University of Glasgow

Roderic Page

[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEglOrWrYrri_oSQKEr2tYFIJLMnbaVw9rMjcyf2xR2Q08KCDrCqSkKSoVbIafAfGKPZL0ftwjPC7m8DkuRz8ueoRDqs1D_rFDVtO8MFLrBiwzZ5fXz-w1UdTxEeZ8sKGL81Spyh/s200/dryadLogo.png){#BLOGGER_PHOTO_ID_5338722072146557970
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For the last two days I\'ve been participating in a NESCent meeting on
[Dryad](http://www.datadryad.org/repo/), a \"repository of data
underlying scientific publications, with an initial focus on
evolutionary biology and related fields\". The aim of Dryad is to
provide a durable home for the kinds of data that don\'t get captured by
existing databases such as GenBank and TreeBASE (for example, the Excel
spreadsheets, Word files, and tarballs of data that, if they are lucky,
make it on to a journal\'s web site as supplementary material (like
[this example](http://systbio.org/?q=node/295)). These data have an
alarming tendency to disappear (see \"Unavailability of online
supplementary scientiﬁc information from articles published in major
journals\"
[doi:10.1096/fj.05-4784lsf](http://dx.doi.org/10.1096/fj.05-4784lsf)).  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmTrAsU2g9TQDV6F16r7wv-S093DXC_4xWmf_Yz1rEMoUdZp34R1Zn-spvC6LCNHk5u4aQf489aXmCMiXhLVs1_W2I0KN8SAwxHFudECbtsSjkne3L7V0Lvy55bnb419LNQB2h/s200/connect.png){#BLOGGER_PHOTO_ID_5338723628849637522
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it was because I was participating virtually (via [Adobe
Connect](http://www.adobe.com/products/acrobatconnectpro/), which worked
very well), but at times I felt seriously out of step with many of the
participants. I got the sense that they regard the scientific article as
primary, data as secondary, and weren\'t entirely convinced that data
needed to be treated in the same way as a publication. I was arguing
that Dryad should assign DOIs to data sets, join CrossRef, and ensure
data sets were cited in the same way as papers. For me this is a no
brainer \-- by making data equivalent to a publication, journals don\'t
need to do anything special, publishers know how to handle DOIs, and
will have fewer qualms than handling URLs, which have a nasty tendency
to break (see \"Going, Going, Gone: Lost Internet References\"
[doi:10.1126/science.1088234](http://dx.doi.org/10.1126/science.1088234)).  
  
Furthermore, being part of CrossRef would bring other benefits. Their
[cited-by linking](http://www.crossref.org/citedby.html) service enables
publishers to display lists of articles that cite a given paper \--
imagine being able to do this for data sets. Dryad could display not
just the paper associated with publication of the data set, but all
subsequent citations. As an author, I\'d love to see this. It would
enable me to see what others had done with my data, and provide an
incentive to submit my data to Dryad (providing incentives to authors to
archive data is a big issue, see Mark Costello\'s recent paper
[doi:10.1525/bio.2009.59.5.9](http://dx.doi.org/10.1525/bio.2009.59.5.9)).  
  
Not everyone saw things this way, and it\'s often a \"reality check\" to
discover that things one takes for granted are not at all obvious to
others (leading to mutual incomprehension). Many editors,
understandably, think of the the journal article as primary, and data as
something else (some even struggle to see why one would want to cite
data). There\'s also (to my mind) a ridiculous level of concern about
whether ISI would index the data. In the age of Google, who cares?
Partly these concerns may reflect the diversity of the participants.
Some subjects, such as phylogenetics, are built on reuse of previous
data, and it\'s this reuse that makes data citation both important and
potentially powerful (for more on this see my papers
[hdl:10101/npre.2009.3173.1](http://hdl.handle.net/10101/npre.2009.3173.1)
and [doi:10.1093/bib/bbn022](http://dx.doi.org/10.1093/bib/bbn022)). In
many ways, the data is more important than the publication. If I look at
a phylogenetics paper published, say 5 or more years ago, the methods
may be outmoded, the software obsolete (I might not be able to run it on
a modern machine), and the results likely to be outdated (additional
data and/or taxa changing the tree). So, the paper might be virtually
useless, but the data continues to be of value. Furthermore, the great
thing about data (especially sequence data) is that it can be used in
all sorts of unexpected ways. In disciplines such as phylogenetics, data
reuse is very common. In other areas in evolution and ecology, this
might not be the case.  
  
It will be clear from this that I buy the idea articulated by Philip
Bourne
([doi:10.1371/journal.pcbi.0​010034](http://dx.doi.org/10.1371/journal.pcbi.0010034))
that there\'s really no difference between a database and a journal
article and that the two are converging (I\'ve argued for a long time
that the best thing that could happen to phylogeneics would be if
*Molecular Phylogenetics and Evolution* and
[TreeBASE](http://www.treebase.org) were to merge and become one
entity). Data submission would equal publication. In the age of Google
where data is unreasonably effective
([doi:10.1109/mis.2009.36](http://dx.doi.org/10.1109/mis.2009.36), PDF
[here](http://www.computer.org/portal/cms_docs_intelligent/intelligent/homepage/2009/x2exp.pdf)),
privileging articles at the expense of data strikes me as archaic.  
  
So, whither Dryad? I wish it every success, and I\'m sure it will be a
great start. There are some very clever people behind it, and it takes a
lot of work to bring a community on board. However, I think Dryad\'s use
of Handles is a mistake (they are the obvious choice of identifier given
Dryad is based on DSpace), as this presents publishers with another
identifier to deal with, and has none of the benefits of DOIs. Indeed, I
would go further and say that the use of Handles + DSpace marks Dryad as
being basically yet another digital library project, which is fine, but
it puts it outside the mainstream of science publishing, and I think
that is a strategic mistake. An example of how to do things better is
[Nature Precedings](http://precedings.nature.com/), which assigns DOIs
to manuscripts, reports, and presentations. I think the use of DOIs in
this context demonstrated that *Nature* was serious, and valued these
sorts of resource. Personally, I\'d argue that Dryad should be more
ambitious, and see itself as a **publisher**, not a repository. In fact,
it could think of itself as a journal publisher. Ironically, maybe the
editors at the NESCent meeting were well advised to be wary, what they
could be witnessing is the formation of a new kind of publication, where
data is the article, and the article is data.


For the last two days I've been participating in a NESCent meeting on Dryad, a "repository of data underlying scientific publications, with an initial focus on evolutionary biology and related fields". The aim of Dryad is to provide a durable home for the kinds of data that don't get captured by existing databases such as GenBank and TreeBASE (for example, the Excel spreadsheets, Word files, and tarballs of data that, if they are lucky, make it

Messaggi di Rogue Scholar

Dryad, DOIs, and why data matters more than journal articles