Public Library of Science - Open Access

PLoS Author Surveys 2009 – Summary Presentation

Mark Patterson — Wed, 23 Dec 2009 02:45:25 -0800

Earlier this year, PLoS sent out a series of surveys to authors whose work was considered by our journals in 2008. We wanted to find out what authors think about all aspects of our services – from submission and peer review, through to publication and the functionality of the PLoS journal web sites.

We have learned a lot from the surveys, primarily that levels of satisfaction amongst authors are generally very good. We also identified areas where services can be improved, and we’ve adjusted our services in a number ways during 2009.

We have now summarized the results of the surveys along with how we have responded to some of the suggestions during 2009 in a short presentation, which is publicly available. We feel it’s important to share these results in particular with the authors who were kind enough to complete the questionnaires, and we would like to express our thanks to the hundreds of authors who took part. We are planning to repeat the surveys next year, so that we can monitor how views have changed and can respond to suggestions for further improvements.

Meanwhile, we welcome feedback from anyone who is using our services, as an author, reviewer, editor or reader.

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Be heard at the White House - tell them why you support public access to research

Liz Allen — Wed, 16 Dec 2009 10:43:12 -0800

The White House Office of Science and Technology Policy has invited comment on broadening public access to publicly funded research and they want to hear from you. Please post your contributions to this blog.

Their Request for Information (RFI) lasts for just 30 days and expires on 7 January 2010, so we'd like to encourage you to get involved sooner rather than later. This is an opportunity for us to shape a broader public access policy - how it should be implemented, what type of technology and features are needed, and how to manage it.

Adding your thoughts to the blog will help ensure that the administration form a balanced (the comment thread is moderated) view of stakeholders' interest. E-mail comments will also be accepted and will be posted to the blog by the moderators.

There are 3 main topics where the administration would appreciate your input (they also welcome general comments) and each one is open for a set period of time:

1. Implementation - expires 20 December 2009. Which Federal agencies are good candidates to adopt Public Access policies? What variables (field of science, proportion of research funded by public or private entities, etc.) should affect how public access is implemented at various agencies, including the maximum length of time between publication and public release?

2. Features and Technology - 21-31 December 2009. In what format should the data be submitted in order to make it easy to search and retrieve information, and to make it easy for others to link to it? Are there existing digital standards for archiving and interoperability to maximize public benefit? How are these anticipated to change?

3. Management - 1-7 January 2010. What are the best mechanisms to ensure compliance? What would be the best metrics of success? What are the best examples of usability in the private sector (both domestic and international)? Should those who access papers be given the opportunity to comment or provide feedback?

Thanks for supporting this initiative.

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Responding to community feedback - DeepDyve and PLoS - Q & A

Liz Allen — Wed, 04 Nov 2009 10:01:10 -0800

Over the past few days, a company called DeepDyve, who run a search engine that we use on the PLoS.org website, announced a rental service for research articles. DeepDyve offers two types of content on its site - restricted-access content (from traditional publishers such as OUP, Wiley-Blackwell, Sage and others) which can be "rented" for $0.99 on a "pay-as-you-go" model and open-access content, which is always free.

The open-access and library community have been asking some pertinent questions about this new launch and our involvement with it which we'd like to address in this blog post.

Q: Is PLoS charging a fee for access to articles that appear in DeepDyve?

A: There is no financial gain to PLoS - all our content is freely available online to everyone, including commercial organizations, under the terms of the Creative Commons Attribution License that we use.

Q: Why has PLoS agreed to provide its content to DeepDyve?

A. The Creative Commons License means that no permission is required to reuse PLoS content - in fact, creative reuse for commercial as well as non-commercial purposes is encouraged. Readers might like to know that almost every organization that wants to use PLoS content in bulk checks in with us first out of courtesy and this was the case with Deep Dyve.

Q: Is DeepDyve an interim solution that restricts the progress of open-access?

A: When comprehensive open-access is a reality, demand for DeepDyve's service may reduce but since most of the world's research is still locked behind subscription or pay-per-view barriers, DeepDyve at least offers an alternative way to get hold of restricted access articles for an affordable price.

Q. Is PLoS doing this to gain eyeballs on its content?

A. PLoS content is freely available to everyone who wants to reuse it. We want as many people as possible to take advantage of this content because research information is most powerful when more people can discover and use it and naturally, we're in favor of maximum exposure for the work of PLoS authors.

Q. Is this the start of a proliferation of new business models that will make use of open-access content?

A. As the influence of open-access grows, and more content becomes openly available, organizations are going to find new and creative ways to reuse it. Some of the added value that these organizations bring may well come at a cost to users who will exercise their spending power and decide which services will be ultimately successful.

Finally, when we raised some of the concerns of the community, listed above, with DeepDyve they were responsive and immediately made the status of open-access content clearer on their website.

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Open Access Week

Bora Zivkovic — Mon, 19 Oct 2009 11:34:25 -0700

This week - 19th-23rd October 2009 - is the Open Access week around the world - fitting nicely with the 5th birthday of PLoS Medicine. And when I say 'around the world' I really mean it. Just check out all the global events happening this week.

The OA Week is co-organized by Open Access Directory, PLoS, SPARC, Students for Free Culture, eIFL (Electronic Information for Libraries) and OASIS.

Many countries are participating this year, including some with numerous events all around the country. See, for example, all the events in Germany (there are 67 events in that country alone!), Netherlands, China and Japan.

You can get all the information and follow the events on the Open Access Week blog. There is also a nice round-up on the SPARC site.

As the week unfolds, we will blog more about it here. In the meantime, you can follow the news of the OA week on Facebook or by following PLoS on Twitter.You may also want to sign up to participate in the OASPA webinar (locationless - sign up to participate online).

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PLoS Journals – measuring impact where it matters

Mark Patterson — Mon, 13 Jul 2009 05:22:00 -0700

In 2009, in this online world, how do most scientists and medics find the articles they need to read? The answer for the content published by PLoS (and no doubt by many other publishers) is via one of the now ubiquitous search engines, be it one that only searches the scientific literature, or more likely, one that searches the entire web. Given that readers tend to navigate directly to the articles that are relevant to them, regardless of the journal they were published in, why then do researchers and their paymasters remain wedded to assessing individual articles by using a metric (the impact factor) that attempts to measure the average citations to a whole journal? We’d argue that it’s primarily because there has been no strong alternative. But now alternatives are beginning to emerge.

A few months ago, PLoS initiated a program to provide a series of metrics on the individual articles published in all the PLoS Journals. You can see some examples here, here, here and here. There are two complementary benefits to the new approach.

First, we are focusing on articles rather than journals. The dominant paradigm for judging the worth of an article is to rely on the name and the impact factor of the journal in which the work is published. But it’s well known that there is a strong skew in the distribution of citations within a journal – typically, around 80% of the citations accrue to 20% of the articles. So the impact factor is a very poor predictor of how many citations any individual article will obtain, and in any case, journal editors and peer reviewers don’t always make the right decision. Indicators at the article level circumvent these limitations, allowing articles to be judged on their own scientific merits.

Second, we are not confining article-level metrics to a single indicator. As summarized by Michael Jensen, and discussed by many others including recently over at the Scholarly Kitchen, there’s a lot more to scientific impact than citations in the selection of journals covered by the Web of Science – the proprietary source of data that provides the impact factor calculation. Citations can be counted more broadly, along with web usage, blog and media coverage, social bookmarks, expert/community comments and ratings, and so on. Our own efforts are so far confined to citations (as measured by Scopus and PubMed Central), social bookmarks (as made by users of Connotea and CiteULike), and blog coverage (as recorded by Bloglines, Postgenomic and Nature Blogs), and these metrics will be improved and expanded over the coming months. The good news is that many of these indicators can be collated automatically, using openly available web tools that constantly update information on the article itself.

The presentation of a comprehensive array of this data is an enticing prospect. When an article has been published, we have tended to regard that as the end of the story (barring corrections or the occasional retraction). But if, as frequently happens, a very good article has been published in a specialist journal after being rejected from a highly selective one, it would be great to indicate to a user that this article is actually looking pretty significant, and show how its influence develops over the months and years.

Rather than basing judgments on the importance of research on the opinions of two or three reviewers and editors, article-level metrics will attempt to capture the actions and opinions of entire communities of readers to give a rich and sophisticated picture of research impact that will be helpful to authors and readers alike. Readers may then frame that picture in the context of their particular field and their own work.

To realize the vision for article-level metrics there are still some significant hurdles to clear: it won’t be enough simply to provide indicators without some context or guidance on how to interpret them; some indicators (particularly citations) take months to build up limiting their value as early indicators of impact; and standards will need to be developed so that the indicators are reliable and as free as possible from gaming and manipulation.

A clear editorial selection process will always have a place before publication in a scholarly journal. But a reduction in the reliance on the impact factor for so many aspects of research assessment could be massively liberating. PLoS Medicine, to cite an example close to home, has recently restated its mission – focusing on the diseases and risk factors that have the most profound impacts on global health. By carefully selecting articles that are likely to have the biggest influence on global health and using innovative and diverse approaches to assess and indicate that influence, PLoS Medicine will be a greater force, regardless of how many citations an average article accrues

Looking towards other modes of publishing, PLoS ONE is predicated on the notion that judgements about impact and relevance can be left almost entirely to the period after publication. By peer-reviewing submissions purely for scientific rigour, ethical conduct and proper reporting before publication, articles can be assessed and published rapidly. Once articles have joined the published literature, the impact and relevance of the article can then be determined on the basis of the activity of the research community as a whole. Article-level metrics and indicators, along with other post-publication features are part and parcel of the PLoS ONE approach, and could help readers to filter and sort literature after it is published. Ultimately, the aim of adding value to articles after publication is to improve the whole process of scientific communication and accelerate research progress itself. You can read more about article-level metrics in the context of PLoS ONE, and a talk is also available online from Pete Binfield (Managing Editor of PLoS ONE).

Article-level metrics and indicators will become powerful additions to the tools for the assessment and filtering of research outputs, and we look forward to working with the research community, publishers, funders and institutions to develop and hone these ideas. As for the impact factor, the 2008 numbers were released last month. But rather than updating the PLoS Journal sites with the new numbers, we’ve decided to stop promoting journal impact factors on our sites all together. It’s time to move on, and focus efforts on more sophisticated, flexible and meaningful measures.

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Creative Re-Use Demonstrates Power of Semantic Enhancement

Shabnam Sigman — Thu, 16 Apr 2009 15:44:17 -0700

A Review article published today in PLoS Computational Biology describes the process of semantically enhancing a research article to enrich content, providing a striking example of how open-access content can be re-used and how scientific articles might take much greater advantage of the online medium in future.

Dr. David Shotton and his team from Oxford University spent about ten weeks enriching the content of an article published in PLoS Neglected Tropical Diseases, the results of which can be seen online here.

The enhanced version includes features like highlighted tagging which you can turn on or off (tagged terms include disease names, organisms, places, people, taxa), citations which include a pop-up containing the relevant quotation from the cited article, document and study summaries, tag clouds and citation analysis.

With a single click you can re-arrange the reference list by number of times each paper is cited, or add in the authors’ analysis of how the reference is used in the paper (obtains background from, confirms, extends, shares authors with, uses method in). The group has also provided interactive versions of some of the figures: compare the original, static Figure 3 to the moveable, overlaying, enhanced version.

David Shotton’s group hopes that this largely manual effort will demonstrate what practical enhancements can be made to scientific papers through the application of existing technology. These developments significantly enrich the content of a paper, and also demonstrate some of the potential that open-access provides by removing any barriers on the re-use of content. Once the methods employed by Dr Shotton and his colleagues become more routine, all open-access literature could be semantically enhanced and redistributed without restriction. Whether the next steps towards semantic markup are implemented by authors, publishers or post-publication text miners remains to be seen, but we welcome your feedback on this idea, either as a comment to this post, or on the article itself.

By Evie Browne, Publication Manager, PLoS Computational Biology

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Is Society Biased Against "Openness"? A PLoS Board Member’s Perspective on the Future of the Library in the Digital World

Nisha Doshi — Thu, 19 Mar 2009 09:53:37 -0700

The Arcadia Project is a three-year programme based at the University of Cambridge (UK), which aims to explore the role of academic libraries in a digital age. Naturally, we were delighted that a PLoS board member was selected to give the first Arcadia lecture. As well as serving on the PLoS board and being the founder of the Center for the Study of the Public Domain, Professor James Boyle is also the Chairman of the Board of Creative Commons, co-founder of Science Commons, a member of the advisory board of Public Knowledge, and William Neal Reynolds Professor of Law at Duke Law School. He was therefore ideally suited to providing an informed and inspiring vision of the future of the library in the digital world.

Professor Boyle challenged the stereotypical image of libraries as conservative, dusty places, arguing instead that they are extraordinary institutions which combine the fundamental roles of archiving, facilitating research and enabling public access to cultural material. Nevertheless, libraries developed in a world where the container for knowledge was the book: only one person at a time could read any one copy of a book, and libraries provided valuable repositories for these documents. In the age of digitised knowledge, books and papers can be read simultaneously be anyone on the planet – in theory, at least. What effect does this have on the notion of the library?

To address this question, we were asked to consider three trends. Firstly, according to Professor Boyle, attitudes towards information dissemination are characterised by a fear of openness. If asked to predict the outcomes of the World Wide Web in 1992, we would have easily predicted the risks of spam, illicit copying, and pornography, and we may have rejected this decentralised model in favour of a closed, carefully-controlled system. In contrast, he suggests, we would not have been able to imagine the blossoming of information and knowledge sharing which the Internet has enabled, nor the dramatic benefits it has brought in areas such as information layering, blogging, open source software, and whistleblowing. This fear of openness, or “cultural agoraphobia”, leads to an asymmetry in our perception of risks and benefits. As a result, we are too reluctant to embrace open systems and methods of production or distribution, and we are not yet able to differentiate effectively between appropriate and inappropriate developments in the sphere of “openness”.

The development of copyright formed Professor Boyle’s second trend: as the cost of copying has decreased to almost zero via the invention of the printing press, copying technologies, audio recording and the Internet, the perceived need for stronger protection has increased – when you needed a monk to copy a book, copyright wasn’t so much of an issue! The third trend which we were asked to contemplate relates to the contrast between the evidence-based nature of most policy-making (for example, in medicine or environmental science) in contrast with the anecdotal or philosophical basis of most intellectual property debates. Although illicit copying is indeed problematic, Professor Boyle proposed that unnecessarily-tight copyright laws lead to even greater losses, such as failed sharing, inability to conduct research, and inability to access material even where the copyright holders cannot be identified. He explained that US copyright laws have been characterised by a “20^th century black hole”, whereby is it almost impossible to opt out of copyright and copyright is in place for a period of time which is longer than the commercial life of almost every cultural object. All gates lead into copyright and none lead out, he argued. Although these laws were initially designed to provide an incentive for people to allow access to others, they now achieve the opposite.

In a world of open access and digitisation, therefore, do libraries still have a role to play? Absolutely, concluded Boyle. We should increasingly look to digital libraries to provide “global access to everything”, we should invest in ensuring the stability of digital archives to preserve access to cultural objects in the face of evolving technologies, and we should develop novel ways to use and explore the information which is increasingly becoming available to us. Powerful arguments indeed, which seem to reaffirm the Public Library of Science’s mission statement in all respects.

Nisha Doshi, Publications Assistant, Public Library of Science

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Open Access Archaeology and PLoS

Nisha Doshi — Tue, 17 Mar 2009 10:37:46 -0700

Starting work in open-access publishing at PLoS Medicine seemed a sensible step for me, having focused my Masters research on an evaluation of the quality and research dividends of an online archaeological database – a unique resource which holds records of more than 300,000 artefacts from England and Wales and renders information about these finds accessible to any interested party, whilst also facilitating research into previously neglected topics and questions. Yet, many of my colleagues in archaeology insisted that open access had no place in our discipline, arguing that authors would be unable to fund publication fees and traditional subscription-based journals were too central to assessment of academic merit. A quick search of PLoS journal archives reveals, however, that some archaeological scientists have already embraced the open-access model for dissemination of their research.

Perhaps most significant in terms of its contribution to the discipline is a paper by Houyuan Lu and colleagues from the Chinese Academy of Sciences, Beijing, published by PLoS ONE in February 2009. This study represents a valuable step forward in archaeobotanical analysis of common and foxtail millet – important early cultivars in northern China which have been hitherto difficult to identify at archaeological sites. Detailed analysis of phytoliths (microscopic silica bodies found in plants) enabled the authors to establish five diagnostic characteristics which can be used to differentiate between these two species. Since phytoliths are more likely to be preserved than millet grains, this study not only enhances archaeologists’ ability to identify these crops at archaeological sites, but the detailed morphological analyses presented in the paper also provide a useful methodology which can be applied to other cereal crops and wild grasses.

In addition to archaeobotany, research in archaeogenetics is already well represented amongst PLoS papers. For example, Guido Barbujani and colleagues analysed mitochondrial DNA in 28,000-year-old bones from the Paglicci Cave, southern Italy, and not only demonstrated genealogical continuity from this Cro Magnon individual to modern Europeans, but also revealed radical dissimilarity between this early modern human and near-contemporary Neanderthals. Francesco Cucca and colleagues studied the Y chromosomes of 930 Sardinian males to suggest predominantly pre-Neolithic settlement of the island of Sardinia, with little subsequent gene flow from outside populations. As a result, they identified Sardinia as a potentially useful setting for genetic association studies of multifactorial diseases. Similarly, another PLoS ONE paper by Helen Donoghue and colleagues has relevance for both archaeological and present-day studies: using PCR and liquid chromatography, these researchers have identified Mycobacterium tuberculosis in human bones from the 9000-year-old village of Atllit-Yam in the eastern Mediterranean, and shed light on the co-evolution of this pathogen with human and animal hosts.

Like the phytolith-based analysis above, Ruth Bollongino and colleagues also chose PLoS ONE to report research into early domestication, using DNA analysis to suggest rapid introduction of domestic cattle into central Europe without significant crossbreeding with local wild aurochs. A PLoS Genetics paper by Agnar Helgason and colleagues reports mitochondrial DNA analysis of 1000-year-old Icelandic skeletal remains, revealing sequences which are more similar to contemporary populations in Scotland, Ireland and Scandinavia than they are to modern Icelandic inhabitants. Likewise, Li Jin and colleagues analysed mitochondrial DNA from human remains believed to be construction workers for the mausoleum of the First Emperor of China (famous for its Terracotta Warriors) and suggested that these workers originated from diverse regions of China and beyond. As ever in archaeology, it is important to take stock of the limitations of our techniques and, in a paper entitled “Cryptic Contamination and Phylogenetic Nonsense”, Anna Linderholm and colleagues raise important questions about the risk of contamination of archaeological samples with modern human DNA.

Open-access archaeological papers published by PLoS are not limited to archaeobotany and archaeogenetics. For example, William Banks, Francesco d’Errico and colleagues present archaeological and chronological data, coupled with high-resolution palaeoclimatic simulations, to argue that Neanderthal extinction did not result from climate change but from competition with anatomically modern humans. Research articles are also complemented by essays and interviews, notably a PLoS Genetics interview with Svante Pääbo (Director of Evolutionary Genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig) – a key player in archaeogenetics whose work has ranged from Neanderthals to Egyptian mummies.

Far from representing a dead end, this range of research hints that the open-access model has an important role to play in archaeology. Already, one major field unit (Oxford Archaeology) has committed to “making archaeological knowledge free to access” as part of its Open Archaeology programme and the Alexandria Archive Institute has developed an international facility for open access archiving of primary data from archaeology and related disciplines. Hopefully, the coming months and years will see increasing publication of archaeology in open-access journals such as PLoS ONE, to enable widespread dissemination of research and facilitate international and interdisciplinary access, dialogue and debate.

Nisha Doshi, Publications Assistant, Public Library of Science

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"Ten Simple Rules" Collection: Chinese Translation

Rosemary Dickin — Fri, 27 Feb 2009 08:20:33 -0800

In a wonderful example of creative reuse of open literature, PLoS Computational Biology’s “Ten Simple Rules” collection of Editorials has recently been translated into Chinese by members of the EpiMan discussion forum. Originally written by Editor-in-Chief Philip E. Bourne and collaborators, this collection of 11 articles (October 2005 – June 2008) offering professional tips and advice has proved to be a popular and valuable resource and focus of discussion for scientists and other professionals at every stage of their career.

The members of epiman.cn, a non-profit academic forum based in China, saw the potential value of a translation of this work, and a collaboration of 18 members of the forum translated the articles into simplified Chinese. The resulting PDF, which is now available to download on PLoS Computational Biology’s website was first distributed by the EpiMan forum in December 2008. The group is currently seeking a publisher to produce print copies of the translation for distribution in the Chinese mainland.

PLoS actively encourages the free dissemination and reuse of information to maximise the impact and value of our published work. Under the Creative Commons Attribution License, material may freely be copied, translated, distributed and re-imagined (providing the original authors are credited).

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Save the date - Open Access Week 19-23 October 2009

Liz Allen — Wed, 14 Jan 2009 12:11:24 -0800

After the resounding success of our first ever Open Access Day in 2008, where we had nearly 130 participating organizations from almost 30 countries, we are pleased to announce that this year's events will be scheduled during the week of 19-23 October 2009.

Why a week rather than a day? When we asked for feedback from the folks taking part last year, while they said that they had enjoyed the "event-in-a-box" approach, many of them found that cramming everything into one day was tricky (especially given international time differences) and that spreading activities over a week to suit their individual needs would be easier.

What is also particularly pleasing about choosing this week is that 19 October is PLoS Medicine's fifth birthday so any planned community-led events to celebrate this important milestone can do double duty.

The organizing forces behind Open Access week remain unchanged from last year namely: PLoS, SPARC and Students for FreeCulture but we also wish to add a technology partner who could assist us with streaming live web coverage of round table discussions or talks from prominent advocates and post event delivery. So if you are reading this and you work in this field or have significant experience of it and want to join the team please email Donna Okubo (dokubo@plos.org).

We will be launching our Open Access Week 2009 site shortly but in the meantime, you can sign up here.

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Open Access Week is held in 19-23 October 2009.

from Keitabando's Blog on Tue, 2009-03-10 00:42

Last year, I lectured in the event named Open Access Day.
国際学術情報流通基盤整備事業　│　イベント情報　│　SPARC Japanセミナー【Open Access Day特別セミナー】「日本における最適なオ-プンアクセス...