Dryad curators: wizards behind the curtain?

Did you ever wonder what goes on behind the scenes when Dryad curators review data files submitted by authors?  There are no wizards behind our curtains, just real live information specialists and trained data curators.

by Kaptain Kobold via Flickr

by Kaptain Kobold via Flickr

Dryad’s curation process is intentionally lightweight, so it doesn’t delay the availability of the data. Curators don’t review the scientific merit of the files – that is left to peer reviewers and the scientific community. Instead, we rely on our curators’ expertise in library and information science to ensure the integrity and preservation of the data.

Curators perform basic checks on each submission (can the files be opened? are they free of copyright restrictions? do they appear to be free of sensitive data?). The completeness and correctness of the metadata is checked and the DOI is officially registered. During their work, Dryad curators encounter thousands of data files in any number of file formats. Our team examines all of these data files to ensure they do, in fact, include data, and not manuscripts, or pictures of kittens.

Curators may communicate directly with submitters to address issues and/or to make suggestions about enhancing the description and reusability of the data package. They can also create new versions of data packages should corrections or additions be needed after archiving. Ultimately, the responsibility for the content of the files rests with the submitters, but Dryad’s curators can help to catch and fix many common problems – and some rare ones, too.

fileTypes_wordleSince Dryad’s inception, curation operations have been led by the Metadata Research Center (or MRC) directed by Dr. Jane Greenberg, initially at the University of North Carolina at Chapel Hill, and now at Drexel University. The team is supervised by Senior Curator Erin Clary, and currently includes all students in, or graduates of, Library and Information Science (LIS) or Informatics Master’s programs.

So, (wizard) hats off to all our behind-the-curtains data curators, whose vital contributions ensure that the data in the repository is findable and usable. If you have a question about Dryad curation or need advice on preparing your data for archiving, don’t hesitate to email us at curator@datadryad.org.

40 Years of Data

We are delighted to announce the availability of the data underlying the book “40 Years of EvGrant 40yrs of evol cover copyolution” by Peter and Rosemary Grant. In this new book, the Grants give an account of their classic, long-term study of Darwin’s finches on one of the Galápagos Islands.  From the announcement by Princeton University Press.

The authors used a vast and unparalleled range of ecological, behavioral, and genetic data–including song recordings, DNA analyses, and feeding and breeding behavior–to measure changes in finch populations on the small island of Daphne Major in the Galápagos archipelago. They find that natural selection happens repeatedly, that finches hybridize and exchange genes rarely, and that they compete for scarce food in times of drought, with the remarkable result that the finch populations today differ significantly in average beak size and shape from those of forty years ago. The authors’ most spectacular discovery is the initiation and establishment of a new lineage that now behaves as a new species, differing from others in size, song, and other characteristics. The authors emphasize the immeasurable value of continuous long-term studies of natural populations and of critical opportunities for detecting and understanding rare but significant events.

“40 Years of Evolution”, which is written a style that will be accessible to researchers, students and a more general audience, includes over 100 line drawings illustrating quantitative patterns among the many variables the authors have studied. There are 82 data files being made available in Dryad for researchers and students to explore the numbers behind those figures.  We are proud to be the custodians of this unique scientific resource.

For students and teachers interested in the Grants’ long-term studies of Darwin’s Finches, we also recommend the excellent background material and hands-on data analysis activities from the HHMI BioInteractive site.

Data citation: Grant PR, Grant BR (2013) Data from: 40 years of evolution. Darwin’s finches on Daphne Major Island. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.g6g3h

 

Ecology and Evolution integrates with Dryad

Ecology and Evolution is the latest journal to integrate submission of manuscripts with data to Dryad.  Ecology and Evolution is a Wiley open access journal supported by other journals published by Wiley, including journals owned by the British Ecological Society, the European Society for Evolutionary Biology and the Society for the Study of Evolution.

Ecology and Evolution’s integration with Dryad means that all authors will be invited to archive the data supporting the conclusions in the article, and their process of depositing data files has been simplified by the behind-scenes-coordination between the journal and the repository. Authors are invited to submit data to Dryad when their manuscript is accepted, and have the option to set a one-year embargo on the availability of their data files. There are already 50 articles in the journal with their underlying data archived in Dryad.

EcologyEvolution_DryadThe journal has a strong data policy, requiring “as a condition for publication, that data supporting the results in the paper should be archived in an appropriate public archive, such as GenBank, TreeBASE, Dryad, the Knowledge Network for Biocomplexity or other suitable long-term and stable public repositories.”

Editor-in-chief Allen J. Moore  says “We are fully behind Dryad… and I think things are going well.”  Moore is a strong proponent of open data, a former Dryad Board member, and an experienced data depositor.

The journal covers Data Publishing Charges for its authors.

 

New open access journal Elementa integrates with Dryad

We are pleased to announce that Elementa is the latest journal to integrate submission of manuscripts with data to Dryad.  Elementa’s integration with Dryad means that all authors will be invited to archive the data supporting the conclusions in their article, and their process of depositing data files has been simplified by the behind-scenes-coordination between the journal and the repository. Authors will be invited to submit data to Dryad when their manuscript is accepted, and will have the option to set a one-year embargo on the availability of their data files.

The journal has a strong data policy, requiring “all major datasets associated with an article to be made freely and widely available.” The journal is also a Dryad member, and will be covering the charges for its authors when Dryad begins assessing Data Publishing Charges (DPC) on September 1.

Elementa: Science of the Anthropocene is a new open access scientific journal publishing original research reporting new knowledge of the Earth’s physical, chemical, and biological systems.

logo The journal is a nonprofit collaborative involving BioOne, Dartmouth, the Georgia Institute of Technology, the University of Colorado, the University of Michigan, and the University of Washington. Elementa is comprised of six inaugural knowledge domains: Atmospheric Science, Earth and Environmental Science, Ecology, Ocean Science, Sustainable Engineering, and Sustainability Transitions.

The journal is now welcoming article submissions, and the first articles will be published in September.

Ecology Letters integrates with Dryad

We are pleased to announce that Ecology Letters is the latest journal to integrate submission of manuscripts with data to Dryad.  In this process, the journal and repository communicate behind the scenes in order to streamline data submission for authors, and also to ensure that the article contains a permanent link to the data.

EcolLettCover copyEcology Letters is published by The French National Center for Scientific Research (CNRS), a public basic-research organization that defines its mission as producing knowledge and making it available to society. Marcel Holyaok, the journal’s Editor-in-Chief, has been actively involved with Dryad since 2009, serving on the Consortium Board from 2009-2011, and currently on the elected Board of Directors.

There are already a number of articles in Ecology Letters with associated data in Dryad, including the most frequently downloaded data file in Dryad, The Global Wood Density Database, which has been downloaded nearly 6000 times:

Zanne AE, Lopez-Gonzalez G, Coomes DA, Ilic J, Jansen S, Lewis SL, Miller RB, Swenson NG, Wiemann MC, Chave J (2009) Data from: Towards a worldwide wood economics spectrum. Dryad Digital Repository. doi:10.5061/dryad.234

Article:

Chave J, Coomes D, Jansen S, Lewis SL, Swenson NG, Zanne AE (2009) Towards a worldwide wood economics spectrum. Ecology Letters 12: 351-366. doi:10.1111/j.1461-0248.2009.01285.x

Dryad is delighted to welcome Ecology Letters to the growing group of journals that have taken this important step to support and facilitate their authors’ data archiving.

Elsevier and Dryad implement reciprocal linking

We are pleased to share below the text of a press release from Elsevier, announcing use of this image to direct viewers of online articles to the underlying data in Dryad. Dryad_web_banner_small_v4eSee below for sample articles; the image displays on the right sidebar, under Applications and Tools. This Dryad widget may be used by any publisher or journal to facilitate access to related publicly available data that authors have archived in Dryad.

Elsevier, a world-leading provider of scientific, technical and medical information products and services, and the Dryad Digital Repository, a leading archive for scientific and medical research data, today announced that they have implemented two-way linking between their respective content.

The Dryad Digital Repository provides facilities for archiving, discovery and accessibility of data files associated with any published article in the sciences or medicine, as well as software scripts and other files important to the article. Dryad is a nonprofit organization committed to its mission of making data publicly available for research and educational reuse. All data files stored in Dryad receive persistent, resolvable Digital Object Identifiers (DOIs) to ensure their proper citation.

Scientific and medical research datasets stored by Dryad for research articles published in 28 Elsevier journals can now be immediately accessed from the online articles on ScienceDirect and vice versa. This allows readers to easily find the background information they need in order to develop a deeper understanding of the article, and also helps to place the article in a larger context.

Dr. Todd Vision, Associate Director for Informatics at the National Evolutionary Synthesis Center and Principal Investigator on the primary NSF grant funding Dryad since 2008, said, “We are delighted to work with Elsevier in cementing the union between scientific articles and research data. Molecular Phylogenetics and Evolution was one of the first journals that joined the Dryad consortium and we would like to applaud them for recognizing that the integrity, rigor, and long-term impact of the science published by the journal is strengthened by archiving the associated data at the time of publication. We also believe that authors themselves will ultimately benefit, in the form of increased citations and other forms of professional credit, for making their data available for others to reuse.”

Dr. Derek Wildman, Editor in Chief of Molecular Phylogenetics and Evolution, a journal which has successfully incorporated and uses the reciprocal linking option between Dyrad and ScienceDirect, said, “DNA sequence data serves as the basis for the majority of the studies we publish. Dryad has done an excellent job in establishing a public archive for all types of data used in evolutionary biology. By making these data sets public and allowing for direct linking between a published research papers, scientists can more efficiently build on the work of their predecessors, strengthening scientific research enterprise. We see the incorporation of the two-way linking as a win for all parties.”

The first 28 journals hosted on ScienceDirect to feature the reciprocal linking option, displayed in the right hand sidebar of the online article page view, are:

  • Animal Behaviour
  • Applied Soil Ecology
  • Behavioural Processes
  • Biological Conservation
  • Comparative Biochemistry and Physiology. Part D, Genomics and Proteomics
  • Ecological Indicators
  • Environmental Pollution
  • Fisheries Research
  • Fungal Genetics and Biology
  • Gene
  • Hormones and Behavior
  • Infection, Genetics and Evolution
  • International Journal for Parasitology
  • Journal of Biomedical Informatics
  • Journal of Human Evolution
  • Journal of Informetrics
  • Marine Genomics
  • Molecular and Biochemical Parasitology
  • Molecular Phylogenetics and Evolution
  • Palaeogeography, Palaeoclimatology, Palaeoecology
  • Protist
  • Quaternary Science Reviews
  • Science of the Total Environment
  • Soil Biology and Biochemistry
  • Theoretical Population Biology
  • Toxicon
  • Trends in Ecology and Evolution
  • Virus Research

This type of linking between articles and data is one of the pillars of Article of the Future, Elsevier’s on-going program to improve the format of the scientific article. Elsevier collaborates with more than thirty data repositories, and is continually looking to collaborate with other relevant organizations.

View article examples on ScienceDirect:

R. Alexander Pyron, John J. Wiens, A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians, Molecular Phylogenetics and Evolution, Volume 61, Issue 2, November 2011, pp. 543-583, http://dx.doi.org/10.1016/j.ympev.2011.06.012.

Peter J. Unmack, Gerald R. Allen, Jerald B. Johnson, Phylogeny and biogeography of rainbowfishes (Melanotaeniidae) from Australia and New Guinea, Molecular Phylogenetics and Evolution, Volume 67, Issue 1, April 2013, pp. 15-27, http://dx.doi.org/10.1016/j.ympev.2012.12.019.

James Starrett, Marshal Hedin, Nadia Ayoub, Cheryl Y. Hayashi, Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae, Gene, Volume 524, Issue 2, July 2013, pp. 175-186, http://dx.doi.org/10.1016/j.gene.2013.04.037.

Mercy Y. Akinyi, Jenny Tung, Maamun Jeneby, Nilesh B. Patel, Jeanne Altmann, Susan C. Alberts, Role of grooming in reducing tick load in wild baboons (Papio cynocephalus), Animal Behaviour, Volume 85, Issue 3, March 2013, pp. 559-568, http://dx.doi.org/10.1016/j.anbehav.2012.12.012

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About Dryad

The Dryad Digital Repository is a curated resource that makes the data underlying scientific and medical publications discoverable, freely reusable, and citable. By providing a general-purpose home for a wide diversity of data types, Dryad benefits individual researchers, educators and students as well as a diversity of stakeholder organizations. Dryad is a member-based nonprofit organization incorporated in North Carolina, USA with users around the world.

About Elsevier

Elsevier is a world-leading provider of scientific, technical and medical information products and services. The company works in partnership with the global science and health communities to publish more than 2,000 journals, including The Lancet and Cell, and close to 20,000 book titles, including major reference works from Mosby and Saunders. Elsevier’s online solutions include ScienceDirect, Scopus, Reaxys, ClinicalKey and Mosby’s Suite, which enhance the productivity of science and health professionals, and the SciVal suite and MEDai’s Pinpoint Review, which help research and health care institutions deliver better outcomes more cost-effectively.

A global business headquartered in Amsterdam, Elsevier employs 7,000 people worldwide. The company is part of Reed Elsevier Group plc, a world leading provider of professional information solutions. The group employs more than 30,000 people, including more than 15,000 in North America. Reed Elsevier Group plc is owned equally by two parent companies, Reed Elsevier PLC and Reed Elsevier NV. Their shares are traded on the London, Amsterdam and New York Stock Exchanges using the following ticker symbols: London: REL; Amsterdam: REN; New York: RUK and ENL.

Media contact

Dale Seaton
Executive Publisher, Journals
Elsevier
+1 212 633 3862
d.seaton@elsevier.com
 
**Update: In addition to DOIs, the banner widget also works with PubMed IDs

Odd couples in the animal kingdom, but not in a data repository

We are celebrating the recent publication in Dryad of the first data to accompany a book [1, 2]. Odd Couples: Extraordinary Differences Between the Sexes in the Animal Kingdom, from Princeton University Press, examines the occasionally surprising gender differences in animals, and what it means to be male or female in the animal kingdom. It is intended for both general and scientific readers.

The author, Daphne Fairbairn, a professor of biology at the University of California, Riverside, and Editor-in-Chief of Evolution, a Dryad partner journal, describes the data as:

…a survey of all recorded sexual dimorphisms in all of the animal classes that contain dioecious species (species with separate sexes).  It categorizes the prevalence of dioecy, the types of differences between the sexes (size, shape, color, etc.) and the magnitude of the differences.  I use this survey to construct frequency plots in the book, but there was no room to publish the full survey results.  This is the first time that such a survey has been done and I am hoping that it will prove useful to other biologists who might use the data for hypothesis testing.  I might even get around to this myself!

I think these archived data are one of the most significant contributions of the book to the scientific literature, even though they will not be important for non-specialist readers.

While most data in Dryad accompany journal articles, we are happy to see data archiving catching on with other types of publications such as books, thesis dissertations and conference proceedings.  Please contact us if you are interested in submitting data and have any questions about its suitability for Dryad.

[1] Fairbairn DJ (2013) Data from: Odd couples: extraordinary differences between the sexes in the animal kingdom. Dryad Digital Repository. doi:10.5061/dryad.n48cm

[2] Fairbairn DJ (2013) Odd Couples: Extraordinary Differences Between the Sexes in the Animal Kingdom, Princeton University Press, ISBN:9780691141961.