Open Access News

Jonathan Gray, Big Art Mob, public art and open heritage resources, Open Knowledge Foundation blog, November 30, 2007.  Excerpt:

I’ve just been poking around at the Big Art Mob website which was launched by Channel 4 earlier this year and picked up a Royal Television Society Innovation Award earlier this month. It aims to “create the UK’s first comprehensive survey of Public Art” using user-submitted camera phone pictures and a Google maps API....

In keeping with the ‘public spirit’ of the project, the terms and conditions state that images contributed will be made available to others under a Creative Commons Attribution-NonCommercial-ShareAlike license.

It looks like a great project, and...as if it could generate a significant collection of CC licensed images displayed on the Big Art Map. However it would be even better if their images were fully open, and if the project made raw dumps of site location data and associated tags available for others to re-use!

The potential of open heritage resources....

Some of us at the OKF have been brainstorming about local heritage projects like this for a while. One line of thought is that linking user-generated material (including material from Flickr, Wikipedia, and so on) to material from local museums, libraries and archives could encourage the growth of a ‘public information ecology’ for local heritage. Naturally we think open licensing would help such an ecology to flourish - and would let developers to experiment with different kinds of interfaces to enable users explore, modify, extract and reuse material they are interested in. ‘Public art’ such as architecture, sculpture, and other landmarks is ideal subject matter for this! ...

Many freely available resources out there are still not open. Imagine what kinds of applications would be possible if more hobbyists and institutions allowed the fruits of their labour to be re-combined and built upon!

Marc, Der weite Weg von der Einstellungs- zur Verhaltensänderung » Hürden auf dem Weg zu Open Access, Wissenswerkstatt, November 30, 2007.  (Thanks to Basic Thinking Blog.)  Read it in German or Google's English.  How academic conservativism is slowing the adoption of OA. 

Jean-Claude Guédon, Open Access and the divide between “mainstream” and “peripheral” science, a preprint forthcoming in Sueli Mara S.P. Ferreira and Maria das Graças Targino (eds.), Como gerir e qualificar revistas científicas, 2007 (in Portuguese).  The preprint is in English. 

Abstract:   Discusses the potential of open access to overcome the divide between the mainstream and the peripheral in science, including the divide between the developed and developing world. Specific open access implementation strategies are examined with respect to this role. For example, subsidized open access journals with no article processing fees, a common practice in many if not most of the world's countries, are helpful to overcoming the divide, as is a coherent system of institutional and thematic repositories.

Update. Also see Heather Morrison's comments on this article.

Chris Soghoian, AOL, Netflix and the end of open access to research data, Surveillance State, November 30, 2007. Excerpt:

Over the past year, there have been a number of high-profile incidents in which sensitive user data was accidentally revealed to the Internet at large. As a result, I believe that high-tech companies will never again share anonymized data on their users with academic researchers, at least not without requiring contracts and nondisclosure agreements. For the users and privacy advocates, this is probably a good thing. However, for researchers, the scientific community, and Internet users who want cool new technologies, this is almost certainly a change for the worse.

In 2006, Netflix released over 100 million movie ratings made by 500,000 subscribers to their online DVD rental service. The company then offered $1 million to anyone who could improve the company's system of DVD recommendation. In order to protect its customers' privacy, Netflix anonymized the data set by removing any personal details.

Researchers announced this week that they were able to de-anonymize the data, by comparing the Netflix data against publicly available ratings on the Internet Movie Database (IMDB). Whoops....

The same thing happened back in 2006 when AOL released the search records of 500,000 of its users. Within days of the database's release, journalists from the New York Times had revealed the identity of user number 4417749 to be Thelma Arnold, a 62-year-old widow from Lilburn, Ga. Over 300 of the woman's searches were traced back to her, ranging from "60 single men" to "dog that urinates on everything." ...

Comments

• In the Netflix case, the anonymized data could only be de-anonymized because researchers could leverage the independent, publicly-accessible ratings at IMDb, and they could only de-anonymize data for those Netflix users who had made a good number of ratings at both services.  In the case of AOL, researchers could leverage the user searchstrings, and could only get leverage when they had a good number of searchstrings from the same person.  So in both cases, they could only identify a subset of users, not all users.  (However, I agree that even this is a deplorable invasion of privacy.)
• Although the Netflix and AOL datasets show two different kinds of vulnerability, most datasets on human beings will show neither kind.  For example, anonymized data on medical patients could only be de-anonymized if researchers could go backwards from clusters of symptoms and treatments to individuals.  Neither the Netflix nor AOL episodes raises the risk of that. 
• I believe that Soghoian meant to limit his claim to data on users of web services, even though his headline goes well beyond that category.  I understand that headlines cannot capture every nuance of the articles they describe, and run into this problem with my own blog every day.  But I want to underscore the point about the larger world of open data in case someone draws the wrong conclusion.  In the research landscape at large, very few open datasets are about human beings at all, and even fewer are about users of online web services.  Even under the worst-case scenario in which all anonymized user data could be de-anonymized, the impact on open research data would be relatively small.

The UK DataShare Project has released a State-of-the-Art Review.  Although dated September, it was apparently released today.  Excerpt:

DataShare is a collaborative project led by the University of Edinburgh, with the University of Oxford, the London School of Economics (LSE) and the University of Southampton. Its central aim is to develop a model for the deposit of social science datasets in institutional repositories (IRs). Lyon (2007, p.45) notes that, whilst many institutions have developed IRs over the last few years to store and disseminate their published research outputs, “…there is currently no equivalent drive to manage primary data in a co-ordinated manner.”

As this review will show, although policies and practices currently operate to gather, store and preserve data, chiefly in national, subject-based data centres, much data remains unarchived and is at serious risk of being lost. DataShare believes that IRs may be developed to rescue some of this ‘orphaned data’ and make it available for future research, to the benefit of research communities and wider society....

Good news from Queensland University of Technology:

The Open Access to Knowledge (OAK) Law team led by Professor Brian Fitzgerald has received a Vice-Chancellor’s Award for Excellence in a ceremony held on 31 October, 2007 at Kelvin Grove. The Awards are offered annually to recognise exceptional performance of staff who demonstrate sustained and outstanding achievement in activities that are aligned to the University’s vision and goals....

PS:  Kudos to Fitzgerald and the rest of the OAK Law team!  (Disclaimer:  I'm on the OAK Law advisory group, which means I know enough to appreciate its work, but have much too little involvement to take any credit.)

Yesterday the European Parliament recommended compulsory licenses for "environmentally necessary technologies" in order make those technologies available to developing countries.  For details, see Section 9 of the Parliamentary resolution.  (Thanks to IP Watch.)

Comment.  Good move.  If A and B are in a lifeboat with leaks fore and aft, A in the bow has extra bailing cans, and B in the stern has none, then how much should A charge B for a can?  Now if you were sitting between them and the question were put to a vote....

The presentations from the IEEE Library Advisory Council Meeting (New York, October 26, 2007) are now online.  (Thanks to John Dupuis.)  See especially these four:

• Jens Vigen, Extracting Trends from an Emerging Publishing Market
• Catherine Forestier, IR and OA in France + INP Toulouse's Experience
• David Alsmeyer, Open Access Journals in the Telecoms Sector
• John Dupuis and Mike Buschman, Nature as an example of Web 2.0

MIT launches web site for high school students, MIT News, November 28, 2007.  Excerpt:

MIT President Susan Hockfield announces today the launch of a new web site, Highlights for High School, that will provide resources to improve science, technology, engineering and math (STEM) instruction at the high school level.

The web site builds on the success of MIT's revolutionary OpenCourseWare initiative and is designed to inspire the next generation of engineers and scientists and to be a valuable tool for high school teachers....

"Highlights for High School will provide students and teachers with innovative tools to supplement their math and science studies," she added. "We hope it will inspire students to reach beyond their required classwork to explore more advanced material through OCW and also might encourage them to pursue careers in science and engineering."

Highlights for High School features more than 2,600 video and audio clips, animations, lecture notes and assignments taken from actual MIT courses, and categorizes them to match the Advanced Placement physics, biology and calculus curricula. Demonstrations, simulations and animations give educators engaging ways to present STEM concepts, while videos illustrate MIT's hands-on approach to the teaching of these subjects....

Andrew Mowbary and three co-authors, Improving stability and performance of an international network of free access legal information systems, Journal of Law and Technology, November 2007.

Abstract:   High quality legal research must increasingly be global and comparative. This is hindered by the limited range of countries’ laws covered by the centralized systems of the multinational commercial legal publishers and by the costs of accessing their materials. Networking of online legal information by commercial legal publishers goes back to the 1970s. Over the last decade a global decentralised network of Legal Information Institutes (or LIIs) has emerged, providing free access to legal information which is comparable with and sometimes better than the commercial providers. Australia’s LII - AustLII, has been a lead player, and created and runs the World Legal Information Institute (WorldLII), the principal interface into the shared LII legal data.

The ad-hoc nature of the technical networking between the dozen existing LIIs means that the effective utilisation of this shared infrastructure has previously been sub-optimal and increasingly fragile. This has been exacerbated by the network’s constant expansion. This paper outlines an initiative funded by the Australian Research Council’s E-Research programme to address these problems by building a flexible generic set of tools to support and enhance access to WorldLII and more generally, any network of geographically distributed set of web-based systems.

Jim Downing has released "a stable version of the SPECTRa tools" which allow chemists to deposit data directly into an OA repository.  (Thanks to Peter Murray-Rust and Charles Bailey.)

"SPECTRa" stands for "Submission, Preservation and Exposure of Chemistry Teaching and Research Data."

At the Internet Governance Forum in Rio de Janeiro (November 12-15, 2007), Brazil and Italy agreed to draft an Internet Bill of Rights.  From the Italian announcement:

Privacy, data protection, freedom of expression, universal accessibility, network [neutrality], interoperability, use of format and open standards, free access to information and knowledge, right to innovation and a fair and competitive market and consumers safeguard.

On these principles the Internet Bill of Rights will have to be set up, an idea produced by our country and supported by the Italian delegation, led by the Communications’ Undersecretary, Luigi Vimercati....

Convened at the Forum liked the idea which roused also the Brazilian government members. So formally, Italy and Brazil endorsed a joint declaration committing themselves to reach as soon as possible a shared and planned resolution of network rights, a theme that, in the next 2008 Internet Governance Forum of New Delhi, will have to be prioritized. This paper was signed by Undersecretary Vimercati and the Brazilian Minister for Culture, Gilberto Gil. “We deem important to held an introductory meeting, to which invite everyone is interested”, said Vimercati....

Sara Forster, Sigma Xi Lecturer Explores Open-Notebook Science, The Daily Gazette, November 27, 2007.  Excerpt:

Jean-Claude Bradley of Drexel University came to Swarthmore College this Tuesday for a Sigma Xi Lecture on Open Notebook Science....

Bradley argued that as science moves toward being more open, computers and machines will be able to perform more of the scientific process itself without humans—and this might allow more science to be released in a public open format....

At Drexel, Bradley has what he calls an open lab. He started by blogging about everything he does there, and has solicited comments from peers in the scientific community to help him with his research. He now has a Wiki, called UsefulChem that has all the experiments his lab has conducted. It functions as his students’ lab notebook and has all their information so that outside scientists can see the entire process of the experiments.

This method has many advantages. In his lecture, Bradley said that because of his strategy, “I can share my raw data with the world.” When everything is public, he explained, nothing can get lost. Although some scientists are worried about getting scooped since anyone can see their work, Bradley argued that open-notebook research makes finding collaborators easier, allows exchange for discussing vendor reliability and hypotheses, and allows undergraduates to see real research in action.

The Journal of Trauma Management & Outcomes is a new peer-reviewed OA journal BioMed Central.  From the BMC blog:

...The journal considers articles on all aspects of trauma research, with a focus on interventions demonstrating efficacy and effectiveness in improving clinically relevant outcomes for severely injured patients such as mortality, morbidity, quality of life, function, and costs....

Vikas Anand has launched Vikas PSOAR, a Google Coop search engine for "pharmaceutical sciences open access resources" (PSOAR).  From the FAQ:

[Vikas PSOAR is] a custom search engine tailored to explore the internet for scholarly literature (articles, thesis and drug information) in the fields of pharmaceutics, pharmacognosy, analysis, chemistry, biotechnology, microbiology, bioinformatics, pharmacology, toxicology, pathology, physiology, and multidisciplinary pharmaceutical sciences....

The Cape Town Open Education Declaration will officially launch in mid-January.  But it made a soft launch today in order to gather pre-launch signatures.  If you or your institution is committed to open education, please consider signing the declaration before it launches.

The Cape Town Declaration aims to unify and accelerate the open education movement, roughly as the Budapest Open Access initiative did for open access.  The text and FAQ are provisional until January.  Read them closely and send the drafters your feedback.  Meantime, here's an excerpt from the text:

We are on the cusp of a global revolution in teaching and learning. Educators worldwide are developing a vast pool of educational resources on the Internet, open and free for all to use. These educators are creating a world where each and every person on earth can access and contribute to the sum of all human knowledge. They are also planting the seeds of a new pedagogy where educators and learners create, shape and evolve knowledge together, deepening their skills and understanding as they go.

This emerging open education movement combines the established tradition of sharing good ideas with fellow educators and the collaborative, interactive culture of the Internet. It is built on the belief that everyone should have the freedom to use, customize, improve and redistribute educational resources without constraint. Educators, learners and others who share this belief are gathering together as part of a worldwide effort to make education both more accessible and more effective....

The expanding global collection of open educational resources has created fertile ground for this effort. These resources include openly licensed course materials, lesson plans, textbooks, games, software and other materials that support teaching and learning....

However, open education is not limited to just open educational resources. It also draws upon open technologies that facilitate collaborative, flexible learning and the open sharing of teaching practices that empower educators to benefit from the best ideas of their colleagues....

PS:  For earlier previews of the declaration, see my past blog posts on it.

Pitt’s Libraries and University Press Collaborate on Open Access to Press Titles, a press release from the University of Pittsburgh, November 29, 2007.  Excerpt:

The University of Pittsburgh’s University Library System (ULS) and University Press have formed a partnership to provide digital editions of press titles as part of the library system’s D-Scribe Digital Publishing Program.  Thirty-nine books from the Pitt Latin American Series published by the University of Pittsburgh Press are now available online, freely accessible to scholars and students worldwide.  Ultimately, most of the Press’ titles older than 2 years will be provided through this open access platform.

For the past decade, the University Library System has been building digital collections on the Web under its D-Scribe Digital Publishing Program....

The D-Scribe Digital Publishing Program includes digitized materials drawn from Pitt collections and those of other libraries and cultural institutions in the region, pre-print repositories in several disciplines, the University’s mandatory electronic theses and dissertations program, and electronic journals during the past eight years, sixty separate collections have been digitized and made freely accessible via the World Wide Web....The D-Scribe collections are accessible free-of-charge on the World Wide Web....

More titles will be added to the University of Pittsburgh Press Digital Editions each month until most of the current scholarly books published by the Press are available both in print and as digital editions....

Comment.  Kudos to Pitt.  This is a model for other university presses and institutional repositories.  If a press is nervous about publishing dual (OA and non-OA) editions of new books, it could emulate the Pitt model:  start with a non-OA edition and after two years add the OA edition.  If an institutional repository is reaching out to different parts of campus for content, it could emulate the Pitt model:  offer to host OA editions of backlist titles from the university press. 

Update.  Also see the article in today's Library Journal Academic Newswire.  Excerpt: 

In an ambitious expansion of its existing D-Scribe program, the University of Pittsburgh University Library System (ULS) and the University of Pittsburgh Press (UPP) have announced a partnership that will eventually offer open access to digital editions of the press's entire backlist. The partnership kicks off with 39 books from the Pitt Latin American Series, now available online and freely accessible to scholars and students worldwide.

"The goal of our collaboration is to digitize and make available all, or almost all, of the UP Press backlist and then to continue to place online all imprints after two years," Pitt director of libraries Rush Miller told the LJ Academic Newswire. "In other words, the press will continue to produce the hard copy and sell it for two years," he explained, "then the title goes open access via D-Scribe." ...

The press currently has about 500 backlist titles.

While many university presses have looked warily upon open access, Pitt's commitment represents a significant partnership between libraries and presses. UPP director Cynthia Miller (no relation) is "a cautious supporter" of open access, Miller noted. "We have been in discussions for several years about this type of project. She does not believe that this arrangement with us will cut into her initial sales," he explained, adding that the UP Press has largely moved to print on demand for its older titles. "This is just another step." ...

The Charleston Advisor's Seventh Annual Readers’ Choice Awards are now public.  Some highlights:

Best Content.  Google Book Search –– This project has seen unprecedented expansion as Google has added a great number of new libraries including many outside of the United States. “By the pound,” this is one of the most ambitious digitization projects ever done....

Best Pricing.  NYTimes.com –– The free Web version of the New York Times and its backfile represents one of the best opportunities on the Web. The addition of video, podcasts, and other features shows how newspapers can transform themselves.

Lemon Award.  PRISM (The Partnership for Research Integrity in Science and Medicine) –– The Association of American Publishers (AAP) has announced a partnership to oppose efforts to put publicly funded research in the public domain. They oppose “the risks of proposed government interference with the scholarly communication process.” These publishers should not bite the hand that feeds them....

Electronic Information for Libraries (eIFL) has joined the membership program of the Directory of Open Access Journals (DOAJ).

The University of Maryland has launched an institutional repository.  From this week's announcement:

...This release marks two and a half years of work in the creation of a repository that serves the teaching and research mission of the University of Maryland Libraries. Many of the objects are digital versions from Maryland's Special Collections (such as A Treasury of World's Fairs Art and Architecture) or are new virtual collections (The Jim Henson Works). Other collections (such as Films@UM) support the teaching mission of the Libraries. This release also marks the integration of electronically available finding aids, ArchivesUM, into the repository architecture, creating a framework for digital objects to be dynamically discovered from finding aids.

The repository is based on the Fedora platform, uses Lucene for indexing, and Helix for streaming video. The repository features almost 2500 digital objects, with new objects added monthly. Object types currently delivered include full text (both TEI and EAD), video, and images. Objects can be discovered within a collection context or via a search across multiple collections. Cross-collection discovery is achieved through a common metadata scheme and controlled vocabulary. This metadata scheme also provides for individual collections to have more granular domain-specific metadata.

We welcome feedback and comments [here].

Ian Gallacher, Aux Armes, Citoyens!:' Time for Law Schools to Lead the Movement for Free and Open Access to the Law, a preprint self-archived November 28, 2007.  Gallacher teaches at the Syracuse University College of Law.  (Thanks to Lawrence Solum.)

Abstract:   This article is a manifesto that outlines the principles of the open access to legal information movement and sounds a call to action for law schools to become leaders in that movement. The article surveys the present legal information environment, reviews the development of computer-assisted legal information and the long-term future of book-based legal research, and discusses the problems inherent in a system where two large 'information resource' corporations control access to legal information. After considering the need for open access to the law for pro se litigants, scholars from outside the legal academy, and practicing lawyers, after considering and rejecting courts and legislators as viable guarantors of open access, and with the model of the clinical legal community's tradition of engaged scholarship as an example, the article concludes that America's law schools have both the opportunity and obligation to provide an alternative to the commercial legal information sites and make America's law freely available to all. The article ends with a series of proposed principles that might guide such an open-access legal information site.

From the body of the paper:

The bedrock principle of an open access legal information site is that it be free and accessible to everyone, not just those who have a professional interest in the information, who live in this country, or who can afford to pay for it: access to American legal information should not be limited by economic status, geographical location, or any other barriers....

Yet for all the innovation and change that has occurred, the internet has not changed the way in which legal information is made available, and American legal information is still the hostage of commercial interests. The large commercial vendors are being challenged by smaller upstart companies offering services like Fastcase and Versuslaw, but they are really only offering alternative versions of the same thing; the law is still being treated as a commodity to be bundled, sold, and profited from rather than being offered free to the citizenry that has already paid once for it through taxation....

Heather Morrison, DOAJ: 80 new titles in the last 30 days, Imaginary Journal of Poetic Economics, November 28, 2007.  Excerpt:

...As of today, November 28, 2007, the Directory of Open Access Journals (DOAJ) has added 80 new titles in the last 30 days. That's an average of 2.67 per calendar day!

While some journals appear to be new, a number have start years going back as far as 1992, indicating a mix of new journals and OA conversions. Only 4 of these titles are from Bentham Open. Bentham Open is a new open access publisher, with plans to launch over 300 OA journals in the coming year, so clearly DOAJ staff have their work cut out for them!

This post is part of the Dramatic Growth of Open Access Series.

DOAJ has already added 451 titles in 2007 so far, for an average growth rate of a minimum of 1.24 titles per calendar day - and a month to go! This is not only a healthy growth rate; it's a healthy, increasing growth rate. For the full story of 2007, watch for year-end numbers!

Antony Williams, The Entire ChemSpider Database is On Its Way to PubChem! ChemSpider Blog, November 28, 2007.  Excerpt:

I have blogged previously about the fact that we are willing to share the entire ChemSpider structure collection with anyone who wants it. Specifically PubChem are willing to accept it..and YES, I have pointed out that they will be receiving back their own structure collection too since we deposited it on ChemSpider.

What’s the value of redepositing the same structures to PubChem? There are actually many - structures on PubChem connected out to ChemSpider will now be connected to Patents, those structures will be connected to analytical data, they will be connected to additional identifiers not available on PubChem, they will be connected to curated identifiers (compare the list of names for methane on PubChem versus ChemSpider), they will be connected to Supplementary Data, and they will be connected to additional predicted properties. So, there is actually a LOT of value in having the links back to ChemSpider from PubChem.

Our best estimate is that there will be about 8 million new structures finding their way to PubChem from ChemSpider.

Now, I was close to thinking that we could declare that the ChemSpider structure collection was Open Data. I’ve posted about Open Data and it’s definitions and challenges previously (1,2). PMR , one of the primary evangelists of Open Data and its definitions is continuing to refine the definitions of Open Data....

Linda Quattrin has blogged some notes on a discussion of OA at the University of Toronto.  Excerpt:

What lies ahead for patients and practitioners as the world of information technology converges ever deeply with the art and science of medicine and research?

That was among the questions informing a lively conversation last week between Dr. John Hoey, former editor-in-chief of the Canadian Medical Association Journal, and Dr. Richard Smith, former editor-in-chief of the British Medical Journal and author of The Trouble with Medical Journals (2006).

The discussion, held at U of T’s Trinity College, was the prelude to a fundraiser for Open Medicine, an open-access peer-reviewed journal that is itself part of a social movement to ensure access to scientific knowledge is free and content is widely disseminated...

A long-time advocate of open-access medical publishing – the BMJ first posted its content free online for non-British users nearly a decade ago – Smith offered a range of sacred-cow tipping opinions, delivered with classic Brit candor and self-deprecating irreverence, on the evolution of medical publishing, the influence of Web 2.0 and the challenge of finding sustainable financial models for open-access journals.

Would the author-pays model of Public Library of Science (where he is an unpaid board member) hold if the venerable Nature and Science journals charged, say, $10,000+ a paper? (Smith thinks so, although in my non-academic view such steep fees would seem to set the bar precipitously high for a new investigator still building grant-writing prowess or an institution with lighter pocketbooks.)

If a journal’s research is freely available, should it charge instead for the premium analysis or opinion pieces it offers?...Are Google-informed patients starting to level the informational playing field and subsequent power balance by forcing doctors to more openly acknowledge the current limits of medical practice? ...

Tom Tivnan, EU open access push, Bookseller.com, November 28, 2007.  Excerpt:

The European Union has moved towards recommending wider open access publishing, a move hailed as a "step in the right direction" by open access campaigners but provoking concern among publishers. The Council of the EU released a report last week inviting member states to support various open access options including delayed open access journals and research into how scientific information is accessed. According to EU statistics, member states account for 43% of the world’s scientific research.

David Prosser, director of the Scholarly Publishing and Academic Resources Coalition (SPARC) Europe, said: "The recommendations could have been stronger but this is a good next step. The really important thing is that this is the first time we have seen actual political support in the EU for open access."

The EU is pushing for a "mandated" open access model to ensure that all publicly funded research is freely available. Some learned societies, such as the Wellcome Trust, already fund mandated OA so that journals can be both peer reviewed and freely available. But publishers are concerned the EU is pushing for an unfunded mandate with delayed open access, where access to journals is exclusive through the publishers for a period of time, after which the articles become completely open access.

Stephen Barr, m.d. of Sage Publications, said there has been an "unwillingness" from the EU to consider funded open access. He added: "Publishers generally believe that it [unfunded open access] will cause damage to the existing business model and may over time destroy the economic basis of many journals."

While publishers are wary, some open access campaigners believe the EU's recommendations do not go far enough. Prominent open access campaigner Peter Suber called the report "weak tea". He said: "It takes the problem seriously, as well as the opportunity and the previous studies and recommendations. But it stops far short of the near-consensus recommendation for an open access mandate for publicly-funded research."

Launch of European digital library "on track", a press release from the European Commission, November 29, 2007.  Excerpt:

On 27th November, a high level group on digital libraries met Commission officials in Brussels to discuss progress towards launching the European digital library. A European digital library foundation has recently been created. This formalises the agreement of European archives, museums, audiovisual archives and libraries to work together and to provide a common access point to Europe's cultural heritage online.

“Europe's citizens should all be able to enjoy our rich cultural heritage. This foundation is a significant step towards making that ambition come true," commented Information Society and Media Commissioner Viviane Reding. "It shows the commitment of Europe's cultural institutions to work together and make their collections available and searchable to the wide public through a common and multilingual access point online." ...

Europe's cultural institutions plan to launch a prototype of the European digital library in November 2008....

For a steady growth of the European digital library, two key issues need to be tackled: the financing of digitisation and solutions for making copyrighted works searchable through the European digital library. In its meeting the high level group discussed:

• new ways for funding digitisation through public private partnerships;
• solutions for mass-digitisation of out of print works and orphan works (for which it is very difficult to locate the rightholders). By June next year the group should find an agreement on dealing with orphan works (including criteria for searching for rightholders);
• the issue of access to and preservation of scientific information (see IP/07/190). Scientific publishers, libraries and scientists confirmed their intention to work together in an experiment with open access to scientific publications after an embargo period.

David Beaver and Kai von Fintel, Semantics and Pragmatics - A New Journal, Semantics and Pragmatics, vol. 0 (2007).  Editorial in the inaugural issue of a new OA journal.  Excerpt:

...Our field, like most of academia, has a long history of interdependence with big commercial publishers. The need to make a profit forces these publishers to limit circulation to those who can pay a hefty subscription, mostly libraries in large academic institutions in first world nations. But, the world has changed rather dramatically....

[I]n the internet age, most of the distribution infrastructure we need has been paid for by others. At a low cost (which we can bear without charging readers) we can make everything we publish in our journal permanently accessible within minutes at any hour of any day to a billion or more people....

Thus it seems to us that a move to open access, electronically distributed noncommercial journals is inevitable. Overdue, even....

We should note that open access journals such as S&P are the second step in a hoped for open access revolution. The first step, which we urge all authors that publish their work in non-open-access journals to take, is to deposit “postprints” (the final manuscript version of an article after peer review and revisions) in open access archives and/or on the author’s or their institution’s website. This is commonly called “Green Open Access” and is within reach for virtually all of the output of our field, since even commercial publishers will grant authors the right to deposit the postprint on the web (some even do this routinely in their standard authors’ agreement now, and some even allow the author to put the journal’s final pdf version of the article on the web). If the standard author agreement does not include this right, we encourage authors to see whether they can amend the agreement to include that right; standard tools for adding such amendments are easily available on the web.

With journals like S&P, this process of freely distributing the results of scientific research is made even smoother. Open access is a central part of the journal’s mission. Advocates of open access call this “Gold Open Access”. In fact,...S&P is a “platinum open access” journal, which does not levy any kind of author charge. It is entirely free for authors and for readers. This is made possible by a support structure consisting of multiple institutions:

• Infrastructure and technical support provided by the Linguistic Society of America under its eLanguage initiative.
• Free and open source software available without cost, especially the OJS journal management software and the LATEX typesetting system.
• Start-up funding (and a small amount of continuing funds) provided by the MIT Library, the MIT Department of Linguistics and Philosophy, the MIT School of Humanities, Arts, and Social Sciences, and the University of Texas at Austin.
• The usual pro bono work of academics in writing, reviewing, and editing research articles....

The Albert Einstein Science Park library serves three research institutions specializing in the Earth sciences.  It recently launched a search engine which covers the library's digital holdings, the institutional repository for GeoForschungsZentrum Potdam, and 30,000 OA resources on Earth science worldwide.  For details, see Roland Bertelmann's announcement on SOAF.

The three research institutions served by the library are GeoForschungsZentrum Potsdam (the German National Research Center for Geosciences), the Potsdam Institute for Climate Impact Research, and the Research Unit Potsdam of the Alfred Wegener Institute für Polar and Marine Research.

The newly elected President of the American Fisheries Society, Mary Fabrizio, plans to launch the society's first OA journal.  From yesterday's announcement of her election:

...Fabrizio will also promote a continued shift toward electronic communication of AFS findings, including creation of an open-access electronic journal in coastal and marine fisheries. AFS already publishes several leading peer-reviewed print journals, including Transactions of the American Fisheries Society, North American Journal of Fisheries Management, North American Journal of Aquaculture, and the Journal of Aquatic Animal Health.

Digital communications, writes Fabrizio, can "deliver fisheries information to professionals working in remote areas or in parts of the world where one of the few links to science-based information is through the Internet. Such information strengthens the knowledge base upon which we manage our resources." ...

Eve Gray has blogged some notes on the SARUA Open Access Leadership Summit (Gaborone, Botswana, November 20-21, 2007).  Excerpt:

On the second day of the Southern African Regional Universities Association (SARUA) Open Access conference last week, the penny suddenly dropped. From the start, the signs were good – the conference...was, after all, focused on open access. The Chair of SARUA, Professor Njabulo Ndebele of the University of Cape Town, the Botswana Minister of Education, J D Nkate and the CEO of SARUA, Piyushi Kotecha, opened the conference with strong statements on the value of Open Access in their respective constituencies. This is echoed on the SARUA website which, unusually for a university association site, acknowledges the importance of dissemination as a core value and makes a clear statement of its commitment to Open Access both as one of its programme areas and as a core principle, as well as its policy for its own communications. The central statement is perhaps this:

Promoting Open Access for increased quality research, enhanced collaboration, and the sharing and dissemination of knowledge, is a central principle for SARUA’s work. The Association is already engaging with groups and networks of expertise and good practice locally and globally in order to support the development of Open Access benefits for HE.

At the conference, the comments of these opening speakers did not therefore appear to be glib statements of openness as a worthy value, but seemed firmly embedded in a recognition of the need to create equity for the developing world in its contribution to global knowledge. What emerged, particularly from Piyushi Kotecha, was a vision which could move SARUA universities on from the current post-colonial reliance on the North for standards for research competence, to a situation in which they could promote their own competence as knowledge producers. As Alma Swan commented later in the proceedings, she thought that, with hindsight, the Open Access movement should perhaps have named itself Open Dissemination, to get away from the implicit dependence on access to knowledge from the North-West that can sometimes emerge in development-speak. And it goes further than Open Access alone....

More connections emerged as Johannes Britz, echoing what Amanda Barrett had said, spoke of the importance of education as a human freedom, citing the unhappy statistics of education and research on the continent. He charted the difference between the old information world in which richness had to be sacrificed for the sake of wide reach and the new digital paradigms in which we can combine reach and richness. However, 80% of the world lives, he said, where infrastructure is lacking for unbundled,digital information and education is therefore dependent on physical objects such as books. He brought this down to a moral issue – the bread principle, as he called it. If we can make information and distribute it for a very marginal cost, then we have a new economic model that could serve those deprived of access to education. This is a moral imperative, but IP gets in the way. What also gets in the way is the excessively high cost of telecommunications in countries like South Africa and many other African countries. This means, he said, that the moral agenda becomes a money agenda. The bottom line, he argued, is that access to information is a basic human right and information infrastructure is fundamental to making access work.

It all came together just after Derek Keats, of the University of the Western Cape, had talked about the ways in which web 3.0 could break out of the narrower confines on university walls and the covers of books, offering abundance rather than the limitations of a physical environment....

This all suggests that in the context of higher education in southern Africa, open access, combined with innovative use of mobile technology and a recognition of the transformative potential of social networking, offers considerable potential to move research and teaching away from anachronistic hierarchical and locked-in models inherited from the colonial era. Open access can therefore mean not only improved research communications and a greater global contribution by African research, but the use of open education and social networking might offer great potential in under-resourced countries to provide access for greater numbers of students to a well-supported, relevant and effective higher education system.

PS:  Also see the conference program, now online.

Stevan Harnad, Administrative Keystroke Mandates To Record Research Output Can Serve As Open Access Mandates Too, Open Access Archivangelism, November 28, 2007.

There is no need to keep waiting for governmental OA mandates.

Harnad, Stevan (2005) The OA Policy of Southampton University (ECS), UK: the "Keystroke" Strategy [Putting the Berlin Principle into Practice: the Southampton Keystroke Policy] . Delivered at Berlin 3 Open Access: Progress in Implementing the Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities, University of Southampton (UK).

University OA mandates are natural extensions of universities' existing record-keeping, asset management, and performance-assessment policies. They complement research-funder OA mandates, and are the most efficient and productive way to monitor and credit compliance and fulfillment for both. Australia's Arthur Sale has done the most work on this. Please read what he has to say:

Arthur Sale wrote in the American Scientist Open Access Forum:

The evidence is quite clear that advocacy does not work by itself, and never has worked anywhere. To repeat the bleeding obvious once again: depositing in repositories is avoidable work under a voluntary regime, and like all avoidable work it will be avoided by most academics, even if perceived to be in their best interests, and even if the work is minor. The work needs to be (a) required and (b) integrated into the work pattern of researchers, so it becomes the norm. This is the purpose of mandates - to make it clear to researchers that they are expected to do this work.

My research and published papers show that mandates do work, and they take a couple of years for the message to sink in. Enforcement need only be a light touch - reporting to heads of departments for example. (See references below.) ...

Peter Lewis, Copyright Abuse, Significant Figures, November 28, 2007.  (Thanks to David Bradley.)  Excerpt:

...I first came across the problem of copyright abuse by numerous commercial image databanks, in 2004. At the time, I was writing my book on the Tay Bridge disaster (Tempus 2004). My reanalysis of the disaster...involved systematic examination of the many high quality photos taken for the Official Inquiry of 1880. We asked Dundee City Library and St Andrews University Library to make high resolution scans, which my university paid for in the usual way. When I produced my book, however, St Andrews protested that I had wrongly used their images, despite the fact the images dated from 1879 and earlier and were clearly out-of-copyright. They eventually backed down but they, and many others, seem to think that if they posses an old image, they possess the copyright forever....

Worse still, modern image companies such as Getty and the UK’s Science Museum/NRM possess public domain images which they have scanned from original periodicals such as the Illustrated London News, and claim new copyright in those images. I protested to the Science Museum about their policy, and was told that "it was too difficult to remove the copyright watermark for one or two images"!

Another example occurred more recently when we were designing new covers for one of our teaching blocks. It was a book about intellectual property, and the designer had used an old image from a US Patent which he had found in a commercial image library. They wanted to charge £600 (about $1200). I pointed out to the designer that the image was in the public domain and could be downloaded for free from the US Patent Office website, and so we saved the money. Many designers and others are apparently totally unaware of this scam, and will happily pay large sums for public domain images when they can be obtained for free. One irony in this case was that the quality of the US Patent Office image was much better than that offered commercially....

The National Museum of Natural History in the Netherlands has launched the Naturalis Digital Academic Repository, an OA repository for Naturalis publications.  (Thanks to Klaus Graf.)  From the site:

The Digital Academic Repository of Naturalis is a service which is part of a national and international network of scientific and scholarly information services. In the Naturalis repository, the scientific staff of Naturalis stores the electronic version of its publications for future use. The repository also makes sure that references to the publications become available within a international network of information services, hereby increasing the visibility of the publications.

Also see the November 20 press release (in Dutch).

Online library gives readers access to 1.5 million books, a press release from Carnegie Mellon University, November 27, 2007.  Excerpt:

The Million Book Project, an international venture led by Carnegie Mellon University in the United States, Zhejiang University in China, the Indian Institute of Science in India and the Library at Alexandria in Egypt, has completed the digitization of more than 1.5 million books, which are now available online.

For the first time since the project was initiated in 2002, all of the books...are available through a single Web portal of the Universal Library, said Gloriana St. Clair, Carnegie Mellon’s dean of libraries.

“Anyone who can get on the Internet now has access to a collection of books the size of a large university library,” said Raj Reddy, professor of computer science and robotics at Carnegie Mellon. “This project brings us closer to the ideal of the Universal Library: making all published works available to anyone, anytime, in any language. The economic barriers to the distribution of knowledge are falling,” said Reddy, who has spearheaded the Million Book Project.

Though Google, Microsoft and the Internet Archive all have launched major book digitization projects, the Million Book Project represents the world’s largest, university-based digital library of freely accessible books. At least half of its books are out of copyright, or were digitized with the permission of the copyright holders, so the complete texts are or eventually will be available free.

The collection includes a large number of rare and orphan books. More than 20 languages are represented among the 1.5 million books, a little more than 1 percent of all of the world’s books.

Many of the books, particularly those in Chinese and English, have been digitized — their text converted by optical character recognition methods into computer readable text. That allows these books to be searched and, eventually, reformatted for access by PDAs and other devices.

An outgrowth of Reddy’s Universal Library, the Million Book Project received $3.5 million in seed funding from the National Science Foundation and substantial in-kind contributions from hardware and software manufacturers....The U.S., China and India provided $10 million each in cash and in-kind contributions to the project. More recently, the Library at Alexandria, Egypt, has joined the effort....

Though the long-term goal of the Universal Library is to make books, artwork and other published works available online for free, about half of the current collection remains under copyright. Until the permission of the copyright holders can be documented, or copyright laws are amended, only 10 percent or less of those books can be accessed at no cost.

The project has surpassed one million books, but the participants are looking to expand to all countries and eventually every language....

PS:  Also see the project Progress Report (last updated November 24, 2007).

Update.  Also see the profile of Raj Reddy in the November 30 issue of INDOLink.

BioMed Central upgraded its Open Repository service.  From today's announcement:

BioMed Central today announced the latest upgrades to Open Repository, the open access publisher's hosted repository solution.  The upgrades include new features from DSpace, the open-source platform for accessing, managing, and preserving scholarly works.  Open Repository now offers institutions increased customization options and a new and improved user interface.  Also, two prestigious organizations have recently elected to host their repositories on Open Repository: Roehampton University and Medecins Sans Frontieres, demonstrating that Open Repository is the first choice for a wide variety of organizations....

Open Repository version 1.4.9 has several new features that are designed to enhance the customer experience.  The release offers an improved user interface, making it easier for customers to browse and submit their material online.  Additionally, institutions can convert their Word, Excel, PowerPoint, Text and RTF documents to PDF format.  Customers can also set up RSS feeds, and customize lists and search fields, adding value to the already robust platform.

"Open Repository provides a hosted solution that is quick and simple to set up, customizable to our needs and easy to use," said Pat Simons, Bibliographic and Technical Services Manager, Roehampton University. "We switched from Proquest's repository service because Open Repository offered better value for money and all the features we plan to use...."

Open Repository from BioMed Central gives institutions the personalization of an in-house repository at a fraction of the cost....

The November issue of the Journal of Digital Imaging is devoted to free and open source imaging software, and all the articles in the issue are free online. JDI is published by Springer.  (Thanks to PowderMonkey.)

Update. When I first posted this note, I used the wrong URL in my link to the journal. I've now fixed it. If you tried it when the link was broken, please try again --and blame the initial mistake on me, not Springer.

Free O’Data: Ireland makes (some) data free, Free Our Data: the blog, November 26, 2007.  Excerpt:

...Ireland’s geographical agency, the GSI, has made a number of its datasets about boreholes available for free online.

Announced by the minister, the web page itself is a bit spartan: “Minister Ryan launches Spatial Data Projects to allow free online access to Departmental data. GSI, along with PAD, EMD and Engineering Divisions of DCENR, all contributed data to these series of web map viewers, data download pages and GIS web services. Click on www.dcenr.gov.ie/spatial+pages [Note: this isn’t a valid page, or at least not to me on my Mac] or http://www.gsi.ie/mapping for further details.” ...

An interesting contrast with the Environment Agency for England and Wales, which as we pointed out in May, is trying to charge people for details about water extraction locations....

NKC for online educational resources to promote higher education, India EduNews, November 27, 2007.  Excerpt:

In a recent letter to the Prime Minister Dr. Manmohan Singh, the National Knowledge Commission [NKC] Chairman Mr. Sam Pitroda has suggested that India should use the broadband internet connectivity to spread high quality educational resources throughout the globe.

The NKC chairman states that, "One of the most effective ways of creating knowledge economy in the country is to stimulate the development and dissemination of quality open access materials and open educational resources through broadband internet connectivity." ...

Among other recommendations, the NKC suggests that all research articles published by Indian authors who receive financial assistance from the government should be available under the open access format. The government should also invest in the digitization of books and journals, which are outside copyright protection....

The suggestions made by Mr Pitroda have been welcomed by several intellectuals and academicians of the country....

Alfred Hero, Opening Access, Signal Processing Magazine, September 2007 (accessible only to subscribers).  Hero is the President of the IEEE Signal Processing Society (SPS).  Excerpt:

...[O]pen access to electronic media has become prevalent. This is particularly true in the biological and physical sciences where, in some subdisciplines, a veritable open access movement has taken hold. Some learned societies have responded to this movement by making at least a portion of their publications open access. Others have preferred to stay on the sidelines, waiting to see how things shake out. The stakes for an organization like the IEEE SPS are high.

What are the stakes? Our journals are among the most highly ranked in the discipline —for example, in past years, our IEEE Signal Processing Magazine and (cosponsored) IEEE Transactions on Medical Imaging have been ranked number one in impact factor among all IEEE publications. Thus, we benefit from significant download activity within our journals on IEEE Xplore. A large part of Society income is derived from fees collected from these downloads. Loss of this income could affect the Society’s operations and our ability to invest in worthy causes and initiatives. On the other hand, if the
Society provided open access to our publications, it would potentially broaden the readership. This could translate into more citations, higher impact factors, and higher visibility. But at what cost?

It costs the Society several thousands of dollars to publish a typical article....Except for IEEE Signal Processing Magazine, which is partially supported by advertiser revenues, annual subscription income and Xplore download revenues have covered the full cost. A sustainable open access system would require a different financial model.

I know of three financial models that have been proposed for electronic open access, yet each has drawbacks, and none are provably sustainable. The author-pays model requires authors to pay all publication costs, shutting out those of insufficient means. The advertiser- pays model depends on “double-click” income, e.g., from pop-up ads on the Web server, a level of commercial intrusion that might be unsavory for some readers. The sponsor-pays model requires the cost of publication to come out of research grants to the author or foundation grants to the publisher, but few sponsors are willing to pay the full costs. A few for-profit publishers have adopted the author-pays model. Several not-for-profit organizations, such as the ArXiv, have adopted the sponsor-pays model. Other not-for-profit publishers have chosen the middle ground of limited open access: access to recent journal issues is restricted to paid subscribers while back issues are available as open access. The IEEE has begun experimenting with limited open access; selected articles in current issues of IEEE Spectrum are freely accessible.

While the IEEE SPS currently has no limited or unlimited open access journals, we are open access friendly. In the spirit of motivating reproducible research, authors of papers in our journals are encouraged to post open access electronic reprints and other supporting materials on their personal Web sites. When our new IEEE SPS Web pages come online in the next few months, you will see several open access features there. For example, the IEEE SPS e-newsletter will be publicly accessible there. Other open access features are being considered. As usual, I welcome your suggestions.

Comments

• First I commend IEEE SPS for its bright green policy --not just permitting author self-archiving, but actively encouraging it. 
• I also commend it for thinking about gold OA, and for doing so in public.  I appreciate that Hero recognizes three business models for OA journals, not just one (author-side publication fees).  But in fact there are more than three.  As I put it an article last year:  "Some no-fee OA journals have direct or indirect subsidies from institutions like universities, laboratories, research centers, libraries, hospitals, museums, learned societies, foundations, or government agencies.  Some have revenue from a separate line of non-OA publications.  Some have revenue from advertising, auxiliary services, membership dues, endowments, reprints, or a print or premium edition.  Some rely, more than other journals, on volunteerism.  Some undoubtedly use a combination of these means.  But we don't know how many other sources of revenue might be missing from this short list...."
• Hero is right that OA "would potentially broaden the readership [which]...could translate into more citations, higher impact factors, and higher visibility."  But it would do more:  it would accelerate research on signal processing. 

Elsevier announces launch of 2collab, new research 2.0 platform, a press release from Elsevier, November 27, 2007.  Excerpt

Elsevier, the world's leading publisher of science, technology and medical (STM) information, today announced the official launch of 2collab, a free online platform for scientific collaboration....

2collab allows researchers to add, share and rate bookmarks, tag resources, and to add comments and create topical groups. Each user is encouraged to create a personal profile, which everyone can view to ensure the authenticity of fellow users. This creates an accessible environment where specialists can work together on evaluating new research, discussing current controversies and opportunities as well as providing a place for first-time authors to promote their research....

New open access proceedings service supports earth and environmental science conferences, a press release from the Institute of Physics, November 22, 2007.  (Thanks to KnowledgeSpeak.)

Monday 19 November 2007 saw the launch of IOP Conference Proceedings: Earth and Environmental Science (EES) a fast, efficient and low-cost open access proceedings service dedicated to conferences specializing in the earth and environmental science disciplines.

Based on IOP Publishing’s highly successful open access proceedings in physics, EES allows conference organizers to create a comprehensive record of their event and make a valuable contribution to the open access literature that will be of long-lasting benefit to their research communities.

As part of the service’s launch, EES is waiving a total of US$5000 of publication fees for a number of conferences who expect to publish their proceedings during 2008....

We are delighted to announce that the first conference to qualify for this is the 14th International Symposium for the Advancement of Boundary Layer Remote Sensing (ISARS2008) which takes place on 23–25 June 2008, Risø National Laboratory, DTU, Roskilde, Denmark....

Visit IOP Conference Proceedings: Earth and Environmental Science to find out more about publishing your proceedings.

Žiga Turk, Council on Scientific Information in the Digital Age: Too Little Too Late, Growth, jobs and more, November 27, 2007.  Turk is the Slovenian minister for growth.  Excerpt:

I have been involved in publishing on the World-Wide-Web since 1992 and with scholarly publishing since 1995, also as a co-editor of a peer-reviewed journal ITcon and a coordinator of a framework program SciX, that was studying the topic in depth.

The bottom line is that in the scientific publishing process there is a decreasing value added by the publishers. The research is funded by the governments or the industry, performed by the researchers, papers are written and reviewed by them for free, only at the very end a publisher comes along that takes over the copyright, publishes the work and sells the journal at great expense to the community that created and edited the content for free.

At the Competitiveness (Internal market, Industry and Research) Council meeting in Brussels, on 22 and 23 November 2007 a conclusion has been reached on scientific information in the digital age: access, dissemination and preservation....

The Council underlines

the importance of scientific output resulting from publicly funded research being available on the Internet at no cost to the reader under economically viable circumstances, including delayed open access;

Why just no cost to the reader. Why only delayed open access. This section should underline "the importance of scientific output resulting from publicly funded research being available on the Internet at no cost under economically viable circumstances, including open access"....

Rather than making a clear statement that results of EU funded research should be published using open access paradigm, the suggestion to the commission is quite watered down:

experiment with open access to scientific data and publications resulting from projects funded by the EU Research Framework Programmes in order to assess the appropriateness of adopting specific contractual requirements;

Experiment ... in order to assess the appropriateness of adopting specific contractual requirements. Now this is a good example of the Brussels parlance! ...

In all, its good to see the Council take interest in open access publishing. However, one can clearly feel that someone managed to dilute a potentially powerful documents. As it stands it hardly brings anything new. Most of the other actions suggested, such as "debating", "experimenting", "exploring", "bringing together stakeholders" are either long overdue or have been done already.

In the context of the Lisbon strategy that should be driving Europe towards a knowledge based economy, one should note that the explosion of the internet based technologies in the US have been made possible by the (1) open access to software, (2) open standards and (3) freely available scientific articles on the subject. The cited document brings nothing like that to Europe.

Update (11/29/07). Also see the EurActiv article on Turk's assessment of the Council conclusions.

Update (12/6/07). Also see the EDRI-Gram article on Turk's assessment.

Update (12/7/07). Also see Bruce Sterling's comments on the EDRI-Gram article.

J. Christopher Bare and three co-authors, The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications, BMC Bioinformatics, November 19, 2007.  (Thanks to ResourceShelf.)  Abstract:  

Background.  Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data.

Results.  The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved.

Conclusions.  The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools.

Matthew Cockerill, Open access for biotechnology research, Biotech International, June/July, 2007.  (Although dated June/July, the article only appeared online recently.)  Excerpt:

Science publishing is changing. The internet has created the possibility of universal access to scientific research, and the broad benefits of such “open access” have become clear....

Most scientific journals have been online since the late 1990s, but for the most part they retained the same business model that was used in print. Authors of research articles transfer exclusive rights to the publisher, and the publisher then sells access back to the scientific community.

While this model has served the community well for centuries, it fails to make the most of the potential of the web to universally distribute the results of scientific research....An article can be shared with the whole world as easily and cheaply as with a single reader.

From the perspective of the author who carried out the research, the institution that hosted it, and the funder that paid for it, the widest possible distribution and readership of an article is of course desirable....

BioMed Central not only makes its research articles freely accessible on its own website, but also uses the Creative Commons Attribution License....

One of the reasons that freedom of reuse is so important is that humans are increasingly not the only readers of scientific articles. Computer programs are continually trawling the web, harvesting scientific content, and seeking to make sense of it....

The largest traditional STM publisher, Reed Elsevier, recently boasted that the average cost-per-download for its subscribers in the UK had fallen to only £2 per article. However, BioMed Central’s open access publication system is demonstrably able to deliver far broader access to articles at lower cost. The overall cost to the research community per full text download, for BioMed Central’s articles, is less than £0.25....

Open access archives and open access journals are sometimes presented as alternative solutions to the challenge of making research universally available, but in fact, the two are highly complementary.

Open access journals address a key criticism of open access archives, which is the suggestion that they pose a threat to subscriptions and hence to the peer review system.  It is true that, if freely accessible copies of all research articles were to be widely available via repositories, libraries would have little incentive to continue to subscribe. And if subscriptions were the only viable model on which peer-reviewed publications could operate, this would indeed be a concern....Open access repositories and open access journals benefit from each other and are evolving....

It is strongly desirable that the results of biofuels research should be disseminated as widely as possible, both to allow the cross-fertilisation of ideas between different fields and to facilitate informed public debate on matters of policy in this area....

C.Y. Lee, T.E. Davis, and E.K. Noji, Suicide bombing of the Mineralnye Vody Train: case study in using open-source information for open-source health intelligence, Prehospital and Disaster Medicine, July/August 2007.  Not even the abstract or table of contents is free at the journal site, so I'm linking to the abstract at PubMed:

Objective: Open-source information consists of a range of publicly available material, including various periodicals, news reports, journal publications, photographs, and maps. Although intelligence agencies regularly use open-source information in developing strategically important intelligence, the disaster community has yet to evaluate its use for planning or research purposes. This study examines how open-source information, in the form of Internet news reports and public access disaster databases, can be used to develop a rapid, 72-hour case report.

Methods: Open-source information was extrapolated from several news reports on a terrorist bombing that occurred in Russia on 05 December 2003, using a self-devised "data" collection sheet, and background information collected on the nature of similar disasters using three public access databases.

Results: The bulk of health-related information was collected in the first 13 hours after the event, including casualty demographics, immediate dead, total dead, admitted, and treated-and-released. The complex and prolonged rescue of casualties was identified, as well as the presence of unexploded ordnance. This incident also was identified as the first publicly reported suicide terrorist bombing of a commuter train.

Conclusions: Open-source information has the potential to be a helpful tool in reconstructing a chain of events and response. However, its use must be validated further and used appropriately. Standards for collection and analysis also must be developed.

PS:  For more on open source intelligence, see my blog posts on OSS.net.

Robert Davies, Opening up information for better public value, New Library World, 108, 11/12 (2007) pp. 490-503.  Only this abstract is free online, at least so far:

Purpose – The purpose of this paper is to provide an introduction to a number of initiatives in train at European and international level to promote the value of public investments in digital information from different perspective.

Design/methodology/approach – Major developments in three key areas are described and assessed in terms of their potential impact on libraries in the digital era.

Findings – Significant progress is being made in opening up digital information for wider use but major barriers and constraints remain to be addressed.

Originality/value – The paper brings together inter-related perspectives, e.g. those of public and private sector users, which are not always seen as part of the same picture. It is of interest to a wide range of stakeholders in the information society and the knowledge economy.

Heather Morrison, Open Access and Accessibility for the Print Disabled, Imaginary Journal of Poetic Economics, November 25, 2007. 

Abstract:   Open Access and Accessibility for the Print Disabled are two goals that fit together like hand and glove. In the online environment, it just makes sense to think about accessibility as we create information, rather than creating inaccessible information and building expensive services to overcome barriers that we have built later on. A document in XML or HTML is more accessible than one in PDF. A PDF that is not locked down with permissions, and not image-based, is more accessible than a PDF that is either locked down or image-based. The Budapest Open Access Initiative was not designed specifically to meet the needs of the print disabled; but a document that meets the BOAI definition of open access will be accessible for the print disabled, too. Similarly, when advocates for the print disabled convinced Adobe to build accessibility into their product (1), they were not thinking about accessibility for the rest of us, but their efforts have already (inadvertently) meant that many a PDF - whether published by a traditional or open access publisher - is much closer to meeting the BOAI definition of open access. This post includes a listserv message and comments, some from experts, and concludes with some final thoughts, including whether this might be considered a peer-reviewed listserv / blogpost, whether the publisher's PDF is, as often referred to, a value-add - or a value-subtract.

The November issue of Serials is now online.  Here are the OA-related articles.  (Only abstracts are free online, at least so far.)

• Stephen Pinfield, Can open access repositories and peer-reviewed journals coexist?  Abstract:   It is often assumed that open access repositories and peer-reviewed journals are in competition with each other and therefore will in the long term be unable to coexist. This paper takes a critical look at that assumption. It draws on the available evidence of actual practice which indicates that coexistence is possible at least in the medium term. It discusses possible future models of publication and dissemination which include open access, repositories, peer review and journals. The paper suggests that repositories and journals may coexist in the long term but that both may have to undergo significant changes. Important areas where changes need to occur include: widespread deployment of repository infrastructure, development of version identification standards, development of value-added features, new business models, new approaches to quality control and adoption of digital preservation as a repository function.

• Sally Morris, Will the parasite kill the host? Are institutional repositories a fact of life - and does it matter?  Abstract:   Despite an apparent lack of enthusiasm among academics themselves, institutional repositories seem set to grow. Two studies have highlighted the possible damage which could be caused to journal subscriptions by widespread self-archiving. If journals were damaged financially, the scholarly community would lose some functions which it appears to value very highly: management of peer review; editing; selecting and collecting content into a convenient package. It would also suffer indirectly, if learned societies were no longer able to give the same support to their disciplines. However, publishers cannot afford simply to oppose these developments; rather, they need to work with the scholarly community to identify those functions which are of greatest importance to the community in the digital era, and then to work out how to deliver and market these.

• Sarah Watson, Authors' attitudes to, and awareness and use of, a university institutional repository.  Abstract:   This article reports the findings of an author study at Cranfield University. The study investigated authors' publishing behaviours, attitudes, concerns, and their awareness and use of their institutional repository (IR), Cranfield QUEprints. The findings suggest that despite a reasonable amount of advocacy many authors had not heard of QUEprints and were not aware of its purpose. Once explained, all authors saw at least one benefit to depositing a copy of their work to QUEprints, but many were unsure how to deposit, preferring to depend on the Library to do the work. The authors voiced few concerns or conditions regarding the inclusion of their work in QUEprints, but felt that it would be an extra, inconvenient step in their workload. This research led to the development of the Embed Project which is investigating how to embed the IR into the research process and thereby encourage more authors to deposit their work.

• Frederick J. Friend, UK access to UK research.  Abstract:   Technological changes are providing opportunities for easier access to publicly-funded research. While these opportunities for easier access have been growing, concerns have been expressed that current business models are preventing their realization. Even well-funded university libraries are unable to purchase all the books and journals required by researchers and learners. A survey conducted by JISC, CURL and SCONUL looked at six situations of access in one UK university to the research papers and books written by researchers in another comparable UK university. The survey indicates that UK researchers and learners may not have access to around one-third of publications by researchers in other UK universities. The shortfall in access varies from university to university and relates to all types of content but particularly to books and journals from smaller publishers. Targeted additional funding and support for new access models are suggested to improve access for UK researchers to UK research.

The Dutch medical journal, Nederlands Tijdschrift voor Geneeskunde, has had its 150 year back run online for paying customers for more than two years.  Yesterday it announced that it will make it freely available to everyone --but with a five-year moving wall.  (Thanks to Wouter Gerritsma.)

David Prosser, Public Policy and the Politics of Open Access, Liber Quarterly, 17, 2 (2007).  Only the abstract is free online at the journal site, but David self-archived a full-text preprint back in August 2007.

Abstract:   In the five years since the launch of the Budapest Open Access Initiative in February 2002, one of the most striking developments in the scholarly communications landscape has been the increasing interest taken in open access at a policy level. Today, open access (in the form of both self-archiving and open access journals) is routinely discussed and debated at an institutional-level, within research-funding bodies, nationally, and internationally. The debate has moved out of the library and publisher communities to take a more central place in discussions on the ‘knowledge economy’, return on investment in research, and the nature of e-science. This paper looks at some of the public policy drivers that are impacting on scholarly communications and describes the major policy initiatives that are supporting a move to open access.

Paul Ayris, Embedding Open Access into the European Landscape – the Contribution of LIBER, Liber Quarterly, 17, 2 (2007).  Only this abstract is free online, at least so far:

Abstract:   This paper continues an earlier published history of the OAI Workshops, organised under the aegis of the LIBER Access Division, in CERN Geneva. It discusses the OAI5 Workshop, held on 18-20 April 2007, which underlines the emerging importance of Open Access to support information provision and exchange across Europe.

Alma Swan, African genesis, OptimalScholarship, November 25, 2007.  Excerpt:

Last week a two-day conference on Open Access took place in the University of Botswana in Gaborone. So what? Open Access conferences are not unusual these days. This one was, though, for two reasons. First, it is the first time that the terms 'Open Access' and 'Leadership Summit' have ever come together in a conference title. Second, the vice chancellors of Southern African universities - for it was their meeting - sat through two days of presentations and discussions on the topic. Having the attention of a group of vice chancellors focused on Open Access for two days has to be a first, too.

It is said that once someone in the world has an idea it is easier for everyone else to have it too. That has been hard to believe where Open Access is concerned. The uptake of the concept has been appallingly slow and embarrassingly cock-eyed in many cases. Yet we seem to be entering a new phase. University leaders are starting to understand the messages about the new opportunities for science and scholarship now that we have the Web. It's not just Open Access. The issue is far broader, deeper and important for mankind than even that. But OA is the start, the founder principle upon which the rest can be built, and thinking leaders in the academic world are seeing this. In the last few weeks we have had the initiation of movements at university level to promote and further Open Access and its associated benefits in Brazil, Europe and now Southern Africa....

I want to highlight...the significance of this meeting in the context of world scholarship. The problems of African scholarship are in general more than, and different to, those in the developed economies. Eve Gray set this scene in the most authoritative and impressive of ways in her opening talk at the meeting. Nonetheless, there are also difficulties that are shared, and the suboptimality of communication is one. Hussein Suleman followed up on the second day, from his perspective as a computer scientist, with an excellent overview of what can and should be done in Africa to address this issue. The vision and actions he promoted apply everywhere else, too. Africa's uniqueness in certain respects does not simply read-over into the scholarly communications arena too. True, the problems in this respect are exacerbated in Africa, but they are not confined there, nor even to the developing world as a whole. All parts of the globe share that particular suboptimality.

Alma Swan, Dancing with words, Optimal Scholarship, November 24, 2007.  Excerpt:

The Council of the European Union yesterday issued its "Conclusions on scientific information in the digital age: access, dissemination and preservation". From the language in the Conclusions (Euro-speak, of course) it is clear that the Council has taken on board the arguments that scientific communication is suboptimal and can be improved. It also makes the step of linking this with doing science better in Europe, and with the benefits to the people of Europe that would ensue from such improvements. So far, so good. The overall outcome, though, is that the Council recommends 'more studies'. Who would ever have predicted that? This is Eurocracy at its best....

There were also several mentions in the Conclusions of the term 'delayed open access'. I would call that an oxymoron except that oxymorons are meant to be deliberate and done for effect. I doubt the Council intended such an outcome. The Budapest Open Access Initiative and the Berlin Declaration gave us nothing on timing, but the Bethesda Statement did: it specifically defines Open Access as 'immediate', as of course it must be....There is a great attraction to publishers in finding ways to describe Restricted Access as open. Carried to its logical conclusion, all publications thus become Open Access....

Though we should be grateful that there are signs of some sort of grasp of the issues at stake, we have to conclude that the Council still hasn't got the point....

Dear Council members: European scientists are every bit as good as any elsewhere in the world. If you think European science doesn't work as well as it should, you are right. We have major problems with our science in Europe - structural, economic, political. Seeing to it that the fabric of communication is optimal would help a very great deal. Come up with a proper policy on the use of taxpayer-funded research. You can do it if you try.

In a book just published on exam howlers, one schoolboy quote is this: "The USSR and the USA became global powers but Europe remained incontinent." From the mouths of babes ....

The November issue of Kunstchronik is devoted to open access.  The issue is not itself OA, at least so far, but Klaus Graf (who conceived the issue) expects that all the articles will soon be self-archived.  Watch his version of the TOC for links to OA editions of the articles, as they become available.

These articles from the issue are already OA:

• Klaus Graf, Kulturgut muß frei sein.  An argument for OA to digital images of cultural heritage objects, free even for commercial use.
• Klaus Graf, Neues Urheberrecht: Autoren müssen reagieren.  A recapitulation of his call to German authors to claim the rights, and authorize OA, to their works published before 1995.

From Arthur Sale in the American Scientist Open Access Forum (thanks to Stevan Harnad):

Yesterday [November 23, 2007], Australia held a Federal Election. The Australian Labor Party (the previous opposition) have clearly won, with Kevin Rudd becoming the Prime-Minister-elect.

What has this to do with the American Scientist Open Access Forum? Well the policy of the ALP is that the plans for the Research Quality Framework (the RQF - our research assessment exercise) will be immediately scrapped, and it will be replaced by a cheaper and metrics-based assessment, presumably a year or two later.

At first sight this is a setback for open access in Australia, because institutional repositories are not essential for a metrics-based research assessment. They just help improve the metrics. However, the situation may be turned to advantage, and there are several major pluses.

(1) Previous RQF grants should have ensured that every university in Australia now has a repository. Just mostly empty, or mostly dark, or both.

(2) The advisers in the Department of Education, Science & Technology (DEST) haven’t changed. The Accessibility Framework (ie open access) is still in place as a goal....

(4) If the Rudd government is serious about efficiency in higher education, they could simply instruct DEST to require universities to put all their currently reported publications in a repository (ID/OA policy), from which the annual reports would be automatically derived. In addition all the desired publication metrics would also be derived, at any time. The Accessibility Framework would be achieved....

Any university that fails to immediately implement an ID/OA mandate (Immediate Deposit, Open Access when possible) in its institutional repository is simply deciding to opt out of research competition, or mistakenly thinks that it knows better. Although I suppose there is still the weak excuse that it is all too hard to understand or think about....