Archiving Research Data,
Dryad,and Publishers
Neil Beagrie, Charles Beagrie Ltd
Bloomsbury Conference June 2010
With contributions from Julia Chruszcz, Peter Williams, and Todd Vision
Overview
• The Challenge;
• The Dryad Consortium;
• Supplementary Data and Publishers;
• Research Data Preservation Costs (KRDS);
• The Future.
The Challenge
PRC Global Study
n=3759
n=2940
n=1262
n=1653
n=2989
n=2118
n=1294
n=2565
n=1868
n=2273
n=841
n=2362
4
Source: PRC global study (forthcoming)
Requesting Data
• Wicherts et al. (2006 Am. Psychol. 61, 726)
requested data from the 141 most recent
articles in American Psychological
Association (APA) journals.
“6 months later, after … 400 emails, [sending]
detailed descriptions of our study aims, approvals
of our ethical committee, signed assurances not to
share data with others, and even our full
resumes…”
Only 27% of authors shared their data
The Dryad Consortium of
Scholarly Societies and
publishers (and libraries)
Archiving at publication
• Avoids loss, corruption, obsolescence of data files;
• The point in time when authors are best able to ensure
the correctness of data and metadata;
• Authors have incentive to deposit their data in order to
complete the publication process;
• Journals are best able to monitor compliance with policy;
• In short, the “Genbank model” works.
Incentives to authors
• Access to colleagues’ data
• Visibility and citability
– Another way for work to have high impact
• Integration
– Combinability with other data adds value
• Long-term preservation
– Including data format migration
• Ad hoc data sharing can be burdensome
– Deposition to multiple specialized repositories
– Fulfilling individual requests for data takes effort
Joint Data Archiving Policy
• DEPOSIT AT PUBLICATION
– As a condition for publication, all data used in the paper should be
archived in an appropriate public archive.
• REPEATABILITY
– Data should be given with sufficient detail so that together with the
paper content, each result in the published paper may be re-created.
• EMBARGO
– Authors may elect to have the data publicly available at time of
publication, or if the archive allows opt to embargo access to the data.
• EXCEPTIONS
– Exceptions may be granted at the discretion of the editor, especially
for sensitive information such as the location of endangered species.
• COORDINATION
– The aim is for the Dryad consortium of journals to adopt this policy
simultaneously.
That’s all well and good, but
where’s this “appropriate
public archive”?
A mosaic of specialized
databases
• There are a growing number to which deposition
is encouraged/required (Genbank, Treebase)
– And others are emerging
• A world in which every datatype had its own
required database, each with its own submission
system:
– Would be a huge burden on authors
– Would inevitably leave some data orphaned
– Might never be financially possible
Overcoming the submission
burden
• Integrating journal submission and data
submission
– Prepopulating bibliographic metadata
– “Handshaking” with specialized repositories
• Enhancing low-quality author-provided
metadata
– Human curation
– Machine assisted metadata enhancement
The Dryad Digital Repository
The Repository
• Dryad is a repository (at Duke) for datasets
underlying scientific research articles;
• ƒ
Its initial focus has been evolution and ecology;
• ƒ
Participating journals subscribe to the Joint Data
Archiving Policy;
• ƒ
Dryad datasets will have (DOIs), and Creative
Commons ‘CC-Zero’ licenses;
• Project ƒ
Funded by the National Science Foundation
2008-2012;
• Sustainability plan a key deliverable.
Supplementary Data and
Publishers
Overview
• Consultancy for Dryad Sustainability: covered areas of draft
business plan and sustainability for Dryad
• Presenting one of the contributions(publishers) to section on
Comparators and Costs
• Outcomes from desk research and 12 interviews with
publishers/data publishers + some additional input drawn
from Keeping Research Data Safe
• Very brief presentation – article in preparation for Learned
Publishing Oct 2010 issue….KRDS2 available from JISC
Interviewees
•
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•
•
•
•
•
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Journal of Clinical Investigation
Journal of the American Medical Association
Molecular Phylogenetics and Evolution (Elsevier)
Journal of Heredity (OUP)
Ecological Society of America
Wiley-Blackwell + Ecology Letters
Royal Society
Federation of American Societies for Experimental Biology
OECD Publishing
Internet Archaeology and Archaeology Data Service
Pangaea: Publishing Network for Geoscientific &
Environmental Data
• Dataverse Network (Social Sciences, Harvard)
Some Findings: growth
• Many interviewees stated that supplementary data and
materials are showings rapid growth
• 3 gave figures: from 32 articles in 2000, to 251 in 2009 – an
increase of 784%; from 6% in 2005 to 38% in 2009; from
2% a decade ago to 87% in 2009.
Some Findings: workflow
• supplementary data have grown organically at the various
journals investigated (author driven);
• Both the work and the costs being absorbed into the daily
running of journals;
• in 4 cases minimal impact on work duties; in 5 others there
was a significant but often unquantified impact (two of these
might be considered data publications with a focus on
publishing data papers or datasets); and in 3 cases the
information was not available or unknown;
• can be explained in terms of level of effort or importance
applied : the greatest levels of effort are associated with
copy editing, format migration, addition of metadata, etc,
whilst the least effort is required for simply hosting the
material; and/or high-levels of automation in the workflow.
Some Findings: costs
• These were in most cases unknown or only partially known;
• Costs mentioned but usually not quantified include: digital
storage costs, salary costs of journal staff; and long term
preservation costs;
• detailed cost information was really only available from
Internet Archaeology via Archaeology Data Service which
had participated in an activity based costing study (KRDS2);
• Internet Archaeology archiving costs reflect those for a
“dataset publisher” so only a comparator for part of Dryad’s
content – large datasets.
Some Findings: revenue
• only author fees and journal subscription fees were
mentioned as current revenue sources for the
supplementary materials in journals;
• 3 journals interviewed have author charges for
supplementary materials (see next slide);
•
The data archiving and sharing organisations interviewed
relied primarily on (uncertain) research grants and
temporary or re-current core funding, but one had access to
a small endowment and another has a charging policy for
some depositors.
Some Findings: author charges
• Journal of Clinical Investigation - authors are charged $300
for supplemental data to appear online with accepted
articles;
• Ecological Archives - submission of ‘appendices and
supplements’ is free up to 10MB. Above this, there is a fee
of $250 for the first 1 GB and $50 for each subsequent GB.
The fee for publication of a data paper is $250 for
publication of the abstract in the relevant journal plus
publication of up to 10 MB in Ecological Archives. An
additional $250 is charged for data sets between 10MB and
1GB, and for larger datasets there is an additional $50 per
GB fee;
• The Federation of American Societies for Experimental
Biology (FASEB) charges $100 for each Supplemental file.
Keeping Research Data Safe
(KRDS1 & KRDS2):
JISC-funded studies of Research Data
Preservation Costs
(separate Dryad costing project by Lori EakinRichards based on KRDS approach)
KRDS: what did we learn?
Whole of Service costing/Seeing the“Big Picture”
Selection of 2009 Allocation of UKDA Activity Costs
Acquisition
5.8%
Ingest
21.5%
A. Storage +Pres. Planning
3.1%
Access
16.9%
KRDS:Implications
• Changing view of digital preservation costs:
– “getting stuff in and out” costs much higher than
“keeping it (bit preservation + migration)”;
– Staff costs c.70% of total costs;
– Importance of economies of scale and
automation;
– Findings of KRDS and Dryad Repository’s own
activity costing projections fed into Dryad
sustainability planning.
Future Plans
• Dryad sustainability plan being put to Dryad
member societies and publishers;
• Dryad extending consortium to new members
–achieving economies of scale;
• Bid to JISC to establish Dryad-UK;
• Extending KRDS research and
implementations.
Further Information
Dryad see www.datadryad.org
Keeping Research Data Safe2 (KRDS2)
webpage at www.beagrie.com/jisc.php
KRDS2 report available from JISC website
http://www.jisc.ac.uk/publications/reports/20
10/keepingresearchdatasafe2.aspx#downlo
ads
Email: neil@beagrie.com