The Official PLOS Blog

You’ve always relied on PLOS to make scientific and medical research freely accessible to all. Now we’re introducing a number of tools and services to unlock the full potential of the data that currently exists in the Figures and Supporting Information files of our journals but has to this point been just beyond easy reach and these include:

Expanding our partnership with Dryad – since July 2012, PLOS Biology has been encouraging authors to deposit their underlying data (and here’s a great blog post on why that’s important) in this open access repository at submission so that it is available during the peer-review process and safely secured for future reference.  PLOS Genetics is the latest journal to offer this option and will be joined by all our other titles in due course.

Providing more Digital Object Identifiers (DOI) – previously only available for the entire article, we’ve expanded the number of citable objects to include Figures and SI files with the goal of encouraging more granular linking to and re-use of smaller units of content.

Introducing a widget from figshare – now you can see inside the SI files (datasets, text files, documents, animations, videos and presentation files) without leaving the article or opening them. When you spot interesting files you can download them singly or altogether.

Here’s what Theo Bloom, Editorial Director for Biology, had to say about these developments “in our 10^th anniversary year, we are delighted to see the expansion of our efforts to encourage data access and sharing to the other PLOS journals. By supporting openness in data use and re-use, and open access to the literature, we hope to drive the PLOS mission of leading a transformation of research communication forwards”.

Look out for more announcements about data as we continue to improve the accessibility of our content so that others can build on more of it than ever before. If you have ideas or thoughts to share on this topic, please let us know via Twitter, Facebook or email.

At our ten year mark as a publisher of Open Access journals, PLOS announces a year-long series of events to recognize and advance the innovations brought about through the adoption of Open Access publishing. These activities will target both the scientific  community and the public at large.

The history and benefits of Open Access remain a largely untold story. In 2000, to address a lack of access to the majority of scientific research published behind paywalls, our founders shook up the academic science establishment with an Open Access petition.  Two years later, incorporated as the non-profit  Public Library of Science, PLOS created an Open Access publishing model by launching its first journal, PLOS Biology, followed by six other journals over the decade that followed.  Today, working as advocates, publishers and innovators, in tandem with a vibrant and growing community of supporters, we continue our founders’ mission to transform research communication.

During our tenth anniversary year, PLOS will partner with media organizations to demonstrate the many ways in which biomedical research published on an open access platform can affect peoples’ lives for the better. With monthly online dialogues, we’ll invite leading advocates in conversation to look ahead at the possible future of open access scientific discovery and publishing.

Additional offerings during our tenth anniversary year will include programs to increase adoption of Open Access, deliver more innovations in publishing, and expand peer-review , including pre-and post-publication. Our vision is to help the research community build a truly open, distributed, and reusable public repository of ideas and data. Here are details of what we’re working on for 2013. Stay tuned to the Official PLOS Blog, Twitter, and Facebook for the latest news.

• Reinventing Science:  Stories of Open Discovery: This multimedia series, consisting of feature articles, research summaries and podcasts, will profile researchers who are tapping into the knowledge of Open Access journals and collections to help accelerate their own research and enhance collaboration with peers around the globe. The series will be produced in collaboration with an online news and broadcast radio partner and will debut in early spring.
• PLOS Conversations on Open Access:  Hosted by Cameron Neylon, this regular podcast will round-up the latest happenings and discussions about Open Access, open research, and open data. Look for the series to debut in early spring on the PLOS Blog and social media sites.
• More About “HowOpenIsIt?”: The conversation has moved from “is it open?” to “HowOpenIsIt?”, and to continue this discussion, PLOS will unveil new resources and tools that help authors, readers, and funders understand the benefits of Open Access and how to apply components of the HowOpenIsIt? Open Access Spectrum at the article and journal level.
• Article-Level Metrics: Through ongoing forums, live and virtual events, and other activities, PLOS will continue to make advances in article-level metrics and other mechanisms for broadening peer review to include post-publication impact indicators, along with better tools for assessing organizing, and reusing research ideas and data.
• The PLOS Journals: In 2013, PLOS Medicine turns its attention to non-communicable diseases and the burden of disease they cause, while PLOS ONE continues its growth as the world’s largest peer reviewed journal.  In October, PLOS Biology celebrates the journal’s tenth birthday with special activities and events to be announced — look for details in PLOS Biologue. The community journals, PLOS Pathogens, PLOS NTDs, PLOS Genetics and PLOS Computational Biologywill continue to publish the research of an international roster of authors, working, as do all our journals,  with the help of dedicated volunteer editors and peer reviewers who are the backbone of these publications. Look for announcements of new collection launches in PLOS journals throughout the year.
• Journal Enhancements: PLOS is increasing user interaction and readability, such as the recently announced redesign of the PLOS journal interface, and investing in enhanced tools for article authoring and submission.

PLOS is grateful to the authors, readers, reviewers, editors, advisors, librarians, funders, and collaborators who have supported our mission as an advocate, publisher, and innovator. We look forward to continuing to shape the future of scientific research communications.

Keep up with these tenth anniversary programs and new ones to come on the PLOS home page and the Official PLOS Blog.

On the eve of our tenth anniversary, we’re pleased to announce that the redesign of all PLOS journals is now live. The three goals of this initiative were to:

1. Ensure that readers can quickly assess the relevance and importance of an article through a figure browser and highly visible Article-Level Metrics
2. Improve site navigation to help users discover content more easily
3. Launch a flexible platform from which to build out future innovations

This refresh offers users more effective ways to access and read content, updates the overall appearance of the sites and harmonizes them with our new PLOS look announced earlier this year.

Many of you will have noticed some ongoing enhancements to the journals this year, for example figures and Article-Level Metrics (ALM). You can expect similar developments to continue to roll out starting in early 2013 and into the future as we continue to adapt to meet user needs.

After extensive research into how researchers find and use content, we’ve focused our attention on refining and improving our article layout and functionality so that we can help you to locate relevant articles more quickly and enrich your reading experience. Here’s a short video, and a brief rundown of the new user features that you can see from today:

• More prominent figures – featured throughout articles and search so that you can quickly determine if an article is relevant
• Enhanced Discovery – Search now reflects our new expanded taxonomy of subject categories
• Metrics Signposts – sub-sets of ALM data, provide at-a-glance measures of article reach and impact
• Custom Saved Search – log in, enter your keywords and save, then receive new content that precisely meets your interests via email
• Author data – clear presentation of affiliations/attribution for each author as well as grouped by institution
• Abstract and Figure viewer – providing new ways for you to get around and find what matters
• Faster navigation – persistent (so you never get lost) and floating (follows you down the page)
• Clearer Tabs – easier to see and use, providing enriched article information

To find out more about our new features and get tips on navigating the new site please visit our updated Help page.

PLOS is taking advantage of the most powerful web technologies to improve our reader experience, promote Open Access and encourage conversation around the latest research to accelerate progress in science and medicine and lead a transformation in research communication.

We’re proud to have self-funded this project using revenue generated from our publishing business. It’s of prime importance for us as a non-profit that we give back to the researchers who publish with us and what better way to say thank you than with an improved journal experience.

Here’s what Kristen Ratan, PLOS’ Chief Products and Publications Officer, had to say about this project. “PLOS’ top priority is meeting the needs of our researcher community and the new sites focus on accessing and assessing the article content and data as quickly as possible. The enhanced publishing platform will also allow us to quickly deploy new functionality and take our reader experience to a whole new level.  We look forward to continuing to roll out improvements over the coming year and enriching our content still further”.

We welcome your feedback on our redesign in any one of a number of ways:  comment on this post; Twitter; Facebook; or just plain old fashioned email.

On the eve of our tenth anniversary, we’re pleased to announce that a redesign of all PLOS journals is around the corner.  The three goals of this initiative were to:

1. Ensure that readers can quickly assess the relevance and importance of an article through a figure browser and highly visible Article-Level Metrics
2. Improve site navigation to help users discover content more easily
3. Launch a flexible platform from which to build out future innovations

Here’s a sneak preview of our new journal home pages so that you know a little more about what to expect.

Many of you will have noticed some ongoing enhancements to the journals this year, for example figures and Article-Level Metrics (ALM). You can expect similar developments to continue to roll out starting in early 2013 and into the future as we continue to adapt to meet user needs.

After extensive research into how researchers find and use content, we’ve focused our attention on refining and improving our article layout and functionality so that we can help you to locate relevant articles more quickly and enrich your reading experience. Here’s a brief rundown of the new user features:

• More prominent figures – featured throughout articles and search so that you can quickly determine if an article is relevant to you
• Enhanced Discovery – Search now reflects our new expanded taxonomy of subject categories
• Metrics Signposts – sub-sets of ALM data, provide at-a-glance measures of article reach and impact
• Custom Saved Search – log in, enter your keywords and save, then receive new content that precisely meets your interests via email
• Author data – clear presentation of affiliations/attribution for each author as well as grouped by institution
• Abstract and Figure viewer – providing new ways for you to get around and find what matters
• Faster navigation – persistent (so you never get lost) and floating (follows you down the page)
• Clearer Tabs – easier to see and use, providing enriched article information

PLOS is taking advantage of the most powerful web technologies to improve our reader experience, promote Open Access and encourage conversation around the latest research to accelerate progress in science and medicine and lead a transformation in research communication.  We look forward to introducing our redesign shortly.

Today PLOS Computational Biology launched a collection of seven existing Software articles which present novel biological insights on an open access platform and break new ground by sharing the open source software that enabled the featured discoveries. This combination of Open Access and Open Source can only help push the development of computational biology’s many diverse fields – and create a model for other scientific disciplines.

According to the criteria for publication, all articles in the PLOS Computational Biology Software collection must use a license approved by the Open Source Initiative (OSI), thus enabling the modification of source codes for follow on innovations by subsequent researchers. Source code provides a human readable language for programmers to use when working with the machine code that drives a computer program. The early adoption of free and open source software by biologists was a direct result of the Herculean task they’ve faced over two decades of unprecedented progress in genomics and biomedical research – progress which has often depended on processing massive amounts of data about how cells, genes and proteain interact under various conditions. “Existing methods are often challenged by new types and amounts of data, so computational biologists create new pieces of software to analyze and interpret the data deluge.

The availability of open source software is of increased importance in the context of research where peer review, reproducibility, and building upon prior work are integral to the advancement of the science.  Source code access also helps researchers quickly identify and remedy bugs that might lead to spurious results and adapt programs or pieces of code to suit individual needs, and allows expert users to contribute to code development on an informal basis.

The seven articles released today describe approaches to a wide range of biological problems that could enable advances in fields such as drug development and environmental cleanup.  In an editorial introducing the collection, Software editors Andreas Prlić and Hilmar Lapp cite their objective to provide recognition to software developers who they propose are generally under appreciated by the current academic system. This Software Collection, part of The PLOS Computational Biology community journal, remains open for submissions.

PLOS Computational Biology is a peer-reviewed, open-access journal featuring works of exceptional significance that further our understanding of living systems at all scales through the application of computational methods. It is an official journal of the International Society for Computational Biology. The International Society for Computational Biology (ISCB) is a scholarly society dedicated to advancing the scientific understanding of living systems through computation.  The Society serves over 3,000 members from more than 70 countries.

You can visit the collection at www.ploscollections.org/software.

On November 1^st – 3^rd  2012, PLOS welcomed 45 thought leaders in the rapidly emerging field of Article Level Metrics (ALM) to a Workshop on new ways to measure science and a Hackathon (co-sponsored by ImpactStory) to highlight the opportunities of the altmetrics field for the developer community.

ALMs offer direct, first-hand views of the dissemination and reach of research articles through an ever-increasing range of different metrics, from the more traditional usage and citation data, to the mosaic of social media data. This multi-dimensional suite of indicators captures the research footprint from the moment of publication and dynamically tracks its impact over time.

Building off last year’s Beyond Impact Workshop and altmetrics11 & 12, representatives from notable universities, funders, libraries, publishers and developers gathered at the Fort Mason Conference Center for an in-depth discussion of current challenges and future opportunities in the altmetrics community.

During the event, the group had the opportunity to provide input on the most pressing and compelling areas of ALM advancement. Topics such as community structures, advocacy, anti-gaming mechanisms, scalability, relevance, sentiment analysis, personalization, data presentation and many others were the subjects of thorough examination and lively discourse. A full report of the entire proceedings will be available shortly on the PLOS ALM website and some interesting personal impressions of the workshop are provided by Martin Fenner (PLOS ALM technical lead).

The Hackathon was held at the PLOS San Francisco office and brought the research community and developers together to identify solutions to current challenges in the field of altmetrics Group members worked on a number of different projects including:

•  ReRank It – allows ranking of pubmed search results based on the impact they have had
• AltViz – focused on better ways to visualize altmetric data at various levels
• Other projects –  Author Centrality Measurement, Altgaming and One article, Many URL’s

PLOS also made two important announcements at the Workshop. Firstly, the launch of the Altmetrics Collection which brings together current research to seed further study and use in this field. As an ever-growing collection, it covers a range of research relating to scholarly impact in online tools and environments. The Collection remains open to all authors who wish to submit research in these areas.

PLOS also promoted the availability of a new release of our open source application (API) which enables API users the ability to access historical data, giving a more accurate picture of the manner and frequency with which readers interact with published content. The code is hosted on GitHub.

PLOS’s unique position as a publisher, an Open Access advocate and a technology-led innovator combine to allow us to successfully leverage its mission of leading a transformation in research communication. It’s gratifying that ALM have attracted support as a new way to measure the reach and impact of an article in and across different research disciplines.  Just recently, Nature Publishing Group announced that that they would be joining PLOS and a growing number of publications by providing ALM’s on twenty journals.

PLOS is delighted to support community momentum coming out of this meeting. To get involved simply add a comment to this post, send us a Tweet or share your thoughts on our Facebook page.

One of the many joys of OA Week is the opportunity to reflect on the movement’s progress. It has been a watershed year for Open Access advocates as evidenced by the surge of momentum since last year.  Just this week a new study published in BMC Medicine shows that OA publishing is growing faster than previously thought. Last week,  the European Science Foundation’s (ESF) membership organization for all medical research councils in Europe, the European Medical Research Councils (EMRC) released a Science Policy Briefing (SPB) entitled ‘Open Access in Biomedical Research’ highlighting the need to accelerate the adoption of open access to research articles in the biomedical sciences across Europe. Governments, funders, publishers, and academic institutions are also leading the way by adopting Open Access policies more firmly than ever before. Here’s a snapshot of recent progress.

Government

In July, three concurrent announcements–Research Councils UK – RCUK; the government response to the Finch Report, and Higher Education Funding Council for England – HEFCE–established a framework for introducing Open Access to the UK over a short period of time with implementation starting in April 2013.  Also in July, the European Commission (EC) published its own set of documents on Open Access, which further raises the possibility that Open Access will become a prevalent mode of dissemination of scientific research, and widened the set of potential publishing models. In the U.S., Open Access advocates are eagerly awaiting a response from the White House after successfully garnering more than 27,000 signatures on a petition that urges expanding Open Access to research funded by all U.S. federal science agencies.

Funders

The World Bank announced an Open Access policy that went into effect in July in  which its data and publications will be licensed under Creative Commons copyrights and made free to the public. In June, the Wellcome Trust announced that it will more strongly enforce its Open Access policy. Noncompliance could result in final grant payments being withheld. Last month, the Budapest Open Access Initiative issued a new set of recommendations, which reaffirmed and expanded on the original Budapest Declaration:

Publishers

This summer also ushered in additional Open Access publishers that will contribute to our important cause. eLife and PeerJ are among those now accepting submissions. PLOS welcomes all new and existing publishing efforts that make research Open Access. Several other publishers are moving toward Creative Commons Attribution (CC-BY) license licensing. John Wiley & Sons, Inc., announced revised licensing arrangements for proprietary journals published under the Wiley Open Access program. The journals will adopt the CC-BY, which allows commercial use of published articles. The Wiley Open Access portfolio also includes journals published with society partners, many of which will similarly transfer to the CC-BY license. A similar  development comes from Nature Publishing Group: Scientific Reports offers authors the option of using a CC-BY license. Scientific Reports published its 457^th article on June 14, its first birthday, making it Nature Publishing Group’s fastest-growing journal. Springer also shifted this year.

Academic Institutions

The Faculty Advisory Council at Harvard University announced that it can no longer afford to maintain its subscriptions to academic journals. The announcement offers advice on what staff can do to alleviate the problem:

Consider submitting articles to Open Access journals, or to ones that have reasonable, sustainable subscription costs; move prestige to Open Access. If on the editorial board of a journal involved, determine if it can be published as Open Access material, or independently from publishers that practice pricing described above. If not, consider resigning.

Purdue University passed a recommendation in 2012 for all faculty to follow Harvard University’s policy with similar licenses, requirements, and options. The recommendation includes modifying Purdue epubs, the existing university repository, as an Open Access repository.

In May, the University of California, San Francisco (UCSF) became the latest academic institution to adopt an Open Access policy for scholarly publications.

The steady progress toward Open Access is encouraging but our work is not yet done. Let’s continue this momentum and transform research communication together.

Welcome to OA week, a celebration of Open Access principles and progress around the world. In preparation for this year’s activities PLOS, SPARC, and OASPA recently released the final version of the Open Access Spectrum guide. This resource outlines the core components of Open Access across the continuum from “open access” to “restricted access”. Its aim is to help authors make informed decisions on where to publish based on journal policies. It also provides a resource for funders and other organizations to help establish criteria for the level of open access required for their policies and mandates. Ultimately, the conversation must shift from “Is It Open Access?” to “HowOpenIsIt?”

To kick off OA Week, SPARC and the World Bank are hosting a live blog and webcast today at 4:00 EST.

PLOS will celebrate the week in a number of ways:

Monday, October 22

• Wide release of the Open Access Spectrum guide
• PLOS is a member organization of the The Humanitarian Centre,  which has launched its 2012 Cambridge International Development report. The report is a collection of original pieces from speakers and participants in the Humanitarian Centre’s ‘Global Health Year’: a year of events and activities designed to explore ways that people from different disciplines, sectors and countries can work more effectively together to tackle global health challenges.
• PLOS Advocacy Director, Cameron Neylon, examines the next phase of Open Access in a blog post: Free and Open Data as a Worldwide Economic Engine
• Guest blogger Barbara Fister provides an educator’s perspective in an post that considers open science as an alternative to the “science-as-property” model used in most schools and colleges

Tuesday, October 23

• Cameron Neylon publishes an editorial in PLOS Biology titled, “Open Access: Delivering on its Potential”
• Cameron Neylon, as a guest speaker at the University of Nijmegen, delivers a talk entitled, “More than just access: The road to delivering networked research”
• Guest blogger Daniel Mietchen, a research physicist, blogs on how Open Access transforms the way research is published, focusing on the importance of licensing in enabling reuse on Wikipedia

Wednesday, October 24

• Guest blogger Mark Thorley (Natural Environment Research Council and lead for Research Councils UK on their Open Access policy) provides a funder’s perspective on why Open Access matters when spending public funds to advance scientific research
• Cameron Neylon is a guest speaker at the University of Exeter delivering a talk entitled, “Realizing the full potential of Open Access: How I learned to stop worrying and love the RCUK policy”
• Kristen Ratan, PLOS Chief Publications and Products Officer, participates in an Open Access publishing day forum at the National Science Library, Chinese Academy of Sciences

Thursday, October 25

• To celebrate the 5^th anniversary of PLOS Neglected Tropical Diseases,  the journal will be publishing a number of items around the theme of progress made in the NTDs field and challenges that remain. We will be publishing a commemorative Editorial, two collections, and a call for Historical Profiles and Perspectives submissions. The primary collection is called “The Geopolitics of Neglected Tropical Diseases”.  The collection is a compilation of previously published review articles focusing on the geographic distribution of NTDs by region, inspiring readers to think about the geopolitics of the infectious diseases affecting the most marginalized populations and the unique perspective of the burden of disease within a global context. A secondary collection compiles our top-viewed research articles from each year of publication to highlight the continued impact of our primary research.
• A Q&A with Peter Hotez and Serap Aksoy, Editors-in-Chief of PLOS Neglected Tropical Diseases, on how far the journal has come in the past five years.

Friday, October 26

• Guest blogger Christy Collins, Founder and President of M-CM Foundation, patient advocate, and parent, gives us a closer look at how patient advocates are using data from open source medical research
• Cameron Neylon is attending the launch of the Open Access policy at the University of Oslo

On behalf of PLOS, SPARC, and OASPA I want to thank everyone who contributed during the open review process of the Open Access Spectrum guide. In preparation for Open Access Week (October 22-28), we are issuing the final version today so that people can download and print it for their use next week and beyond. This resource outlines the core components of open access (e.g., reader rights, reuse rights, copyrights, author posting rights, etc.) across the continuum from “open access” to “restricted access”.  Its aim is to help authors make informed decisions on where to publish based on journal policies. It also provides a resource for funders and other organizations to help establish criteria for the level of Open Access required for their policies and mandates. Ultimately, the conversation must shift from “Is It Open Access?” to “HowOpenIsIt?” The phrase “HowOpenIsIt?” will be used for a family of offerings to foster and promote open access in research communications.  The Open Access Spectrum is our first program with more to come. Today’s content also includes an FAQ and a Chinese translation (Spanish translation coming soon).

The public comment period, which lasted two weeks, generated 60 responses from 11 countries. We received input from publishers, librarians, authors, editors, and research funders, among others. Of the 26 entries in the draft table, 18 were edited and improved as a result of this feedback. The most notable change was an additional entry to the “Copyrights” category. The draft version included four definitions along the Open Access Spectrum. The final version added a fifth: Publisher holds copyright, with some allowances for author and reader reuse of published version.

We deeply appreciate all the suggestions that we received. Your feedback provided greater clarity and precision to the final document.

Not all Open Access is created equal.  To move beyond the seemingly simple question of Is it Open Access?” PLOS, SPARC and OASPA have collaborated to develop a resource called HowOpenIsIt?” This resource identifies the core components of open access (OA) and how they are implemented across the spectrum between “Open Access” and “Closed Access”.  We recognize there are philosophical disagreements regarding OA and this resource will not resolve those differences.

We are seeking input on the accuracy and completeness of how OA is defined in this guide. Download the open review draft and provide feedback via the comment form on the SPARC site.  In its final form, this guide will provide an easily understandable, comprehensive, and quantifiable resource to help authors make informed decisions on where to publish based on publisher policies.  In addition, funders and other organizations will have a resource that indicates criteria for what level of OA is required for their policies and mandates.

This OA guide is aimed toward a wide audience of researchers, authors, and policy-makers.  Your feedback will help us more precisely define OA across a number of categories.  The goals of the guide are to:

•  Move the conversation from “is it open access?” to “how open?”
• Clarify the definition of OA
• Standardize terminology
• Illustrate a continuum of “more open” versus “less open”
• Enable people to compare and contrast publications and policies
• Broaden the understanding of OA to a wider audience

In 2002, the Budapest Open Access Initiative articulated the basic tenets of OA for the first time.  Since then, thousands of journals have adopted policies that embrace some or all of the open access core components related to: readership; reuse; copyright; posting; and machine readability

Why now and why this resource?

OA is gaining momentum and we are seeing a groundswell of support from authors and funders to colleges and governments. Despite this progress there is still confusion about OA.  With this guide we aim to provide greater clarity regarding its definition and components.  All suggestions will be considered and a final version will be released during Open Access Week (October 22 -28, 2012).  The comment period will close on Monday, October 8, at 5:00pm (EST).