Introduction to Dryad !

Martin Fenner Dryad Board Member Technical Lead Article-Level Metrics Public Library of Science (PLOS) http://orcid.org/0000-0003-1419-2405

SummaryResearch data repository for the data underlying scholarly publications. !

Publishers are encouraged to facilitate data archiving by coordinating the submission of manuscripts with submission of data to Dryad. !

Dryad is governed by a nonprofit membership organization. Membership is open to any stakeholder organization, including but not limited to journals, scientific societies, publishers, research institutions, libraries, and funding organizations.

http://datadryad.org/pages/organization

Journal Policies on Research DataTherefore, a condition of publication in a Nature journal is that authors are required to make materials, data and associated protocols promptly available to readers without undue qualifications. http://www.nature.com/authors/policies/availability.html !To allow others to replicate and build on work published in PNAS, authors must make materials, data, and associated protocols available to readers. http://www.pnas.org/site/misc/iforc.pdf

!

PLOS journals require authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception. http://www.plosone.org/static/policies.action#sharing

Most Ecology Data become Irretrievable when Preserved by Researchers

Vines TH et al. (2013) Current Biology http://dx.doi.org/10.1016/j.cub.2013.11.014

Our results reinforce the notion that, in the long term, research data cannot be reliably preserved by individual researchers, and further demonstrate the urgent need for policies mandating data sharing via public archives.

Joint Data Archiving Policy (JDAP)Data are important products of the scientific enterprise,

and they should be preserved and usable for decades in the future.

As a condition for publication, data supporting the results in the article should be deposited in an appropriate public archive.

Authors may elect to embargo access to the data for a period up to a year after publication.

Exceptions may be granted at the discretion of the editor, especially for sensitive information.

http://datadryad.org/pages/jdap

Roche et al. (2014) PLOS Biology http://dx.doi.org/10.1371/journal.pbio.1001779

Embargoes chosen by Dryad Authors

Embargo selections of Dryad data authors for the 10,108 files in Dryad (http://datadryad.org/) deposited from inception to September 20, 2013. Data include only datasets related to articles published in journals for which the authors had the option of selecting an embargo.

Tables, figures, supplements = publishers

Analyzed data = repositories

Raw data = institutions

Research data and publications

The Long Tail of Orphan DataV

olum

e

Rank frequency of datatype

Specialized repositories (such as GEO)

Orphan data

Heidorn PB (2008) http://hdl.handle.net/2142/9127

The large volume of long-tail data is rarely preserved, less standardized, rich in information content and often irreplaceable.

Disciplinary Scope

As a community-driven project Dryad started in the Life Sciences, but is open to submissions from all disciplines, including Physical and Engineering Sciences, Social Sciences and Humanities.

What do the data look like?• Size –Mean number of files: 2.4 –Mean storage requirement: 9.7 Mb

• Format types – 60% plain text (unrecognized content standard) – 11% Excel – 5% PDF – 3% Word

Materials and Methods

References

Quality of DataCuration of all datasets: checks that data files are readable,

metadata complete and correct, etc. Description of data, methods and other relevant

information in the related journal article Availability of datasets during journal article peer review

(some journals).

Materials and Methods … As recombination events can lead to over-estimation of nucleotide substitution rates, each dataset was scanned for recombination using seven different algorithms (RDP, GENECONV, Bootscan, MaxChi, Chimaera, SiScan, and 3seq) implemented in RDP v3.44 [83]. Sequences implicated as recombinant by two or more algorithms were excluded from further analysis. These finalized alignments were deposited into Dryad (doi:10.5061/dryad.58ss8). Modeltest v3.7 [84] was used to determine the best-fit model of nucleotide substitution for each dataset (by AIC)…

http://dx.doi.org/10.1371/journal.ppat.1003838

Dryad uses DataCite DOIs and Metadata Schema

http://dx.doi.org/10.5438/0008 http://datacite.labs.orcid-eu.org/?q=10.5061%2FDRYAD.8271F

Required fields needed for data citation: identifier, creator, title, publisher, publication year

Describes related documents e.g. parts, related journal article, or newer version

Link to ORCID identifiers

Metadata of Related Article can provide additional information

Korpela K, Flint HJ, Johnstone AM, Lappi J, Poutanen K, et al. (2014) Gut Microbiota Signatures Predict Host and Microbiota Responses to Dietary Interventions in Obese Individuals. PLOS ONE http://dx.doi.org/10.1371/journal.pone.0090702

Funding: The study involved samples from previously published studies including the Belgian trial funded the FNRS grant, British study funded by World Cancer Research Fund and the Finnish trials funded by EU 6th Framework Programme in project HEALTHGRAIN. WMdV and AS are funded by the grants to WMdV by Academy of Finland (grant 1141130) http://www.aka.fi/en-GB/A/ and ERC (grant 400795) http://erc.europa.eu/advanced-grants. KK is funded by the Helsinki Biomedical Graduate Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. !Author Contributions: Conceived and designed the experiments: AS KK. Performed the experiments: KK. Analyzed the data: KK. Contributed reagents/materials/analysis tools: HF AJ JL KP ED ND WMdV. Wrote the paper: KK AS WMdV HF ND.

http://europepmc.org/abstract/MED/24453561

Metrics for Related Article: Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux

http://dx.doi.org/10.5061/dryad.j08jp http://dx.doi.org/10.1371/journal.pone.0041389

Dryad Revenue Model• Deposit fees (started September 2013)

• Pay upfront for both ingest and long-term preservation • At 10K data packages/year, ~ €40 per deposit • Non-operational costs covered by membership fees, grants for R&D, etc.

• Payment schemes • Journal subscription • Per-deposit fees, covered by journal (pre or post-submission), institution

or funder • Author-pays (last resort!)

• Neutral with regards to the business model of journals • National Science Foundation (NSF) grant until 2016

Beagrie N, Eakin-Richards L, Vision TJ (2009) Business models and cost estimation: Dryad repository case study. http://www.ifs.tuwien.ac.at/dp/ipres2010/papers/beagrie-37.pdf

Data Publication Charges

• Waivers • for authors from countries classified by the World Bank as low-income

or lower-middle-income economies • Surcharges • for non-integrated submissions • for data packages greater than 10 GB

Dryad MembershipDryad is a nonprofit membership organization. Membership is open to any stakeholder organization, including but not limited to journals, scientific societies, publishers, research institutions, libraries, and funding organizations. !Members have a say in the governance of the organization through nomination and election of its Board of Directors and voting on amendments to its Bylaws at the Annual Meeting; receive discounts on submission fees; participate in an active knowledge sharing network; and help advance the mission of the organization through their financial support.

https://trello.com/b/dlAq9aSV/dryad-developmentDryad uses DSpace open source software for digital repositories