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Celebrating a diversity of journals

2011/12/21 by Peggy Schaeffer

Our last post celebrated the 1000th data package in Dryad. This week, with the release of two data packages associated with articles in Ecological Monographs, we celebrate another important milestone, our 100th journal.

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.

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1E+3

2011/10/07 by tjvision

Fig 1. Helen of Troy, detail from an Attic red-figure krater, c. 450–440 BC

It is said that a picture is worth a thousand words and that Helen of Troy (Fig 1) had a face that launched a thousand ships.  Why is the number 1000 significant to those of us at Dryad today?  (Especially since its place in literature is ultimately an accident of our decimal number system [1]).

The reason is that Dryad released its 1000th data package.  The lucky submission is: Hager R, Cheverud JM, Wolf JB (2011) Data from: Genotype dependent responses to levels of sibling competition over maternal resources in mice. doi:10.5061/dryad.8qq3p0d8  [2]. This (arbitrary, but see [3]) milestone has put us in a reflective mood, and so here we take the opportunity to consider what it means.

First, it encourages us that Dryad’s multipronged approach to making data available for reuse (raising awareness of the issues, coordinating data archiving policy across journals, providing a user-friendly submission interface, paying attention to the incentives of researchers) is bearing fruit.  As a result of this strategy, the rate of submissions continues to grow; over 60% of submissions are from the past nine months alone.  Since a picture is worth a thousand words, see Fig 2.

Figure 2. Data packages submitted to Dryad through September 2011

We are mindful will take some time before we can measure the impact of the availability of these data for reuse, but there are encouraging signs from the frequency with which data are being downloaded.  We will discuss those results in a separate post.

What else can we learn from these first 1000 submissions?  One is the importance of making data submission integral to publication. While there are 88 different journals in which the corresponding articles appear, about three quarters of the submissions come from the first nine journals that worked to integrate manuscript and data submission with Dryad [4].  Journal policy matters, and the enthusiasm with which journals implement policy matters.

As far as disciplinary diversity goes, the first 1000 submissions are dominated by journals in evolutionary biology and ecology.  Dryad’s first biomedical journal partner, BMJ Open, was integrated within the past few months, and as a result of many other new journal partnerships being developed, we expect submissions to the repository to represent a much broader array of basic and applied biosciences in the near future.

Interestingly, most of the deposits are relatively small in size. Counting all files in a data package together, almost 80% of data packages are less than one megabyte.  Furthermore, the majority of data packages contain only one data file and the mean is a little less than two and a half.  As one might expect, many of the files are spreadsheets or in tabular text format.  Thus, the files are rich in information but not so difficult to transfer or store.

We are pleasantly surprised to report that most authors, most of the time, see the value in having their data released at the same time as the article is published.  Authors are making their data available immediately upon publication, or earlier, for over 90% of data files.  In nearly all cases where files are put under embargo, authors choose to release them one-year post-publication rather than requesting a longer embargo from the journal.

Thomson Reuters indexes more than half a million abstracts annually in BIOSIS.  A difficult-to-estimate, but undoubtedly substantial, fraction of this literature reports on data that cannot be, or is not, archived in a specialized public data repository.  This helps put Dryad’s 1000 data packages in perspective.   As a discipline, we still have a long way to go to preserve and make available for reuse all the “published” data that has no home.  But every data package that is submitted to Dryad is a little victory for the transparency and robustness of science.

So here’s to the first thousand.  May they have plenty of company in the coming years.

Footnotes:

  1. Things might have turned out very differently judging by the presence early vertebrate fossils with more than five digits (see http://en.wikipedia.org/wiki/Polydactyly_in_early_tetrapods)
  2. To celebrate, we are sending a Dryad-logo coffee mug to Dr. Reinmar Hager, who submitted the 1000th data package.
  3. Random cool fact about the number 1000.  It is “the smallest number that generates three primes in the fastest way possible by concatenation of decremented numbers (1000999, 1000999998997, and 1000999998997996995994993 are prime) … [excluding] the number itself” (see http://primes.utm.edu/curios/page.php/1000.html).
  4. This includes a collection of legacy data packages from the Systematic Biology archives that was submitted en masse to Dryad in mid-2009.

Posted in Dryad features | Tagged | 1 Comment »

Why does Dryad use CC0?

2011/10/05 by Peggy Schaeffer

Early in the process of depositing data to the Dryad repository,  authors are asked to consent to the explicit release of their data into the public domain under the terms of a Creative Commons Zero (CC0) waiver. We are frequently asked why Dryad uses CC0 rather than a license such as CC-BY, and it is important for all users to understand the rationale for this, as well as its implications.

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.

Posted in Dryad features | Tagged | 1 Comment »

UK Parliament report supports Dryad and data access

2011/07/28 by Peggy Schaeffer

Dryad has won high-level support from the UK Parliament. Its Select Committee on Science and Technology has been reporting on the peer review of scientific publications. Among the questions it considered was:  How far should reviewers be expected to go to assess technical soundness? The report discusses the feasibility of reviewing the underlying data behind research, and how those data should be managed.

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

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Looking for Research Data? What Matters to You?

2011/07/24 by whangusa

What matters to you when looking for research data in a repository? UK based Digital Curation Centre is looking for Dryad users to complete a 10 minute questionnaire on this. Results will contribute to an assessment framework for Dryad, and the questionnaire includes entry to a competition for $80/ £50 Amazon tokens. DCC are carrying this out as part of the Dryad UK project, which also involves the British Library and Oxford University’s Image Bioinformatics Lab.

Posted in Uncategorized | 1 Comment »

Why aren’t cancer microarray datasets archived more often?

2011/07/13 by tjvision

A new study in PLoS ONE by Heather Piwowar, a postdoctoral associate affiliated with DataONE, Dryad, and NESCent, reveals interesting trends in the archiving of data underlying published microarray results.  From the press release:

By querying the full text of the scientific literature through websites like Google Scholar and PubMed Central, Piwowar identified eleven thousand studies that collected a particular type of data about cellular activity, called gene expression microarray data. Only 45% of recent gene expression studies were found to have deposited their data in the public databases developed for this purpose. The rate of data publication has increased only slightly from 2007 to 2009. Data is shared least often from studies on cancer and human subjects: cancer studies make their data available for wide reuse half as often as similar studies outside cancer.

“It was disheartening to discover that studies on cancer and human subjects were least likely to make their data available. These data are surely some of the most valuable for reuse, to confirm, refute, inform and advance bench-to-bedside translational research,” Piwowar said.

“We want as much scientific progress as we can get from our tax and charity dollars. This requires increased access to data resources. Data can be shared while maintaining patient privacy,” Piwowar added, noting that patient re-identification is rarely an issue for gene expression microarray studies.

Reference:  Piwowar, H. (2011). “Who shares? Who doesn’t? Factors associated with openly archiving raw research data.” PLoS ONE 6(7): e18657. doi:18610.11371/journal.pone.0018657

“In the spirit of the topic”, the data behind the study are publicly available in Dryad at doi:10.5061/dryad.mf1sd

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BMJ Open: a new partner and an expanded scope

2011/06/27 by Peggy Schaeffer

Dryad is pleased to welcome BMJ Open as a new partner journal, reflecting the recently expanded scope of repository to be inclusive of all of basic and applied biosciences, including medicine. BMJ Open is a new online-only, open access journal from the esteemed London-based BMJ Group.  It is dedicated to publishing medical research from all disciplines and therapeutic areas, utilizing fully open peer review and immediate online publication.

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.

Posted in Data sharing | Tagged , | 3 Comments »

Request for input: archiving and licensing software

2011/06/19 by drycafe

Behind a scientific finding, in addition to unique data, there is often unique software. If Dryad archives data in part to allow others to validate the findings reported in the literature, then should we not also enable researchers to archive the software that was used to process, analyze and, in the case of simulations — create those data?

Some users have already deposited software source code alongside their data (e.g. doi:10.5061/dryad.8384, doi:10.5061/dryad.18) [1]. If users are willing and able to release their code under a CC-Zero waiver [2], then there is nothing stopping this practice. In fact, Creative Commons and the Free Software Foundation have recently stated that CC-Zero is appropriate for release of software to the public domain [3].

Yet, a number of journal partners and users have requested that Dryad provide more, or different, options for software, and that authors should not be required to waive legal rights with CC-Zero. Since software is clearly a creative work, source code unambiguously carries copyrightable intellectual property. Enabling a greater range of licensing options could open the door to more authors archiving software that is integral to their paper, and this would further Dryad’s mission of enabling scientists to validate and build upon previously work. So, how should we do that?

One important consideration is that we aim to make the submission process as easy as possible for users. This would be compromised by presenting a confusing array of licensing options, and having those differ between types of files.

The principle desiderata of a license for deposited software are more or less the same as for data: freedom to reuse, modify (analogous to the “recombine” for data), and redistribute (in original or modified form), with no more than attribution expected or required. It turns out that these are also the principles common to all licenses approved by the Open Source Initiative, or OSI [4].

So, could we just pick one of the minimally restrictive OSI-approved licenses (since we want to facilitate reuse rather than hamper it), and require release of software under those terms? We are currently of the opinion that the answer is “no”, for a couple of reasons:

(1) Some, though not all, software will already be licensed. Asking a user to choose a different one would clearly be a burden, since changing a license requires express consent from all copyright holders, including possibly the employer or funder.

(2) If the software includes third-party code to which a ‘share-alike’ license has been assigned (e.g. the GNU Public License, or GPL [5]) , then the user is required to release the code under equivalent licensing terms. Unlike for data, it would be highly unusual to combine software source code from many different sources, and so this does not pose an insurmountable barrier to archiving and reuse for scientific purposes.

Given the above, our current thinking is that Dryad should enable users to select any OSI-approved license they deem appropriate. However, we also wish to strongly guide users, when there is no prior license assigned to any part of their software, to choose either a non-share alike OSI license or a CC-Zero waiver. It is currently unclear whether dedicating software to the public domain with CC-Zero would be of as much value as it is for data [6]. We’d welcome your thoughts on that.

There are some other considerations on our plate, as well:

  • We want to be careful to avoid steering users away from using a public source code repository when that is more appropriate [7]. Is it better for Dryad to host code snapshots, or to direct users to specific versions of software in a public code repository?
  • Some users bundle software and data together in tarballs or zip archives. Since we cannot easily assign different terms to the data and software within such a combined file, it could increase the burden on users to separate these components out.
  • In addition to software, there is other content that publishers host in Supplemental Materials that some of our partner journals would like Dryad to host, instead. To the extent that some of this content is neither data nor software, should we be recognizing a third category of intellectual property, to which a license such as CC-BY [8] would be assigned?

If you have opinions or ideas, we would like to encourage you to share them with us as public comments on this blog. What’s the best way to accommodate software (and other non-data material) within Dryad?

Notes

[1] Some software source code in Dryad is already available under grandfathered license terms, such as in doi:10.5061/dryad.18.

[2] Dryad currently requires users to assign CC-Zero to all archived files. This waives all copyright and related rights in the data (to the extent legally possible in an author’s jurisdiction), effectively dedicating the data to the public domain. The use of CC-Zero is predicated on most data being “facts”, and facts in most jurisdictions cannot be copyrighted, although this not universally true (e.g. photographs). Note that Dryad has a policy that the original article and the data package are to be cited when the data are reused, but we feel that this is most appropriately enforced through scholarly practice, not through a license.

[3] According to Creative Common’s FAQ, CC-Zero “is suitable for dedicating your copyright and related rights in computer software to the public domain, to the fullest extent possible under law. Unlike CC licenses, which should not be used for software, CC0 is compatible with many software licenses, including the GPL“.

[4] http://www.opensource.org/

[5] http://www.gnu.org/licenses/gpl.html

[6] For the motivation behind the recommended use of CC-Zero for data, see the Science Commons Protocol for Implementing Open Access Data

[7] Public open source code repositories include generic ones, such as Sourceforge, as well as those specific to particular types of code, such as R-forge for R, and CPAN for Perl. For more about best practices in scientific software development, see Baxter SM, Day SW, Fetrow JS, Reisinger SJ (2006) Scientific Software Development Is Not an Oxymoron. PLoS Comput Biol 2(9): e87. doi:10.1371/journal.pcbi.0020087

[8] http://creativecommons.org/licenses/by/3.0

[9] Many thanks to H. Lapp for starting this post. I (T. Vision) take responsibility for the opinions expressed here, as well as any sins of omission or commission.

Posted in Dryad features, Uncategorized | 9 Comments »

A new creature in the biodiversity world: the data paper

2011/06/03 by tjvision

Dryad is happy to announce a new initiative with Pensoft Publishers, the pioneering publisher behind ZooKeys and other rapid-publication open access journals, including BioRisk, Comparative Cytogenetics, International Journal of Myriapodology, Journal of Hymenoptera Research, NeoBiota, PhytoKeys, and Subterranean Biology.  Dryad is working with Pensoft to support publication of data papers in the area of biodiversity, together with the Global Biodiversity Information Facility and the Barcode of Life.  Through this effort, we aim to make the data publishing experience as smooth and rewarding as possible for authors, while at the same time making sure these important data are vetted through peer review and available for reuse in public repositories.  The full press release from Pensoft is below.

Data publishing policies and guidelines for biodiversity data published by Pensoft

Pensoft Publishers announced a data publishing project for biodiversity data in response to the increasing demands from institutions and scientists to open scientific data to anyone who would be interested to use them.

“An opinion survey amongst the authors, readers and editors of the Pensoft journal ZooKeys carried out in April convinced us that the majority of participants (84 %) are willing to publish their data, so that to make them available to anyone to use, share or integrate with other data” said Dr Lyubomir Penev, managing director of Pensoft Publishers. Among the most important incentives to publish data, the scientists mentioned  that  “open data increases transparency and the overall quality of science, the potential for collaborative research as well as an opportunity to increase academic credit in the form of citations. Therefore, providing a service to ensure a permanent publication record for published data is of key importance for the success of the project”, adds Dr Penev.

The core of the project is the concept of the “Data Paper” developed in a cooperation with the Global Biodiversity Information Facility (GBIF). Data Papers are peer-reviewed scholarly publications that describe the published datasets and provide an opportunity to data authors to receive the academic credit for their efforts. Currently, Pensoft offers the opportunity to published Data papers describing biodiversity data, Barcode of Life genome data and biodiversity-related software tools, such as interactive keys and others.

Pensoft reached an agreement for cooperation in data hosting and developing of data publishing workflows with the GBIF, the Dryad Data Repository and the Consortium for Barcode of Life.

“Data publishing becomes increasingly important and already affects the policies of the world’s leading science funding frameworks and organizations. Opening and integrating biodiversity data will be the future basis to increase efficiency of monitoring the processes of global change, conservation of nature and saving life on our planet” concluded Dr Vincent Smith, coordinator of the European Union FP7 project ViBRANT, in the framework of which a part of the work has been carried out.

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

2011/02/22 by Peggy Schaeffer

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

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