Open Access News

News from the open access movement

Saturday, May 26, 2007

Internet Archaeology converting to OA

Internet Archaeology: creating an Open Access success story, a press release from JISC, May 25, 2007.  Excerpt:

Internet Archaeology was established in 1996 with funding until July 2001 from the JISC eLib programme. Innovative since its inception, it was the first refereed online e-journal in Archaeology and has been very successful in gaining international recognition as a high-quality academic journal....

Internet Archaeology is unique in Archaeology in that it is a multi-media journal available exclusively on the Web; it has no print equivalent. It includes elements that would be impossible in a paper publication, such as searchable databases to analyse online; full-colour, interactive images; video footage; virtual reality models and access to related digital archive material. This allows the subscriber to choose the level of detail required through a variety of indexing and searching methods to provide new opportunities to enrich teaching and research. For example students can work interactively with archaeological material, which facilitates active learning. Archaeologists can use this resource to examine examples of best practice when designing fieldwork projects and data management systems.

Internet Archaeology 2008-2009: Open Access for UK HE and FE

Two year funding from JISC Collections will help Internet Archaeology with the transition to Open Access. The funding for the period from 1st January 2007 to 31st December 2009 will allow free access, from January 2008, (to issues 22-25 of the journal) to the growing number of universities and colleges that teach Archaeology....

The funding period also provides Internet Archaeology with the opportunity to develop its long-term Open Access model as it seeks to generate a growing proportion of its revenue from publication subventions from research councils, commercial developers, and state funding archaeological agencies....

Internet Archaeology Archive 1996-2006

JISC Collections has also purchased the Internet Archaeology Archive 1996-2006 (which includes issues 1 to 21 inclusive) on behalf of UK higher and further education institutions, which means they can now have permanent access to ten years of rich multimedia scholarly content completely free of charge. Content ranges from excavation reports (incorporating text, photographs, data, drawings, reconstruction diagrams, interpretations) and analysis of large data sets along with the data itself, to visualisations and applications of information technology in archaeology....

PS:  I can't tell whether the free online access will be limited to users from UK institutions.  If anyone knows the answer, please drop me a line.

Update. I just learned from Liam Earney at JISC that the newly-funded free online access will be limited to the UK. However, Lorraine Estelle at JISC reassures me that IA plans to use some of its new funding to prepare for full worldwide OA.

Overview of OA publishing in Canada

Heather Morrison, Demystifying open access journals: pure gold, a presentation at the Canadian Library Association Annual Conference (St. John's, May 23-26, 2007).  Self-archived May 24, 2007.

Abstract:   A brief overview of open access publishing (pure gold, i.e. no delayed back access) and library involvement, with a focus on the Canadian scene. Includes audience quizzes. Part of a panel designed to stimulate discussion on open access publishing.

OAN is five

Today is fifth birthday of Open Access News.  Blogger says it has 11,066 posts, which comes to about six a day.  (About 200 were written by my co-contributors during the period when OAN was a group blog.)  I'm sure that the last couple of years bring up the average and that the slope of the curve is rising rather than falling.  There's nothing else I'd rather be doing right now, but that relentless growth is ominous and I have to keep reminding myself that it reflects the steadily mounting worldwide momentum for OA.

Friday, May 25, 2007

Presentations on OA at the CSE meeting

The presentations from the session on the current status of open access at the Council of Science Editors 2007 Annual Meeting (Austin, May 18-22, 2007) are now online at the home page of the DC Principles Coalition:

Profile of LEAP

Judith Winters, New ways to unlock potential of research, AHDS Newsletter, Spring/Summer 2007.  Excerpt:

AHDS Archaeology and the e-journal Internet Archaeology are working together on the LEAP project: Linking Electronic Archives and Publications. Judith Winters (editor of Internet Archaeology) provides a short summary of the main aims and objectives of the project

What is LEAP?

LEAP is a project to investigate novel ways to combine the interpretive analysis of publications with the underlying data of archives. To do this, the project will use four exemplars of multi-layered e-publications and e-archives. LEAP will also examine how new ways of combining publications and data can be applied beyond archaeology across the arts and humanities.

Aims of LEAP

  • To explore questions of linking between distributed archives and e-publications and to investigate the ways in which e-publications can be interactive, multi-layered and underpinned by supporting data.
  • To look at how multiple forms of dissemination can be used for different audiences.
  • To implement dynamic interfaces between and within resources that can accommodate different types of user.
  • To assess how far tailored interfaces are capable of long-term preservation.
  • To examine other questions which arise from this means of dissemination: quality control, peer review, IPR, citation....

Public access to surgery mortality data decreases risk of mortality

Ben Bridgewater and eight co-authors, Has the publication of cardiac surgery outcome data been associated with changes in practice in northwest England, BMJ, June 2007.  Abstract:  

Objectives: To study changes in coronary artery surgery practice in the years spanning publication of cardiac surgery mortality data in the UK.

Methods: A retrospective analysis of prospectively collected data from all National Health Service centres undertaking adult cardiac surgery in northwest England was carried out. Patients undergoing coronary artery surgery for the first time between April 1997 and March 2005 were included. Changes in observed, predicted and risk adjusted mortality (EuroSCORE) were studied. Evidence of risk-averse behaviour was looked for by examining the number of patients at low risk (EuroSCORE 0–5), high risk (6–10), and very high risk (11 or more), before and after public disclosure.

Results: 25 730 patients underwent coronary artery surgery during the study period. The observed mortality decreased from 2.4% in 1997–8 to 1.8% in 2004–5 (p = 0.014). The expected mortality (EuroSCORE) increased from 3.0 to 3.5 (p<0.001). The observed to expected mortality ratio decreased from 0.8 to 0.51 (p<0.05). The total number and percentage of patients who were at low risk, high risk and very high risk was 2694 (84.6%), 449 (14.1%) and 41 (1.3%) before and 2654 (81.7%), 547 (16.8%) and 47 (1.4%) after public disclosure, respectively, demonstrating a significant increase in the number and proportion of high risk patients undergoing surgery (p<0.001).

Conclusions: Publication of cardiac surgery mortality data in the UK has been associated with decreased risk adjusted mortality on retrospective analysis of a large patient database. There is no evidence that fewer high risk patients are undergoing surgery because mortality rates are published.

In the same issue, also see Steven Livesey's comment, Is public access to surgeon-specific data affecting practice adversely?  (No abstract available.)

Call for OA to Brazilian research

Roberto Meneghini of BIREME has called for OA to Brazilian research.  Read the Portuguese original in the Jornal da Ciênca or Google's English.  (Thanks to Donat Agosti.)

PS:  Just last week BIREME required the journals indexed in LILACS or SciELO, and publishing articles on clinical drug trials, to require OA to the underlying trial data.

The OA decision of Germany's Bundesrat

The International Publishers Association (IPA) has released released an English translation of the Bundesrat Decision of May 11, 2007.  Excerpt:

Decision of the Bundesrat

Communication from the Commission of the European Communities to the European Parliament, the Council and the European Economic and Social Committee on scientific information in the digital age: access, dissemination and preservation

COM (2007) 56 final; Council Doc. 5748/07

In its 833rd session on 11 May 2007, pursuant to §§ 3 and 5 EUZBLG (Act on Cooperation between the Federation and the Federal States in European Union Affairs), the Bundesrat adopted the following Opinion:

1. The Bundesrat generally welcomes the Communication from the Commission taking up the increasingly important topic of knowledge dissemination in the digital age....

The call for the freest possible, immediate and open access to information corresponds with the aim of the EU to increase the competitiveness of the European economy.

2. At the same time, the Bundesrat points out that the call for the freest possible, immediate and open access to scientific information may conflict with the protection of intellectual property, and in particular copyright, which is also a significant criterion for the success of the internal market and the promotion of innovation and creative activity....

3. The Bundesrat therefore welcomes that the Communication does not only present ways to facilitate knowledge transfer, but also outlines the position of publishers, emphasising their central role in the scientific information system.

In this context the Bundesrat particularly welcomes that the Commission recognises the quality control function of publishers of scientific publications, and that it intends to monitor open access experiments - also offensively pursued by publishers, as well as to support their publication costs.

Publishers, and particularly the scientific journals they publish, play a pivotal role in the scientific information system. Over the past years, the publishing industry has undertaken substantial investments in the area of “online publishing”, thereby already contributing to an efficient dissemination of information. In doing this, publishers constantly compete for authors and readers. This ultimately guarantees the high quality of scientific publications....

5. The Bundesrat regards open access publication as an additional method of knowledge dissemination, in particular with regard to research results. However, the Bundesrat also points out that open access does not avoid the costs of knowledge processing and knowledge transfer, but rather shifts them from the users to the authors; that there are also reasons in favour of publishing scientific publications through a publisher.

The Bundesrat welcomes that the Communication does not regard changes, in particular limitations on copyright, as necessary to reach the goals....

6.  The Bundesrat points out that in the light of predominantly effective competition in the market for scientific information, public intervention is advisable only in demonstrably necessary cases and with as low in intensity as possible.

In the view of the Bundesrat, the co-financing of research infrastructures (in particular “digital repositories”) announced by the Commission does raise the fundamental question of the extent to which the supply of information is a public duty. This question should receive particular attention within the framework of the discussion process now launched by the Commission....

Also see the IPA press release accompanying the translation (May 24, 2007).  Excerpt:

IPA welcomes the statement by the Bundesrat. Says IPA Secretary General Jens Bammel: “IPA appreciates the balanced arguments and constructive tone chosen by the Bundesrat. Open access is a great opportunity which must be explored. At the same time care must be taken that we do not lose what is in fact working so well in other business models. This debate should be conducted in a measured way, based on sound arguments and empirical facts reflecting the high standards of academic debate in the journals themselves. The Bundesrat statement is a welcome contribution to this debate.“

Adds Jens Bammel: “The principle must be that business models for publishing scientific information should not be mandated by governments but should prove their own value and sustainability in the marketplace, and with the researchers how freely chose the most appropriate journal for each article.”

Comments. For background, the Bundesrat was discussing the EC's Communication on access to scientific information in the digital age, February 15, 2007.  For my thoughts on the same EC Communication, see SOAN for March 2, 2007,

  1. First I thank the IPA for making and circulating this English translation.
  2. The good news for OA supporters is that the Bundesrat endorses the goal of OA, more or less ("The call for the freest possible, immediate and open access to information corresponds with the aim of the EU to increase the competitiveness of the European economy.")
  3. The good news in a minor key is that the Bundesrat's reservations about OA are based on misunderstandings.  There's hope that we can educate the members and counteract the publisher lobbying whose effects show so strongly here.  On the other hand, the Bundesrat has already acted and the chances for reconsideration any time soon are slight.
  4. OA needn't interfere with copyright.  If the Bundesrat objection ("the call for the freest possible, immediate and open access to scientific information may conflict with...copyright") is abstract, and includes sloppy or careless implementations of OA, then it's true.  But in exactly the same way, TA publishing may also conflict with copyright.  If the claim is more specific, that certain OA proposals conflict with copyright, then the Bundesrat has not specified the proposals or the conflicts and we can only wait until it does so.  Moreover, the objection is contradicted by the Bundesrat's own acknowledgment in #5 that "the [EC] Communication does not regard changes, in particular limitations on copyright, as necessary to reach the goals...."
  5. [T]he Bundesrat also points out that open access does not avoid the costs of knowledge processing and knowledge transfer, but rather shifts them from the users to the authors.... Where does one start with this bolus of misinformation?  First, no serious proponent of OA ever said that OA publishing was costless.  Second, the Bundesrat is apparently focused on fee-based OA journals.  But let's disentangle this.  Even fee-based OA journals do not usually shift costs to authors.  They charge publication fees but the fees are usually paid by funders or employers, not by authors out of pocket; and many fee-based journals will waive the fees in cases of economic hardship.  Beyond this, most OA journals do not even charge fees.  And beyond this, the EC Communication was not even talking about OA journals.  It was talking about OA repositories, which never charge fees.
  6. The Bundesrat points out that in the light of predominantly effective competition in the market for scientific information.... This is an unfunny joke that could only have been written by a publisher lobbyist.
  7. Finally, Jens Bammel's argument that we should let the market decide which models to adopt is easily answered.  Scientific research and publication are permeated by government spending and government policies, and do not represent a market in any ordinary sense. In Europe, as in the US and around the world, most scientific research is funded by taxpayers, most scientists work at public institutions and are paid by taxpayers, and most subscriptions to subscription-based journals are bought by public institutions and paid by taxpayers. If publishers really mean that government money and policymaking should keep out of this sector, then they should say so. But they would go bankrupt under such a rule. What they really want is the present arrangement of government subsidies for the work they publish, government subsidies for their own subscription fees, and double-payments by taxpayers who want access. (That's a market?)

New blog on open education

WideOpenEducation is a new blog devoted to open access and open source, especially in higher education.  It's sponsored by the Online Education Database.  From its inaugural post:

The term ‘open education’ refers to the free exchange of educational ideas among universities, organizations, educators, and students. The widespread use of the Internet has made it possible for these groups to collaborate more efficiently than ever before and create a robust system that benefits everyone. According to Chris Lehmann, “[T]eachers have long known that the best methods of teaching are only made better with collaboration with peers.” This collaboration forms the core of open education.

Open education takes shape in the form of open educational resources, or OERs. There are three different types of OERs:

  1. Learning content, which may include journals, collections, and open courseware.
  2. Learning tools, which may include software, content management systems, content development, and publishing and development initiatives.
  3. Implementation resources, which may include intellectual property licenses, design principles, and localization of content.

Wide Open Education’s focus will be on all of these aspects of open education as well as any tangentially-related matters. Enjoy!

Google restrictions on public-domain works hurt users and Google too

Cory Doctorow, Google Print doesn't do exclusive deals with libraries, but still holds the public domain tight to its chest, Boing Boing, May 24, 2007.  Excerpt:

A couple weeks back, I blogged about NPR's segment on digital libraries, where Brewster Kahle criticized Google for striking exclusivity deals with libraries that prohibited Google's competitors from scanning their collections.

Google has replied, saying that it doesn't have any such deal with the libraries, and they've put it in writing. They've even included one of their library contracts. This is really, really good news.

I'm still disappointed that Google puts restrictive notices on their public domain works (these aren't licenses, just "polite notices") that tell what you're not allowed to do with these books. I know they're worried about their competitors getting ahold of those documents, but that's the deal with the public domain: it doesn't belong to you, period, it belongs to all of us. Just because you scan a public domain book, it doesn't confer the right to control it to you.

More importantly: Google is betting that it will make more money by locking these books up to be merely read than it could by making them available as a giant tarball for the Internet to bend, spindle, mutilate and fold. That merely hosting these will generate more pageviews than turning them loose for remix, mashup, scholarship and other forms of inventive re-use.

It just doesn't seem like Google, betting against the Internet's creativity and capacity to innovate. I know they've got a lot of smart people there, but I hope they understand that they don't have all the smart people. Google makes the bulk of its money by indexing the cool stuff other people make. Why restrict people from making more cool stuff? ...

More on CERN's project to convert particle physics journals to OA

Travis C. Brooks, Open Access Publishing in Particle Physics: A Brief Introduction for the non-Expert, a preprint posted to arXiv May 23, 2007. 

Abstract:   Open Access to particle physics literature does not sound particularly new or exciting, since particle physicists have been reading preprints for decades, and for 15 years. However new movements in Europe are attempting to make the peer-reviewed literature of the field fully Open Access. This is not a new movement, nor is it restricted to this field. However, given the field's history of preprints and eprints, it is well suited to a change to a fully Open Access publishing model. Data shows that 90% of HEP published literature is freely available online, meaning that HEP libraries have little need for expensive journal subscriptions. As libraries begin to cancel journal subscriptions, the peer review process will lose its primary source of funding. Open Access publishing models can potentially address this issue. European physicists and funding agencies are proposing a consortium, SCOAP3, that might solve many of the objections to traditional Open Access publishing models in Particle Physics. These proposed changes should be viewed as a starting point for a serious look at the field's publication model, and are at least worthy of attention, if not adoption.

Proposing an OA, open review journal for educational technology

George Siemens, Scholarship in an age of participation, Emerald InTouch, March 27, 2006.  Siemens proposes an open access, open review journal for "emerging trends in educational technology and pedagogy, exploring fields of social software, connectivism, and networked learning" and calls on interested colleagues to contact him.

More OA archaeology

Wessex Archaeology adopts Creative Commons license for photos, Past Thinking, May 24, 2007.  (Thanks to Jo Cook.)

[Disclaimer: I work for Wessex Archaeology]

Wessex Archaeology have just announced that they will be using a Creative Commons license for the 600+ photos that they have on Flickr and in their gallery.

Let’s hope that other heritage organisations follow suit. The “All Rights Reserved” copyright model is very restrictive when you study and record the past, and want to share some of that work with others to aid and encourage further learning.

By adopting the Creative Commons “Attribution-NonCommercial-ShareAlike 2.0? license, they are actively saying to people “we want you to use our photos”. Which for a heritage organisation, is fairly novel!

Another society journal backfile goes OA

The British Epigraphy Society is digitizing and providing OA to the backfile of BES News.  (Thanks to Charles Ellwood Jones.)

More on finding articles in PubMed and PubMed Central

Sandra Porter, Finding scientific papers for free, one more experiment, Discovering Biology in a Digital World, May 24, 2007.  Excerpt:

I meant for this to be a three part series, but in part II, I learned that one more experiment had to be done. I had to know if the articles I found in PubMed Central were the same articles that I found in PubMed.

Part I and part III cover the background and my favorite method. Now, we're going to find out if my favorite method is really enough....

To test this, I did a PubMed search with term "cancer," as before, and limited the search to free, full, text.

Then, I clicked the Preview/Index tab, opened the Filter field, and selected either the pubmed pmc free filter or the pubmed pmc filter....

Then, I clicked the AND button to add that term to my query. (Using the AND, OR, or NOT buttons works wonderfully, because everything is properly formatted with quotes and brackets.)

In part II, I found 220,219 articles on cancer in PubMed and 171,702 articles in PubMed Central. In today's experiment, I found that only 52,160 articles (a little more than a third, were shared between the two databases).

What's the take home message?

PubMed Central contains articles that are not available in PubMed (with limits). So, to get as many articles as you can, you do need to search both databases. And, if that doesn't work, my commenters (here and here) have left a number of excellent suggestions!

More on Eigenfactor for measuring citation impact

Carl Bergstrom, Eigenfactor: Measuring the value and prestige of scholarly journals, C&RL News, May 2007.  This is the first full account of the Eigenfactor as a measurement of citation impact, its algorithm, its intended uses, and its advantages over other impact measurements.  I won't post an excerpt because the article doesn't directly touch on OA issues.  But I will point out that Eigenfactor results are free of charge.

JSTOR is considering OA

Tom Matrullo, A conversation with JSTOR's Bruce Heterick, Improprieties, May 24, 2007.  (Thanks to David Weinberger.)  Excerpt:

I had a good conversation the other day with Bruce Heterick, Director, Library Relations, at JSTOR.... 

[My] recent interest in JSTOR [is] mainly derived from (1) searching for certain topics in the Humanities and Social Sciences, (2) discovering with glee that interesting articles from scholarly journals are now online, (3) realizing with consternation that such articles lie behind an institutional barrier that blocks access to anyone not affiliated with a participating institution, and (4) registering puzzlement that anyone would take all sorts of pains to firewall knowledge -- knowledge mainly produced by scholars at not-for-profit institutions of higher learning devoted to bringing light into our world.

Heterick was generous with his time, and patient with my questions....

[H]ere's the maybe-if-and-when good news, the presiding lights behind JSTOR are now looking at various ways and means to open its treasurehouse to all, because they understand that that makes all sorts of sense. They simply have to ensure that by doing so, they don't remove the parts of their economic model that have enabled them to build a self-sufficient, independent 501(c)3 organization in a relatively short time.

Let me back up and offer some of what Heterick shared with me about JSTOR (more background here and, in book form via here.)

The founding aim of JSTOR was less dissemination than preservation....

[PS:  Here omitting good detail on the current JSTOR business model, range of content, and range of paying users.]

[A]long the way [JSTOR has] begun to look at the possibilities for more open access to its collections. Any qualifying institution in Africa can get access to its entire collection for free. There are special rates for high schools and an effort to get more public libraries to buy in.

Enter Google

Now, all this was taking place in the background, without much in the way of public notice, until last year, when JSTOR allowed Google to spider its online archives....

At which point, Heterick said, requests for JSTOR's online material "exploded." JSTOR found itself in the interesting position of letting it teasingly be known that it has an astonishing wealth of scholarship at the same time as it was saying to any unaffiliated researcher at its gate: "Not now."
JSTOR hadn't thought of offering a pay-per-view access before Google crawled its archive. Now, as of January, JSTOR has invited its publishers to make their titles available to unaffiliated researchers on a pay-per-view basis....

[S]till, the goal of open access is very much on its mind.

“It’s not a question of if we should do it but when we can do it and not devolve our preservation goals,” he says. “Would people or libraries be willing to pay to maintain JSTOR and maintain its long term mission of archiving? We don’t know… .”

Would institutional libraries continue to pay the subscription fees if the journals were openly available to all? On one hand, why should they? Still, it's not impossible: after all, JSTOR is ensuring the immortality of the work of...scholars at these same universities. It's also saving the costs of continually adding space....

Comment.  This is important and could become be a huge step toward OA in the social sciences and the humanities.  I talked to the Mellon Foundation in 2004 about the possibility of OA to sufficiently old and amortized back issues of participating journals, and the answer was not a flat no.  The door was ajar.  It's very heartening to hear that the door is opening further and that JSTOR now considers OA to be a goal.

Thursday, May 24, 2007

NSF launches data interoperability project

The NSF Office of Cyberinfrastructure has launched the Community-based Data Interoperability Networks (INTEROP) project and is now soliciting proposals (May 23, 2007).  (Thanks to Clifford Lynch.)  From the solicitation:

Synopsis of Program.  Digital data are increasingly both the products of research and the starting point for new research and education activities.  The ability to re-purpose data – to use it in innovative ways and combinations not envisioned by those who created the data – requires that it be possible to find and understand data of many types and from many sources. Interoperability (the ability of two or more systems or components to exchange information and to use the information that has been exchanged) is fundamental to meeting this requirement.   This NSF crosscutting program supports community efforts to provide for broad interoperability through the development of mechanisms such as robust data and metadata conventions, ontologies, and taxonomies. Support is provided for Data Interoperability Networks that will be responsible for consensus-building activities and for providing the expertise necessary to turn the consensus into technical standards with associated implementation tools and resources.  Examples of the former are community workshops, web resources such as community interaction sites, and task groups.  Examples of the latter are information sciences, software development, and ontology and taxonomy design and implementation....

Approximately 10 awards may be made in each of the fiscal years 2008, 2009, and 2010 subject to the quality of proposals and pending the availability of funds. Awards may be up to $250,000 total costs per year for three to five years....

The due date for the first round of funding is August 23, 2007.

Open data presentations at XTech

Abstracts of the presentations on Open Data at XTech 2007 (Paris, May 15-18, 2007) are now online.

Open data and linked data

Paul Miller, Linked Data - the real Semantic Web? Nodalities, May 22, 2007.  (Thanks to Peter Murray-Rust.)  Excerpt:

It has been interesting to follow the rise of the 'Linked Data' meme in the Semantic Web community recently, and to track it alongside longer term (but quieter) mutterings around 'Open Data' from the likes of Tim O'Reilly and XTech programme committees past and present.

The recent push is due in no small part, I believe, to the sterling efforts of the Linking Open Data community, and to the support they've been receiving from W3C's Semantic Web Education & Outreach (SWEO) group, of which I'm a rather quiet member.

Listening to Tim Berners-Lee's keynote in Banff a week or so back, there was a strong steer toward 'Linked Data', and the opportunities presented by the relationships between resources and the aggregate of those resources. This thread came up again and again, most notably in the Linked/Open Data sessions. Thinking about it again, the whole Linked Data thrust actually comes across as a far more compelling way to describe the value of the Semantic Web to the non-geek audience....

If the Web of Data is the target, of course, the thorny issue of to whom the data belong, and the ways in which the data may be used, come to the fore once more. This is an area we've been tackling with contributions such as the Talis Community License, and it came up in Rob's contribution in Banff [Rob's audio here, PDF of everyone's slides here], as well as papers from both of us at XTech last week....

One conversation from last week that has carried over onto email this week was with Rufus Pollock of the Open Knowledge Foundation. They don't have a license, but they do usefully define a set of principles to underpin the notion of 'open knowledge', and they explicitly include the separate notion of data....

We're seeing movement as a growing body of implementors, commentators and analysts recognise the potential of linking disparate data resources together, leveraging some of the more basic capabilities of RDF and other Semantic Web enabling technologies. We're also seeing a matching awareness of the need to protect use of those data sets (and not merely to safeguard the interests of data owners, but also - and far more tellingly - to give confidence to data aggregators and users), and a refreshing willingness to engage openly and cooperatively in reaching a pragmatic solution. It's a great time to be involved in this space, and Talis looks forward to playing our full part across the piece.

Author attitudes toward OA repositories for teaching and learning

Melanie Bates and three co-authors, Attitudes to the rights and rewards for author contributions to repositories for teaching and learning, ALT-J, March 2007.  Only this abstract is free online for non-subscribers, at least so far:

In the United Kingdom over the past few years there has been a dramatic growth of national and regional repositories to collect and disseminate resources related to teaching and learning. Most notable of these are the Joint Information Systems Committee's Online Repository for [Learning and Teaching] Materials as well as the Higher Education Academy's subject specific resource databases. Repositories in general can hold a range of materials not only related to teaching and learning, but more recently the term 'institutional repository' is being used to describe a repository that has been established to support open access to a university's research output. This paper reports on a survey conducted to gather the views of academics, support staff and managers on their past experiences and future expectations of the use of repositories for teaching and learning. The survey explored the rights and rewards associated with the deposit of materials into such repositories. The findings suggest what could be considered to be an 'ideal' repository from the contributors' perspective and also outlines many of the concerns expressed by respondents in the survey.

More on AZoM's OA journals that pay authors

Financial rewards for nanotech science authors and peer reviewers, a press release from ("The A to Z of Materials"), May 22, 2007.  (Thanks to Jim Till.)  Excerpt:

The AZo Journal of Nanotechnology Online...has recently notified all authors and peer reviewers of their revenue share earnings for the last 12 month period.

Authors of the most popular papers have earned in excess of $500 for their contributions under the AZoNetwork Patented OARS (Open Access Revenue Share) scheme and peer reviewers have earned between $100 and $500 for their efforts.

Due to the free and open access nature of the journal and the size of the online audience, which now exceeds 350,000 monthly visitor sessions, the most popular AZoJono paper has been viewed more than 17,000 times in the last 12 months.

Professor Chennupati Jagadish, Federation Fellow at the Australian National University and member of the AZoJono peer review team commented, "The AZo Journal of Nanotechnology Online (AZoJono) has been leading the open access publications in Nanotechnology with timely publication of manuscripts as well as rewarding authors, reviewers and editors for their efforts. The number of downloads of some of the papers published in AZoJono has been phenomenal."

Don Maclurcan, from the Institute for Nanoscale Technology, University of Technology, Sydney and an AZoJono author commented, "Quality publishing with an online, open-access journal that financially rewarded its authors and reviewers seemed beyond belief. I was wrong. Not only were my papers rapidly disseminated around the globe but I also received a nice Christmas bonus!"

Dr. Ian Birkby, the inventor of the OARS scheme and CEO of the operator of, the online publisher, AZoNetwork, commented,... "Although we accept it is unlikely that financial reward is the main aim of authors, it is nevertheless significant that we have proved that high quality science writing can be rewarded financially whilst at the same time be distributed in a true open access format. Although the current results are but a small beginning, we believe they nevertheless represent a significant change in the scientific publishing landscape and we look forward to employing our Open Access Revenue Share scheme into other scientific disciplines."

PS:  Recall that earlier this month AZoM won a Hitwise Australia award for online leadership in manufacturing and industry.  For more on AZoM's patented OA business model, my comment in SOAN for October 2005.

Asking the German govt to strengthen its support for OA

Germany's Aktionsbündnis: Urheberrecht für Bildung und Wissenschaft (Coalition for Action: Copyright for Education and Research) issued a press release yesterday on its communications with the national ministries of science and culture.  The coalition asked the ministries whether they agree that the government has a role to play in providing access to publicly-funded research, and where they stand on the conflict between the upper house of Parliament's 2006 support for OA and its May 2007 deference to private publishers.  The coalition also calls on Parliament to resolve its conflicting positions in favor of OA for publicly-funded research.  Read the press release in German or Google's English.

Carl Zimmer contrasts Wiley and PLoS

Carl Zimmer, An Open Mouse, The Loom, May 24, 2007.  Excerpt:

[This] is also a chance to add my two cents to a discussion that's been bubbling for a few weeks: the clash between bloggers and scientific journal publishers. Last month Shelley Batts at Retrospectacle wrote a post about a paper, and included a chart that appeared in it. She promptly got a letter from Wiley, the journal's publisher, menacing her with legal action unless she took the chart down. A long discussion then unfolded about fair use, a concept so mystical that I get a headache every time I try to figure out whether it applies to some text or image I'd like to use in my own work. Once the controversy reached Boing-Boing proportions, Wiley sent Batts a note telling her that it was all a big misunderstanding and that they "would typically grant permission on request in order to ensure that figures and extracts are properly credited."

For us science writers, there's a huge irony to this episode. Scientific journals like attention. The better-funded ones will go to great lengths to get stories written about their papers. They offer us science writers elaborately appointed press packages offering sneak peeks at papers coming out in the near future. They sometimes give us the cell phones of the authors of those papers, in case we need to call them in the middle of the night....

But scientific journals also cling to conventions that block the news from spreading --particularly through the online world. Wiley, for example, initially reacted to Shelley not with enthusiasm, but with a menacing note. When Shelley responded by politely asking for permission, she was told to contact another person at Wiley. And when Wiley finally sort-of apologized, they still expected Shelley to jump through conventional hoops to get permission. All this kerfuffle over a little graph. It might have taken days to get permission to reprint it, which in the blogosphere is a geological era. Wiley was, consciously or unconsciously, going out of their way to squash interest in their papers.

Compare Shelley's experience to what I'm about to do. I'm going to --shudder-- reprint a diagram from a journal. Just lift it straight out....

[PS:  Omitting chart and discussion of it.]

[The chart is from] a paper they published last summer in the journal PLOS Genetics....

And what do I now hear from PLOS? Do I hear the grinding of lawyerly knives?  No. I hear the blissful silence of Open Access, a slowly-spreading trend in the journal world.  PLOS makes it very clear on their web site that "everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish." No muss, no fuss. If I want to blog about this paper right now, I can grab a relevant image right now from it. In fact, I just did.

I certainly appreciate the importance of copyrights (as the owner of many for my articles and books), but in these situations, keeping information behind a thick wall starts to seem a bit crazy, like the loss of precious bodily fluids. Far from committing some sort of violation to the PLOS paper, I have actually just spread the word about it. A few readers may even go back to read the original. And it was so easy and straightforward for me to do so that I will be very reluctant to bother with anything else.

PS:  The Batts/Wiley story broke in late April when I was traveling.  If I'd been at my desk, I'd have covered it or at least I'd have tried.  But because the comments proliferated explosively, I wasn't at my desk, and I had a full load of other work, I decided that I had to let it go.  I'm glad to catch up a bit with this post.  I'm also glad to have the chance to recommend comments by Mark Chu-Carroll, Cory Doctorow, Matt Hodgkinson, Bill Hooker, Rob Knop, Brock Read, Kaitlin Thaney, Bryan Vickery, and Alan Wexelblat.  Finally, Katherine Sharpe at ScienceBlogs, where the controversy began, solicited comments from five "experts and stakeholders" (Jan Velterop of Springer, John Wilbanks of Science Commons, Mark Patterson of PLoS, Matt Cockerill of BMC, and me.)

Ghent U joins the Google Library Project

Ghent University has joined the Google Library Project, becoming its 16th library partner and the fifth from a non-English speaking country.  From Ghent's announcement:

Until now all we have done is to accumulate treasures and carefully arrange them on the shelves of our libraries. … We seem to have forgotten that this immense capital, little used today, could bear abundant fruit. Let us hasten, therefore, if it is possible … to make it completely available to scholars by publishing a universal catalogue.

          (Ferdinand Vander Haeghen, 1867)

Ferdinand Vander Haeghen (1830-1913), Chief Librarian in the nineteenth century already had an Open Access attitude....

It is 140 years later now and Ghent University still has this open mind to projects like Google Book Search. Ghent was the first Belgian University to sign the Berlin declaration on Open Access last February. The Berlin declaration encourages researchers to publish in Open access and holders of cultural heritage to support open access by providing their resources on the internet.

Ghent University is the Belgian partner in the European DRIVER project that aims to create a portal for freely accessible European research output. The University library already added 40,000 cultural heritage photographs and almost 2,700 publications in Open Access. 

And now we are really excited by the perspective of adding so many out op copyright books in Open Access through the partnership with Google’s Library Project. An important asset for the cooperation is the wonderful collection  kept in [our] Booktower. These books came into the library with the French revolution when convents and abbeys were confiscated. The chief librarians in the nineteenth century succeeded in bringing together valuable and unique collections. The most active one was the above mentioned Ferdinand Vander Haeghen. More details can be found in background information.

The partnership with the Google Library Project is the result of an ICT-mission from the Flemish Minister for Science and Innovation Fientje Moerman in which the Interdisciplinary Institute for Broadband Technology (IBBT) participated....

Also see the shorter announcements from Google Book Search and Google Librarian Central.

PS:  Google says Ghent is the 15th library partner, but I've been counting the Library of Congress, which participates through the World Digital Library.

Wednesday, May 23, 2007

Social scholars support OA

Laura Cohen, Social Scholarship on the RiseInmersión Educativa, May 23, 2007.

As an academic librarian, I've been trying to get a handle on the emerging parameters of social scholarship. This is the practice of scholarship in which the use of social tools is an integral part of the research and publishing process. The process gains a number of characteristics, including openness, conversation, collaboration, access, sharing and transparent revision.

In this entry, I'm going to paint an idealized picture of this process, gathering together both observations and speculations. I'm not suggesting that any one individual would do all of these things. I'm just looking at the options - or better yet, the opportunities....

A social scholar contributes to the conversation about her research topic by discussing her findings and ruminations on her blog and by inviting comments....

During the source gathering phase of her research, a social scholar shares important citations by depositing and tagging them on academic-oriented bookmarking sites such as Connotea and CiteULike....

A social scholar deposits her works-in-progress in a pre-print repository in order to take advantage of useful comments from peers.

Post publication, a social scholar provides open access to her works by depositing them in a post-print repository, institutional repository, personal Web site, etc....

Whenever possible, a social scholar publishes in open access journals....

OA panel at Copyright Utopia

MollyK has blogged some notes on the Open Access Panel at Copyright Utopia: Alternative Visions, Methods and Policies (Adelphi, Maryland, May 21-23, 2007). 

Closed is Not Necessarily the Opposite of Open: Open Access Initiatives
Paul Jaeger (moderator), Ann Bartow, Brian Crawford, Heather Joseph, Denise Troll Covey

This session was remarkably hostile, and unfortunately given the complexity of the topic, did little to clarify the issue at hand: Open Access and its potential for radical (and in my opinion, greatly needed) change in the scholarly communications arena. While I don't claim to be an OA expert, I do feel that I have a solid understanding of the principles and issues, and this session made me anxious and frustrated as I realized that people without my background were undoubtedly more confused afterward than before we even began. Despite Heather Joseph's "modern interpretive copyright dance", the session was truly characterized by the following phrases (supplied by panelists, not audience): "pit bull", "fired up", drank a bottle of Tabasco". Nevertheless, there were good points made, which I share below.

  • faculty are more concerned with what their peers are doing with OA journals, not about the dysfunction in scholarly communications or serials pricing
  • if everyone waits to see what their peers do (chicken & egg issue), then nothing will change!
  • to get faculty to go green, must understand current culture in order to change it
  • advancement & stature in field are key issues for faculty, not public access; faculty don't understand that there is an access issue...until you cancel journals
  • if ILL changes to strict document delivery (current section 108 review) then faculty will likely become interested in publicly accessible materials
  • lobby for OA resolution to be adopted by Faculty Senate
  • publishing agreements are contracts, and contracts are negotiable
  • what is in it for individual researchers? what are the carrots?
  • only through use of research findings by others is research impact maximized

New blog on data sharing

On April 30, Heather Piwowar launched Research Remix, a new blog on data sharing and reuse.  (Thanks to Bill Hooker.)  From her about page:

[T]he goal of this blog is to capture my notes as I flail around learning everything I can about data sharing and re-use, with the short-term goal of writing my biomedical informatics doctoral dissertation literature review. Taking notes here out in the open in case it interests anyone else along the way.

See for example her post from yesterday, Nonresponse to data sharing requests:

A few years ago, as I expressed frustration due to lack of a reply from a corresponding author, a professor summarized his experience: one third of authors do not reply when contacted, one third reply but are not able or willing to supply requested data, and one third reply and do supply the information.

I’ve since run across two published reports [one, two] which quantify the nonresponse to data sharing requests. Does anyone have others? ...

What a sorry state of affairs.  In some ways it is understandable. Sharing data is hard. People are busy.  But isn’t sharing data part of a scientist’s job description?

More on finding OA papers in medicine

Sandra Porter, Finding scientific papers for free, part III: my new favorite method, Discovering Biology in a Digital World, May 23, 2007.  Excerpt:

This is the third, and last part in a three part series on finding free scientific papers. You can read the first part here: Part I: A day in the life of an English physician and the second part, where I compare different methods, here.

Today, I will show you how to use my new favorite method....

1. Go to the NCBI.

2. Choose the link to PubMed. (It's in the top blue bar, under the DNA icon)

3. Click the Limits tab....

4. Click the box next to "Links to free full text."

5. Select any other Limits that might apply.

I often pick English for the language since I can't read any other language. I wouldn't try to impose too many limits at first....You can always narrow the search later.

6. Enter your search terms and click "Go."

7. Click the Review tab if you wish to read reviews, click links to the articles if you wish to see the abstract and get a link to the publication....

Where to find more info...

1. Cancer Biology covers the different types of literature databases, Boolean operators, combining queries, limiting searches, and using the search history.

2. Allelic Variants of Superoxide Dismutase demonstrates many ways to find information about genetic diseases, and includes my topic for today; how to find free papers in PubMed.

3.  Some of yesterday's readers contributed their favorite search strategies in the comments section.  If you're looking for specific papers, these are some great ideas....   

PS:  For background, see the excerpts from Part I and Part II that I blogged here yesterday.

Paris meeting on open archives

The presentations from the Couperin Consortium meeting, Journée d'étude sur les Archives Ouvertes (Paris, May 21, 2007), are now online.   (Thanks to the INIST Libre Accès blog.)

OA to clinical trial data working as intended

GlaxoSmithKline's own OA Clinical Trial Register was a major source of data for a new study showing that Avandia, GSK's drug for diabetes, increases the risk of heart attack.  For details see yesterday's Wall Street Journal.  (Thanks to Ari Friedman.)

Update. Apparently scientists studying Avandia risks don't have access to all the GSK data they'd like. See Jonathan Eisen's post about a radio discussion of the problem and his own phoned-in contribution.

Update. Cory Tomsons warns that the role of open data in this case doesn't mean that we can relax efforts to regulate and improve drug safety. Excerpt:

Open access to the data is a good idea, but it is not enough. Public health cannot take place voluntarily or in a legal vacuum. We need regulation to enforce that open access, we need regulation to uncover harmful effects and screen for snake-oil ‘alternative therapies’, and we need regulation to free doctors and patients from biased sales pitches. Absent this, informed choice about medical treatment is a myth.

Software to automate OA queries to authors

News from Ari Friedman's Self-Archiving Initiative:

There is now software available, written in PERL, to check journal policies in a long list of citations and e-mail the authors to ask them to provide archivable versions. If you have any problems adapting the code to your own purposes, please e-mail the author.

I wrote him for additional details and learned this:

It was designed to help create this page

Given a webpage of articles in that particular citation format (can be changed with some minor coding), it runs through a list of articles, looks their open access status up in ROMEO, then embeds comments next to each article with that status.  A separate script can then run through and e-mail all the authors whose works are not currently OA.  The text of the e-mail is customizable.  We used it to ask the author to send us a version which we were allowed to make publicly available on our page, but I imagine if it gets any use outside of its original use it will be to ask authors to self-archive the works and provide the link.

PS:  Unlike the email request buttons now available for EPrints and DSpace, Friedman's software applies to online bibliographies, not repositories, sends many queries at once, and can ask authors to deposit their articles, not merely to forward copies of articles already on deposit.  This could be very useful. 

Turkish guide to launching an IR

ANKOS (Anatolian University Libraries Consortium) has published a guide to establishing an institutional repository, in Turkish with an English summary.  (Thanks to Bulent Karasozen.)

Demystifying OA

The slides and video of the colloquium by CERN's Salvatore Mele at Stanford's SLAC, Demystifying Open Access (Palo Alto, May 14, 2007), are now online.  (Thanks to Jens Vigen.)

The MRC and BHF OA mandates in action

James Mitchell Crow, Scientists seek indicators of illness, Chemistry World, May 22, 2007.  Excerpt. 

A £17 million fund has been set up by the UK's Medical Research Council (MRC) for research into biomarkers, the tell-tale body chemicals that are associated with particular diseases....

The MRC have contributed £8 million to the fund, with a further £1 million from the British Heart Foundation and £8 million from a range of pharmaceutical and analytical science companies. Money has been awarded on condition that the results are made freely available in open access scientific journals. The projects will run for three years....


  • Both the Medical Research Council and British Heart Foundation require OA to the research they fund.  But their policies require deposit in an OA repository, not publication in an OA journal (see their policies here and here respectively).  I suspect that Crow simply mixed these up. 
  • What's new and promising (but not unprecedented) is that "a range of pharmaceutical and analytical science companies" would contribute to a research fund with an OA mandate.  Kudos to the leadership in all the contributing companies.

More on how copyrights hinder research

Donat Agosti, Das Urheberrecht behindert die Forschung, Handelszeitung, May 16, 2007.  How copyrights hinder research and how OA accelerates it.

(Because the original is a PDF, I can't link to a machine translation.)

New prize for openness and innovation in cancer research

The Gotham Prize is a new annual $1 million award for innovation in cancer research.  It doesn't specifically require OA for research results, but it does specifically try to counteract the data hoarding and secrecy that often accompany promising new ideas, especially in their early stages.  From the FAQ:

For competitive reasons, preliminary research and ideas are often not widely shared. (Though a handful of foundations insist on sharing of preliminary research, this is not the norm)....Research that leads to non-patentable treatments or cures is not usually funded by the for-profit world. Most areas of prevention are ignored. Research that involves long lead times and/or basic science also does not receive enough support. Sharing of preliminary research and new ideas is limited. In recognition of these issues, it is hoped that the Gotham Prize for Cancer Research will help to fill in some of these gaps and lead to accelerated progress in the prevention, diagnosis, etiology and treatment of cancer.

OpenBusiness on Freebase

Wikipedia for Data - Freebase, OpenBusiness, May 23, 2007.  Excerpt:

Want to know how many dentists are in one mile vicinity, if they are next to tube stop and are specialists in teeth whitening? Freebase say they can not only give you this information, but that the database behind it will be build Wikipedia style.

Normally one would say this is ‘nuts’, but the team behind it seems promising (and Tim O’Reilly thinks the idea is HUGE).
OpenBusiness has interviewed one of the minds behind Freebase.

Robert Cook is one of the co-founders of Metaweb, the company behind Freebase. The company attempts nothing less than to build a ‘better infrastructure for the Web’.

Behind the Metaweb is also Danny Hillis, serial inventor and entrepreneur who was behind the Connection Machine a parallel supercomputer at MIT....

Freebase aims to be the Wikipedia for data. So naturally OpenBusiness was interested. Also their business model seems cool. They say they will make money through an through an API program. Depending on the commercial vs. non-commercial nature, and extent of services required by a developer, they will charge fees. How this all works, why they use Creative Commons and what they think about OpenAPI’s read below:

1. Why did you start Freebase?

Freebase’s goal is to be a database of the world’s knowledge.  As a single unified database, Freebase will prove to be far more powerful than the sum of its data sources, as it connects people to films, films to places, places to science, science to schools, schools to sports and so on…

As a database, it lets people ask complex and extemporaneous questions like, “Find me child-friendly dentists within 10 miles of my home,” or “Give me photographs of John F. Kennedy in Europe prior to 1962,” or even “Find me all of the Venture Capitalists in Silicon Valley who share a board membership and went to college together.” ...

Even more than the technology, the bigger question for us was where all of this the data would come from.  The internet has many thousands of significant databases, but most are hidden within websites or have restrictive licenses so that the data is locked up.  Fortunately, there are several hundred significant open databases that are in machine readable form, and we have begun to import these.

But most importantly, there are now many examples of sites where people are eager to build collective knowledge.  Wikipedia is the best example of this, but there are countless other sites built from user contributions, the biggest being IMDb (which has since become a closed model) and Musicbrainz, a music database which in many ways surpasses commercial alternatives.  It’s this phenomenon that makes us believe that a large database can actually be built....

We...learned two critical things from Wikipedia:

A. Wikipedia has radically embraced a ‘post-hoc’ moderation model....

B. Wikipedia has exactly one article for one idea....

Freebase has adopted the radically open contribution model (our current closed Alpha notwithstanding), where users can add structured information with minimal effort, such as the closing time of a restaurant, a link to a digital camera’s online manual, or the name of a company’s founder.  Experts in a field are unimpeded by process.  Bad data becomes good data as many people find problems and fix them.

Also, like Wikipedia, Freebase has the same one-to-one mapping of database records (what we call “Topics”) to things in the world.  For instance, we have a single “Austin, Texas” topic that points to all of the companies based there, the movies filmed there, the tree species growing there and the famous people born there.  If there are two “Austin Texas” topics, they will get joined into a single one.

3. You are using a CC license - why? ...

Freebase uses the very open “Creative Commons Attribution License” that allows anybody to use the data for any purpose, as long as they give attribution to the contributor.....

We believe that the more open the license is, the larger the set of users, the larger the set of contributors, and therefore the larger and higher quality the data set.  We allow and encourage commercial use because we want people to start building businesses that use and contribute back data to Freebase....

PS:  For more background, see my post from 3/9/07 on the Freebase launch.

Tuesday, May 22, 2007

New OA journal of urban life

Métropoles is a new peer-reviewed OA journal of cities and urban life published with support from the French Ministère des Affaires Etrangères, Région Rhône-Alpes, CNRS, Ministère de l’Ecologie, du Développement et de l’Aménagement Durables, Cluster 12 de la Région Rhône-Alpes, and the Ecole Nationale des Travaux Publics de l’Etat.  (Thanks to Klaus Graf.)

New OA journal of semio-linguistics

Semen: Revue de sémio-linguistique des textes et discours is a new peer-reviewed OA journal published by the Presses Universitaires de Franche-Comté.  (Thanks to Klaus Graf.)

Finding OA papers in medicine

Sandra Porter, Finding scientific papers for free, part I, Discovering Biology in a Digital World, May 21, 2007.  Excerpt:   

This three part series covers the problem of finding scientific articles, compares results from a few different methods, and presents instructions for the best method.

A day in the life of an English physician

In April, I had the great fortune to attend (and speak at) a conference on scientific publishing sponsored by the Association of Learned and Professional Society Publishers. One of the first speakers was an English physician who described his trials and a typical ordeal in trying to use the medical literature....

This doctor, a thoughtful and well meaning young man, had reviewed the X-ray results for one of his patients. She listened quietly and asked if him if her results could mean lung cancer.  He went to the internet to find out.

First, he tried PubMed.

But many of the papers were in journals that he couldn't access because his hospital didn't have subscriptions.

Next, he tried Google.

But his Google results all seemed to be same, and they failed to provide his answer.

Last, he tried Google scholar and finally found a place to begin. Luckily, he happened on a paper, written by someone that he knew worked in the field....

The talk was over and it was time for questions. One of audience member, an older gentlemen with a crisp English accent, angrily questioned the young man, in disbelief. How could it be that he, a doctor, couldn't access this information? Surely, he must have access through his University?

Calmly and carefully, the young physician explained that he worked in a hospital, run by the National Health Service. Yes, he said, he could access publications if he were at the University....

Furthermore, he explained that the computer he uses is situated in a central work station, shared with the nurses, and other doctors; and used for multiple tasks. With others waiting to access to patient records, check medication details, and review lab results, it's impossible for him to monopolize the computer for more than a few minutes at a time....

I sat in the audience, simply amazed. Not that he couldn't access information for free, mind you, but that he didn't know how to find freely accessible information in PubMed....

Also see Part II: comparing methods:

Today, we do an experiment with PubMed and PubMed Central to determine the best way to search for free articles....

I searched either PubMed or PubMed Central through the National Center for Biotechnology Information (NCBI) with the term "cancer." Then, I either limited the search (using Limits, shown as "PubMed Limits" in my graphs below) or I used the Display menu to filter the results (shown as "PubMed PMC" links in the table). Last, I sorted the results by date to see which search method gave the newest publications....

In my experiment, only 11 percent of the articles that I found [in PubMed] were freely available, and that was when I used the best method....

The least successful method was to use the PMC links filter....

If I searched PubMed Central directly, I obtained more articles, but the most recent articles were from May. My PubMed search, on the other hand, had located articles, from June. (Yes, June hasn't happened yet, but some articles can be found before they're officially published.).

Overall, I found the best method, with the most results, was to use PubMed and limit the articles to those with free full text. While it's certainly true that 219,985 articles are way too many for me to read, at least I know I'm getting the most recent articles, and that I will be able to view the articles that I choose to investigate.

Plus, one of the tabs limits the results to review articles....

More on the limited knowledge of OA in Africa

Charles Mkoka, Open access blocked by unawareness and librarians,, May 22, 2007.  Excerpt:

African scientists are making increased use of online scientific journals but many are still not aware of free access, according to a study.

Researchers also warned that slow Internet connections and librarians' control over passwords is hindering what access there is.

The study was published in BioMedCentral's Health Services Research last week (17 May)....

[M]any respondents complained they had difficulty obtaining passwords from librarians, who often failed to make them available.

Maurice Long, publisher coordinator of the International Association of Scientific, Technical and Medical Publishers says over four million articles were downloaded from HINARI in 2006, indicating that the majority of librarians do distribute HINARI passwords.

In the cases where they don't, there is a need for information literacy training, Long told SciDev.Net.

Barbara Aronson, HINARI's programme manager at the World Health Organization agreed. She said that, in the study, those from institutions whose librarians and researchers had been trained at HINARI workshops reported better results in working together to use HINARI....

PS:  For background, here's the original article and my blog post about it.  I'm glad to hear that HINARI is working on the password availability problem.  On the other hand, straight OA requires no passwords.

Sean Eddy on open access and open source

Kevin Davies, Eddy Celebrates Open Access in Franklin Speech, BioIT World, May 22, 2007.  Excerpt:

Sean Eddy accepted the 2007 Benjamin Franklin Award....

Open access to software, journal articles, and data is an issue of profound importance to researchers across the community. The first journals, created in the mid 1600s, were founded with a tacit quid pro quo: disseminate your research, allow others to reproduce your work, and gain a measure of fame in the process....

Four centuries later, the issue hasn’t changed so much. In 2001, Celera published its assembly of the human genome in Science, but refused to freely distribute the sequence without restrictions. Eddy said he uses Celera’s DVD as a coffee coaster, because the terms barred him from redistributing the sequence data.

In the aftermath of the controversy, the National Academy of Sciences convened the Cech Report, reaffirming the quid pro quo of science publication. “If you’re not disclosing anything, why should you get credit?” said Eddy. “All members of the scientific community … are playing on the same playing field. [If] Celera publishes a paper, their genome sequence should be available. [If] I publish a paper, my software should not be made available to academics only, but to [everyone].”

Eddy devoted most of his talk to the topic of data dissemination and open access. “We want not just humans to be able to read the literature, but computers to be able to read the literature.” Said Eddy: “The bioinformatics community is the canary in the coalmine for this kind of issue, we’re affected by this issue. We’re the ones trying to integrate large datasets. If the dataset is there but not integratable, we know about it first…. The literature affects us very much.” ...

“For me, open access is secondary. The goal is to create systems that work… open access is necessary but not sufficient.” Eddy made a strong case that it is worth academics taking time away from their top priority – writing papers – to “create tools and make sure that they get used by the community.” There are several keys to doing that successfully, including choosing the right problem, preparing a simple manual, making it freely and readily available, and ensuring that it is integrated into the community’s system.

Eddy is best known for a program called HMMER, for running profile hidden Markov models on sequence families. The software is easily downloadable, and runs on anything, said Eddy. There is one page of instructions for installation, another page for getting started....

Curiously, Eddy noted that the International Society for Computational Biology has a policy against open source software. Some members, he said, think they should be able to make money from industry for writing software. “Some people with a similar mindset as me have infiltrated the board of directors,” and will work to change the system....

"Emancipatory teaching in an electronic age"

James Neill, Journey into use of free software, open formats, open access, and open licensing in academia, University of Canberra wiki, May 22, 2007. 

Abstract:   This article overviews an action-inquiry-based experimentation with an emancipatory approach to academic work in the 21st century electronic age. Universities generally request of academic staff the pursuit of three (inter-related) missions: teaching, research, and service. This article suggests four pillars which could help to support authentic pursuit of these missions: the use of free software, open file formats, open access materials, and placing of materials into the public domain or use of copyleft licensing. This approach was pursued within the the the context of teaching Survey Design & Methods in Psychology during Semester 1, 2007 at the University of Canberra as part of the institution's Researching Online Learning project. Institutional support and encouragement to experiment with an open academic approach was critical to the progress made.

More on a possible OA journal of computational linguistics

The blog-based discussion of a possible OA journal for computational linguistics and natural language processing has moved to a wiki

Monday, May 21, 2007

More on open data at XTech 2007

Rufus Pollock has blogged some notes about XTech 2007: The Ubiquitous Web (Paris, May 15-18, 2007).  Excerpt:

Last week I was at the XTech conf along with Jo Walsh in order to present in the Open Data track. We built on our recent discussion to argue for the fundamental importance of componentization in developing the Open Data/Knowledge ecosystem — you can find the slides of our talk (entitled Open Data and Componentization) here.

Being here for the week has been a great experience. With one of the four streams being dedicated to Open Data the conference has been a chance to see and chat with a whole bunch of other projects and people, some of which I knew about before, but many of which I did not (or had not met in person).

Coming out of this was a really good sense of convergence in understanding as to what we need to do: add licenses to data, get a consensus on what ‘openness’ is, find ways to add knowledge APIs so we can plug difference corpora together. It is also very heartening to see the growing maturity of many of the tools and resources — e.g. PubMed, the World Wide Molecular Matrix, time visualization tools, gene databases — though I would say we still find it very hard to plug different resources together — where that has been achieved it is usually thanks to a high degree of agreement in terminology and standards combined with a significant commitment to add the associated structures into the data....

Video about the the global commons movement

From the iCommons blog:

...[I]f you want to watch a great film about Creative Commons, iCommons and the Global Commons movement, watch this great film by Rehad Desai from Uhuru Productions....

New OA journal on biofuels

Biotechnology for Biofuels is a new peer-reviewed OA journal from BioMed Central.  For details, see today's announcement.

Podcasts on open data

Danny Ayers has posted five podcasts on open data, from the WWW2007 Developers Track (Banff, May 10, 2007).  (Thanks to Peter Murray-Rust.)

Google will digitize 100,000 ancient Indian texts

Charles Huckabee, Google to Digitize Ancient Texts at University in India, Chronicle of Higher Education News blog, May 20, 2007.  Excerpt:
Google has agreed to digitize some 800,000 books and manuscripts at the University of Mysore, in Karnataka, India, the Indo-Asian News Service reported. Some of the documents are written on palm leaves, and some on paper. Among them are India’s first political treatise, the Arthasastra, dating from the fourth century BC.

J. Shashidhara Prasad, vice chancellor of the university, said the project would “restore and preserve this cultural heritage for effective dissemination of knowledge,” according to the news service....

Of the 800,000 texts Google will digitize from the Mysore library, about 100,000 date from the eighth century.

PS:  The Indo-Asian News Service adds that the works will be "patented" after they are digitized and before Google may link to them.  Did it mean "copyrighted"?  Either way, will Google display full-texts (as it may do with public-domain works) or limit itself to fair-use snippets (as it must do with works under copyright)?

Update. Library Journal Academic Newswire reports that early reports of this project have been exaggerated:

...[R]eports circulating on the Internet are...claiming Google has struck a deal to digitize more than 800,000 books and manuscripts at the University of Mysore, Karnataka, India....There's just one catch --that agreement is news to Google. Google officials confirmed they were in discussions, but that there was no agreement in place with Mysore.

Another reason for OA in anthropology

Alexandre Enkerli, AAA on OA, Lorenz on AAA, Open Access Anthropology, May 21, 2007.  Excerpt:

...One argument I don't hear being made very frequently is that OA is perfect for ethnographers working abroad. Few of the people with whom we collaborate "in the field" have access to [American Anthropological Association publications] but many do have some form of Internet access....OA makes it relatively easy for people with whom we work to look at some of the things we have published "about them."

Of course, the same argument can be made in local communities. But I think it's more forceful a concept when applied to "remote communities." It might sound too "Crisis of Representation circa 1990" but I personally see benefits to making our writings available to people who can relate to them. After all, such a practise goes well with both the spirit and the letter of our codes of ethics....

Cancer Research UK announces its OA mandate

Cancer Research UK released its OA policy today.

The CR-UK pledged to adopt an OA mandate back in January 2007, at the launch of UK PubMed Central (UKPMC).  (It's a member of the UKPMC Funders Group and all members of the Funders Group pledged or adopted OA mandates.)  But it took some time to deliberate and didn't announce its policy until today.  Excerpt:

From June 2007 it is a condition of funding that Cancer Research UK-funded researchers deposit an electronic copy of peer-reviewed, published papers arising from their Cancer Research UK funded work in the UKPMC database.

This applies to research papers resulting from new awards made after 1 June 2007, as well as to existing grants. It also applies to researchers within our institutes.

Cancer Research UK is introducing an open access policy because we believe that improving access to research papers will help scientists throughout the world to make the discoveries we need to beat cancer.

To ensure that the output of the research we fund is available to the widest possible audience, we believe it is necessary to provide open and unrestricted access to it....

As a Cancer Research UK-funded author you should ensure in advance of making any agreement with or commitment to a publisher that there is no conflict with your obligations under Cancer Research UK's open access policy. For details of compliant publishers visit the ROMEO database.

However, we accept that some Cancer Research UK-funded authors will wish to publish their research in journals that do not comply with UKPMC requirements, because these journals are the most appropriate for their subject matter.

Cancer Research UK's open access policy allows for publication in non-compliant journals in exceptional circumstances. If you wish to publish in one of these journals, you will need to make a case for this course of action in advance of submitting your manuscript by emailing

There are two ways to comply with the policy:

  • Submit your paper to a journal that offers an open access option, usually on payment of a fee. The publisher will then take responsibility for uploading the final, published version of your article into UKPMC.
  • Submit your paper to a journal that does not offer an open access option, but will either allow a copy of your research to be deposited after the embargo period or permit you to self-archive in UKPMC.

Cancer Research UK will not make additional funds available to cover the costs of open access publishing at this stage. However, the situation will be closely monitored and actual costs to researchers will be reviewed in summer 2008....

A range of further information is available to help you understand how this policy and UKPMC will affect you:

PS:  The main page on the policy doesn't talk about timing, but the FAQ fills in the gap:  "All deposited papers must be made freely accessible from the UKPMC as soon as possible, and in any event within six months of the journal publisher's official date of final publication."  Kudos to all involved at CR-UK.

A German review of Willinsky's Access Principle

Daniel Zimmel has written a review of John Willinsky's book, The Access Principle, MIT Press, 2005 (print edition, OA edition), for Bibliothek: Forschung und Praxis, 2007.  The review is in German.  (Thanks to Klaus Graf.)

Because the review is a PDF, I can't link to a machine translation.

Wishful thinking in the publisher position paper on balancing rights

Kevin Smith, Publisher position on author rights, Duke Scholarly Communications, May 20, 2007.  Excerpt:

Three academic publishing organizations recently released a short position paper called “Author and Publisher Rights for Academic Use: An Appropriate Balance” that is worth a look from all who are concerned about scholarly communications.  For higher education, the position paper contains elements that evoke hearty agreement and others that demand objection.

If, as a recent comment on the LibLicense list suggested, the purpose of the paper is to call wide attention to two facts, that many scholarly journals already have very “scholar-friendly” policies built into their publication agreements and that copyright is not necessarily a barrier to academic discussion and comment, there would be little to argue with.  It is quite true that many academic journals already allow authors to retain many or most of the rights necessary for subsequent teaching and research uses....

On the issue of digital “open access” availability, the position paper takes an awkward stance....[T]he paper marshals several arguments against mandated public access for research funded with public money.  Some of these arguments are self-contradictory; if one fear about open access is that it will “confuse the scientific record,” why is it suggested that a better course than mandating access to the final version of an article is to post pre-prints?  While pre-print repositories seem less threatening to the traditional business model of journal publishing, the scientific record is best preserved when access to the scholar’s final word is available to all.

One comment at the very end of the report deserves comment.  The publishing organizations take note of the educational exceptions and limitations built into copyright law but assert “that these exceptions are thus far limited to traditional photocopying and do not permit the exploitation of such materials [journal articles] over the Internet.”  This is wishful thinking; no court, that I am aware of, has decided one way or another about how far educational exceptions apply in the digital realm.  The TEACH Act, although largely a failure at its stated purpose, is clearly intended to apply some leeway for education to the Internet.  And the oft-repeated assertion that copyright law is technology neutral implies that there is fair use on the Internet, as the recent Perfect 10 decision held, even if its educational boundaries have not yet been clarified.

More on MIT and the SAE

Elia Powers, Standing Up for Open Access, Inside Higher Ed, May 21, 2007.  Excerpt:

Professors at the Massachusetts Institute of Technology were perplexed: How could a membership organization that gladly accepts and archives their scholarly work turn around and limit transmission of the material?

[A]bout two years [ago, the SAE]...began requiring users to download a plug-in that prevented sharing encrypted documents over a network. Users could only view a paper on a single desktop computer and were allowed one printed copy per access code. No saving a copy to the computer. No photocopying. SAE also changed pricing models so that users were charged per view....

Last month, MIT Libraries explained in a blog posting its decision to cancel access to the database because of the restraints. The decision set off a chain of events that has led SAE to reconsider its policy. The case shows, among other things, the extent to which faculty members will go to protect the free flow of academic information in a time when technology allows for greater research sharing.

Wai K. Cheng, a professor of mechanical engineering at MIT and an SAE fellow who led the faculty charge against the restrictions, presented his concerns to SAE’s publications board last month. The organization prides itself on its efficient search engine and comprehensive database, he said in an interview, which made the change in policy all the more annoying.

“It is a step backwards,” Cheng said. “All of the sudden we’re back to archiving papers by printing them out. They want to put a lock on this thing and make it more difficult to operate.”

As a result of his and others’ lobbying efforts, the panel last month announced plans to form a task force of professors, librarians, its own board members and others to rethink the policy....

[Ellen] Duranceau, [MIT's] licensing consultant, said faculty at MIT are committed to keeping their papers open to as many eyes as possible.

“The core issue is the reaction of the authors here in discovering that when they had written papers and given SAE the right to the materials, [the group] betrayed their trust,” she said. “No one was under a naive assumption that everything should be free, but there was an understanding that things should be made as barrier-free as possible.”

PS:  For more background, see my posts from March 21 and April 23, 2007.

Sunday, May 20, 2007

OA collection of Darwin's letters

For more than 20 years, the Darwin Correspondence Project has been collecting Darwin's letters for a series of priced, printed volumes.  It has now started releasing them in an OA edition.  From the site:

Welcome to the Darwin Correspondence Project's new web site. The main feature of the site is an Online Database with the complete, searchable, [OA] texts of around 5,000 letters written by and to Charles Darwin up to the year 1865. This includes all the surviving letters from the Beagle voyage - online for the first time - and all the letters from the years around the publication of Origin of species in 1859.

The letter texts, and the contextual notes which help make them accessible, are taken from the first thirteen volumes of the Correspondence of Charles Darwin (Burkhardt et al., Cambridge University Press 1985-).  Letters from later volumes will be added on a rolling programme following behind publication of the print edition. Volumes 14 (1866) and 15 (1867) are already published and Volume 16 will be published in 2008.

The database also includes summaries of a further 9,000 letters still to be published.There will be 30 volumes of the print edition in total.  Previously unknown letters continue to come to light....

OA collection of radical small-press writing

The University of Utah has launched Eclipse, "a free on-line archive focusing on digital facsimiles of the most radical small-press writing from the last quarter century."  (Thanks to the Prelinger Library blog.)


For the past three days, Blogger hasn't listed all my archive files in my sidebar.  But the problem is now fixed, thanks to an anonymous contributor to the Blogger Help Group

OA collection at the U of Vermont

Back in April, the University of Vermont launched an OA repository for rare and fragile works from its special collections.  From its announcement:

The University of Vermont Libraries launched the Center for Digital Initiatives (CDI) on Monday, April 16....The CDI is a new online resource that allows any user with Internet access to view and search documents and photographs from the university's Special Collections.

Previously, library patrons had to visit Bailey/Howe Library and wear white gloves to view these often fragile materials.  The CDI allows them to access UVM's signature collections in digital form from a remote location. CDI's initial collection — more will follow — is a rich, searchable archive of more than 1,000 pages of materials generated by eight Vermont Congressmen, including such well known figures as George Aiken and Robert Stafford, documenting topics ranging from the abolition of slavery to social life in Washington, D.C. The first document dates from 1818, the most recent from 2004. The collection also includes photographs....

[Quoting Vermont Senator Patrick Leahy, who helped secure funding for CDI:]  "CDI creatively harnesses modern technology to open windows to earlier periods of Vermont’s history. By making these archives more accessible, it will also make them more useful." ...

New material will be added on a daily basis.

No comment

In a New York Times op-ed, Mark Helprin argues for permanent copyrights.  He refers to the expiration of a copyright as "expropriation" and "confiscation".

Update. See the lengthy response evolving at Lawrence Lessig's wiki.

The internet as a platform for pursuing truth

Time Magazine has published an excerpt from Al Gore's new book, The Assault on Reason (Penguin Press, to be available on May 22).  Excerpt from the excerpt:

...[T]he Internet...has extremely low entry barriers for individuals. It is the most interactive medium in history and the one with the greatest potential for connecting individuals to one another and to a universe of knowledge. It's a platform for pursuing the truth, and the decentralized creation and distribution of ideas, in the same way that markets are a decentralized mechanism for the creation and distribution of goods and services. It's a platform, in other words, for reason. But the Internet must be developed and protected, in the same way we develop and protect markets —through the establishment of fair rules of engagement and the exercise of the rule of law. The same ferocity that our Founders devoted to protect the freedom and independence of the press is now appropriate for our defense of the freedom of the Internet. The stakes are the same: the survival of our Republic. We must ensure that the Internet remains open and accessible to all citizens without any limitation on the ability of individuals to choose the content they wish regardless of the Internet service provider they use to connect to the Web. We cannot take this future for granted. We must be prepared to fight for it, because of the threat of corporate consolidation and control over the Internet marketplace of ideas....

The democratization of knowledge by the print medium brought the Enlightenment. Now, broadband interconnection is supporting decentralized processes that reinvigorate democracy....

Giving readers one more reason to look at OA articles first

Heather Morrison, Does Open Access correlate with quality and recency? Imaginary Journal of Poetic Economics, May 20, 2007.  Excerpt:

A recent study by the Publishing Research Consortium (PRC) postulates that the most prominent (and thus most citable) authors are more likely to make their articles available in an OA model, and that they are more likely to do so with their most important (and thus most citable) articles. (Executive Summary, 5B).

The PRC also postulates that there is an Early View effect with open access articles, which relates only to articles posted before final publication, and suggests that the period between the early posting of an article (either pre-print or post-print) and the appearance of the cognate published journal article allows for earlier accrual of citations.
If these postulations are correct, this is good news for open access, readers, and authors!

Readers will have yet another way to sort through all of the research literature that is being produced nowadays. If one does not have time to read everything, then start with open access resources. Not only are they easier to access, they may be higher quality and more important too....

More on OA to clinical drug trial data

Pat McCaffrey, Clinical Trial Data: Fit for Public ConsumptionAlzheimer Research Forum, March 13, 2007.  Excerpt:

This week, two independent groups of academic researchers call for more transparency in the conduct of clinical trials. One focuses on the structure of industry-academic partnerships in clinical trials, while the other argues for a more open airing of safety results from large-scale clinical trials that are submitted to the United States Food and Drug Administration (FDA)....

[According to Piccart et al. in Nature] academic independence and openness with the data is the key to successful clinical investigation. “Only by ensuring untrammeled access to long-term data, both good and bad, can we conduct clinical trials in a credible manner,” the authors conclude. “This access will ensure that those patients who consent to participate in them maintain faith in the clinical trial process.”

That theme of the importance of open access to data is echoed in the second report, from Aaron Kesselheim from the Brigham and Women’s Hospital and Michelle Mello of the Harvard School of Public the March/April issue of Health Affairs.

When companies conduct a trial, all the safety and efficacy data is submitted to the FDA. The primary data stays under wraps, with the results presented in a summary report, which is often written by the applicant company. The presumption behind this scheme is that releasing the raw data could harm the business interests of the company by helping their competitors....

Kesselheim and Mello question whether the FDA’s default policy of keeping safety data secret is consistent with public’s interest in disseminating the information, which not only protects people using existing drugs, but also can help efforts to make future drugs safer.

While it may be true that the release of some kinds of information, such as data on chemical composition and formulation, and sometimes efficacy, can put companies at a disadvantage, this is rarely the case with safety data, the authors write....


Piccart M, Goldhirsch A, Wood W, Pritchard K, Baselga J, Reaby L, Kossler I, Kyriakides S, Norton L, Coates A. Keeping faith with trial volunteers. Nature. 2007 Mar 8;446(7132):137-8. Abstract

Kesselheim AS, Mello MM. Confidentiality laws and secrecy in medical research: Improving Public Access to Data on Drug Safety. Health Affairs. 2007 March; 26(2): 483-491. Abstract

CCAHTE Journal converting to OA

Cheryl McLean, CCAHTE Journal Achievements and Challenges, Crossing Borders, May 17, 2007.  McLean is the editor and publisher of the CCAHTE Journal.  (CCAHTE = Canadian Creative Arts in Health, Training and Education.)  Excerpt:

Back here again on the business front, as founder and publisher of CCAHTE Journal, it has been an exciting and challenging ride. I have personally invested a year and a half to launch this endeavor and I have done this enthusiastically and without guarantees. However, the excitement and privilege of being active in the publishing industry in Canada and evolving toward Open Access at this historic time in academic publishing has been infinitely rewarding....

There are many Open Access academic journals coming on line today, and a number of these sustain their free and open accessible operations with some form of publisher's fees so that publishers can continue to make the information available via internet and web technology while covering the costs to do so. These fees are frequently offset or covered by funding agencies, as part of the grant that their publicly funded research can reach the widest possible audience....

We will be seeking potential corporate sponsorships. As is the case with the Open Access journal, Open Medicine, we will not be accepting advertising or sponsorships from the pharmaceutical industry. We will be seeking sponsors, advertising and other funding avenues to help sustain what has become an important, even critical, new international vehicle for research and information in the field and we will be open to your thoughts and suggestions in this regard.