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Archive for October, 2011

1E+3

Posted in New features, tagged on 2011/10/07 | 1 Comment »

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.

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Why does Dryad use CC0?

Posted in New features, tagged on 2011/10/05 | 3 Comments »

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.

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