Call for Papers: PLoS Text Mining Collection

The Public Library of Science (PLoS) seeks submissions in the broad field of text-mining research for a collection to be launched across all of its journals in 2013. All submissions submitted before October 30th, 2012 will be considered for the launch of the collection. Please read the following post for further information on how to submit your article.

The scientific literature is exponentially increasing in size, with thousands of new papers published every day. Few researchers are able to keep track of all new publications, even in their own field, reducing the quality of scholarship and leading to undesirable outcomes like redundant publication. While social media and expert recommendation systems provide partial solutions to the problem of keeping up with the literature, systematically identifying relevant articles and extracting key information from them can only come through automated text-mining technologies.

Research in text mining has made incredible advances over the last decade, driven through community challenges and increasingly sophisticated computational technologies. However, the promise of text mining to accelerate and enhance research largely has not yet been fulfilled, primarily since the vast majority of the published scientific literature is not published under an Open Access model. As Open Access publishing yields an ever-growing archive of unrestricted full-text articles, text mining will play an increasingly important role in drilling down to essential research and data in scientific literature in the 21st century scholarly landscape.

As part of its commitment to realizing the maximal utility of Open Access literature, PLoS is launching a collection of articles dedicated to highlighting the importance of research in the area of text mining. The launch of this Text Mining Collection complements related PLoS Collections on Open Access and Altmetrics (forthcoming), as well as the recent release of the PLoS Application Programming Interface, which provides an open API to PLoS journal content.

As part of this Text Mining Collection, we are making a call for high quality submissions that advance the field of text-mining research, including:

  • New methods for the retrieval or extraction of published scientific facts
  • Large-scale analysis of data extracted from the scientific literature
  • New interfaces for accessing the scientific literature
  • Semantic enrichment of scientific articles
  • Linking the literature to scientific databases
  • Application of text mining to database curation
  • Approaches for integrating text mining into workflows
  • Resources (ontologies, corpora) to improve text mining research

Please note that all submissions submitted before October 30th, 2012 will be considered for the launch of the collection (expected early 2013); submissions after this date will still be considered for the collection, but may not appear in the collection at launch.

Submission Guidelines
If you wish to submit your research to the PLoS Text Mining Collection, please consider the following when preparing your manuscript:

  • All articles must adhere to the submission guidelines of the PLoS journal to which you submit.
  • Standard PLoS policies and relevant publication fees apply to all submissions.
  • Submission to any PLoS journal as part of the Text Mining Collection does not guarantee publication.

When you are ready to submit your manuscript to the collection, please log in to the relevant PLoS manuscript submission system and mention the Collection’s name in your cover letter. This will ensure that the staff is aware of your submission to the Collection. The submission systems can be found on the individual journal websites.

Please contact Samuel Moore (smoore@plos.org) if you would like further information about how to submit your research to the PLoS Text Mining Collection.

Organizers
Casey Bergman (University of Manchester)
Lawrence Hunter (University of Colorado-Denver)
Andrey Rzhetsky (University of Chicago)

Category: Alt-Metrics, Open Access, PLoS Collections, Publishing, Technology | Leave a comment

PLoS Appoints Two New Members to Board of Directors

PLoS is pleased to announce that Heather Joseph and Robin Lovell-Badge will join the PLoS Board of Directors, effective May 19, 2012. “Heather and Robin will be terrific additions to the board, significantly broadening our expertise in outreach, policy, and research,” said board chairman Gary Ward. Both Heather and Robin have long-standing associations with PLoS and play active roles in policy and scientific publication now and throughout their careers, albeit in much different capacities.

Heather Joseph

Heather serves as the Executive Director of the Scholarly Publishing and Academic Resources Coalition (SPARC) (Washington, DC). Under her leadership, SPARC is a strong ally with PLoS in the Open Access movement to eliminate barriers in the dissemination of scholarly research. Heather is also the convener of the Alliance for Taxpayer Access, a coalition of universities, libraries, and advocacy groups for patients, consumers, and students that influences policy and legislation to promote unrestricted access to publicly funded research. Prior to joining SPARC, Heather worked for 15 years as a publisher in commercial and nonprofit organizations, including five years as the President of BioOne and nearly three years as the Director of Publishing for the American Society for Cell Biology.

Robin is Head of the Division of Stem Cell Biology and Developmental Genetics at MRC National Institute for Medical Research (London, UK). His research into sex determination, the nervous system, and early embryo stem cell biology has been published in PLoS journals, among many other scholarly publications. Robin has become increasingly active as a leader in public engagement and policy work related to stem cells, genetics, and human embryo and animal research. His focus on the ways science is regulated, conducted, and disseminated led to his involvement with PLoS. In 2004, he published Ethereal Ethics in PLoS Biology to describe the differences in the politics of bioethics between the US and UK. Robin received his PhD in Embryology at University College London and conducted postdoctoral research in Cambridge, UK and Paris, France.

Robin Lovell-Badge

Robin and Heather join sitting board members David Liddle, Rosalind Smyth, Marty Tenenbaum, and Beth Weil serving with Gary Ward as chairman and Patrick Brown and Michael Eisen as co-founders on the board.

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Latest Developments in PLoS Article-Level Metrics

PLoS continues to expand and refine Article-Level Metrics (ALM). This suite of performance measures (including usage statistics, citations, trackbacks from blogs, bookmarks, social media coverage and user comments and ratings) are available on every PLoS article so that authors and the scientific community can assess the impact of the research. We are also broadening our outreach activities to spread the word on ALM to more researchers, technical experts, other publishers, funders, and institutions.

A key part of the current effort is to convene scholarly metrics thought leaders to help spearhead the widespread adoption of ALM. By engaging leading authorities in metrics, and bringing them together in a working group, PLoS can better coordinate the development of ALM. The following experts serve on the ALM Technical Working Group in an advisory role to help steer the direction of PLoS ALM implementation:

  • Pedro Beltrao, University of California San Francisco
  • Phil Bourne, University of California Santa Cruz
  • Bjoern Brembs, Freie Universität Berlin
  • Martin Fenner, PLoS
  • Duncan Hull, European Bioinformatics Institute
  • Cameron Neylon, Science and Technology Facilities Council Oxford
  • Heather Piwowar, NESCent, Duke University
  • Jason Priem, University of North Carolina at Chapel Hill
  • Dario Taraborelli, Wikimedia Foundation
  • Jevin West, University of Washington
  • Johan Bollen, Indiana University

Starting May 16, 2012, Martin Fenner will join PLoS as the ALM Technical Lead. Martin announced the news on his PLoS blog Goobledygook last month. Martin has been a leading advocate of scholarly metrics and has worked on several article usage applications. As ALM Technical Lead, he will not only help with the development of the PLoS ALM application, he will also lead developer outreach for the project.

Further information on all these developments are available on a new ALM website launched today, please take a moment to check it out. We also encourage you to visit our journals and to view ALM by clicking on an article metrics tab.

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Publisher of PLoS ONE moves to new Open-Access initiative

After four years of dedicated service and steady leadership, Peter Binfield, Publisher of PLoS ONE, will be leaving us on May 18th.  Under his stewardship, PLoS ONE has grown into the largest peer reviewed journal in the world. In the process, PLoS ONE has pioneered new editorial models that are being widely adopted by many publishers.  We part on the best of terms – Pete is leaving to start his own company, and so we wish him well in this new Open Access Initiative. PLoS ONE is in very capable hands under the expert guidance of Executive Editor Damian Pattinson and Senior Editorial Manager Jackie Thai.  Damian and Jackie already run day to day publishing operations, and they will continue to do so.

We are also pleased to announce that Kristen Ratan has been appointed head of a united Publications and Products group. Kristen brings a wealth of experience in both scientific publishing and product development, and has quickly made significant contributions to PLoS. Kristen’s passion for innovation, people, and publishing will be a tremendous asset for us as we continue our leadership in Open Access publishing.  With the extensive experience of Ginny Barbour and Theo Bloom, both recently promoted to Editorial Directors, PLoS has strong editorial leadership in place that complements Kristen’s product and platform development experience. The Open Access movement is increasing in momentum and we appreciate the support of the community as we continue our effort to accelerate progress in science and medicine by leading a transformation in research communication.

Category: Publishing | 2 Comments

Bridging the Journal-Wikipedia gap

In March 2012, PLoS Computational Biology took what we hope will be a first step in a new level of interaction between publishers, researchers and the public. “Topic Pages” are a new article type, written in the style of a Wikipedia article. The page, which should fill a gap in Wikipedia’s computational biology content, is peer reviewed. Once accepted, a version of record is published in PLoS Computational Biology, with the text being uploaded to Wikipedia very soon afterwards to undergo the usual updates and edits of articles on the site. In the following guest post, our Topic Pages Editor, Daniel Mietchen, explains the motivations and hopes for this experiment.

PLoS Computational Biology Meets Wikipedia | Topic Pages

Guest post by Daniel Mietchen, the PLoS Computational Biology technical editor for Topic Pages. As Wikimedian in Residence on Open Science, he helped to define the workflow for Topic Page article submission and peer review.

On Tuesday morning, the English Wikipedia’s main page contained a short statement informing visitors “that the protein Concanavalin A (pictured) cuts itself in two and then reassembles in a circularly permuted order” when cut in half, with the bolded link inviting clicks from those wishing to find out more.

Two proteins that are related by a circular permutation. (Image from Bliven S, Prlić A (2012) Circular Permutation in Proteins. PLoS Comput Biol 8(3): e1002445. doi:10.1371/journal.pcbi.1002445)

The clicks led to Circular permutation in proteins, an article that describes circular permutation in proteins as

“a type of relationship between proteins, whereby the proteins have a changed order of amino acids in their protein sequence, such that the sequence of the first portion of one protein (adjacent to the N-terminus) is related to that of the second portion of the other protein (near its C-terminus), and vice versa.”

Subjecting the quote to a Google search reveals that there is an article in PLoS Computational Biology that is also entitled Circular Permutation in Proteins, in which the concept is defined in exactly the same way.

Rather than a bug, this striking similarity between the Wikipedia and journal articles is a feature, reflecting the new manuscript track of Topic Pages at PLoS Computational Biology. As explained in an accompanying editorial (whose title has been circularly permuted to yield the title of this blog post), “Topic Pages are the version of record of a page to be posted to (the English version of) Wikipedia.”

In other words, Topic Pages expand on earlier attempts to add a dynamic component to scholarly publishing. They provide the English Wikipedia with expert-written and expert-reviewed content, and allow authors to get credit for their work.

Like the phrase quoted above, the paper contains direct links to Wikipedia pages for background, which dramatically reduces the need to rehash what is already known, while still allowing for a minimum of context.

The reviews that have been produced as a result of the journal’s peer review process have since been posted to the talk page of the Wikipedia entry (along with some further procedural explanations) and as comments to the paper itself.

While the workflow for the initial Topic Page at PLoS Computational Biology was a work-in-progress (as described by both authors), we anticipate considerable streamlining of the workflows for future ones.

Other journals wishing to experiment with wiki contributions are invited to use the dedicated Topic Pages wiki for preparing articles in their respective manuscript track. To further stimulate such experiments, Wikimedia Germany has approved funds to help other journals integrate their workflows with those of Wikimedia projects.

We hope that such a shared experimental environment and code base can provide fertile ground for publishers to develop best practices and standards on the way towards more dynamic modes of publishing. We acknowledge the help and support we have received from several WikiProjects, most notably those on Computational Biology, Molecular and Cellular Biology, and Open Access.

Category: Publishing | 1 Comment

PLoS Currents Has a New Publishing Platform

We are pleased to announce that PLoS Currents has moved to a new publishing platform, offering easier interaction to all users.

This innovative, online publication channel for the rapid communication of new scientific research and ideas aims to minimize delays between the generation and publication of new research. All content published is peer-reviewed, citable, publicly archived in PubMed, and indexed by Scopus.

PLoS Currents removes barriers to communication and exchange through:

  • A single, integrated solution for writing and publishing
  • Flexible article format for increased ease of submission
  • Streamlined peer-review process that establishes the legitimacy of the work
  • Individual sections tailored to a specific research community

Its six sections include:

For this redesign, we partnered with Solvitor LLC* to implement Annotum (the name of this new publishing platform). Carl Leubsdorf, Jr., founder of Solvitor LLC, describes Annotum as “an open-source, open-access, open-process authoring and publishing system based on WordPress.”

We welcome you to browse articles and submit your research to one of the PLoS Currents sections today. Contact us at currents@plos.org.

*Annotum is a product of Solvitor LLC with heavy lifting by Crowd Favorite, and with special thanks to Google, PLoS, NIH/NLM/NCBI, and Automattic.


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Announcing PLoS Currents: Disasters

This blog post originally appeared on Speaking of Medicine March 27.

Today, there are ever more pressing needs for up-to-date information to be quickly available and easily accessible. This has never been more true than in the field of disasters, where slowness in sharing knowledge can be the difference between life or death for thousands of people, or the avoidance or mitigation of catastrophic outcomes for an ecosystem.

Image Credit: http://firepix.blm.gov, English Wikipedia

Despite the breadth of technological possibilities available, publishers and scientific journals have not provided adequate solutions for publication during fast moving emergencies. One study, published in 2009 showed that the majority of the epidemiological articles on the SARS epidemic of 2003 were submitted after the epidemic had ended, many several years after – and this for an emergency that lasted just a few months. The UNIDSR has identified that, “the sharing of research findings, lessons learned and best practices” are a priority in its Hyogo Framework for Action 2005-2015.

PLoS is proud therefore to announce the launch of PLoS Currents: Disasters, a new, innovative open-access publication for the rapid communication of new research results and operational analyses derived from the study or management of all types of disasters. All research is citable and permanently archived in PubMed Central as well as indexed in Scopus and PubMed.

Our primary aim is rapid dissemination to make essential, and in many cases otherwise hard to publish, findings as widely available as possible as quickly as possible, so they can be used and built upon. We have implemented an integrated authoring, editorial, and peer-review system called Annotum, a new publishing platform, which we believe can cut the publishing time down to a few weeks, or even days. Authors directly compose or insert their manuscript in the web-based application and peer review occurs within it. All of the content is published under a Creative Commons Attribution License (CCBY), which means that articles are immediately free to read but more importantly can then be reused in any way, provided that the authors and original sources are attributed correctly.

PLoS Currents is a flexible publishing channel, which responds to the particular needs of the community of disasters-related researchers and practitioners. In addition to the decreased publishing time through a streamlined review and production process, it offers:

  • Flexibility: open article formats to reflect the diverse types of disasters-related research
  • Revisions: updated versions of articles that document the latest results or analyses.

The most recent article, from 16 international experts in the fields of research, education, ethics and operational aspects of disaster medical management, highlights a critical issue in disaster management and describes a template for uniform data reporting of acute medical response in disasters.

PLoS Currents: Disasters is supported by an international group of researchers, practitioners, who serve on its editorial and review board.

Professor Virginia Murray, an Editor for PLoS Currents: Disasters, and the Head of Extreme Events and Health Protection at the Health Protection Agency, said “evidence based advice is essential for providing relevant up-to-date evidence based information to support the development of planning for extreme events – PLoS Currents: Disasters is a valuable publication resource to help to build the information that is so vitally needed for this purpose.”

Professor Mike Clarke, also an Editor for PLoS Currents: Disasters, and the current Chair of the MRC Network of Hubs for Trials Methodology Research and one of the founders of Evidence Aid, said “We are increasingly aware of the problems caused by research not being published in a timely and accessible way, and the damage this does to decision making and, consequently, to health care and health. The arrival of PLoS Currents: Disasters will help ensure that we learn from those lessons, by improving access to the knowledge needed in disasters. Evidence Aid is trying to make it easier for people to use systematic reviews of relevant information, and this new resource is a landmark step in making this information available.”

Fabrice Renaud, Head of the Environmental Vulnerability and Ecosystems Services Section, United Nations University Institute for Environment and Human Security, Bonn, Germany and an Editor of PLoS Currents: Disasters said: “PLoS Currents: Disasters will enable scientists and practitioners who directly work on the many facets of disaster prevention, disaster management and disaster response to rapidly share their on the ground expertise, observations and research results with a wide range of stakeholders.

Professor David Sanderson, Director, Centre for Development and Emergency Practice (CENDEP) and an Editor of PLoS Currents: Disasters said: “PLoS Currents: Disasters aims to fill an important gap – that of getting good evidence-based research out fast to those working in disasters.”

PLoS Currents started with its first section, Influenza, in 2009. Today, we continue the spirit of innovation with the launch of our sixth and newest member, PLoS Currents: Disasters, which we will be developing over the next few months. Contact us at disasters@plos.org with any questions, comments, or suggestions on further developments or leave a comment below.

PLoS Currents: Disasters welcomes your submissions.

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Cameron Neylon to Join PLoS as Director of Advocacy

PLoS is pleased to announce the appointment of Cameron Neylon as Director of Advocacy. Cameron is well known in the scientific community, recognized for his professionalism, experience, vision and influence in scholarly publishing, communication, and research. His attendance at the Budapest Open Access Initiative meeting, advisory role for the Scholarly Communication in Africa Program, and leadership of the Open Society Foundation-funded Beyond Impact project are recent examples of his focus on web technology to enhance research communication. After earning his PhD in Chemistry from Australian National University, Cameron worked as a Wellcome Trust International Fellow at the University of Bath; a lecturer in chemical biology at the University of Southampton; and most recently a senior scientist at the Science and Technology Facilities Council, UK. He has also served as an academic editor for PLoS ONE—one of many commitments he will transition prior to joining PLoS in early July.

In early July 2012, Cameron Neylon will join PLoS as Director of Advocacy.

In his new position, Cameron will promote advocacy of Open Access and develop strategies to drive the broader reinvention of research communication, both within the existing PLoS journals and beyond. He will work with other Open Access advocates, funders, publishers and scholarly societies to raise awareness and promote the adoption of research communication systems that support the public’s access and contribution to research. Cameron’s passion and dedication to Open Access are manifest in his speaking engagements and leadership in online media. His knowledge of policy and the scientific community in the EU and Asia/Pacific region will be a great asset to PLoS. He is among the most effective, articulate and balanced advocates of open and collaborative science, and of quality, speed and sustainability in research communication. Please join us in welcoming Cameron and congratulating him on his new role.

Category: Publishing | 1 Comment

New data sources added to Article-Level Metrics

In 2009, PLoS became the first publisher to add comprehensive usage and reach data to every published article so that the entire academic community could form their own assessments of their value.  Today, we’re pleased to announce the addition of 3 new data sources to our Article Level Metrics (ALM) program: article usage from PubMed Central; number of users via Mendeley; and number of Facebook mentions. We have also re-vamped the display of ALM data on the ‘Metrics’ tab of each article.

To find out more about these article enhancements, you can watch a short (<2 minute) video and browse these screen shots.

Article-Level Metrics now displayed on the article itself

New data source: article views from PMC

New visual display of data sources

This is the first in a series of forthcoming developments to ALM that we expect to roll out in the next 12 months – you can expect to see the addition of Twitter as a data source in the next few weeks and a number of tools will be added to make use of ALM data in the journals this year – so watch this blog for tagged posts.

Talking to various participants at the excellent Science Online 2012 event in North Carolina earlier this month it became clear that while some are ALM experts there are many who haven’t heard that PLoS provides performance data for every article including the following data from the sources noted:

  • Article usage – PLoS:  page views, PDF and XML downloads. NEW: PubMedCentral:  page views, PDF downloads
  • Citations–CrossRef, PubMed Central, Scopus, ISI Web of Science
  • PLoS reader evaluation –Comments, Notes, Star rating
  • Blog coverage – Research Blogging, Nature Blogs
  • Social tools –CiteULike and Connotea. NEW: Mendeley and  Facebook.

Additionally, PLoS provides context for the performance of each article by providing journal and topic averages so researchers can see how their research compares with that of others.

The best way to get familiar with ALM’s is to click on the metrics tab at the top of your article – then you can understand more about the impact of your research and the discussions that it inspired!

Category: Alt-Metrics, Publishing | 3 Comments

Genetically Modified Insect Collection from PLoS Neglected Tropical Diseases

PLoS Neglected Tropical Diseases presents a new collection of articles on the use of genetically modified (GM) insects for controlling some of the most widespread infectious diseases. Articles from across the PLoS journals describe the technological advances these tools represent, the regulatory framework, and the societal dialogue that is necessary for their wide-scale application for disease control.

Diseases transmitted by insects form a huge burden on human and animal populations. Insect control has historically been one of many strategies for control of diseases such as dengue, malaria, and sleeping sickness. The debate on whether GM insects could be used for disease control began as soon as transgenic insects were first produced in the 1980s. Since then, several experimental releases of GM insects have taken place. These trials show promise for limiting the spread of many vector-borne diseases (most notably Dengue fever). Articles in this collection showcase different aspects of this new technology including development, environmental impact, and regulation. Public discussion of the science and application of GM insects is necessary as new developments bring potential wide releases closer to a reality.

In an Editorial, Michael J Lehane (Liverpool School of Tropical Medicine) and Serap Aksoy (Yale School of Public Health) state that GM insects “may provide great promise for new means of controlling diseases with a devastating impact on people’s lives. If so, then public acceptance is likely to be a key issue in their implementation.” With many countries considering open field trials of GM insects, a Viewpoint by Guy Reeves et al. examines the regulation process of the first 3 countries that have had field trials of GM insects. Commentary by John Mumford highlights that both national and international regulations are required due to factors regarding each country’s individual environmental risk to GM insects.  In a Commentary from an industry perspective, Luke Alphey and Camilla Beech argue that “the agencies tasked to regulate GM insects have appropriately taken a cautious, thorough approach that allows progress towards realisation of the substantial benefits GM insect technology could potentially provide, while rigorously protecting the public and environment.”

The articles in this collection highlight many different points of view surrounding the research into GM insects. As the recent history of GM insect development demonstrates, public discussion is necessary as scientists continue to research GM insect technologies to control some of the world’s most devastating diseases.

This blog post was written by Renata Santillan (Publications Assistant of PLoS Neglected Tropical Diseases). Image Credit: James Gathany, Centers for Disease Control and Prevention.

Category: PLoS Collections, PLoS Neglected Tropical Diseases, Publishing | 1 Comment