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Archive for the ‘Journals’ Category

In our latest post, our Executive Director Melissanne Scheld sits down with Dryad’s Board of Directors Chair, Professor Charles Fox, to discuss challenges researchers face today, how Dryad is helping alleviate some of those pain points, why Dryad has had such staying power in a quickly changing industry,  . . . and then we move on to dessert. 

Chuck Fox

Can you tell us a little about your professional background and how that intersects with Dryad’s mission?

I wear two hats in my professional life – I am an evolutionary ecologist who studies various aspects of insect biology at the University of Kentucky, and I am a journal editor (Executive Editor of Functional Ecology).

My involvement with open data and Dryad began fortuitously in 2006. The British Ecological Society was invited to send a representative to a Data Registry Workshop, organized by the Ecological Society of America, to be held that December in Santa Barbara, California. I am (and was at that time) an editor of one of the British Ecological Society’s journals, Functional Ecology, and I live in the U.S. So Lindsay Haddon, who was Publications Manager for the BES, asked me to attend the workshop  as their representative. Before that meeting I don’t recall having thought much about open data or data archives, but I was excited to attend the meeting in part because the topic intrigued me and, selfishly, because my parents live in southern California and this was an opportunity to visit them. The discussions at that meeting, plus those at a couple follow-up meetings over the next couple years, including one at NESCent in Durham, North Carolina, and another in Vancouver, convinced me that data publishing, and open data more generally, should be a part of research publication. So I began lobbying the BES to adopt an open data policy and become a founding member of Dryad. I wrote a proposed data policy – just a revision of the Journal Sata Archiving Policy, JDAP, that many ecology and evolution journals adopted – and submitted that proposal to the BES’ publication committee. It took a few years, but in 2011 the BES adopted that data policy across their suite of journals and became a member of Dryad. The BES has since been a strong supporter of open data and required data publication as a condition of publishing a manuscript in one of their journals. Probably because I was a vocal proponent of data policies at BES meetings (along with a few others, most notably Tim Coulson), I was nominated to be a Dryad board member, and was elected to the board in 2013.

As an educator,  what are some of the biggest changes you’ve seen in the classroom during your career?

When I started teaching, first as a graduate student (teaching assistant) and then as a young university professor, we didn’t have Powerpoint and digital projectors. So I made heavy use of a chalkboard (or dry erase board) during lecture, and used an overhead projector for more complicated graphics. Students had to take detailed notes on the lecture, which required them to write furiously all throughout the class. Nowadays I produce detailed PowerPoint slides that include most of the material I cover, so I write very little on the chalkboard. And, because I can provide my slides to students before class – as a pdf that they can print and bring to class – the students are freed from scribbling furiously to capture every detail. Students still need to take some notes (my slides do not include every detail), but they are largely freed to listen to lecture and participate in class discussions. I am not convinced, though, that these changes have led to improved learning, at least not in all students. Having information too easily available, including downloadable class materials, seems to cause some students to actually disengage from class, and ultimately do poorly, possibly because they think they don’t need to attend class, or engage when they do attend, since they have all of the materials easily accessible to them outside the classroom?

What do you think the biggest challenges are for open science research today?

I have been amazed at how quickly open data has become accepted as the standard in the ecology and evolution research communities. When data policies were first proposed to journals there was substantial resistance to their adoption – journals were nervous about possibly driving away authors, and editors (who are also researchers) shared the views that were common in the community regarding ownership of their own data – but over just a few years the resistance largely disappeared among editors, societies and publishers, such that a large proportion of the top journals in the field have adopted policies requiring data to be published alongside research manuscripts. That said, some significant challenges remain, both on the researcher side and on the repository side. On the repository side, sustainable funding remains the largest hurdle. Data repositories cost money to run, such as for staff and infrastructure. Dryad has been relying on a mix of data publication charges (DPCs) and grants to fund its mission. This has worked for us so far, but constantly chasing grants is a lot of work for those writing grants, and the cost to researchers paying DPCs, albeit small, is not trivial for those without grant support.

On the researcher side, though data publishing has mostly become an accepted part of research publication in the community, there remain many important cultural and practical challenges to making open data universally practiced.  These include the development of standards for data citation and reuse (not restrictions on data reuse, but community expectations for citation and collaboration), balancing views of data ownership with the needs of the community, balancing the concerns of researchers that produce long-term datasets with those of the community, and others. We also need to improve education about data, such as teaching our students how to organize and properly annotate their datasets so that they are useful for other researchers after publication. Even when data are made available by researchers, actually using those data can be challenging if they are not well organized and annotated.

When researchers are deciding in which repository to deposit their research data, what values and functions should they consider?

Researchers should choose a repository that best fits the type of data they have to deposit and the community that will likely be reusing it. There are many repositories that handle specialized data types, such as genetic sequence data or data to be used for phylogenetic analysis. If your data suits a specialized archive, choose that. But the overwhelming majority of data generated by ecologists don’t fit into specialized archives. It’s for these types of data that Dryad was developed.

So what does Dryad offer researchers? From the perspective of the dataset author, Dryad links your dataset directly to the manuscript you have published about the dataset. This provides users detailed metadata on the contents of your dataset, helping them understand the dataset and use it correctly for future research. Dryad also ensures that your dataset is discoverable, whether you start at the journal page, on Dryad’s site, or any of a large number of collaborator services. The value of Dryad to the dataset user are similar – easy discoverability of data and clear links to the data collection details (i.e., links to the associated manuscripts).  

You’ve held several roles on Dryad’s Board of Directors – what about this organization compels you to volunteer your free time?

My experiences as a scientist, a journal editor, and participating in open data discussions have convinced me that data publication is an essential part of research publication. For decades, or even centuries, we’ve relied on a publishing model where researchers write manuscripts that describe the work they have done and summarize their results and conclusions for the broader community. That’s the typical journal paper, and was the limit of what could be done in an age where everything had to fit onto the printed page and be distributed on paper. Nowadays we have near infinite space in a digital medium to not just summarize our results, but also provide all of the details, including the actual data, as part of the research presentation. It will always be important to have an author summarize their findings and place their work into context – that intellectual contribution is an essential part of communicating your research – but there’s no reason that’s where we need to stop. I imagine a world where a reader can click on a figure, or table, or other part of a manuscript and be taken directly to the relevant details – the actual data presented in the figure, the statistical models underlying the analyses, more detailed descriptions of study sites or organisms, and possibly many other types of information about the experiment, data collection, equipment used, results, etc. We shouldn’t be constrained by historical limitations of the printed page. We’re not yet even close to where I think we can and should be  going, but making data an integral part of research publication is a huge step in the right direction. So I enthusiastically support journal mandates that require data to be published alongside each manuscript presenting research results. And facilitating this is a core part of Dryad’s mission, which leads me to enthusiastically support both Dryad’s mission and the organization itself!

Pumpkin or apple pie?  

Those are my two favorite pies, so it’s a tough question. If served a la mode, i.e., with ice cream, then I’d most often pick apple pie. But, without ice cream, I’d have to choose pumpkin pie.

Stay tuned for future conversations with industry thought leaders and other relevant blog posts here at Dryad News and Views.

 

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Chain link fence with highway in backgroundDryad is a curated, non-profit, general-purpose repository specifically for data underlying scientific and medical publications — mainly journal articles. As such, we place great importance on linking data packages to the articles with which they are associated, and we try our best to encourage authors and journals to link back to the Dryad data from the article, ideally in the form of a reference in the works cited section. (There’s still a long way to go in this latter effort; see this study from 2016 for evidence).

Submission integration provides closer coordination between Dryad and journals throughout the publishing workflow, and simplifies the data submission process for authors. We’ve already implemented this free service with 120 journals. If you’re interested in integrating your journal, please contact us.

We’re excited to share a few recent updates that are helping to make our data-article linkages more efficient, discoverable, and re-usable by other publishers/systems.

The Automated Publication Updater

One of the greatest housekeeping challenges for our curation team lies in finding out when the articles associated with Dryad data packages become available online. Once they do, we want to add the article citation and DOI link to our record as quickly as possible, and to release any data embargoes placed “until the article appears.” Historically, we’ve achieved this through a laborious patchwork of web searches, journal alert emails, and notifications from authors or editors themselves.

But over the past year or so, we’ve built and refined a webapp that we call the APU (or Automated Publication Updater). This super-handy tool essentially compares data packages in the Dryad workflow with publication metadata available at Crossref. When a good match is found, it automatically updates article-related fields in the Dryad record, and then sends our curation team an email alert so they they can validate the match and finalize the record. The webapp can be easily run by curators as often as needed (usually a few times a week).

While the APU doesn’t find everything, it has dramatically improved both efficiency with which we add article information and links to Dryad records — and our curators’ happiness levels. Big win. (If you’re interested in the technical details, you can find them on our wiki).

Scholix

Dryad is also pleased to be a contributor to Scholix, or Scholarly Link Exchange, an initiative of the Research Data Alliance (RDA) and the World Data System (WDS). Scholix is a high-level interoperability framework for exchanging information about the links between scholarly literature and data.

  • The problem: Many disconnected sources of scholarly output, with different practices including various persistent identifier (PID) systems, ways of referencing data, and timing of citing data.
  • The Scholix solutionA standard set of guidelines for exposing and consuming data-article links, using a system of hubs.

Here’s how it works:

  1. As a DataCite member repository, Dryad provides our data-publication links to DataCite, one of the Scholix Hubs. 
  2. Those links are made available via Scholix aggregators such as the DLI service
  3. Publishers can then query the DLI to find datasets related to their journal articles, and generate/display a link back to Dryad, driving web traffic to us, increasing data re-use, and facilitating research discovery.

Crossref publishers, DataCite repositories/data centers, and institutional repositories can all participate — information on how is available on the Scholix website.

Programmatic data access by ISSN

Did you know that content in Dryad is available via a variety of APIs (Application Program Interfaces)? Details are available at the “Data Access” page on our wiki.

The newest addition to this list is the ability to access Dryad data packages via journal ISSN. So, for example, if you wanted access to all Dryad content associated with the journal Evolution Letters, you would format your query as follows:

https://datadryad.org/api/v1/journals/2056-3744/packages

If you’re a human instead of a machine, you might prefer to visit our “journal page” for Evolution Letters:

https://datadryad.org/journal/2056-3744

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Dryad is committed to values of openness, collaboration, standardization, seamless integration, reduction of duplication and effort, and increased visibility of research products (okay, data especially). The above examples are just some of the ways we’re working in this direction.

If you’re part of an organization who shares these values, please contact us to find out how you can be part of Dryad.

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oupDryad is very pleased to announce more integrations from charter member and partner Oxford University Press Journals. Oxford University Press (OUP) publishes over 300 journals, many with the support of learned societies. As part of Oxford University, OUP brings a rich history of working with researchers.

OUP has integrated seven more journals with Dryad, all of which can provide secure links to data during the peer review process:

oup_covers

  • Behavioral Ecology – published on behalf of  The International Society for Behavioral Ecology, Behavioral Ecology publishes studies on the whole range of behaving organisms, including plants, invertebrates, vertebrates, and humans. Data publication is sponsored for Behavioral Ecology authors.
  • BioScience – published on behalf of the American Institute of Biological Sciences, BioScience has been publishing current research in Biology since 1964.
  • Environmental Epigenetics is an open access journal that publishes research in any area of science and medicine related to the field of epigenetics.
  • Toxicological Sciences is the official journal of the Society of Toxicology and publishes influential research in toxicology. Data publication is sponsored for authors for Toxicological Sciences.
  • Journal of Urban Ecology is an open access journal which covers all aspects of urban environments. This includes the biology of the organisms that inhabit urban areas, the diversity of ecosystem services, and human social issues encountered within urban landscapes.
  • Virus Evolution serves the community of virologists, evolutionary biologists and ecologists who are interested in the genetic diversity and evolution of non-cellular forms of life.
  • Work, Aging and Retirement reflects a broad community of professionals in the fields of psychology, sociology, economics, gerontology, business and management, and industrial labor relations.

Integration with Dryad ensures bidirectional links between the article and the data, and increased visibility for both. It also simplifies the process of data submission for authors. All data in Dryad is reviewed by professional curators who perform basic checks to ensure discoverability and proper metadata, and becomes freely accessible online once approved.

Oxford University Press is increasing its commitment to authors and to quality by making it easy to publish datasets alongside the manuscript, and by allowing data to be available during the peer review process.

We’re delighted to build our partnership with Dryad by integrating this set of OUP journals. Providing authors with a simple and user-friendly route to data sharing helps to increase transparency and reproducibility of published research, and ultimately must be good for science. We hope to integrate more of our journals in the near future.

– Jennifer Boyd, Senior Publisher Life Science Journals, OUP

To learn more about journal integration with Dryad and DPCs, contact us.

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We are delighted to announce the launch of a new partnership with The Company of Biologists to support their authors in making the data underlying their research available to the community.

COBNewLogo300dpiThe Company of Biologists is a not-for-profit publishing organization dedicated to supporting and inspiring the biological community. The Company publishes five specialist peer-reviewed journals:

The Company of Biologists offers further support to the biological community by facilitating scientific meetings, providing travel grants for researchers and supporting research societies.

Manuscript submission for all COB journals is now integrated with data submission to Dryad, meaning COB authors can conveniently submit their data packages and manuscripts at the same time. Dryad then makes the data securely available to journal reviewers, and releases them to the public if/when the paper is published.

We congratulate The Company of Biologists on taking this important step to help facilitate open data. To learn more about how your organization or journal can partner with Dryad, please contact us.

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UCP logoDryad is very pleased to announce a new partnership with the University of Chicago Press – Journals Division. Founded in 1890, Chicago is one of the oldest and currently the largest continuously operating university press in the United States. Chicago has recently integrated two additional journals with Dryad: Physiological and Biochemical Zoology (PBZ) and International Journal of Plant Sciences (IJPS) and is sponsoring Data Publication Charges (DPCs) for both titles. PBZ and IJPS join sister publication, The American Naturalist, a Dryad partner since its inception.

Integration with Dryad

  • Ensures bidirectional links between the article and the data, and increased visibility for both
  • Simplifies the process of data submission for authors
  • Takes advantage of Dryad’s professional curators who perform basic checks to ensure discoverability and proper metadata
  • Ensures that the data is freely accessible once the article becomes available online

Physiological and Biochemical Zoology publishes original research in the areas of animal physiology and biochemistry. PBZ focuses on ecological, evolutionary and behavioral aspects of morphological, physiological, and biochemical mechanisms. PBZ’s integration will allow authors to make their data available to journal editors during peer review.

The International Journal of Plant Sciences has been publishing plant science research since 1875. IJPS covers a wide range of topics including genetics and genomics, developmental and cell biology, biochemistry and physiology, morphology and anatomy, systematics, evolution, paleobotany, ecology, and plant-microbe interactions. IJPS will accept data from authors at the time of article acceptance.

The University of Chicago Press – Journals Division is increasing its commitment to authors and the STM field by making it easy to publish datasets alongside the manuscript, and by taking the extra step of covering the cost of data publication on behalf of authors. To learn more about journal integration with Dryad and DPCs, contact us.

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We are delighted to announce the integration of three new journals: The Bone & Joint Journal, Bone & Joint Research and Bone & Joint360.

BJJBJRBJ360

The British Editorial Society of Bone & Joint Surgery is a not-for-profit charity formed in 1953 for “the advancement and improvement of education in orthopaedic surgery and allied branches of surgery,” achieved through publication of The Bone & Joint Journal (formerly known as JBJS (Br)). With all three journals, authors should submit the data to Dryad after the manuscript has been accepted.

Please see here for more information about how your journal can integrate manuscript and data submission to Dryad.

 

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We are delighted to announce the integration of four new journals: Ecography, Journal of Avian Biology, Nordic Journal of Botany, and Oikos.

OIKOS_123_01_COVER.inddJABY_I_45_05_COVER:JABY_I_45_05_COVER.qxp.qxdNJBY_I_32_02_COVER.inddECOG_Issue Information.indd

The Nordic Society Oikos, which supports scientific research in ecology and related disciplines and to stimulate and enhance communication between stakeholders in ecological research in the Nordic countries and beyond, owns these journals, and is generously sponsoring Data Publication Charges on behalf of its authors. The Oikos Editorial Office, based in the Department of Biology at Lund University, manages the publication of these journals in partnership with Wiley. For all four journals, authors should submit the data to Dryad after the manuscript has been accepted.

Please see here for more information about how your journal can integrate manuscript and data submission to Dryad,

 

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