Posts Tagged 'data sets'

LabArchives and the BioMed Central Research Awards

I have just returned from London where, among other things, I was proud to represent LabArchives in presenting the BioMed Central “Open Data Award” that was sponsored by our organization. At the well attended 6th Annual event, BioMed Central’s Research Awards celebrated excellence in scientific research made freely available through open access publishing within their portfolio of over 200 journals and are much like the “Academy Awards” for science.

We are very proud to be sponsoring the Open Data Award this year and are also very excited about our recently announced partnership with BioMed Central.  As you may know, LabArchives offers a web-based solution for the problem of storing, organizing, sharing and publishing scientific data.  Investigators who use LabArchives are able to automatically share data sets with individuals or with the public at large and can easily assign a Digital Object Identifier (DOI) to these data.

BioMed Central authors can obtain a complimentary subscription to LabArchives that enables them to store up to 100 MB of data, a portion or all of which can be published in connection with, or separately from, a journal article.

As the scientific community continues to embrace the concept of open data, it is important that the process of sharing information be as simple and seamless as possible. At LabArchives, we are dedicated to creating easy-to-use and affordable products to bring this important goal to fruition.

The Open Data Award seeks to recognize researchers who have published in BioMed Central journals and have demonstrated leadership in the sharing, standardization, publication, or re-use of biomedical research data. This year we genuinely had the strongest shortlist yet, with excellent nominees from fields as diverse as microbiology, health geographics, rheumatology, clinical medicine, genomics and chemistry.

This  year, the winning paper was “The International Stroke Trial database” by Peter AG Sandercock, Maciej Niewada, Anna Członkowska, the International Stroke Trial Collaborative Group, published in the journal: Trials

Peter Sandercock and colleagues published “The International Stroke Trial database” paper and data set in the journal Trials with the primary purpose of making individual patient data from the International Stroke Trial (IST) available for public use. With more than 19,000 patients this was one of the largest randomized trials ever conducted in acute stroke. The results of the International Stroke Trial were first published in the Lancet in 1997 but the data, which are highly valuable for secondary research, were not publicly available until this article was published, in April 2011.

Sharing and publishing clinical trial data is much needed to improve the reliability and efficiency of health research but remains very uncommon, particularly on such a large scale. Included with the paper was a spreadsheet with the anonymized data from the many patients in the trial. As well as being transparent the authors have been responsible and adhered to available best practice guidelines on protecting anonymity. The paper got the judges’ attention right from the start of and the decision was, remarkably and uniquely for this award, unanimous.

The authors should be commended for their efforts to make such a large amount of data available as data sharing on this scale in clinical medicine shows real leadership. The background care patients received in the nineties is representative of stroke trials currently ongoing in developing countries making the data particularly helpful for planning new trials in these areas – which face a future epidemic of non-communicable diseases such as stroke.

In addition to the well-deserved recognition for their contribution, the authors receive a cash award which we hope will serve as a small token of the appreciation from the publishing and scientific communities, as well as an additional incentive for other scientists to publish important data that may more quickly advance the progress of science in ending disease and improving our understanding of the world around us.

LabArchives is very proud to be participating in these awards, and looks forward to continuing our involvement for many years to come.  I would like to personally thank the members of the BioMed Central team who organized and attended the Awards and created a truly enjoyable evening for me personally as well as everyone in attendance.

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LabArchives and BioMed Central: a new platform for publishing scientific data

Note from the Editor:  This guest blog is written by Iain Hrynaszkiewicz, Journal Publisher at BioMed Central

Introduction

One reason that the worldwide web worked was because people reused each other’s content in ways never imagined or achieved by those who created it. The same will be true of open data.
– Tim Berners-Lee and Nigel Shadbolt, The Times, New Year’s Eve 2011

As part of our commitment to reproducible research and transparency, BioMed Central has partnered with LabArchives to work together for the shared goal of making datasets supporting peer-reviewed publications available and permanently linked to online publications – and available under terms which permit reuse freely, as Open Data.

A growing number of repositories for scientific datasets – which with persistent identification can be cited in and linked from published articles – are available but many fields still lack an obvious repository. There has been debate about whether institutional or subject-specific repositories (and journals) are the best solution for data archiving and publishing. But what is absolutely clear is that, for data, one size does not fit all – literally and metaphorically.

When available, data repositories are usually the best place for larger datasets which cannot be included as additional files, and we have been working to increase awareness of repositories of interest to our authors. But some scientists who are willing to share data may, understandably, be reluctant to deposit data in a repository with which they are not familiar, or which cannot guarantee permanence, or perhaps has suboptimal or ambiguous licensing terms.

LabArchives, an Electronic Laboratory Notebook, enables individual scientists to manage, share and publish data files, providing an accessible platform for sharing and publication which is controlled by authors themselves. LabArchives is web-based, or may also be installed on a local server, enabling a user to access their laboratory documents, protocols, notes and data from any location (you can read more about the features of LabAchives on their website).

As part of this partnership, all BioMed Central authors are entitled to an enhanced free version of LabArchives. This ‘BioMed Central Edition’ of the software offers additional storage capacity compared to the standard free edition, integrated manuscript submission to BioMed Central journals, along with important open data publishing features.

Key data publishing features of LabArchives – BioMed Central Edition

Permanence, citation and linking of datasets
In 2011 LabArchives introduced the ability to assign digital object identifiers (DOIs) to datasets stored and shared with the software. DOIs facilitate data citation, discovery and earning of academic credit for data publication, and datasets assigned DOIs through LabArchives will remain available in perpetuity. The DOI system is used by journal and data publishers, such as DataCite members, to ensure online permanence of published articles. DOIs are indexed permanently by the International DOI Foundation and are much more favorable than URLs for permanently linking content online.

DOIs are assigned in LabArchives through the ‘DOI Management’ tab in the software’s share settings (pictured). DOIs should only be assigned in instances in which data are to be permanently shared with the public.

Image

A LabArchives user can choose to share a data set as it exists at the time of publication, or they may enable users to continue to view changes as they are made, while, importantly, maintaining the version which supports a peer-reviewed publication.  So, a DOI can be assigned to data as of the time the article was published and authors or re-users of the data may then continue with their research.

Data which are available for integration and reuse
Datasets published via the LabArchives platform and assigned DOIs are available under a Creative Commons CC0 waiver. CC0 helps dispel legal uncertainties about what a person or machine can do with data – or any other content – they discover on the web. CC0 enables cultural (scholarly) norms of citation to take precedence over legal conditions, such as requirements for attribution, for ensuring scientists receive appropriate credit for their contributions. CC0 furthermore complies with the Panton Principles for Open Data in Science, which hold that for society to gain the full benefits of scientific endeavors, data must be free to reuse, integrate and build upon without legal or other barriers. In short, data published through the LabArchives – BioMed Central Edition are open data.

Anyone publishing data through LabArchives should ensure that CC0 is appropriate for their data and that they are in the position to apply this waiver to the data.

Complimentary additional storage
The enhanced free version of LabArchives has an increased allotment of 100MB of storage (the standard free edition includes 25MB), enabling publication of larger datasets which cannot be published as additional files with journal articles. BioMed Central authors can continue to submit virtually unlimited numbers of additional files to our journals, up to 20Mb per file –  twice as much as some publishers, but in the age of ‘big data’ this can still sometimes be limiting . Users who choose to upgrade to the full version of LabArchives can store up to 100GB of data (see footnotes).

Integrated file viewers
LabArchives includes viewing software for a variety of file types.  This feature enables those who discover your information to be able to see the data, even when stored in certain proprietary formats.  Viewers are currently included for Microsoft Office files, PDFs, and all standard image formats.  The list of viewers is regularly expanded by LabArchives.

View data in context
Readers (and reusers) of data published and shared through LabArchives can view files in context.  LabArchives’ hierarchical file structure enables meaning to be conveyed to the reader through logical organization of data files.

Integrated manuscript submission to BioMed Central journals
Publishing data permanently online – especially when well-labelled, conforming to community standards, and in open file formats – increases potential for data reuse and collaboration. But peer-reviewed journals undoubtedly add value to data, such as detailed methods, context and discussion. For publishers to continue adding value to science communication, to speed publication and reduce barriers to data sharing it’s important to better integrate with scientists’ workflows and tools, upstream of journal submission and publication. The LabArchives – BioMed Central Edition includes integrated manuscript submission to BioMed Central journals. Authors submitting research manuscripts can, directly from LabArchives, choose the most appropriate of any BioMed Central journal, and authors preparing data notes can link directly to BMC Research Notes’ submission system. Our manuscript templates for research and data notes are also incorporated to help speed the process of manuscript preparation.

With transparency comes responsibility
We encourage authors to comply with available field-specific standards for the preparation and recording of data. We recommend authors review the BioSharing website, and a special article series published in BMC Research Notes, for information on best practice in their field for sharing of data, with particular attention to maintaining patient confidentiality.

All journals in the BMC Series including BMC Research Notes now include information about LabArchives’ BioMed Central Edition in their instructions for authors, and the feature will be added to other journals as, when and if the Editors feel it is service that will be valued by their authors. The first articles which describe and link to data hosted in LabArchives are currently undergoing peer review.

As John Wilbanks, Senior Fellow at the Kauffman Foundation and Open Network Biology Editorial Board member said on the BMC Blog in November 2011: “[M]aking data available will serve as a strong attractor for the smartest people in the world to come and begin building things that utterly surprise and shock us.”

We are looking forward to working with our authors and LabArchives to make more data openly available for integration and reuse in 2012 – and beyond.

Footnotes

Use of LabArchives’ software will have no influence on the editorial decision to accept or reject a manuscript, and use of LabArchives or similar data publishing services does not replace preexisting community data deposition requirements set out in individual journals’ instructions for authors.

The full version of LabArchives including 100GB of storage requires payment. BioMed Central does not receive any commission from LabArchives.

BioMed Central remains committed to work with all data repositories which enable linking of data to publications particularly where specific journals and communities endorse them – such as for example the Dryad repository, with which we are working towards submission system integration with BMC Ecology and BMC Evolutionary Biology. More information on data deposition requirements relevant to BioMed Central’s journals can be found on our supporting data resources page.


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