PLOS Opens Roundup (March 7)


In this issue, Obama signals a commitment to open access and the Dutch libraries start cloudsharing, whilst in other news there is a new science magazine published by the Wellcome Trust, a round-up of the posts surrounding the withdrawal of nonsense papers published by Springer and IEEE, a curious case of the London mathematical society,  an interview with Sydney Brenner discussing why the current culture of some labs stifles innovation, a thought experiment of why publishers don’t need embargoes, a brief review of the cost of hybrid publishing, and the odd mention of data sharing policies….[and see the update added on March 09 to the entry ‘PLOS’s Bold Data policy’]

With thanks to Heather Joseph, Alma Swan, Ginny Barbour and Susan Au for links and tip-offs.


US: The President’s 2015 Budget Request – Public Access Language

US Flag 04 March: President Obama released his FY15 Budget request. As you may know, this request essentially represents the President’s policy “wish list” for the year, and signals the official start to the federal budget process. In the budget released on the 3rd, there is a section titled “Creating a 21st Century Government,” which includes a subsection on “Economic Growth: Open Government Assets as a Platform for Innovation and Job Creation.” It includes language discussing the need for greater public access to government-generated assets, including scientific research. The budget explicitly states:

By opening up Government-generated assets including data and the fruits of federally funded research and development (R&D)—such as intellectual property and scientific publications—to the public, Government can empower individuals and businesses to significantly increase the public’s return on investment in terms of innovation, job creation, and economic prosperity.

While it carries no executive or legislative force, the language signals a continued commitment to the issue of ensuring public access to the results of publicly funded research. For full details and context, please see pages 41-42 of the main link. (Thanks to Heather Joseph for providing this update)

Australia: The National Health and Medical Council sign up to DORA and a guide for researchers to the ARC data management plan

Feb 24: Both announcements are noted by Stephen Matchett in different issues of the ‘Campus Morning Mail’ (you need to scroll down).  On the San Francisco Declaration on Research Assessment (DORA), he notes that the Australian Research Council (ARC) have still to sign up to this (and should). He also adds that “hoping the publishers will actually acknowledge a reform not in their interests is probably too much to expect.” But there are several publishers, such as PLOS, the Royal Society and AAAS, as well as individual journals that have signed up to DORA, in addition to the growing number of funders. Lagging behind even some publishers, however, are the signatories of actual institutions. On the data front, the Australian National Data Service has produced a guide for researchers about creating the required data management plan for ARC, which has to include details for how they will store and share their data (sound familiar – see later).

Netherlands: Dutch consortium of university libraries and the National Library of the Netherlands move to cloudshare their metadata with OCLC Worldshare

Netherlands FlagFeb 19: Not strictly a policy move but a significant move by the libraries of an entire country to shift their services services to OCLC WorldShare. “WorldShare provides an open cloud-based approach for sharing metadata, applications and innovation, enabling library consortia to collaborate at a national or regional level as well as connecting globally to raise visibility and awareness of their institutions on the web, and take advantage of the economies of scale that global collaboration brings.” As Eric van Lubeek, Managing Director, OCLC EMEA notes in the press release: “UKB’s move will serve as an example for other libraries and library consortia, not just in the Netherlands, but around the world.”


Thoughts on journal embargoes

March 05: Ben Johnson provides a thoughtful thought experiment re-imagining scholarly communication and deconstructing the arguments about why publishers think they need to impose embargoes on the final version of the manuscript. He discusses what publishers add that is considered ‘essential’ – i.e. peer-review and ‘brand-recognition’ – and shows that neither has to be supplied by the publisher or subject to embargo because both are available via the accepted version of the article, which can generally be posted to a repository immediately. He goes on to argue that if embargoes were completely lifted, libraries would still continue to subscribe to journals because 1) that’s how articles get cited, 2) readers like all the peripheral content in journals (book reviews etc) , 3) it’s easier to find the article, 4) librarians cancel journals because of price, rather than embargo length, and 5) most librarians won’t cancel anyway as they are tied into big deals.

It’s an interesting analysis and I think he’s right but I think that it also omits one other service. He doesn’t discuss the role of either marking up the html or xml version of the article or ensuring that the article adheres to the appropriate standards of metadata (including metadata that enables you to know what licence is associated with the article). Again, this is not something that publishers need to do but it is currently a service that most established publishers provide because it makes their content more discoverable on the web (until you come up against that paywall). And it is also these jewels of the digital age that subscription publishers are protecting by trying to restrict text mining. They want you to find their version of the article but only to use it under the conditions they stipulate (thus protecting potential revenue stream).

A new way to explore the science of life: Mosaic launches today

Mosaics LogoMarch 04: In another pioneering move, the Wellcome Trust has launched a new #OA magazine about science called ‘Mosaic’, which will feature in-depth stories (including video) across the biosciences but will also include some topics from the humanities (reflecting Wellcome’s roots and focus of funding). A cross between a blog and more formal online magazine, with a wonderfully sleek design, it has a really strong line-up of regular contributors including people like Oliver Burkman (well known to Guardian readers) whose opening feature is an interview with Steven Pinker, as well as Emily Anthes writing on the female condom (no interest there then…) and Michael Regnier exploring Alzheimer’s Disease. Mosaic actively encourages you to not only read the written content for free but also share it and, yes, even republish it –  even commercial re-use is permitted (as long as there is appropriate attribution). Giles Nelson, the editor of Mosaic, provides the rationale for why they opted for a CC BY licence. Such a licence is still rare for this type of ‘ front-section’ content and represents a potential game changer among science writing – (although note it doesn’t apply to all of the content). For example, it is sometimes argued that the front section of journals like Science and Nature could never convert to OA because the work is often commissioned from e.g. science writers and journalists and you therefore have to charge for access because it is not feasible to recoup the cost with e.g. an APC (although this wouldn’t apply to practicing scientists writing in these sections – they generally aren’t paid a commission and often acknowledge funders). Certainly there is a cost that has to be paid for somewhere – but Wellcome have obviously decided that footing the entire bill for the sake of engaging the public with the research they are funding is worth it. Fantastic initiative.

Update (March 07): The SpotOn London conference last fall had a session on Creative Commons journalism and the video is available.

UKSG official journal fully Open Access (without publishing charges) with special issue on OA

Insights coverMarch 04: UKSG, an organisation with a mission to “connect the information community and encourage the exchange of ideas on scholarly communication”, has just flipped its official journal, Insights, to OA. To mark the occasion, they commissioned a special issue on Open Access, featuring articles from speakers at a conference they hosted last year. Among contributions are those focusing on policy (e.g. about Finch by Michael Jubb, and HEFCE from David Sweeny and Ben Johnson), on publishers (e.g. by PLOS ONE’s Damian Pattinson and myself, and by Taylor and Francis on how they’re riding out the transition), on OA in the humanities (by Caroline Edwards, co-founder and co-director of the Open Library of Humanities) as well as OA developments in China by Xiaolin Zhang (Chinese Academy of Sciences).

PLOS’ Bold Data Policy

Image by planeta (CC BY-SA 2.0)

Image by planeta (CC BY-SA 2.0)

March 04: There will be more to come on the PLOS data policy* [see update below] but in the meantime, here is a list to some of the many links and posts that have discussed it. From PLOS, there is an article in PLOS Biology detailing the policy, our FAQ page, and a  post on the EveryONE blog. As well as the numerous tweets, there are reactions from Ian Dworkin, Edmund Hart, Practical Data Management for Bug Counters, DrugMonkey, the MacManes Lab., Erin C. McKiernan, Neuropolarbear, motorcar nine, Small Pond Science and David Crotty over at Scholarly Kitchen (main link). Note that the comments are often as interesting and revealing as the posts and there is a focus on behavioural, neurological and ecological data. Be sure to check out related discussion articles by e.g.  by Joel Hartter et al , Bryan Drew et al and Dominique Roche et al all in PLOS Biology with  associated blog posts from Roli Roberts and Emma Ganley (editors on PLOS Biology). And then read Cameron Neylon’s post ‘Open is a state of mind’.

Update (March 07): Please also see this post by Björn Brembs and another by ecologist Timothée Poisot .

*Update March 09: Theo Bloom (PLOS Editorial Director, Biology) has provided a correction, apology and further clarification about our data sharing policy given “the extraordinary outpouring of discussions on open data and its place in scientific publishing”. As she notes, much of the discussion centered on a misunderstanding in a previous PLOS ONE blog post and also on our site for PLOS ONE Academic Editors: “an attempt to simplify our policy did not represent the policy correctly and we sincerely apologize for that and for the confusion it has caused”. ….”We have struck out the paragraph in the original PLOS ONE blog post headed “What do we mean by data”, as we think it led to much of the confusion.”

As Ivan Oransky reports on Retraction Watch: “The move looks like the right thing to do. The problem seemed to have stemmed from how the policy was communicated, rather than what PLOS actually wanted to accomplish, which is better data sharing. In a time when reproducibility is a growing concern, the latter is a must.

Here’s the salient points of the clarified policy:

“Two key things to summarize about the policy are:

  1. The policy does not aim to say anything new about what data types, forms and amounts should be shared.
  2. The policy does aim to make transparent where the data can be found, and says that it shouldn’t be just on the authors’ own hard drive.”

“We ask you to make available the data underlying the findings in the paper, which would be needed by someone wishing to understand, validate or replicate the work. Our policy has not changed in this regard. What has changed is that we now ask you to say where the data can be found.

As the PLOS data policy applies to all fields in which we publish, we recognize that we’ll need to work closely with authors in some subject areas to ensure adherence to the new policy. Some fields have very well established standards and practices around data, while others are still evolving, and we would like to work with any field that is developing data standards. We are aiming to ensure transparency about data availability.”

She then goes on to demonstrate with an example question and answer. If you have further questions you can post comments to her post, or contact PLOS by email at, and via all the usual channels.

Access and Accessibility for the London Mathematical Society Journals

March 03: Fascinating article by Susan Hezlet in the March issue of ‘Notices of the American Mathematical Society’ about whether the presence of a preprint version on the arXiv has an effect on the usage of the final published version and what the LMS is thinking about open access. The key conclusion is that there is essentially no difference between their usage figures for papers in/not in ArXiv but they still fear that their revenues will be undermined by the UK Government’s open access policies – “…it seems the danger does not lie in the ArXiv version…I believe there would be a threat to the subscription base if we were required to deposit the final published version and not just the authors accepted manuscript. I should be clear that no one is asking this…”.  It is also curious to see that even in a mathematics journal they don’t provide confidence limits on their data (e.g. Fig 1).

Opening Science

Some rights reserved by Martin Clavey. Attribution-ShareAlike 2.0 Generic (CC BY-SA 2.0)

Montage Photoshop by Martin Clavey. Attribution-ShareAlike 2.0 Generic (CC BY-SA 2.0)

March 02: A new book on open science released in January under a CC-BY-NC licence  but with the latest version just out (see menu in the top left). Each chapter has a different author and can be downloaded as a separate pdf (with its own DOI). The chapters span a wide range of topics that covers the basics, such as what ‘open science’ means by Benedikt Fecher and Sascha Friesike, and another on why impact factors and publication pressure reduce the quality of scientific publications by economist Mathias Binswanger, as well as a host of chapters on the tools and the vision for the future. It’s a euro-centric compilation that also includes chapters by many you’ll recognise including Pete Binfield, John Willinsky and Martin Fenner, who told me that they hope to keep the work updated and will consider adding chapters in the future as needed. Be sure to note the fact that you can take all the code for this from Github (‘Fork me on Github’ – top right) and remix it as you see fit (although you can’t then sell it). A great resource

Small firms lack resources to make most of open access

Feb 27: In Times Higher, Paul Jump discusses Elsevier’s contention that small firms lack resources to make the most of open access and that just providing access to the literature wasn’t going to lead to the sort of economic innovation that David Willets (the UK Minister for Sciences) thought it would. According to  David Mullen, Elsevier’s regional sales director of corporate markets in Europe, the Middle East and Asia, when Elsevier provided access to their journals to a dozen small firms in the Netherlands, it had little impact. This directly contradicts a study of small and medium enterprise firms in Denmark however, by John Houghton, Alma Swan and Sheridan Brown. Hougton et al. showed that  it would have taken an average of 2.2 years longer to develop or introduce the new products or processes in the absence of contributing academic research and would cost around DKK210 000 per firm in lost savings (DKK 10 million per year in total across the sample) – see page 47 of the pdf. Elsevier also don’t note that a 2007 study across the EU showed a very weak link between innovative enterprises and public research institutes and universities (see slide 13 and rest of talk given by Alma Swan at the UHMLG Spring Forum).

Mullen does have a point though  – open access to literature is not enough – there also needs to be the social, technological and policy infrastructure in place to ensure seamless searching and filtering between different platforms regardless of the content provider. But I don’t think that Mullen’s solution is the one to adopt. He concludes that the key would be “to provide companies with Elsevier’s entire set of tools for identifying useful research among its journals at an affordable price to help them quickly find the information they needed”…. .

Update (Mar 6): John Houghton responded to the article in Times Higher: “the proposed “tools”, in the form of paywall-controlled proprietary access silos, are the problem, not the solution

Publishers withdraw more than 120 gibberish papers

L0031339 Nonsense talked by a cobbler compared to the talk of a parso

Credit: L0031339 – Wellcome Library, London Nonsense talked by a cobbler compared to the talk of a parson and a surgeon-apothecary. Coloured etching attributed to C. Williams, ca. 1812. (CC BY)

Feb 24:  Richard van Noorden (Nature) covers the story that two publishers – IEE and Springer – have published computer generated papers and were selling them as part of their subscription services. Springer swiftly released a statement on 27th Feb stating that they were removing rather than retracting the papers ‘since they are all nonsense’. The news was covered by both the science press (not just Nature but also in Retraction Watch) and more general media, such as Slate magazine, Fox News, the Wire, and the Telegraph. Most of the posts linked the generation of fake papers with the pressure to publish (and the problems of the impact factor) while raising questions about  whether the rash of fake papers was indicative of ‘slipping standards among scientists’ or the fact that salaries of some professors are linked to the number of papers they publish.

Achilleas Kostoulas lays bare many of the underlying problems in his aptly titled post Fake Papers are not the real problem in Science where he discusses the long history of hoaxes and retractions in science, drawing on Curt Rice’s article in the Guardian about why you can’t trust research. Although papers published as conference proceedings are often not subject to the same rigour of peer-review as articles submitted to journals, there is no doubt that this mess, like others before it (e.g. the OA sting by John Bohannon or the ‘Arsenic Life’ paper in Science), is a larger symptom of a system of peer-review and research evaluation that is increasingly failing. It is not, however, an indictment of the rigour of peer-review for subscription services. Regardless of the type of publisher – OA or subscription –  there is an urgent need to research how research itself is evaluated both before and after publication. One question that remains unanswered is why these computer-generated papers were submitted in the first place. One possibility is that they come from scientists wanting to boost their publication records, although as Richard van Noorden notes (main link), some of the authors were unaware of the submissions. An alternative is that conference organisers might be trying to boost their profile although there is no direct evidence of this.

How Academia and Publishing are Destroying Scientific Innovation: A Conversation with Sydney Brenner

C0009284 Credit: Wellcome Library, London A traditional glass lightbulb with a metal filament against a glowing yellow background. Photograph 1/9/2001 Collection: Wellcome Images

C0009284 Credit: Wellcome Library, London Collection: Wellcome Images Copyrighted work available under CC BY 2.0

Feb 24: In a somewhat related article on the same day as the Nature story above, Elizabeth Dzeng discusses the state of science evaluation with Nobel prize winner Sydney Brenner. Her interview starts out with a fascinating insight into the emerging field of genetics and molecular biology when individuals at the Laboratory for Molecular Biology at Cambridge, such as Brenner, Fred Sanger and Francis Crick, were seen as extremists – part of some kind of evangelical sect. But Brenner goes on to note that the culture of innovation that facilitated their discoveries no longer exists because it has been replaced by a new culture in [US] science that relies on ‘the slavery of graduate students’ and the ‘post-doc as an indentured labourer’. And peer-review is hindering science, he says, and has become ‘completely corrupt’ – “it’s not publish or perish, it’s publish in the okay places [or perish] – while a system of publishing where the author hands over copyright to publishers perpetuates this. He concludes that the open access movement is beginning to shift the culture back  and that even journals like Cell, Nature and Science will have to bow in the end.

ALM community site launched

Feb 24: Jennifer Lin and Martin Fenner have launched a community site, including a blog, which aims to aggregate all the information about ALMs from different sites and to help showcase ALM visualizations of examples “done with d3.js and R, with source code and data openly available to make it easier for people to get started using ALM data.” A great one is the top ten most cited articles on Wikipedia (measured as the number of pages citing a particular article) which lists a paper from Science about life on Mars at the top and also features two PLOS ONE articles (e.g. one about a new species of river dolphin). Notice the source code on the main page re wikipedia citations – which you can lift and use to host the metrics on your own site (you will need an appropriate API key to make it work though).

Update (March 07) from Martin Fenner: The Wikipedia example is based on roughly 320,000 articles from January/February 2014 loaded by CrossRef Labs. So it indicates what recently published papers are popular, not all Wikipedia content (yet!)

Collaborate, co-operate, communicate!

Photo by Krista Baltroka (CC BY)

Feb 20: Over at scholarly kitchen, Alice Medows provides a refreshing post about the need for more collaboration and communication between open access advocates and those from the more traditional wing of the publishing industry with the aim of celebrating success regardless of where it comes from. This is partly in response to less than positive acclaim for initiatives like the ‘Access to Public Research’ (e.g. by Cameron). Much of the discussion has been about the tone adopted by one side or the other and it is worth distinguishing between tone and a genuine difference in substance. As Cameron  notes in his more recent response to this, “Discussion is always more useful than shouting matches. And sometimes that discussion will be robust, and sometimes people will get angry. It’s always worth trying to understand why someone has a strong response. Of course a strong response will always be better received if it focuses on issues. And that goes regardless of which side of any particular fence we might be standing on.”

Cost of hybrid

From Andrew Theo (2012), “Gold Open Access: Counting the Costs”, published in Ariadne, 3 December 2012, maps the cost of article processing fees against journal impact factor.Published under Creative Commons Attribution 3.0 Unported (CC BY 3.0) licence.

From Andrew Theo (2012), “Gold Open Access: Counting the Costs”, published in Ariadne, 3 December 2012, maps the cost of article processing fees against journal impact factor.Published under Creative Commons Attribution 3.0 Unported (CC BY 3.0) licence.

Feb 20: Danny Kingsley discusses the cost of publishing OA in a hybrid journal at the Australian Open Access Support Group blog, including providing this figure of the cost on publishing in a hybrid journal compared with a pure OA journal with an APC. The APC of hybrids are higher, regardless of impact factor of the journal (i.e. used as a surrogate of journal quality). She also discusses other research that shows that most hybrid journals charge about $3000 for access to OA articles. She doesn’t discuss why $3000 is a magic figure but I believe it was a legacy-based estimate that resulted from a calculation by a publisher several years ago. Note that the AOASG also has a page about how different publishers are dealing with accusations of double dipping.

March 5: In a related post Wouter Gerritsma discusses how much the Netherlands is currently spending on article processing charges based on the full list of publications with a Dutch affiliation. It’s worth following the calculation in detail because many more of these estimations will be made over the next few years as the debate on implementing Open Access increases. In particular he reaches a conclusion that a move to Open Access for all Dutch publications at the current average of €1087 per article would increase the cost over what the Netherlands pays in subscriptions by a total of €10.5M. However a similar study in the UK by Alma Swan and John Houghton showed that even the most research intensive UK institutions would save money in an Open Access world once the costs of co-authored papers are evenly distributed. Gerritsma notes that 50% of Dutch papers involve international collaboration suggesting the potential for a saving of up to €10M. Getting the details of these calculations right matters. Look back here next week for a discussion of how these calculations can vary.

Why open access should be a key issue for university leaders

Feb 18: Martin Hall (chair of Jisc and vice-chancellor of the University of Salford) makes an impassioned plea in the Guardian for Universities to be far more proactive about ‘openness’ – “the extent to which those working and studying within the university and college system can get access to any digitally-based information they need without encountering a virtual gateway: a password, subscription requirement or payment.”… “Without openness across global digital networks,” he adds “it is doubtful that large and complex problems in areas such as economics, climate change and health can be solved.” The tagline for the Guardian piece states it’s time senior leaders made openness – and its consequences – their concern.  But everyone can be a leader in this regard; individual researchers, readers and publishers all have the power to influence those in positions to take action.

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One Response to PLOS Opens Roundup (March 7)

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