Open Access News

News from the open access movement

Saturday, July 26, 2008

More on removing price and permission barriers

Jocalyn Clark, Is the NIH open access policy regressive? PLoS blog, July 25, 2008.  Notes from the ISMB 2008 meeting (Toronto, July 19-23, 2008).  Excerpt:

Mark Gerstein from Yale University gave an outstanding talk in a session called The Future of Scientific Publication....He emphasised the use of text mining to study the “structure of science.” ...Whereas conventional challenges have us struggling to keep up with the volume and growth of scientific technologies to structure and text mine scientific publications can help scientists share information and foster collaboration....

But none of this is possible without open access, countered Matt Cockerill from BioMed Central. He said that we absolutely need the raw material (whether it be biological data or bibliometric information) freely and openly available to apply the network algorithms so we can visualise the structure of science. Currently, much information is behind access controls thus disrupting the whole vision of an interconnected and collaborative scientific world.

The second issue of note was raised during the session’s Publishers’ Panel, populated by Catherine Nancarrow (PLoS), Claire Bird (Oxford University Press), and Matt Cockerill (BioMed Central). Panellists noted that the recent NIH public access policy emphasises free not open access. That is, the policy may lead to freely accessible publications (for which publishers or organisations may reap profits from charging authors a fee to deposit their manuscripts), but these will remain under restrictive licenses (thus limiting text-mining).

This, Cockerill argued, makes the NIH policy regressive.

Before blogging this post, I asked Matt Cockerill for his own recollection of what he said.  He gave me permission to quote his reply (Thanks, Matt):

I  don't recall using the word "regressive", though it's not impossible, but obviously context is everything and a single word excerpt doesn't provide it.

I remember making the point that in theory the NIH policy is an important step along the road to full open access, but that there was a danger that the partial form of OA ( embargoes, non final version, no reuse or downloading of bulk XML) could actually end up being an obstacle, used by publishers as essentially a kind of firebreak, to fend of the threat of fuller OA. I didn't use the term firebreak, but that's the idea I was getting at. Certainly at the ISMB meeting, many researchers I spoke to raised this issue as a real concern, as I know it is at NIH too. Which is why I raised it during the panel on the last day of the show....

Comments.  I'm glad Matt was able to clarify.  I agree with his point, but couldn't have agreed that the NIH policy was literally regressive.  Like many of our other success stories, the NIH policy a big step forward even if it stops short of BBB OA.  The NIH policy provides free online access (gratis OA) to an estimated 80,000 peer-reviewed articles per year.  That's unambiguous progress, and it's hard-won.  But the policy removes price barriers without removing permission barriers.  All other funder and university policies in the world do the same thing.  The NIH policy also permits embargoes of up to 12 months, while all other funder policies focused on medical research limit embargoes to six months.  Many funder and university OA policies, including the NIH policy, require immediate deposit in an OA repository, but none requires immediate OA release.  In short, the NIH policy doesn't provide the kind of immediate BBB OA that many OA journals routinely provide, but neither do any other funder and university policies.  The reason is not that NIH came first and set a bad example which late-comers imitated.  The reason is that funder and university policies must mandate OA in a way which is compatible with author freedom to publish in all or most journals as they are today, regardless of what we wish them to be (and what they might eventually become).  I'm whole-heartedly with those who want to solve this problem, go further, and provide BBB OA to all research literature, and at key points in the evolution of the NIH policy I've proposed exactly this tweak.  But we have to make progress in the landscape where we find ourselves, and we shouldn't mistake partial progress for regress.

Update (8/2/08).  Here's how Matt Cockerill made the point in a blog post on August 2, 2008:

...A recurring theme at this year's ISMB conference, especially at the Future of Science Publishing session in which BioMed Central participated, was the need to integrate text mining techniques and biomedical ontologies to make published biomedical articles and data more readily interpretable by computers. Open access is widely agreed to be a basic prerequisite to facilitate such 'semantic enrichment', and several researchers expressed frustration that while the now-mandatory NIH open access policy was driving  the deposit of embargoed manuscripts versions of articles in PubMed Central, due to licensing restrictions those articles were not available for download and text mining, even once converted into XML. The NIH policy is thus only a step along the road towards full open access, though an important one....

PS:  This is true.  Another way to put it is that the NIH policy provides gratis OA, while text mining generally requires libre OA.  (For more on gratis and libre OA, see my article in the August 2008 SOAN.)

Interview with Barbara Aronson about HINARI

El Oso has posted a 16 minute podcast inteview with Barbara Aronson about the HINARI program, and a transcript of the first 10 minutes.  (Thanks to Database Management.)  Excerpt:

DS: ...[W]hat were the greatest obstacles during [2000-2001, when the idea was first implemented]? How did that happen?

BA: There weren’t really any obstacles. It was perfect timing. Kofi Annan that same month announced his millennium agenda and one of the things was that we were supposed to do something about was the digital divide and we were supposed to do it in public-private partnerships with industry. This was the first time that the UN ever said we could work with the private sector....

What we did is we got the six biggest publishers together because they publish between 75% an 85% of the body of journals that we wanted the poorest countries to have access to. We knew that if they would say yes, everybody else would follow suit. We sat down in a room with them and we said, look, here’s what the economies of the world look like. It was a bar graph with four bars: 1.) here are the richest countries of the world - your markets are saturated there, 2.) then you have the fast growing countries - they are quickly approaching the situation of the wealthy countries, 3.) then you have a group of countries with a GNP between $1,000 and $3,000 per capita - we said, OK, you have some subscriptions here, mostly paid for by aid agencies, 4.) then we showed them the last column - there are more than 70 countries in this bar, you don’t have any sales there, you don’t even know the names of these countries, they have the worst health problems in the world, nobody is doing research about their health problems, they need everything, they need to train doctors, nurses, they need to do their own research and solve their own problems. And they are doing the whole thing without access to the latest scientific information or much information at all. And, what do you think about that?

That’s about how long the presentation took - what I just said now. Elsevier, which is the biggest and wealthiest of the publishing groups said, OK, that group gets free access, and the group next to it gets a discounted rate …

And then all the other publishers looked at Elsevier and said, are you really doing this? And Elsevier said yes and then they all said, OK, we are too.


  • It's a good interview and I recommend it.  But I'd skip the introduction, which gives the false impression that the OA movement began with the Bethesda statement, that OA journals are not peer-reviewed, and that OA journals are the only way to deliver OA.
  • My take on HINARI is pretty straightforward.  HINARI improves access and OA improves access better.  Or, HINARI improves access in some places to some extent, but OA improves access everywhere in all the ways that matter.  (1) OA literature, through journals or repositories, is free for everyone with an internet connection, not just for those at designated research institutions in designated developing countries. HINARI doesn't offer free access to physicians, journalists, or policy-makers without institutional affiliations, or even to researchers in India, on the ground that India is too wealthy.  (2) OA literature requires no passwords for access, and no methods for sharing passwords with beneficiaries and hiding them from everyone else.  HINARI's good intentions are often impeded when intended beneficiaries don't know about the program or never get the passwords.  (3) OA journals can easily remove permission barriers as well as price barriers, and often do so, but the TA journals in HINARI almost never do so.  One result is that the HINARI literature is less useful for exploitation than OA literature, and cannot be copied for redistribution to others. 
  • A final point belongs in a different category.  HINARI needn't conflict with efforts to achieve OA.  See, for example, the judicious editorial in the Journal of Cancer Research and Therapeutics calling for the expansion of HINARI while we all work for OA.  But the publishing lobby routinely uses HINARI as a pretext to oppose government OA policies (1, 2, 3).  This non sequitur belongs to the publishing lobby, and should not be attributed to HINARI itself.

Full and partial OA journals from the Philippines

Filipino Librarian has compiled a list of Filipino journals providing OA to all or some of their articles.

The new list supplements an older list from October 2005.

Forthcoming journal on OA databases in biology

Vivien Marx, Oxford University Press to Launch New Journal on Biological Databases, BioInform, July 25, 2008 (accessible only to subscribers).  Excerpt:

Oxford University Press said it plans to launch a new online-only publication that will provide a platform for “novel ideas in database research surrounding biological information” and also “aims to strengthen the bridge between database developers and users.”

The journal, entitled Database: The Journal of Biological Databases and Curation, is scheduled to launch in January 2009.

Computational biologist David [Landsmann] is the journal’s editor-in-chief. He is at NIH’s computational biology branch....Associate editor [Francis] Ouellette of the Ontario Institute for Cancer Research told BioInform that...the journal will only cover open-access databases.

Oxford University Press bioinformatics journals editor Claire Bird said the idea for the journal originated with Richard Roberts, the editor of Nucleic Acids Research, and Alex Bateman, the editor of Bioinformatics, and that it is partially an outgrowth of the popularity of NAR’s annual database issue....

Comment.  The focus on OA databases makes Database blogworthy.  But I wish I could tell you more about the journal's own access policy.  The OUP page on Changes to the journals listing in 2009 says that Database will be "online-only and fully open access during 2009."  So at least it won't merely be a hybrid OA journal in the Oxford Open series.  But is the plan to keep it OA, like OUP's NAR, or to offer just a teaser year of OA and then introduce subscription fees?

Update (7/28/08).  OUP's Kirsty Luff has answered my question and allowed me to post her answer. (Thanks, Kristy.)

We plan for Database to be an open access journal, funded by author charges like the NAR model. The website for Database with all the details are coming soon.

Notes on RepoCamp

Rachel Bruce has blogged some notes on the Library of Congress Repository Camp (Washington, D.C., July 25, 2008).  Excerpt:

Yesterday at the Library of Congress RepoCamp (that is repository camp) took place. The event was organised by the JISC Common Repository Interface Group (CRIG) and the supporting work led by WoCRIG (wisdom of CRIG). Some prize money was contributed by Microsoft for a developer competition.

The list of attendees at RepoCamp was pretty impressive. The majority were technical developers and some gave pitches on particular solutions and technologies that help repository interoperability; attendees at the Camp reviewed these pitches and gave feedback on the ideas. There was also an opportunity for everyone at RepoCamp to pitch prototypes and then to start to develop ideas together. A competition is being held where prizes are being given to motivate developers to develop prototypes. There is a particular focus on using OAI-ORE in ways that bring OAI-ORE functionality into user facing applications.... 

Prior to RepoCamp some developers from the UK have held a CRIG Roadshow in the US. The Roadshow has been focused on interoperability between repositories and eLearning (VLEs), eScience and eAdministration/Library systems. This has been a good way to bring UK and US developers together. After all these issues are global and not something to be dealt with solely within national boundaries.

The approach to WoCRIG has been a way to get technical developers talking and working together to review and develop specifications and solutions. The JISC vision (shared by many others worldwide) of a layer of scholarly content on the web, in part, underpinned by repositories is a challenging one and one way to help achieve this is by getting developers to define problem spaces in repository interoperability based on use cases and to undertake rapid prototyping and testing....

More on depositing in distributed rather than centralized OA repositories

Alma Swan, Here, there, or even everywhere? Where researchers should deposit their articles, Optimal Scholarship, July 25, 2008.  Excerpt:

...Chris Awre and I argued three years ago, in our study on 'Linking UK Repositories' (and in a short paper from that study here) that distributed deposit was the best model to aim for, we were arguing from a theoretical standpoint. Only a handful of universities in the UK had at the time shown any sign of understanding what opportunities lay ahead in the way universities disseminate the results of their efforts, and of the responsibilities they have towards society....

It was the funders who saw the potential, reflected upon the connection between paying for something from public money and handing over the results to a service industry whose business model was mostly predicated upon access control - and disconnected it. The universities continued to snore but while they did so at least the funders were out of bed, showered and breakfasted. Unfortunately, instead of nudging awake the universities...some big funders let them lie, circumventing them in the mechanics of the Open Access process. I would suggest that in doing this they were failing to take the whole research community's interests into account. But with loud snores still emanating from the universities, who could blame them? ...

[U]niversities finally 'get it', which is great for them, for research and for society. Unfortunately, they are getting it later than would have been ideal. In our discussions yesterday [at a "large London medical school" about launching an OA repository] we had to deal with the fact that while over 90% of UK biomedical research is now covered by funder OA mandates (good), many of those mandates stipulate UKPMC as the deposit locus (not so good for the employers of the fundees - the universities). It's not so good because although this medical school can harvest a considerable amount of the material published by its employees from UKPMC, thus finding an easy way to start filling its own repository, this does mean it has an extra job to do. It's not a disaster, and CERN has been doing the same thing with arXiv for years, but it's another task for the repository staff. It also means the medical school has to add a complication to a nice simple wording for its own policy, explicitly allowing those who are already under a funder mandate exemption from the medical school policy. For sure, it would be asking too much to demand that these people deposit BOTH in the institutional repository and in UKPMC. And the funders got there first.

True, we shouldn't get too wound up about this. Interoperability means that back-harvesting, forward-harvesting and upside-down-harvesting can go on wherever appropriate but it is a shame that we have arrived at a point where universities, the mainstays of our societies' research endeavours, have to develop more complex policies than would otherwise have been the case had funders simply directed their grantees to deposit their work in their institutional collections and harvested from there. The funders know where their grantees are, the repository software has a metadata field for funder, so the mechanics are simple. The benefit of such a move would have been to help the universities see the overall plan (earlier than they have done), ensure they put the right infrastructure in place and encouraged them to apply similar polices to cover all the research their employees do. The whole research community would thus be included and benefiting by this time, not just the biomedical community or other communities covered by big funder mandates. I would say that the research funders have rather let down their partners, the universities, in this sense.

Deposit rates for UKPMC are not yet all they should be. Only a minority of the articles expected to be in UKPMC by this time have been deposited, partly because the publishers who said they would do this on behalf of authors have not always done so and partly because some authors have not complied with the mandates from the UK biomedical funders. The UKPMC people are taking steps to remedy this, but how much easier it is for universities to attain a high level of compliance: they say, quite simply, that the repository is where they will be looking for material to be included in research assessment (and for staff appraisals, promotions boards, tenure committees ...)....

Yesterday, the head of one research unit in the medical school, commenting on the figures on one of my slides, said "I think your figures for research papers published from here are a bit low. I know, for instance, that from my own unit we publish something like 100 articles or so a year". He didn't know exactly, he could only guess; but when his repository is up and running he will know precisely what is coming out of his unit and from the medical school as a whole. He will have a whole new box of tools to use in his job.

Friday, July 25, 2008

Italian physics institute signs Berlin Declaration

Italy's Istituto Nazionale di Fisica Nucleare has signed the Berlin Declaration on Open Access to Knowledge.  From its July 15 announcement:

A world in which scientific knowledge can be freely distributed, without barriers, through the Internet (the world’s vast unifying network).

This is the essence of the Berlin Declaration....Now Italy’s National Institute of Nuclear Physics (INFN) has also decided to sign....

In signing the Berlin Declaration, the participating institutions are committing themselves to promoting the Internet as a tool for developing scientific knowledge and to recognising the worldwide strategic role of open access....Encouraging scientific researchers to publish on the web and cultural institutions to make their resources available by creating open archives are fundamental prerequisites for the successful promotion of this new approach to the dissemination of scientific knowledge....

Comment.  Kudos to all involved, especially INFN President Roberto Petronzio.  Now to put the Berlin principles into practice:  Will the INFN follow-up with a policy to provide OA to its research output?

NASA to launch OA image collection

NASA Images will launch next week, according to an article today from (Thanks to ResourceShelf.) From the article:
Nasa is to make its huge collection of historic photographs, film and video available to the public for the first time.

A partnership with the non-profit Internet Archive will see 21 major Nasa imagery collections merged into a single searchable online resource. The Nasa Images website is expected to go live this week.

The launch is the first step in a five-year partnership that will add millions of images and thousands of hours of video and audio content, with enhanced search and viewing capabilities and new user features. ...
See also our previous coverage of NASA Images.

Update. See also the Internet Archive's press release.

Podcast on open science

The Extraordinary Everyday Lives Show posted a podcast on open science on July 24. The audio is about one hour long. The participants are Mike Sefang, Graham Steel, Richard P. Grant, and David Wallace. (Thanks to Graham Steel.)

Oxford lowers prices on hybrid OA journals for third year in a row

For the third year in a row, Oxford University Press has lowered the subscription prices of its hybrid Oxford Open journals to reflect growing author uptake of the OA option.  From yesterday's announcement:

Oxford Open Update

We would like to remind institutions with current standard, print-only, or online-only subscriptions that their authors are eligible for discounted open access charges. From 2009 we will also have a business model for consortia customers which will provide competitive open access charges for their authors of their respective institutions....

You may already have heard that all open access articles are now automatically deposited into PubMed Central, which is helping authors to comply with funding body requirements. Furthermore, for the third year in a row, we have adjusted our online-only prices of journals offering the optional Oxford Open model to reflect any increase in the amount of open access versus non-open access content published in each journal in 2007 compared to 2006. Updated information on our open access pricing adjustments will soon be posted [here]....

The author addendum required for NIH employees

The NIH has released the author addendum (or "cover sheet") it requires when NIH employees publish articles based on NIH-funded research.  (Thanks to Michael A. Rogawski.)  Excerpt:

By signing this Cover Sheet, the Author, on behalf of NIH, agrees to the provisions set out below, which modify and supersede...any conflicting or ambiguous provisions that are in the Publisher’s standard copyright agreement....NIH and Author accept only those provisions of the Publisher’s Agreement that are consistent with the provisions herein....

3. Copyright. Author’s contribution to the Work was done as part of the Author’s official duties as a NIH employee and is a Work of the United States Government. Therefore, copyright may not be established in the United States. 17 U.S.C. § 105. If Publisher intends to disseminate the Work outside of the U.S., Publisher may secure copyright to the extent authorized under the domestic laws of the relevant country, subject to a paid-up, nonexclusive, irrevocable worldwide license to the United States in such copyrighted work to reproduce, prepare derivative works, distribute copies to the public and perform publicly and display publicly the work, and to permit others to do so....

6. Disclaimer. NIH and the Author expressly disclaim any obligation in Publisher’s Agreement that is not consistent with the Author’s official duties or the NIH mission....

7. For Peer-Reviewed Papers to be Submitted to PubMed Central. The Author is a US government employee who must comply with the NIH Public Access Policy....PubMed Central may tag or modify the work consistent with its customary practices....

The NIH cover sheet is part of a newly updated page of NIH Employee Procedures for Complying with NIH Public Access Policy.  The updated page makes clear that employee manuscripts "must be accompanied" by the new cover sheet.

More on publisher deposits in PMC and the APA deposit fee

Should Publishers Have a Role—and an Interest—in Facilitating NIH Compliance?  Library Journal Academic Newswire, July 24, 2008.  Excerpt:

The backlash was so strong, it took less than a day for officials at the American Psychological Association (APA) to rescind a plan to charge a “$2500 fee” to facilitate compliance with the National Institutes of Health (NIH) public access policy. But while that short-lived plan was abruptly abandoned —APA now says it is “reexamining” its policy to “facilitate” NIH compliance— a lingering question remains: what role, if any, should publishers play in NIH compliance?

Although the NIH policy regulates only grantees, publishers have become increasingly involved with facilitating submissions to PubMed Central (PMC)....On its web site the NIH lists hundreds of journals, offering services to aid compliance with funder-mandated public access policies like the NIH’s on behalf of authors....

But is compliance really so odious a task to archive a paper that publishers need to be involved? “No,” Open Access blogger Peter Suber told the LJ Academic Newswire. So why are many publishers taking on the burden of compliance? In a word, control. “The main reason why many publishers want to make deposits on behalf of authors is so that they can specify the embargo period,” Suber observed. NIH’s David Lipman acknowledged many publishers who permit authors to submit “author-final-manuscripts have indicated that they want minimum embargo of 12 months.” ...

Wyatt Hume, provost of the University of California (UC),...urged NIH to offer more concrete guidance on the “complex” relationship between funders, researchers, and publishers, citing the breadth of NIH-related services from publishers.

Suber acknowledged Hume’s point, noting that there are many differing services from publishers because there are many “players with different interests.” Some publishers, he noted, such as the Public Library of Science, simply want all their articles in PMC. Others, he noted, “have nearly the opposite interest,” while some are in between, believing “that NIH-funded authors will gradually migrate to the journals which make their lives easier, and want to be among the winners rather than the losers from that migration.”

Publisher involvement in facilitating NIH compliance, however, shouldn’t create confusion for authors, Suber maintained, especially not over their rights situation. “Authors sign funding contracts before they sign publishing contracts,” he explained. “When they eventually publish articles based on the funded research, they can only sign publishing contracts subject to the terms of their prior funding contracts.”

Against this backdrop of increasing publisher involvement the APA briefly unveiled the most extreme publisher policy to date. While proposing to charge a deposit fee of $2500 per APA manuscript submitted to PMC, APA added no value, Suber noted, observing that NIH charges no fee for deposit, that submission is but a simple clerical process, and that APA didn’t even offer open access for the $2500 fee, still mandating a full 12-month embargo on submitted articles. Suber called it the “worst policy [for NIH-funded authors] to date.”

Although APA seemed to quickly get the message, rescinding the policy within hours of its posting, open access evangelist Stevan Harnad put blame for the fiasco on the NIH’s doorstep. Harnad maintained his oft-cited position that NIH’s requiring deposit in central repositories, like PMC, simply is not needed, and that simply mandating authors to deposit their work in their IRs is the most efficient way to go.

“The simple way to avoid all of this needless confusion and complication is for both institutions and funders to mandate deposit directly in the author’s institutional IR,” he told LJAN. “Services like PMC can then harvest the metadata from there and link to the locus of the full-text in the IR…Immediate IR deposit mandates take the publisher out of the loop completely.”

PS:  To recap, see my posts on the APA deposit fee fiasco from July 15, July 16, and July 19.

More evidence that mandates work

PubMed Central Submissions Jump Sharply Under New NIH Policy, Library Journal Academic Newswire, July 24, 2008.  Excerpt:

In the months since passage of the National Institutes of Health’s (NIH) mandatory public access policy in late December of 2007, the number of submissions to the National Library of Medicine’s (NLM) PubMed Central (PMC) repository, where authors are now required to deposit their NIH-funded research papers, has risen significantly.

According to NIH statistics, submissions to PMC began steadily rising in December 2007, soon after it became clear a mandatory policy would be adopted in 2008. By the first month following passage of the new policy, January 2008, monthly submissions to PMC hit an all-time high of 1255, and have continued to increase significantly every month so far this year. In April 2008, when the policy officially took effect, submissions spiked even more sharply, rising from 1852 total submissions in March, to 2,765 in April and 2,593 in May. The April/May 2008 figures represent well over double the number of submissions for the same months in 2007 (1,198 PMC submissions in April ’07; 948 in May ’07). Although official figures for June have not yet been posted, the NIH’s Dr. David Lipman told the LJ Academic Newswire the submission totals were higher than May.

It’s still too early to compute compliance rates, Lipman noted, but the early returns suggest a stunning turnaround. “Looking at the increase in submissions and the dramatic increase in journals signing PMC Publisher Participation agreements,” Lipman suggested a “reasonable projection” would be a compliance rate “around 55-60 percent.” Adoption of the “mandatory” NIH policy was spurred by abysmal compliance rates under the NIH’s first public access policy, adopted in 2005, which, after considerable pushback from publishers opposed to a deposit mandate, was scaled back to a voluntary policy at the 11th hour. In February, 2006, NIH reported to congress that compliance rates under the voluntary policy lagged around four percent.

SPARC executive director Heather Joseph told the LJ Academic Newswire she expected PMC deposits to remain strong, and said the spike in submissions validated the work done by NIH and the policy’s supporters, including libraries, to educate NIH investigators about the policy, including workshops, podcasts, and an array of web resources.

Comments.  This good news is especially good in light of two background facts:

  1. We're not just comparing deposit rates under a mandatory policy with deposit rates under a voluntary policy.  In the last year or so under the voluntary policy, publishers (led by the AAP/PSP) were trying hard to boost compliance in order to head off pressure to impose an OA mandate.
  2. No one should be surprised if the submission numbers climb slowly.  Before works can be submitted to PMC under the new policy, researchers must receive their grants, do their research, write it up, and get it accepted for publication.  For that reason, most of the recent submissions must be from previous grants and a much larger spike from new research is still to come.

NIH clarifies deposit options under OA policy

The NIH has simplified and clarified its presentation of deposit options under its OA policy.  From the new language on the policy home page:

Authors may submit a paper to the journal of their choice for publication. There are four methods to ensure that a manuscript is submitted to PubMed Central in compliance with the NIH Public Access Policy.

Method A: Publish in a journal that deposits all NIH-funded final published articles in PubMed Central (PMC) without author involvement.

Method B: Make arrangements to have a publisher deposit a specific final published article in PubMed Central.

Method C: Deposit the final peer-reviewed manuscript in PMC yourself via the NIH Manuscript Submission System (NIHMS).

Method D: Complete the submission process for a final peer-reviewed manuscript that the publisher has deposited in the NIH Manuscript Submission System (NIHMS).

These methods vary in the version of the paper submitted, and the actions undertaken by the author and publisher.  Please see Submission Process for more information....

Thursday, July 24, 2008

Journal of emergency medicine converts to OA

The Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine has converted to OA and will be managed by BioMed Central. See the announcement on the BioMed Central blog or the journal's editorial:

... SJTREM has chosen open access publishing for several reasons. Articles are freely and universally accessible online, thus articles are highly visible and read by a wide audience. The authors hold copyright for their work and grant anyone the right to reproduce and disseminate the article provided that it is correctly cited, in accordance with BioMed Central’s open access license agreement. Besides PubMed Central, the journal’s articles are archived in repositories at the University of Potsdam in Germany, at INIST in France and in e-Depot, the National Library of the Netherlands’ digital archive of all electronic publications.

Thanks to substantial funding from The Norwegian Air Ambulance Foundation and The Laerdal Foundation for Acute Medicine, all article-processing charges are covered by the journal. The results of scientific research, as well as clinical experience and commentaries published with SJTREM will be available free of charge to the whole emergency medicine community, both authors and readers. ...

New physics journal from APS is free for now

Physics is a new journal from the American Physical Society.  The inaugural issue (July 2008) is now online. 

Physics won't publish original research articles, but short pieces to highlight, explain, and discuss important articles published in other APS journals.

The articles in the inaugural issue are free online, but the site is as silent on OA as it is on subscription costs.  The articles use all-rights-reserved copyright statements.

Comment.  I try not to blog articles and journals which are only free for an initial trial period.  But I can't yet classify Physics because it doesn't reveal enough about its plans.  On the theory that "free" is an attraction worth mentioning, I suspect that Physics is only free for an initial trial period.  But I really don't know.  If anyone knows more, please drop me a line.

Update (9/23/08). Also see the APS press release. It doesn't answer the question in my comment, but it does say that the journal has been in beta since July. Apparently it's now out of beta.

Four recommendations for open science

Science Commons has released its recommendations for open science, a two-page hand-out prepared for the open science workshop (Barcelona, July 16-17, 2008) held in conjunction with the EuroScience Open Forum 2008 (Barcelona, July 18-22, 2008).  Excerpt:

Open Access to Literature from Funded Research

By "open access" to this literature, we mean that it should be on the internet in digital form, with permission granted in advance to users to “read, download, copy, distribute, print, search, or link to the full texts of articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself.”

Access to Research Tools from Funded Research

By "access" to research tools, we mean that the materials necessary to replicate funded research - cell lines, model animals, DNA tools, reagents, and more, should be described in digital formats, made available under standard terms of use or contracts, with infrastructure or resources to fulfill requests to qualified scientists, and with full credit provided to the scientist who created the tools.

Data from Funded Research in the Public Domain

Research data, data sets, databases, and protocols should be in the public domain. This status ensures the ability to freely distribute, copy, re-format, and integrate data from research into new research, ensuring that as new technologies are developed that researchers can apply those technologies without legal barriers. Scientific traditions of citation, attribution, and acknowledgment should be cultivated in norms.

Invest in Open Cyberinfrastructure

Data without structure and annotation is a lost opportunity. Research data should flow into an open, public, and extensible infrastructure that supports its recombination and reconfiguration into computer models, its searchability by search engines, and its use by both scientists and the taxpaying public. This infrastructure should be treated as an essential public good....

Wednesday, July 23, 2008

Google launches the Knol project

Google has officially launched its Knol project.  From today's announcement:

A few months ago we announced that we were testing a new product called Knol. Knols are authoritative articles about specific topics, written by people who know about those subjects. Today, we're making Knol available to everyone....

The key principle behind Knol is authorship. Every knol will have an author (or group of authors) who put their name behind their content. It's their knol, their voice, their opinion. We expect that there will be multiple knols on the same subject, and we think that is good.

With Knol, we are introducing a new method for authors to work together that we call "moderated collaboration." With this feature, any reader can make suggested edits to a knol which the author may then choose to accept, reject, or modify before these contributions become visible to the public....

Knols include strong community tools which allow for many modes of interaction between readers and authors. People can submit comments, rate, or write a review of a knol. At the discretion of the author, a knol may include ads from our AdSense program. If an author chooses to include ads, Google will provide the author with a revenue share from the proceeds of those ad placements....


  • For background, see my post (and comments) on Google's first announcement of the project in December 2007.
  • There are five knols online at the moment.  Three use CC-BY licenses (1, 2, 3), one uses a CC-BY-NC license, and one uses an all-rights-reserved copyright statement.

Update.  I was wrong to say that there were only five knols online at the time of launch.  Five were highlighted.  But there were already hundreds online.  (Thanks to Adam Hodgkin.)

OA for reproducible research

Patrick Vandewalle, Jelena Kovacevic, and Martin Vetterli, What, Why and How of Reproducible Research in Signal Processing, a preprint submitted to IEEE Signal Processing Magazine.  Self-archived June 20, 2008.  (Thanks to Stevan Harnad.)

Abstract:   Have you ever tried to reproduce the results presented in a research paper? For many of our current publications, this would unfortunately be a challenging task. For a computational algorithm, details such as the exact dataset, initialization or termination procedures and precise parameter values are often omitted in the publication for various reasons. This makes it difficult, if not impossible, for someone else to obtain the same results. To address the problem, we have started making our research reproducible. Instead of only describing the developed algorithms to ‘sufficient’ precision in an article, we give readers access to all the information (code, data, schemes, etc.) that was used to produce the presented results as first advocated by Knuth and Claerbout. We are convinced that making research reproducible is not only a matter of good practice, but also increases the impact of our publications and makes it easier to build upon each other’s work. It is a clear win-win situation for our community: we will have access to more and more algorithms and can spend time inventing new things rather than recreating existing ones.

The authors work in the Audiovisual Communications Laboratory at Switzerland's Ecole Polytechnique Fédérale de Lausanne.  Also see their page on Reproducible Research and their RR Repository, Blog, and Forum.  For background, see my blog post from last year (7/14/08) on their RR work.

U of Milano Bicocca launches an IR

The University of Milano - Bicocca launched an institutional repository, Bicocca Open Archive (BOA) on June 23.  The new IR is supported by CILEA through Italy's SURplus program.  (Thanks to AePIC.)

OA for liberal arts colleges

David Green and Michael Roy, Things to Do While Waiting for the Future to Happen: Building Cyberinfrastructure for the Liberal Arts, Educause Review, July/August 2008. Excerpt:

...In lieu of a grand conclusion, we would like to revisit the eight recommendations published in Our Cultural Commonwealth [American Council for Learned Societies, 2006] and add our own suggestions for steps that liberal arts colleges might take to work toward those goals....

[2] Develop public and institutional policies that foster openness and access. Open access and revised approaches to intellectual property are key components in this effort, since scholars need to have as complete a library as possible of primary and secondary materials in digital form. Liberal arts colleges can track the work of the Create Change educational initiative and follow its recommendations about changing the campus culture to promote open access publishing, although the problem of tenure remains vexing. Colleges can also promote conversations about copyright and fair use that will improve access to the twentieth- and twenty-first-century cultural materials that many humanists and social scientists need to carry out their scholarly and teaching work....

Dan Ariely on the irrationalities of scholarly publishing

The MIT Libraries have released a 20-minute podcast of Dan Ariely speaking about the irrationalities of scholarly publishing.  From the blurb:

The latest in the series of podcasts on scholarly publication and copyright is an interview with Dan Ariely, now James B. Duke Professor of Behavioral Economics [at Duke University].

Professor Ariely recently published the best-selling book Predictably Irrational: The Hidden Forces that Shape our Decisions, ...which...reports on his research showing that emotions, context, social norms, and related factors drive our decisions – and that we are irrational in predictable ways.

In the podcast, Professor Ariely speaks with us about how market and social norms intersect with authors’ decision-making in an evolving system of scholarly communication and publishing. He discusses reward systems, the importance of building an accessible community of knowledge, and the need to lower barriers for information sharing....

More on the OA mandate from the NRC

NRC Publications Archive: Extending the reach and increasing the impact of NRC research, a press release from Canada's National Research Council (NRC), July 23, 2008.  Excerpt:

The National Research Council's Canada Institute for Scientific and Technical Information (NRC-CISTI) is pleased to announce an initiative to create an NRC Publications Archive (NPArC). This searchable, web-based archive will provide access to NRC's record of science and demonstrate the many ways NRC researchers translate science and technology into value for Canada.

NPArC will increase the access to NRC-authored publications, guarantee long-term access to NRC's research output, and serve as a valuable resource for NRC researchers, collaborators and the public.

As part of this initiative, NRC has established a policy making it mandatory, starting in January 2009, for NRC institutes to deposit copies of all peer-reviewed, NRC-authored publications and technical reports in NPArC.

Wherever possible, NPArC will provide access to the full text of these publications. NRC's Licence to Publish (Crown Copyright) will be updated to declare its intent to deposit the full-text of NRC-authored publications in NPArC. However, the nature, timing and extent of access to individual publications depends on a variety of factors, including agreements with publishers, or in the case of technical reports the sensitivity or confidentiality of content.

More information about the NRC Publications Archive will be forthcoming closer to the launch date in December 2008.


  • For background, see my July 16 post on Richard Akerman's preview of the NRC OA mandate.
  • On the one hand, the NRC has adopted a policy "making it mandatory...for NRC institutes to deposit copies of all peer-reviewed, NRC-authored publications and technical reports in NPArC."  On the other, it appears that the policy has a loophole for resisting publishers:  "the nature, timing and extent of access to individual publications depends on a variety of factors, including agreements with publishers...." 
  • I urge the NRC to keep the loophole closed.  There's no need to let publishers opt out by demanding onerous terms incompatible with the NRC's plan for green OA to "all peer-reviewed, NRC-authored publications".  For examples of how to do it, see the OA policies of the Wellcome Trust, NIH, MRC, and others, which simply require, as part of the funding contract, that grantees deposit relevant works in the relevant OA repository.  If grantees find that a given publisher will not permit OA archiving on the terms spelled out in the prior contract, then they must look for another publisher. 


Chinese zoological journal will convert to OA

Acta Zoologica Sinica will convert to OA and change its title to Current Zoology in January 2009.  (Thanks to Kevin Zelnio.)  From yesterday's announcement:

Founded in 1935, and sponsored by the China Zoological Society and the Institute of Zoology (Chinese Academy of Sciences), Acta Zoologica Sinica is the premier Zoological Journal in China. As such it is indexed by major data bases, including BIOSIS, Zoological Record, and Chemical Abstracts.

During the last few years, the Journal has sought to increase its international impact and to publish a substantial portion of papers in English. To further advance this process, the Editors have decided that from now on only manuscripts written in English will be considered for publication. Further, beginning in January 2009, the Journal will be re-launched under a new title CURRENT ZOOLOGY. All manuscripts will be peer-reviewed and, once accepted, papers will be published promptly, without page charges, and read and down-loaded free of charge....

New OA journal of cinema

Wide Screen is a new peer-reviewed OA journal of cinema "from historical, theoretical, political, and aesthetic perspectives."  (Thanks to Reader List.)  The journal has issued a call for papers and expects to publish the first issue in February 2009.

UpdateSubaltern Cinema appears to be another new OA journal, but in fact it uses the same language and lists the same editors as Wide Screen.  It looks like the founders couldn't decide between the two titles.  (PS:  If you're counting votes, I like Wide Screen better.)

More on access for researchers and access for lay readers

Philosophy, Ethics, and Humanities in Medicine has posted three comments in response to Stevan Harnad's article in the December 2007 issue, Ethics of open access to biomedical research: Just a special case of ethics of open access to research.  One comment is by Yuntao Wu, one by Jean-Claude Guédon, and one is a response by Stevan to Jean-Claude's comment (on the relative weight of access for lay readers in the rationale for OA policies).

Is SSOAR deterring deposits?

Klaus Graf argues that the Social Science Open Access Repository (SSOAR), now in beta, (1) requires CC or DIPP licenses and (2) recommends that authors use author addenda which wouldn't allow them to use CC or DIPP licenses.  He warns that if SSOAR is not more flexible, it will block rather than encourage deposits.  Read his argument in German or in Google's English.

The gatekeeping role of search engines

Eric T. Meyer and Ralph Schroeder, The World Wide Web of Research and Access to Knowledge.  Apparently a preprint.  Self-archived June 19, 2008.  (Thanks Branwen Hide.)

Abstract:   This essay presents a framework for understanding formal and informal scholarly communications that are increasingly online. The essay focuses on e-Research, but argues that e-Research cannot be divorced from a larger context which includes search engines for accessing knowledge, and the digitization and use of databases and journals. The essay reviews research related to the shift towards online scholarship, and develops a systematic framework for understanding access to the online realm. While it is true that there are disciplinary differences in the shift to online materials and in the way that e-Research is being promoted in different fields, there are also certain features that disciplines share, such as infrastructures which provide access to e-Research tools and resources. Within this framework, it is possible to identify the various actors that are shaping the digitization of research materials and how they are used. While it is too early to assess long-term impacts on scholarly practices, since many of the changes are still ongoing, it is nevertheless important to identify key emergent factors (competition for attention, online visibility, and gatekeeping) that will play a key role throughout this evolving system.

Presentations on OA in South Africa

Uncovering Open Access: seizing the moment and making it work for you – experiences from the ground, July 22, 2008.  Anonymous blog notes on the OA session at the Locating the Power of In-between Conference (Pretoria, July 3-4, 2008).  Excerpt:

Led by: Martie van Deventer, Head of Information Services Council for Scientific and Industrial Research (CISR) South Africa

There is extensive coverage and discussion in various disciplines and the literature regarding open access. The open access movement is supported and advanced by a wide range of interest goups and activities such as national and international organisations, the academic community, governments and publishers....This session covered challenges and rewards in this area and focuses particularly on the implementation of Institutional Repositories and the development of publishing models.

Siphethile Muswelanto and Dr Martie Van Deventer of CSIR were joined by Ina Smith (University of Pretoria) and Karen Bruns (HSRC Press) to present a compelling case study of efforts to introduce Open Access (OA) across South Africa’s research sector. Whilst uptake of OA - both in the promotion of OA publishing models and the establishment of repositories - still has some way to go progress to date has been good and compares favourably with the comparable situation amongst the development research community in my own country (the UK). Why was this? Dissatisfaction with a system which sees knowledge created in Africa being published in formats which are too expensive for African researchers themselves to access clearly provides an incentive. But, as I listened to the presenters I was struck by two things. Firstly the apparent energy, knowledge and enthusiasm of the participants in their pursuit of this agenda. Secondly their willingness to work together and share knowledge to overcome the barriers they face. This second point has been a recurring theme here and something that bodes well for the future of this emerging intermediaries group being convened here in Centurion.

Of course it’s not all plain sailing - challenges remain and we were cautioned not to regard Open Access as a silver bullet. More remains to be done to encourage uptake, develop skills and connect the different initiatives so that the audience for the research available can be broadened.

Presentations on:

Milestone for RoMEO

SHERPA's RoMEO has passed the milestone of listing more than 400 publisher copyright and self-archiving policies.  (Thanks to Charles Bailey.)

More commercial drug data moves to the public domain

Open access to large-scale drug discovery data, an announcement from the European Molecular Biology Laboratory (EMBL), July 23, 2008.  Excerpt:

The Wellcome Trust has awarded £4.7 million (€5.8 million) [$9.3 million] to EMBL's European Bioinformatics Institute (EMBL-EBI) to support the transfer of a large collection of information on the properties and activities of drugs and a large set of drug-like small molecules from the publicly listed company Galapagos NV to the public domain. It will be incorporated into the EMBL-EBI's collection of open-access data resources for biomedical research and will be maintained by a newly established team of scientists at the EMBL-EBI. These data lie at the heart of translating information from the human genome into successful new drugs in the clinic....

As part of the Wellcome Trust grant announced today, the EBI will obtain the rights to the databases from BioFocus DPI [the service division of Galapagos]. The award will make it possible to provide free access to this information for all researchers. "The scientific community worldwide will greatly benefit from unrestricted access to these data. It will aid their efforts in predictive drug discovery," says Galapagos CEO Onno van de Stolpe. "Galapagos has successfully accelerated its research programmes with these, and BioFocus DPI used the data to deliver on its contracts with customers. After this transfer, which we hope will contribute to the advancement of drug discovery research by improving access to the data that we have collected, we will continue to use these resources."

The transfer will empower academia to participate in the first stages of drug discovery for all therapeutic areas, including major diseases of the developing world....

[S]ays EMBL-EBI Director Janet Thornton: "With this transfer, we aim to facilitate faster and better drug discovery...."


  • Note that Galapagos is not saying that these data have outlived their usefulness.  On the contrary, it will continue to make use of them itself.  The theory here is that open data will accelerate drug discovery, even for the company which formerly held them to itself.  When Novartis did the same thing in 2007, Don Tapscott and Anthony Williams described it this way:  "[B]y placing its data in the public domain, Novartis hopes to leverage the talents and insights of a global research community to dramatically scale and speed up its early-stage R&D activities....By sharing basic scientific data and collaborating across institutional boundaries, companies like Novartis and Intel are challenging a deeply held belief that early stage R&D activities are best pursued within the confines of secretive laboratories. As a result, both were able to cut costs, accelerate innovation, create more wealth for shareholders, and ultimately help society reap the benefits of scientific research more quickly...."  Some now call this practice precompetitive sharing
  • Also note that the Wellcome Trust grant goes to EMBL, to host and manage these data, not to Galapagos, to relinquish them.
  • Kudos to Galapagos and Wellcome Trust not only for opening these data, but for choosing the public domain rather than a license.  This fits with Science Commons' latest thinking on barrier-free research and collaboration in the Protocol for Implementing Open Access Data.

Update.  Also see the comment from John Wilbanks of Science Commons:

...This makes the scientific data that Galapagos has gathered an extraordinary gift — not just to science, but to open science....Returning the data to the public domain removes the legal barriers that prevent us from making full use of the latest technologies for data integration and analysis. The Galapagos data can now be used in ways no one can anticipate — the very definition of innovation....


A wiki of open data on biological pathways

Alexander R. Pico and five co-authors, WikiPathways: Pathway Editing for the People, PLoS Biology, July 22, 2008.

The exponential growth of diverse types of biological data presents the research community with an unprecedented challenge and opportunity. The challenge is to stay afloat in the flood of biological data, keeping it as accessible, up-to-date, and integrated as possible. The opportunity is to cultivate new models of data curation and exchange that take advantage of direct participation by a greater portion of the community....

Each biological pathway must be hewn from a mass of biological information distributed across multiple publications and databases.

The particular challenge of pathway curation is amplified, because pathways are often presented as static images that are not amenable to computation, integration, or data exchange. Furthermore, pathway experts are distributed throughout the world, and most have limited time to learn about complex databases that need their expertise....

Fortunately, the biology community can provide an answer that will scale with the challenge: community curation [through a wiki]....

To facilitate the contribution and maintenance of pathway information by the biology community, we established WikiPathways....

Also see today's announcement of WikiPathways from the Gladstone Institutes at the U of California San Francisco.

Major medical schools announce major medical wiki

A consortium of major medical schools has announced the World’s Largest Collaborative [OA] Online Encyclopedia of Medicine And Health, July 23, 2008.  Excerpt:

The Medpedia Project today announced the formation of the world’s largest collaborative online encyclopedia of medicine called Medpedia. Physicians, medical schools, hospitals, health organizations and public health professionals are now volunteering to collaboratively build the most comprehensive medical clearinghouse in the world for information about health, medicine and the body. This free public site will officially launch at the end of 2008, and a preview site becomes available today....

Harvard Medical School, Stanford School of Medicine, the University of California Berkeley School of Public Health, the University of Michigan Medical School and dozens of health organizations around the world are contributing to The Medpedia Project in various ways. Many organizations will contribute seed content free of copyright restrictions. Harvard Medical School will publish content to uneditable areas that members of their faculty have created as part of a medical school wide effort. Others organizations, such as University of Michigan Medical School will encourage members of their faculty to edit Medpedia as individuals.

Other health and medical organizations that are supporting Medpedia include the American College of Physicians (ACP), the Oxford Health Alliance (, the Federation of Clinical Immunology Societies, (FOCIS), and the European Federation of Neurological Associations (EFNA). These groups are contributing content and promoting participation in Medpedia to their members. Medpedia is also receiving content and cooperation from the National Institutes of Health (NIH), the Centers for Disease Control (CDC), the Federal Drug Administration (FDA) and many other government research groups who are eager to have that public domain information distributed to both the general public and to healthcare professionals.

“Medpedia has the potential to become a vital tool for scientists, researchers and educators, as well as for the general public across the globe, providing easy access to the latest and best information on medicine,” said Dr. Anthony L. Komaroff, Professor of Medicine at Harvard Medical School, and Editor-in-Chief of the Harvard Health Publications Division of Harvard Medical School. “Sharing what we know, we can help each other and help ourselves.” ...

Over the next few years, the growing community of Editors on Medpedia will create and interlink Web pages for the more than 30,000 known diseases and conditions, the more than 10,000 drugs being prescribed each year, the thousands of medical procedures being performed and the millions of medical facilities around the world. These pages will provide insight into the latest health and medical discoveries along with photographs, video, sound, and images. The site has been designed so that everything on a subject will be simple to access. The main topic pages will be written in language the general public can easily understand, and each topic page will have with it a "Technical” page for professionals to discuss the same topic in more clinical and scientific language....

Medpedia runs on open source Mediawiki software, and like Wikipedia, content on the Medpedia site will be available for reuse under GNU Free Documentation License (GFDL)....In the future, in order to cover operating costs, non-invasive, text-based advertising will be shown on the Medpedia website through third-party ad networks such as Google’s Ad Inc. is funded and managed by Ooga Labs a technology greenhouse in San Francisco developing several for-profit, mission-oriented companies to address worldwide needs in health, education, and activism.

While the contents of Medpedia will be OA, editing privileges will be limited to those with an M.D. or biomedical Ph.D. who apply to become an editor.  For more details, see the FAQ.


Berlin survey on OA and OA journals

Karin Weishaupt, Der freie Zugang zum Wissen: auf dem Weg, aber noch nicht am Ziel! Institut Arbeit und Technik, August 2008.  (Thanks to Christine Kant.)  Preliminary results from a survey of author attitudes toward OA journals.  Because the file is a PDF, I can't link to a machine translation.

Weishaupt highlights four conclusions (my paraphrase, not a translation):

  • OA could be implemented much more broadly than it has been to date.
  • OA journals benefit everyone, not just the author.
  • Not all the alleged disadvantages of OA journals turn out, on analysis, to be disadvantages at all.
  • Universities and other research institutions could be doing much more to promote OA.

Weishaupt surveyed about 1,000 researchers at Humboldt University Berlin in May and June 2008.

Tuesday, July 22, 2008

Tracking the openness of databases

Shirley Fung has launched  Molecular Biology Databases, a website to evaluate the openness of databases in molecular biology.  (Thanks to Donna Wentworth.)  From the site:

This work is being developed under the auspices of the Science Commons Data project and builds upon the Science Commons Open Access Data Protocol proposing requirements for interoperability of scientific data. Legal simplicity and predictability can be achieved by waiving copyright and other contractual restrictions, allowing data integrators to reuse, modify and redistribute large datasets. Legal accessibility issues are not the only hurdle to data integration. Technical Open Access should be ensured in order to allow scientists to download data easily and use them in any way, including ways that initial creators are not considered. The objective of this project is to assess the accessibility of databases by analysing their interfaces to access data and their reuse policies in order to identify those that are in the public domain, starting with databases hosted by the Life Science Resource Name (LSRN) Schema registry.

Fung evaluates 34 databases to date, under six criteria:  Downloadable, Offers Batch Processing, Offers a Query Interface, No Registration Required, Policy is Available, Public Domain.  Her website supports the open-data research of Melanie Dulong de Rosnay, described last week by Ethan Zuckerman (and blogged here).

Comment.  This is a very time-consuming but useful job.  Everyone in molecular biology should be grateful, especially if the project leads to more consistent policies on open data across the field.

How universities can support OA textbooks

Kevin Smith, Where should we spend our money?  Scholarly Communications at Duke, July 21, 2008.  Excerpt:

...I think there is also an opportunity here for institutions to be more proactive and seek ways to invest in open access textbooks on a campus-wide level.

Why should schools consider doing this. First, with all the pressure that institutions of higher education are under to reduce the costs for students to attend, open access textbooks offers an avenue for proactive investment that will simultaneously reduce student costs and encourage faculty scholarship. Second, this is a place where universities actually can help combat copyright infringement. Universities have been made the scapegoats in the file-sharing wars, but there is really not a lot they can do to ameliorate that problem, especially since the vast majority of music and movie file-sharing does not occur over college and university networks. But by supporting open access to e-textbooks, we really can reduce the problem of infringement in that realm.

How can universities invest their funds in ways that will encourage open access textbooks and reduce costs (and therefore the incentive to infringe copyright) for students? I can think of three ways, off hand.

First, institutions could invest in infrastructure that would encourage new models for electronic course content. This means a great deal more than simply providing the storage space necessary for an institutional repository. Universities also need to support their faculty authors in efforts to retain copyright so that they can deposit their works in an IR and create new and unanticipated derivative works from those publications. The opportunity to combine materials located in an institutional repository in new ways would create a different spin on the custom textbook; it would offer a heretofore unimagined flexibility based on legal rights retained by the authors of the component parts and licensed to institutions or, using a Creative Commons license, to a broader group of users.

Second, universities and consortia could bring their purchasing power to bear to negotiate multi-user licenses for existing e-textbooks or new ones created in the commercial market....

Finally, universities could make funds available for faculty to encourage the development of open access texts. There has been a great deal of talk recently about funding to support open access via “hybrid” publishing — traditional publications onto which an open access alternative is grafted if the author, or her institution, is willing to pay an added fee. It seems to me that a much wiser investment, and one with a greater return for the dollars spent, could be made by turning those funds to support faculty who want to create online open access textbooks that can be used by students on their own campuses and by others who teach similar courses. Adaptation by others, in that case, would provide an effective “peer-review” to measure the quality of the faculty author’s contribution. In this way, student costs could be reduced, faculty scholarship supported, and the real potential of the digital environment for collaborative learning more fully exploited.

Harvesting chemical info from institutional repositories

Antony Williams, Indexing Institutional Repositories and Authors Self-Archived Collections, ChemSpider, July 23, 2008.  Excerpt:

...What does [institutional self-archiving] mean for indexing of articles and availability for searching in terms of the work we are doing with ChemSpider right now (1,2,3). Text-indexing of chemistry articles would simply mean turning our spider onto the repository. Using the tools we have available now and the database of 21 million compounds and associated dictionary we could also convert the chemical names to structures and make the articles searchable by both text and structure BEFORE publication, in theory, months before. With the work that is already underway on Open Access articles on ChemSpider and SOON to be unveiled, we could also provide tools for authors to markup their own documents. My preference, as for many others, is that authors of Chemistry articles use semantic authoring tools to allow us to grab the appropriate information from the articles for linking as well as provide a path for semantic connectivity.

The question then is whether or not ChemSpider can index institutional repositories or authors self-archived collections on their university research group websites. The authors self-archived collections will be very valuable but of course most likely to upset the publishers. We’d like to do both.

I envisage a time when articles are indexed and searchable even before they are published and indexed by others. Why not? If there are changes to the article between pre-and post-publication both can be indexed.

We welcome your comments! Anyone want to introduce me to the host of an institutional repository?

Monday, July 21, 2008

FOSS tool to validate linked data

An announcement from the W3C, July 17, 2008 (thanks to Pete Johnston):

We're glad to announce Vapour 2.0, a validator for Linked Data and RDF vocabularies. An effort has been made to widen the scope of the validation to cover any kind of Linked Data (Vapour 1.0 was specifically targeted to RDF vocabularies). This new release contains a number of new exciting features, such as checking for meaningful triples in the response documents, links to popular semantic web browsers, and conclusions on the type of the resources per httpRange-14. Moreover, the input form is now simpler, and the reports are even more eye-catching than before.

Validate your linked data! Use our online service

Source code and further details...

PS:  For background, see Tim Berners-Lee's description of Linked Data (July 2006).

OA workshops in Georgia, Ukraine, and Moldova

The July/August issue of the Newsletter is now online.  Excerpt:

Open Access Awareness Raising workshop in Georgia

On May 14-15, the Georgian Integrated Library & Information System Consortium (GILISC) and jointly organised the workshop “Open Access: New Models for Scholarly Communication”. Hosted by the Ilia Chavchavadze State University, the workshop addressed Open Access policies and recommendations and highlighted the benefits of Open Access journals and Open repositories. As a result, workshop participants have created a National Open Access working group. More information and presentations from the workshop are available [here].

Study visit of repository managers to Ukraine

On June 18-21, Informatio Consortium, National University “Kyiv-Mohyla Academy” and organised a study visit of repository managers from Azerbaijan, Belarus, Georgia and Kyrgyzstan to Ukraine. Together with their Ukrainian colleagues they discussed strategies for securing faculty and administration support, management, copyright and interoperability issues, etc. Additional details can be viewed [here].

Open Access: Exploring Scholarly Communication – a workshop in Moldova

On June 23-24, Consortium eIFL Direct Moldova and organised a workshop Open Access: Exploring Scholarly Communication at the Moldova Economics Academy premises in Chisinau. Librarians, scholars and researchers discussed the benefits of Open Access journals and Open repositories, agreed on the need for better promotion of existing Moldavian OA journals and open repository of Moldavian dissertations and decided to work on Open Access declaration and pilot OAI-compliant repository projects. More information and presentations from the workshop are available [here].

Debating the OASPA membership rules

Gunther Eysenbach, Creating an organization for open access publishers - but should we let big publishers dominate?  Gunther Eysenbach's Random Research Rants, July 15, 2008.  (Thanks to Charles Bailey.)  Excerpt:

Dave Solomon has published a draft of possible By-laws for the proposed Open Access Scholarly Publishers Association (OASPA)....

My personal interest in being possibly one of the founding members of this organization (which also may include BioMed Central, Copernicus, Co?Action Publishing, Hindawi, Medical Education Online, Journal of Medical Internet Research, PLoS, and presumably others) is the recognition that some sort of organization is needed to set, promote and enforce professional and ethical standards and OA publishing practices....

But it is important that such an organization is set up and run not to primarily defend the commercial interests of large commercial publishers, but to act as much as possible in the interest of scholarly communication (these are not mutually exclusive goals - but they are not always aligned....)

More specifically, [OASPA is] contemplating the following rules:

Each publisher gets one voting member and an additional voting member for every additional 250 OA manuscripts published in the previous calendar year up to a maximum of 10.

In other words, this will ensure that large publishers have 10 times more votes than small publishers....

Also see Dave Solomon's response to Gunther's concern, and Gunther's reply.

PS:  See my own comments on the draft OASPA bylaws.

More on the Stanford OA mandate

Debra Viadero, Stanford Opens Access to All Its Education Studies, Education Week, July 18, 2008.  Excerpt:

Faculty members at Stanford University’s school of education have voted to make scholarly articles available to the public for free, a policy change that the university says makes Stanford’s education school the first such school in the nation to join the growing “open access” movement in academia.

“We think it’s a huge gain in terms of public access, professional access, policymaker access, and lawmaker access,” said John M. Willinsky, the education professor who proposed the idea to his colleagues at the California university....

“We think [university OA mandates] will become commonplace before too long,” said Mr. Willinsky, who has been active for years in efforts to create software and other tools to support the “open access” movement....

Under Stanford’s new policy, only the author’s final, peer-reviewed copy of the article would be posted online —in some cases, potentially months before the printed version becomes available....

By early fall, the education school plans to have a Web site in place where the articles will be posted and archived in a searchable database. With approximately 50 scholars on Stanford’s education school faculty, the site could accumulate as many as 100 articles a year, by Mr. Willinsky’s estimate.

Publishers, however, would retain the rights to the published version of the articles....

Mr. Willinsky said the policy also includes a waiver so that nontenured faculty, who face the most pressure to “publish or perish,” could ask to opt out of posting their articles online if a potential publisher insists on exclusive publishing rights....

“I think it’s important for Harvard and Stanford to do this, to use our weight to take the stand and give publishers pause before saying, ‘We’re not accepting any articles from Harvard or Stanford,’ ” Mr. Willinsky said....

PS:  Good article until the last two paragraphs (omitted here).  The BOAI is from Budapest, not Bulgaria, and FRPAA has not yet been adopted.

OA to backfile of Max Planck journal of European legal history

The Max-Planck-Institut für europäische Rechtsgeschichte has provided OA to the backfile (1967-2001) of its journal, Ius Commune.  (Thanks to Josef Pauser via Klaus Graf.)

The articles are free online, but I can't find any licensing information about them, either on the TOC or on individual articles.

OAD launches the Bibliography of open access

The Open Access Directory (OAD) is very pleased to announce the Bibliography of open access.

The bibliography is based on Charles Bailey's definitive Open Access Bibliography: Liberating Scholarly Literature with E-Prints and Open Access Journals (ARL, 2005).  We are very grateful to Charles and the ARL for their willingness to move the bibliography to OAD for community updating and revision.  Here's how Charles described the launch on his blog this morning:

...With my permission and the agreement of ARL, most of the Open Access Bibliography has been converted to the MediaWiki format to form the basis of the Bibliography of Open Access. The new bibliography will be authored by registered Open Access Directory users, who can add or edit references. It is under a Creative Commons Attribution 3.0 License.

The initial version of new bibliography has live links; however, they were last updated in August 2004, when the text of the Open Access Bibliography was frozen for print publication preparation. These links can now be updated by registered users.

The Open Access Bibliography, which contains textual sections not found in the Bibliography of Open Access, remains freely available in HTML and PDF formats at Digital Scholarship and as a printed book....

The OAD bibliography couldn't have a better foundation for future development.  It includes all the citations in Charles' original work and omits only his Preface, Acknowledgements, and introductory essay, Key Open Access Concepts.

Remember that OAD is a wiki.  We appreciate your help in keeping its lists comprehensive, accurate, and up to date.


Victorian govt considering OA for PSI and publicly-funded research

Inquiry into Improving Access to Victorian Public Sector Information and Data, a discussion paper from the Economic Development and
Infrastructure Committee of the Victorian Parliament, July 2008.  (Thanks to Tom Worthington.)  Excerpt:

...Question 2: How can improved access to and re-use of PSI [public sector information] drive economic growth, employment opportunities and new commercial ventures? ...

Question 4: If the Victorian public sector is to provide increased access to information, what kind of information would provide the greatest opportunities to improve or develop: ...b) social, medical and scientific research? ...

2.1.1... Emerging evidence suggests that in some cases improved access to and re-use of PSI can increase net returns on investment by government, particularly when access to publicly funded research is improved [citing the important study from Houghton et al, 2006] .... Enhanced access to research may potentially increase the efficiency of R&D investment within scholarly and research communities by reducing duplication of research, and by increasing primary data and information available to researchers. In particular, improved access to R&D research could reduce the number of scientific studies that repeat ‘failed’ research hypotheses. The DEST report also suggested that wider access to PSI would encourage open scientific inquiry and collective learning; allow closer interrogation of research findings and conclusions; and provide researchers with increased opportunities to identify and explore issues not considered in original research briefs, through a re-examination of primary research data.... Another argument for enhanced access to PSI is that it would increase and broaden opportunities for commercial exploitation of research data. Improved access to government research data and information could also potentially benefit the private sector by allowing it to draw on government knowledge and experiences to improve the quality of services, and thereby increase the productivity of the private sector in the economy. The general community can potentially benefit through the development of informed citizens and informed consumers, who by having greater access to research publications and government information would better equip themselves to make efficient use of public and private sector services. An informed community could also, potentially, contribute more actively to the development of effective, efficient, and productive public policy....

Comment.  The committee is soliciting public comments on the paper, which are due by August 22, 2008.  (See the submission details here and on p. ix of the report.)  After digesting the comments, the committee will report back to Parliament by June 30, 2009.  I urge Australians, and especially Victorians, to submit comments to the committee in support of OA for publicly-funded research.


New OA journal of transport and land use

The Journal of Transport and Land Use is a new peer-reviewed, no-fee OA journal from the Center for Transportation Studies at the University of Minnesota.  JTLU publishes under a CC-BY-NC license.  From the editorial by David Levinson and four co-authors in the inaugural issue (Summer 2008):

...JTLU embraces the open-content movement. Most academic publishing, especially in the “traditional model” that comprises most of the journals launched prior to the late 1990s, can be described as a “walled garden.” Inside are the beauties of rich information, but to enter, the costs are steep. Such a model made sense in an age when journals were primarily distributed on paper, and publication costs were high. Today, however, most readers of nominally paper-based journals access the articles online, and the costs such as communications and server space are small enough as to be inconsequential for a single journal.

The main costs —those of writing, reviewing, and editing articles— have historically been gratis (at most, the participants earn social capital which perhaps can later be monetized), while copy-editing and layout do entail real costs and have historically been recovered by charging either readers (through libraries) or authors. But the prices charged by journals publishers to access these journals have increased dramatically, forcing many libraries to cancel subscriptions. In economic terms, these for-profit journals are a privately owned club good, and as the number of club-members decreases, the price per member increases to maintain the facility —a vicious cycle familiar to any analyst of transit ridership.

The model for JTLU differs from that described above in that we see scientific knowledge as a public good best provided without profit by public-minded institutions. The open-content movement is gaining ground throughout scientific literature. In biology, for example, the Public Library of Science (PLoS) has led the way in legitimizing this new model of distribution.

JTLU is open-content, subscription-free, and free to contribute. All of this is enabled by generous financial and administrative support from the Center for Transportation Studies at the University of Minnesota....

Sunday, July 20, 2008

Survey of some learned societies and their members

Learned Societies and Open Access, a report of the results of a survey by the Biosciences Federation, June 2008.  (Thanks to Research Information.)  Excerpt:

The Biosciences Federation (BSF) is the body representing many of the UK’s leading biosciences learned societies. Its thirty-five learned society members have a total membership of almost 40,000 (after allowing for multiple memberships) and they are mostly charities. Twenty-seven of them publish, producing a total of 75 high-quality, relatively low-price journals as part of their charitable educational remit, with a substantial proportion of the content being available online free of charge. Following on from its position statement on Open Access and self-archiving in September 2007, the BSF decided to undertake surveys of its member societies and of the individual researchers who belong to them. The objective was to analyse the experience of its member organisations with regard to their publishing activities, especially as concerns Open Access and self-archiving by authors, and to gather information on the financial contribution made by the societies to their disciplines. Twenty-three societies took part in this exercise. In addition, the societies were asked to encourage their members to complete an online questionnaire on their experience and views of Open Access publishing and self-archiving. There were 1368 usable responses to this questionnaire.

The analysis has highlighted a number of important points:

2. All provide free access to most of their material
Of the 17 societies analysed who publish journals, all provide some form of free access to most of their online journal material. This is usually in the form of delayed free access, usually after 12 months. Some also offer optional immediate open access on payment of a fee, but they report very low take-up so far.

3. Substantial confusion amongst researchers about what Open Access means. Amongst the 1368 researchers who responded to the online survey, there was considerable confusion about what Open Access journals actually are. Almost half of the Open Access journals they said they read, and a third of those they said they published in, were not Open Access journals at all. There seemed to be confusion between online journals (whether providing material free or not) and journals where all material is available free immediately on publication. Thus it is unclear how many of the 74% who said they supported Open Access really understood the issue. Nonetheless, there seems to be substantial support among researchers for the principle of Open Access.

4. Researchers experience difficulty in accessing funds
Only around 15% of survey respondents said they had tried to access OA publication funds from their institutions or research funders to pay for author-side charges. Of these, 53% had found this fairly difficult or very difficult. This adds weight to the BSF’s earlier call for universities to set up ring-fenced funds, and to provide researchers with simple information on how to access them.

5. Researchers prefer publishing in established journals to self-archiving. Although, as mentioned above, almost three quarters of researchers responding to the 2
questionnaire said they considered OA journals a good idea (with the caveat about lack of clarity on the definition), only about one third thought self-archiving (deposit of one of a variety of versions of the paper into university or subject repositories) was a good idea and there was considerable concern about self-archiving. Again, many respondents were confused about what was or was not a repository of self-archived material.

a. Three-quarters of respondents are happy to read the final published journal article, but less than 20% said they were happy with the author’s final version (ie before it is copyedited and laid out by the publisher, but after peer review). This is the version commonly available in repositories.

b. Only 3.5% said they accessed the self-archived version where possible if they also had access to the published version, and 67% never, or rarely, accessed the self-archived version, even if they did not have access to the final published version.

c. Only 12.5% of respondents self-archive whenever possible and 71% never do so. Many cited fears about multiple versions and unedited versions as their reasons for this.

These responses show that, even where some form of OA publication is required by funders or institutions, researchers still prefer to use the final version, as it appears in peer-reviewed journals, to earlier versions in institutional or subject repositories.


Researchers are sympathetic, at least in principle, to funded Open Access publishing, although this is not fully borne out by their practice to date, and there is substantial confusion about what Open Access actually is. Researchers are more worried, however, about self-archive repositories.

Provided it is adequately funded, Open Access publishing could be a viable alternative to the current subscription model in some disciplines. However, there are areas where it is unlikely to work without new funding streams being introduced. This includes subjects such as clinical medicine and systematics, where most research is not supported by grant funding. It also includes review papers, which are often the most highly cited (and by implication most widely read), but which are also not supported by grant funding, and papers from parts of the world where funding would not be available to authors.

If there is a continued expansion of moves by funding bodies and universities to mandate self-archiving with access becoming free within a period that is less than the journals’ current time frames for making material free to all, then a point will come at which so much of the material will be free to readers that the current model of library subscriptions is logically likely to collapse. If peer-reviewed journals are not to cease to exist, this implies a move to author-side payments for journal publication, which will simultaneously achieve funders’ objectives of making articles immediately freely accessible. This could be achieved if funding bodies were to make the money for this available to researchers via their host institutions, and if institutions were to have robust and clear systems to allow researchers to access these funds....


  • In my comments on the BSF's Position statement on Open Access (September 2007) I criticized the organization for putting many secondary objectives ahead of access to research, and asked whether it had consulted its members about their priorities.  I commend it for conducting this survey. 
  • However, it doesn't make a lot of sense to ask societies and researchers what they think about something they don't understand.  I count this survey as good evidence of how much author and society education we still need to do, and not as good evidence for or against OA itself.
  • The BSF understands the problem, and acknowledges that "amongst the 1368 researchers who responded to the online survey, there was considerable confusion about what Open Access journals actually are."  Perhaps as a result, BSF feels free to draw a conclusion undermined by its own survey.  While the vast majority of its respondents (75% v. 20%) would rather read the published editions of articles than the peer-reviewed manuscripts typically self-archived, BSF nevertheless concludes that the rise of green OA will undermine journal subscriptions.  It offers no evidence that this is one of the points on which its respondents were misinformed.
  • One of its key recommendations is based on this conclusion.  The BSF opposes OA mandates with shorter embargo periods than those voluntarily adopted by journals themselves.  The alternative, it says, is that "the current model of library subscriptions is logically likely to collapse".  But it offers no evidence for this conclusion, from the survey or elsewhere, and ignores the counter-evidence from physics.  It also averts its eyes from the 425 learned societies publishing 450 OA journals, which dispense with embargoes altogether.  Moreover, its recommendation assumes that subscription-based journals with OA backfiles are trying to minimize their embargoes, or have already reduced their embargoes to the shortest periods compatible with their survival, which is very unlikely.  Or it assumes that funders have the same interests as publishers, or should put aside their own interests in order to indulge the interests of publishers, which is nuts. 
  • As it did in its position statement on OA, the BSF continues to assume that all OA journals charge author-side fees.  But most OA journals charge no fees at all, and the OA journals published by learned societies are much more likely (83.3%) to charge no fees than OA journals overall (67%).
  • However, I join the BSF in asking funders to allow grantees to use grant funds to pay publication fees at fee-based OA journals, and I join it in calling on universities to set up funds to help faculty pay the same fees.

August Cites & Insights

The August issue of Walt Crawford's Cites & Insights is now online.  This issue contains a lengthy section on Library Access to Scholarship, which covers the OA mandate at Harvard Law School, the OA mandate at the Stanford School of Education, OA library journals, suspicions about Scientific Journals International, the Open Access Directory, the distinction between gratis OA and libre OA, Richard Poynder's inquiry into the costs of OA publishing, and Charles Bailey's 19 years as an internet publisher.

OA research on sepsis

Konstantinos N. Fragoulis, Argyris Michalopoulos, and Matthew E. Falagas, Open-Access World Wide Web Resources on Sepsis, Clinical Infectious Diseases, August 15, 2008.  Accessible only to subscribers, at least so far.