect/cmsctech/856/85602.htm

BMJ Open authors are now being strongly encouraged to deposit the data underlying their articles in Dryad or a more specialized repository, as appropriate.  Authors submitting articles to the journal will benefit from Dryad’s journal submission integration, the process by which data deposit is streamlined for authors through behind-the-scenes communication between the journal and the repository.

An extremely important issue with archiving medical data is, of course, the need to protect patient privacy. To assist its authors, BMJ Open is providing special guidance on data sharing.  Authors must be able to release data to the public domain as with all data in Dryad, and the repository will err on the side of caution by turning back any data that may compromise patient privacy.

To quote from the BMJ Group press release:

Data sharing aims to help scientists and doctors validate and scrutinise researchers’ findings in a bid to prevent fraud and eradicate the kind of selective reporting that has enabled some treatments to acquire regulatory approval, based on incomplete and biased data. In some cases this lack of transparency has prompted the subsequent restriction or withdrawal of certain treatments because of patient safety or effectiveness concerns, which were already evident in the unpublished data.  Data repositories also allow researchers to develop new methods of analysis and use the data to answer questions that the original researchers have not thought of. They also facilitate the acquisition of data for meta analysis (more in-depth comparative reviews).

Commenting on the move, Dr Trish Groves, editor in chief of BMJ Open, said: “Since launch, BMJ Open has championed transparency in medical research through open peer review, open access, and full reporting of studies’ methods and results, all exemplified by last week’s paper on the safety (or not) of medical devices (doi:10.5061/dryad.585t4)…”

This data package in Dryad, which illustrates the tremendous value of medical data for informing medical policy and practice without compromising patient privacy, is available at:

• Heneghan C, Thompson M, Billingsley M, Cohen D (2011) Data from: Medical-device recalls in the UK and the device-regulation process: retrospective review of safety notices and alerts. Dryad Digital Repository. doi:10.5061/dryad.585t4

Groves goes on to say

We strongly encourage authors to share their datasets, and now we’re delighted to be making that easier to do, with the help of DryadUK.

Kudos to the Dryad UK project team, based at the British Library, for facilitating this pioneering partnership.

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.

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

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:

• US funding agencies
• UK funding agencies

Resources on data management & sharing:

• Massachusetts Institute of Technology,  Guide to data management & publishing How to manage your data through the lifecycle.
• Cornell University, Data Management Planning Overview Directed at Cornell affiliates; includes lists of research data services.
• UK Data Centre, Managing and Sharing Data: a best practice guide for researchers. This guide provides best practice guidance for researchers on preparing and looking after data for  their own use and for sharing.
• Columbia University course on Data Acquisition and Management. Overview of data collection issues; includes an extensive list of annotated resources.
• Digital Curation Centre (UK) offers several data management resources, including a Checklist for a Data Management Plan, a Data Management Template, and an online Data Management Planning tool.

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

Credit: adamthelibrarian, from Flickr

This is an important month, because a host of our partner journals are implementing new policies on data archiving, and, in the U.S., the National Science Foundation is asking its new grantees to have explicit data management plans.  There are over 1000 data files from over 50 journals now in Dryad, and much of this content has been submitted only within the past year. Clearly, Dryad’s role in supporting the growing data archiving mandates from journals and funders continues to expand.

New Features
In the past few months, several new features have been added to Dryad.  Users can now save an incomplete submission and come back later to complete it.  They can see a listing of their completed and in progress submissions.  Users can download data citations to their favorite bibliography management programs and upload them to their favorite social bookmarking tools.  A new “faceted search” interface allows users to find data more easily, and also displays related content in other repositories, including ecological and environmental science data (from the Knowledge Network for Biocomplexity) and phylogenetic data (from TreeBASE). To provide an early indication of scientific impact, users can see how often data have been viewed and downloaded.

An important new feature is “handshaking”, which is what we call the process whereby authors upload some of their data to Dryad, and the information is conveyed behind-the-scenes to a specialized repository. The aim of handshaking is to reduce the time and effort need to deposit data when there are different repositories managing different aspects of the data.  Handshaking also enables persistent linkages among data in the different repositories. As a first foray into handshaking, we now offer users the option of initiating a deposit in TreeBASE, the primary repository for published phylogenetic data, whenever a NEXUS file is uploaded to Dryad.  Alternatively, the option is available to deposit in another repository first, and report the identifiers to Dryad to ensure that users can find all the data relevant to a given article.  We will be working in the months ahead to handshake with other specialized repositories required by our partner journals.

See our recent blog post about these features for more details.

Data Deposit in Three Easy Steps: The Movie
Are you looking for a way to show a colleague how straightforward data archiving can be?  We’ve added a short (2-minute) video to the site that walks users through the deposit process in three easy steps.  The video also available at SciVee.

Journals Implement Joint Data Archiving Policy
Starting this month, a number of Dryad partner journals have implemented a Joint Data Archiving Policy that requires, as a condition of publication, that authors deposit the data underlying their article in a public repository.  Some of the journals implementing this policy include: The American Naturalist, Evolution, Evolutionary Applications, Heredity, Journal of Evolutionary Biology, and Molecular Ecology. A recent TREE article by Michael Whitlock suggests how “data generators, data re-users, and journals can maximize the fairness and scientific value of data archiving.”

A growing number of journals now integrate their submission process with Dryad, meaning that the repository and journal exchange information to facilitate the author’s data deposition process and to ensure persistent linkage between articles and data. The current list includes The American Naturalist, The Biological Journal of the Linnean Society, Evolution, Journal of Evolutionary Biology, Journal of Heredity, Molecular Ecology, and Molecular Ecology Resources. And more are on the way (stay tuned).

NSF Data Management Plan Mandate
Starting this month, the U.S. National Science Foundation is requiring grant applicants to provide a data management plan describing how data will be collected, preserved and made available, and these plans will be subject to peer review.  We encourage applicants to leverage Dryad in their data management plans as a solution for the long-term preservation and dissemination of the data associated with their publications.  There are some pointers to resources for data management planning on the Dryad website.

Dryad UK Project
The Joint Information Science Committee (JISC) in the UK has made an award to Dryad and through Oxford University and the British Library to expand the scope of the journals involved, including into the areas of infectious disease and epidemiology, and to create a UK mirror of Dryad.  More information is here and at the Dryad UK site.

New Twitter Feed for Data Deposits
Interested in keeping up with new data available in Dryad?  Follow our Twitter feed (@datadryadnew) or subscribe to our RSS feed. We also Tweet general news about the repository and the world of data science as @datadryad.

Browse and search the repository at http://datadryad.org/
Follow Dryad on Twitter http://twitter.com/datadryad

This blog post is the first issue of the Dryad newsletter, summarizing recent achievements and milestones of the data repository.  If you’d like to receive future newsletters by email, please sign up for the Dryad Users mailing list.

How to deposit data in Dryad

The video is embedded on the Dryad website, and also available on SciVee. Feel free to link to it and share it with colleagues.

It would be a good idea to know and be ready to deposit your files in a data repository, because this month marks the implementation of the Joint Data Archiving Policy.  The policy, endorsed by a consortium of prominent journals and societies, states that journals will require

as a condition for publication, that data supporting the results in the paper should be archived in an appropriate public archive.

The policy can be customized by each journal, and enables both embargoes and editorial discretion to make special exceptions. Blanket exemptions apply to sensitive data such as identifiable human records and endangered species localities.

The journals (and corresponding societies) implementing the policy this month are:

• The American Naturalist (American Society of Naturalists)
• Evolution (Society for the Study of Evolution)
• Evolutionary Applications
• Heredity (The Genetics Society)
• Journal of Evolutionary Biology (European Society for Evolutionary Biology)
• Molecular Biology and Evolution (Society for Molecular Biology and Evolution)
• Molecular Ecology
• Systematic Biology (Society for Systematic Biology)

A sampling of the revised Instructions to Authors includes:

• The American Naturalist: “The American Naturalist requires authors to deposit the data associated with accepted papers in a public archive. For gene sequence data and phylogenetic trees, deposition in GenBank or TreeBASE, respectively, is required. There are many possible archives that may suit a particular data set, including the Dryad repository for ecological and evolutionary biology data (http://datadryad.org). All accession numbers for GenBank, TreeBASE, and Dryad must be included in accepted manuscripts before they go to Production. Any impediments to data sharing should be brought to the attention of the editors at the time of submission.”
• Journal of Evolutionary Biology “The editors and publisher of this journal expect authors to make the data underlying published articles available. An investigator who feels that reasonable requests have not been met by the authors should correspond with the Editor-in-Chief. Authors must use the appropriate database to deposit detailed information supplementing submitted papers, and quote the accession number in their manuscripts.”
• Molecular Ecology: “Data Accessibility: To enable readers to locate archived data from Molecular Ecology papers, as of January 2011 we will require that authors include a ‘Data Accessibility’ section after their references. This should list the data base and respective accession numbers for all data from the manuscript that has been made publicly available…. Please note that this section must be complete prior to the submission of the final version of your manuscript. Papers lacking this section will not be sent to Production.”

At Dryad, we have been working for some time now with editors and publishers at these and other partner journals to support the implementation of this policy. If you submit an article to a “JDAP journal,” you will be invited to simultaneously submit your data to Dryad. This may occur either prior to review or, depending on the journal, at the time your article is accepted. Dryad and the journal communicate behind the scenes to make it as easy as possible for you to deposit your data, and also ensure that a permanent, resolvable, and citable data identifier is published in the final article.  That way, in the future, no one need be frightened by the question “do you know where your data are?”

Our @datadryad feed is also available, for updates on the Dryad repository and data sharing in general.