Open Access News

Library drops BioMed Central's Open Access membership, a press release from the Yale University Libraries, August 3, 2007.  Excerpt:

After careful consideration, the Cushing/Whitney Medical and Kline Science Libraries have decided to end their support for BioMed Central's Open Access publishing effort. The libraries previously covered 100% of the author page charges which allowed these papers to be made freely available worldwide via the Internet at time of publication. This experiment in Open Access publishing has proved unsustainable. The libraries' support will continue for all Yale-authored articles currently in submission to BioMed Central as of July 27, 2007.

The libraries’ BioMedCentral membership represented an opportunity to test the technical feasibility and the business model of this OA publisher. While the technology proved acceptable, the business model failed to provide a viable long-term revenue base built upon logical and scalable options. Instead, BioMedCentral has asked libraries for larger and larger contributions to subsidize their activities. Starting with 2005, BioMed Central page charges cost the libraries $4,658, comparable to a single biomedicine journal subscription. The cost of page charges for 2006 then jumped to $31,625. The page charges have continued to soar in 2007 with the libraries charged $29,635 through June 2007, with $34,965 in potential additional page charges in submission....

We believe in the widest possible access to scholarly research supported by workable business models and should BioMedCentral develop a viable economic model which allows them to more equitably share costs across all interested stakeholders, we would consider renewing our financial support....

Brock Read, Software Weighs Wikipedians' Trustworthiness, Chronicle of Higher Education blog, August 3, 2007. 

The problem with Wikipedia, as most scholars see it, isn’t that the site lacks credible information. There’s plenty of good stuff in the encyclopedia; it’s just that there’s no easy way to separate the wheat from the chaff.

Researchers at the University of California at Santa Cruz are trying to make that process simpler. They’ve designed software that color-codes Wikipedia entries, identifying those portions deemed trustworthy and those that might be taken with a grain of salt.

To determine which passages make the grade, the researchers analyzed Wikipedia’s editing history, tracking material that has remained on the site for a long time and edits that have been quickly overruled. A Wikipedian with a distinguished record of unchanged edits is declared trustworthy, and his or her contributions are left untouched on the Santa Cruz team’s color-coded pages. But a contributor whose posts have frequently been changed or deleted is considered suspect, and his or her content is highlighted in orange. (The darker the orange, the more spurious the content is thought to be.)

The researchers, led by Luca de Alfaro, an associate professor of computer engineering, have posted 1,000 demonstration pages on their Web site, and the samples show that the sorting process is pretty acute. Some articles, like a lengthy entry on the Curtiss P-40, a World War II-era fighter plane, get a nearly clean bill of health. Others, like an article on crochet, fare pretty well. And then there are entries, like a write-up on Polish Christmas traditions, that are drenched in orange.

Because the software assesses the histories of Wikipedia posters without actually fact-checking, it won’t necessarily direct people to Wikipedia’s best, most academically rigorous articles. But the program might be a useful tool for professors who want their students to examine closely how Wikipedia works rather than take it as gospel.

Comment.  Interesting approach. 

• Some bad entries go uncorrected because few people read them.  Hence, I’d trust an entry more if it had a low rate of overwrites and a high rate of readership.  Could the algorithm take the extra variable into account?
• I don’t expect (hope or fear) that algorithms will replace human judgment any time soon.  But there’s no doubt that they can supplement human judgment and already do.  I do look forward to how they can improve as human helpers.  Contrary to sci-fi fantasies, they don’t have to become infallible to cross a significant threshold; they only have to become roughly as fallible as peer review.  And they can be useful immediately, i.e. long before crossing that threshold.

Stevan Harnad, Ethics of Open Access to Biomedical Research: Just a Special Case of Ethics of Open Access to Research, Open Access Archivangelism, August 4, 2007. 

Summary:  The ethical case for Open Access (OA) (free online access) to research findings is especially salient when it is public health that is being compromised by needless access restrictions. But the ethical imperative for OA is far more general: It applies to all scientific and scholarly research findings published in peer-reviewed journals. And peer-to-peer access is far more important than direct public access. Most research is funded to be conducted and published, by researchers, in order to be taken up, used, and built upon in further research and applications, again by researchers, for the benefit of the public that funded it -- not in order to generate revenue for the peer-reviewed journal publishing industry (nor even because there is a burning public desire to read [much of] it). Hence OA needs to be mandated for all research.

Sanjay Kataria, Intellectual Repositories in Institutions of Higher Learning in India: An overview, in Abdullah, et al. (eds.), Proceedings International Conference of Library Information and Society (ICoLIS), 2007, pp. 129-136.  Self-archived August 3, 2007.

Abstract:   The paper discusses the concept of intellectual repository (IR) its need, importance,benefits, critical issues, major problems in establishment & maintenance of IR, role of librarians, intellectual society, academic institutions and the government. It also gives an overview of Intellectual Repository (IR) initiatives taken in the institutions of higher learning in Indian scenario.

The Eduserv Foundation is running a survey on the Use of open content licences by cultural heritage organisations in the UK.  (Thanks to the OKFN.) 

The survey is part of a larger study:

Digital resources produced by publicly funded organisations are a valuable asset to the research and education community. Many people in the sector believe that access to and use of these digital resources could be better and that the wider use of open content licences would help to improve the situation.

A study titled "The Common Information Environment and Creative Commons" was funded by Becta, the British Library, DfES, JISC and the MLA on behalf of the Common Information Environment. The work was carried out by Intrallect and the AHRC Research Centre for studies in Intellectual Property and Technology Law and a report was produced in the Autumn of 2005. During the Common Information Environment study it was noted that there was considerable enthusiasm for the use of Creative Commons licences from both cultural heritage organisations and the educational and research community. In this study we aim to investigate if this enthusiasm is still strong and whether a significant number of cultural heritage organisations are publishing digital resources under open content licences.

For more detailed information about this study, please refer to the full proposal.

Antony Williams, A Plea to Academia to Help Design a Lesson Plan Using ChemSpider, ChemSpider blog, August 3, 2007.  Excerpt:

Over the past 48 hours there has been an interesting discussion on CHMINF. The discussion was around how to teach a large class of students to learn about literature searching, about structure searching, property searching etc. The tools are out there to perform such searches and to facilitate students learning about the types of resources they will need to access if and when they enter industry. The premise of the exchange was that some of the gold standard resources, while excellent, are commonly not affordable at the level necessary to train large classes of students. Below is a posting I placed back onto CHMINF. My question to you readers is as follows “Is there an academic who would like to work with me on a Lesson Plan involving ChemSpider?”. If so…contact me please.

The exchange...

Colleagues,

I wonder whether or not it might be possible to use the ChemSpider service as one of the resources for the classes? For example, relative to some of the comments made below it is possible to perform the majority of searches at www.chemspider.com - this includes structure searches, property searches,name searches as well as LITERATURE searches of Open Access articles. See details below....

A new blog on OA launched yesterday, Indonesian Open Access Initiative.  The blogger goes by the name of Imam.  The inaugural post reprints the Budapest and Berlin statements on OA.

PS. Welcome Imam!  This promises good things for OA and Indonesia.

Bruce Byfield, Academia's Open Access movement mirrors FOSS community, Linux.com, August 2, 2007.  Excerpt:

Free and open source software (FOSS) has roots in the ideals of academic freedom and the unimpeded exchange of information. In the last five years, the concepts have come full circle, with FOSS serving as a model for Open Access (OA), a movement within academia to promote unrestricted access to scholarly material for both researchers and the general public.

"The philosophy is so similar that when we saw the success that open source was having, it served as a guiding light to us," says Melissa Hagemann, program manager for Open Access initiatives at the Open Society Institute, a private foundation for promoting democratic and accessible reform at all levels of society. Not only the philosophy, but also the history, the need to generate new business models, the potential empowerment of users, the impact on developing nations, and resistance to the movement make OA a near twin of FOSS....

By the start of the millennium, a number of academic groups were starting to see the Internet as a solution to these problems. In December 2001, 13 representatives of these groups met in Budapest to organize. They produced a document called the Budapest Open Access Initiative. Starting with the declaration that "An old tradition and a new technology have converged to make possible an unprecedented public good," the initiative called for making all academic articles available online. It was followed in April 2003 by the Bethseda Statement on Open Access Publishing, and in October 2003 by the Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities, both of which suggest how OA could be implemented. Together these three statements -- sometimes known collectively as the BBB Declaration -- provide the practical and philosophical basis for the development of OA.

As with FOSS, the initial reaction to OA was derisive. "They laughed at us," says Hagemann, who is one of the original signers of the Budapest Initiative. "During presentations I would give in various countries, I would be laughed at." At first, the movement's representatives even had trouble gaining membership in the Association of Learned Professional Societies, which issued a news release sharply criticizing OA. Just as with FOSS, these criticisms included claims that OA lacked a business model and was unsustainable. Other criticisms included the claim that OA amounted to vanity publishing and would lack peer reviews, both of which have proved unsubstantiated in practice.

And, in another parallel to FOSS, as OA has spread, so resistance has spread to government lobbying and even threats of lawsuits in some instances. Hagemann alleges that the American National Institute of Health, for instance, has had its implementation of OA delayed through the intervention of Congress and Senate members listening to the publishers' lobbying groups. Similarly, she says the Association of American Publishers has recently hired a Washington lobbyist to campaign against OA.

"They used to laugh at us, but now they're taking us very seriously and working against us politically," notes Leslie Chan, a senior lecturer at the University of Toronto and one of the organizers of online publisher Bioline, as well as an original signatory of the Budapest Initiative. His comments echo a quote by Gandhi often heard in FOSS circles as well: "First they ignore you, then they laugh at you, then they fight you, then you win." ...

Rainer Kuhlen, Open access – ein Paradigmenwechsel für die öffentliche Bereitstellung von Wissen. Entwicklungen in Deutschland, Biblioteconomia i Documentació, June 2007.  BiD published the article in German, Spanish, and Catalan. 

(Google's machine translation isn't working on this file; but just in case the problem is temporary, here's Google's English.)

Last month I blogged the draft Kronberg Declaration on the Future of Knowledge Acquisition and Sharing.  The final edition is now online, dated June 22-23, 2007, but released today:

[O]ver the next twenty-five years:...

Global efforts related to Free and Open Source Software (FOSS) as well as Open Educational Resources (OER) will play a more profound role in knowledge sharing;

Open access to and free flow of content, as well as participation in the creation of this content, will be of crucial importance for equitable knowledge acquisition and sharing;...

We...[s]tress the need to...

Support open access to and free flow of content through the development of open standards, open data structures, and standardized info-structures...[and]

Enable the creation of open content by practitioners in the developing world....

From today's press release from UNESCO:

Knowledge acquisition and sharing will increasingly be technology mediated, and traditional educational processes will be revolutionized, said experts at a UNESCO organized event in Kronberg, Germany, recently.

Adopting the “Kronberg Declaration on the Future of Knowledge Acquisition and Sharing” the high-level experts also said that leaders in the public and private sectors must embrace change in organizations and people by providing opportunities and incentives to facilitate and motivate, as well as to overcome typical barriers in knowledge acquisition and sharing....

The “Kronberg Declaration” that UNESCO and the German Commission for UNESCO have just released summarizes the discussions at the meeting of a UNESCO High Level Group that took place from 22 to 23 June 2007 in Kronberg, Germany. The event was jointly organised by UNESCO and the German Commission for UNESCO, and was sponsored by BASF....

“We have seen over the past 10 years a dramatic increase of the dependence of global development processes from the ability to efficiently produce, disseminate and use information and knowledge” says Abdul Waheed Khan, UNESCO’s Assistant Director General for Communication and Information. ”Lack of access to knowledge increasingly accentuates marginalization and economic deprivation, and we need to join efforts to bridge these gaps”....

The June issue of Access is now online.  This issue has articles on the World Digital Library (from the Library of Congress and Bibliotheca Alexandrina), the Hong Kong meeting on institutional repositories (May 2007), the Bentham Science plan for 300 OA journals, and OA ETDs in the UK.

 The Research Councils UK has released its Annual Review 2006/2007.  Excerpt:

Considerable discussion preceded the publication of the Research Councils’ updated position on access to research outputs in June [2006]. This is a controversial and complex issue, however the Research Councils position is simple: we want the results of the research we fund to be disseminated as widely as possible to ensure that it has the greatest possible impact. The opportunities offered by new communication technologies should be considered by researchers when they are published.  We recognise that the simplicity ends there and our cautious approach will ensure that any impacts on research publication are fully understood. Next year we will commission an authoritative study to report by November 2008, which will guide our developing policy….

Michael Geist has a good suggestion on the CCIA complaint about deceptive copyright notices.  He describes it for Canadian publishers, but the idea would work just as well for publishers from most other countries:

…I raised the same issue last year with regard to Canadian publishers and their use of copyright notices that are exceptionally misleading and that perpetuate the incorrect view that nothing may be copied without prior permission.  While a complaint to the Fair Business Practices Branch of the Canadian Competition Bureau is worth considering (as is statutory reform to address copyright misuse), I argued that there may be another alternative. Book publishing and most other Canadian cultural industries rely on government funding programs - taxpayer dollars - for a portion of their costs.  Indeed, tens of millions are distributed each year to Canadian book publishers, while television programming is among the most heavily subsidized industries in the country.  One way to stop misleading copyright notices would be to require fair copyright notices as a condition of funding.  Publishers and broadcasters that fail to properly balance their notifications by alerting consumers to their fair dealing rights would run the risk of losing access to taxpayer dollars that help fund their business….

Karen G. Schneider, Survival of Small Press Journals: A Librarian Says the Future Is Digital, but We're Not There Yet, Critical Mass, August 2, 2007.  (Critical Mass is the blog of the national book critics circle board of directors.)  Excerpt:

...It's also time to initiate discussions about what a journal should look like five, twenty, or fifty years from now, and what it means to move that journal from print to electronic. The emerging open-access, digital model could eventually save at least some (if not many) members of an endangered genre, given the fragile economics of most small journals, which are further endangered by the recent postal hikes that privilege corporate publishers at the expense of the small press. But even then, this has to be done in partnership with publishers and readers....

Leading the way with a European e-Theses demonstrator project, a press release from the Dutch SURF Foundation, July 31, 2007.  Excerpt:

The organisations JISC (UK), the National Library of Sweden and the Dutch SURFfoundation have tested the interoperability of repositories for e-theses. The result  is a freely accessible European e-Theses portal providing access to over 10,000 doctoral theses.

For the first time ever, various local repositories containing doctoral e-theses have been harvested on an international scale. Five countries were involved in the project: Denmark, Germany, the Netherlands, Sweden and the United Kingdom.

Doctoral theses contain some of the most current and valuable research produced within universities. Still, they are underused as research resources. Nowadays, theses and dissertations no longer have to gather dust in attics or on the shelves of university libraries. By making them available on the Internet, both the author and the university can showcase their research, benefiting not only fellow scientists, but a broad public as well. And when they are publicly available, they are used many times more often than printed theses available only at libraries or by inter-library loan.

The result of this pilot project is described in the report A Portal for Doctoral e-theses in Europe; Lessons Learned from a Demonstrator Project. The report gives practical recommendations to improve the interoperability between the service provider and the data supplier. The recommendations are entirely in line with the guidelines of the DRIVER project.

The report may be useful for institutions that wish to show the world the results of their research. By making their material accessible in a standardised manner and using the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH), they can reach beyond any boundary…. 

Peter Murray-Rust, Cyberscience: Changing the business model for access to data, A Scientist and the Web, July 31, 2007.  Excerpt:

I have been reviewing the availability of Open Data for cyberscience - concentrating recently on crystallography and chemical spectra as examples. I’ll propose a new business model here, still very ill-formed and I welcome comments. It applies particularly to disciplines where the data are collected in a fragmented manner rather than being coordinated as in, for example, survey of the earth or sky. I call this fragmentation “hypopublication”.  However the Internet has the power to pull together this fragmentation if the following conditions are met:

• the data are fully Open and exposed. There must be no cost, no impediment to access, no registration (even if free), no forms to fill in.
• the data must conform to a published standard and the software to manage that standard must be Openly available (almost necessarily Open Source). The metadata should be Open.
• the exposing sites must be robot-friendly (and in return the robots should be courteous).

Such a state nearly exists in modern crystallography….

[C]ouldn’t this be a model for all of science? As I have posted recently I’m going to write to the editors of Elsevier’s Tetrahedron suggesting that they make all their crystallographic data available Openly. They agree it’s not their copyright, so it’s just a question of how to do it - files on a website shouldn’t be a major expense.

And funders should encourage this. If you are urging authors and journals to publish Open full-text, please extend this to data. Yes, there are some technical difficulties in some cases such as metadata, complexity and size but they probably aren’t too scary. And in any case the community will help work out how to use them.

Joanne A. Fox, Scott McMillan, and B. F. Francis Ouellette, Conducting Research on the Web: 2007 Update for the Bioinformatics Links Directory, Nucleic Acids Research, June 22, 2007.

Abstract:   The Bioinformatics Links Directory is an actively maintained compilation of servers published in this and previous issues of Nucleic Acids Research issues together with many other useful tools, databases and resources for life sciences research. The 2007 update includes the 130 websites highlighted in the July 2007 Web Server issue of Nucleic Acids Research and brings the total number of servers listed in the Bioinformatics Links Directory to just under 1200 links. In addition to the updated content, the 2007 update of the Bioinformatics Links Directory includes new features for improved navigation, accessibility and open data exchange. A complete listing of all links listed in this Nucleic Acids Research 2007 Web Server issue can be accessed online [here]. The 2007 update of the Bioinformatics Links Directory, which includes the Web Server list and summaries is also available online, at the Nucleic Acids Research web site.

From the body of the paper:

The Bioinformatics Links Directory is a community resource built on this commitment to the spirit of open access….

Sarah McBride and Adam Thompson, Google, Others Contest Copyright Warnings, Wall Street Journal, August 1, 2007.  Excerpt:

Diehard baseball fans can recite by heart the familiar copyright warnings that run with every game on television.

Now, a computer-industry trade group is crying foul, saying those warnings and others like it on movies and books are trampling over consumers' rights to fair use of copyrighted content.

Today, the Computer and Communications Industry Association -- a group representing companies including Google Inc., Microsoft Inc. and other technology heavyweights -- plans to file a complaint with the Federal Trade Commission, alleging that several content companies, ranging from sports leagues to movie studios to book publishers, are overstepping bounds with their warnings. The group wants the FTC to investigate and order copyright holders to stop wording warnings in what it sees as a misrepresentative way....

Many warnings "materially misrepresent U.S. copyright law, particularly the fundamental built-in First Amendment accommodations which serve to safeguard the public interest," the complaint alleges. CCIA President Ed Black said the warnings create a "chilling effect," dissuading consumers from using portions of the content in ways that are lawful....

A spokesman for Reed Elsevier PLC's Harcourt Inc., one of the publishers named in the complaint, said he hadn't seen it and declined to comment.

From the CCIA's Defend Fair Use page:

...We filed a complaint with the Federal Trade Commission in which we asked the governments foremost enforcer of consumer rights to stop big media from making these ridiculous claims....

Their answer? Threats and exaggerations that misrepresent your rights. Your rights include the right to make Fair Use. But some of the Big Content companies don't like the idea that the law limits their control over how you use what you've legally acquired. These companies know that, by law, anyone can quote, excerpt and even copy their works for things like journalism, homework and research and discussion of all sorts.

Big media companies are turning increasingly aggressive in their efforts to discourage people from doing what they have always done with the media they bought and programs they have recorded in their own homes.

Comment:  Kudos to the CCIA.  Content industries have a natural incentive to minimize fair use, but their public warnings cynically and systematically misrepresent the law.  It's about time that they were called on it by another, larger industry.  The job shouldn't be left to consumers, academics, and non-profits.  BTW, universities are often guilty partners of the content industry in this misrepresentation, distributing its propaganda pamphlets on fair use to “educate” students and faculty about the law.

Update. The Library Content Alliance has sent an open letter to the FTC supporting the CCIA complaint and giving its own examples of misleading publisher FUD about fair use for academic publications. (Thanks to Gavin Baker.) Snippet:

The fair use analysis is complex enough without the obfuscation caused by intimidating, inaccurate copyright warnings. We urge the FTC to investigate this matter carefully, and issue appropriate relief along the lines suggested by CCIA.

Update. Library Journal Academic Newswire for August 2, 2007, has a good article on the LCA letter.

 Chris Surridge, Now we are ONE, PLoS blog, August 1, 2007.  Excerpt:

A week can be a long time in politics; well, a year in scientific publishing can feel like an age. On 1st August last year, PLoS ONE opened its doors for submission and so we have decided to call today our official birthday. So what has the last year been like and how have things changed?

Well, back in August 2006 we were quite excited to have double figures of submissions in our first week. Last month we were averaging 60 submissions a week. Close to two thousand submissions in total.

A year ago we had a dedicated editorial board of 120 people. At the moment that number stands at 386. I cannot thank enough these people who are responsible for assessing all the papers that are submitted, managing their peer review and deciding whether or not they are ready for publication….

Most importantly of all though, in the last year, or, at least, in the months from December 2006, we have published 695 pieces of original research. All of that research is, of course, Open Access and all of that research can be annotated by users, discussed by users and for the last few weeks rated by users….

The initial success of PLoS ONE is something unprecedented in scientific publishing. It has been achieved because of the commitment and faith of hundreds of people: PLoS staff, editorial and advisory board members, reviewers, authors and particularly readers. And yet this is only a very small step towards an open, interactive and efficient literature that will accelerate scientific progress. Over the coming months, we will take further steps with additional functionality on the site, new publishing ventures launching and established ones taking more advantage of the opportunities afforded by the TOPAZ platform on which PLoS ONE is presented.

So, if it is a birthday, what about presents?

Well, PLoS ONE would like three things none of which are particularly expensive and which all of the readers of this blog can give us: three resolutions.

Whenever you write about a published paper, be it in a journal or on a blog, always provide a link to the freely available version of the paper if one exists.

Whenever you read a paper in PLoS ONE, always rate it before leaving.

And most importantly....

Whenever you write a scientific paper, always, always, always publish it Open Access.

PS:  Happy birthday, P1.  I’m glad to spread the word, in hopes that more people will give you the gifts that will benefit everyone.

Update. Klaus Graf has added some tips of his own.

Matt Hodgkinson, BioText - a search engine for open access figures, BioMed Central blog, July 31, 2007.  Excerpt:

At the ISMB conference we met Anna Divoli, a postdoc at the University of California, Berkeley, who showed us the BioText Search Engine, which she was presenting as a poster, and has recently published....

I came across it briefly earlier this month thanks to the blog of medical librarian David Rothman, who described it as "A supercool way to search PubMed Central", which is a pretty good description!

It is part of the text mining BioText project and goes beyond the abstract searching in MEDLINE seen previously to extend searching to the figure legends of Open Access journals in PubMed Central.

As the homepage of PubMed Central notes, "All the articles in PMC are free (sometimes on a delayed basis). Some journals go beyond free, to Open Access". Because Open Access explicitly allows the reuse of the content of the articles in these journals (which include all 170+ BioMed Central journals) this has allowed the BioText people to create a search engine that allows keyword searching of abstracts, figure legends, titles and authors, returning results sorted by date and relevance, and in two formats: abstracts with figure thumbnails and legends, or figure legends with thumbnails....

Anna hinted at upcoming functions such as returning snippets that match the search terms from the full text of the article (much as Google Scholar does). We look forward to these further developments, and we'd like to thank Anna, Marti Hearst and the others on the BioText team for developing such a useful and user friendly tool. This is a great example of how Open Access allows others to make further use of published work, in ways that the authors or publishers had not anticipated.

MMRF, MMRC Launch Multiple Myeloma Genomics Portal, a press release from the Multiple Myeloma Research Consortium, August 1, 2007.  Excerpt: 

The Multiple Myeloma Research Foundation (MMRF) and Multiple Myeloma Research Consortium (MMRC) today announced the launch of the MMRC Multiple Myeloma Genomics Portal, the world's only myeloma-specific repository of genomic data. The MMRC Multiple Myeloma Genomics Portal provides the scientific community with open access to high-resolution genomic data from the MMRC Multiple Myeloma Genomics Initiative pre-publication and in near real-time....

"The MMRC Multiple Myeloma Genomics Portal represents an important step in making genomic data available to the scientific community without restriction. The commitment to make these data available prior to publication means that scientists worldwide will have immediate access to the data, enabling a more rapid pace of scientific inquiry," said Todd Golub, MD, Director of the Cancer Program at the Broad Institute and a pediatric oncologist at Dana-Farber Cancer Institute....

"The MMRF and MMRC's commitment to providing the scientific community with access to this quantity and quality of data offers a remarkable opportunity to advance myeloma research and drug development," said Jeffrey Trent, PhD, President and Scientific Director of TGen. "Ultimately, this can result in better treatment options for patients who so urgently need them." ...

PS:  Apparently the new repository isn't yet online.  MMRC doesn't give a URL in its press release or web site, and Google hasn't heard of it yet.

Jason Bobe, Richter Scale and Your Genomic Portfolio, The Personal Genome, July 31, 2007.  (Thanks to My Biotech Life.)  Jason outlines a way to help people understand their genetic risks for various diseases and get beyond the superficiality and sensationalism of popular media (“scientists discover a gene for Alzheimer’s”).  In the middle of the discussion he pauses for an aside:

Promote open access to scientific and medical literature

This is a plea to scientists and researchers to be more thoughtful about how and where they publish their scientific work. There are lots of interesting possibilities when people can actually access your published work. In return for sharing your data, there may be legions of people that can help ensure that your discoveries and insights can achieve maximum impact.

Since I brought it up, ethicists, legal scholars, policy-makers, public health people and many other stripes of experts should be more conscientious about where they publish their intellectual output. I’m not going to pay $25 per article so that I can get an education about issues that directly affect me. It is easy to attack journalists and bloggers for getting their facts wrong, but we’re living in an information wasteland without access to good scholarly work. Trash in, trash out. This has to change. [Warning: Melodramatic comment dead ahead] We need nothing less than a publishing perestroika.

The Library Journal Academic Newswire for July 31 erroneously reported that Ray English (Director of Libraries at Oberlin College) wrote the July 28 LATimes editorial in support of an OA mandate at the NIH. 

Ray tells me that the report is in error, perhaps arising from the fact that he forwarded a copy of the editorial to LibLicense.  He also tells me that LJAN plans to run a correction.

Update. The Library Journal Academic Newswire ran the correction in its August 2 issue.

Francis Muguet has linked to three OA-related videos from Open-Access.tv:

1. Speech of Dr. Aymar CERN director at ECOSOC / CSTD on 21 May 2007
2. Prof. Stevan Harnad Interview on Open Access to Scientific Information, February 16,, 2007 (Francis is the interviewer)
3. Closing speech by Viviane Reding - 16 February 2007 Scientific Publishing

Compete, collaborate, compel, Nature Genetics, August 2007.  An editorial.  (Thanks to Garrett Eastman.)  Excerpt:

Procedures for microattribution need to be established by journals and databases so that data producers have an overwhelming incentive to deposit their results in public databases and thereby to receive quantitative credit for the use of every published data accession.

The excellent work of database designers at (for example) the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) offers researchers a range of stably funded and user-friendly data repositories in which data producers and annotators can be uniquely identified along with their data across the ubiquitous Web. Accession numbers to database entries are routinely used for data retrieval. They should now also be used to accrue quantitative credit for their authors in a systematic process of microattribution.

Every field of scientific discovery goes through three main stages. First, competitive discoveries result from innovations. Second, competitive collaborations are ventured in an important process of negotiated pooling of resources. Third, standards are agreed upon and data begin to be shared by agreed protocols and databases….

[F]unders are…in an excellent position to maximize the utility of the research they fund by insisting that it be rapidly deposited in public databases—in the case of genome sequences, in advance of the publications that bring credit to the data producers….

When requiring authors to deposit data in public databases, journals, databases and funders should ensure that quantitative credit for the use of every data entry will accrue to the relevant members of the data-producing and annotating teams….

Comment.  This is the second Nature journal in two days with an editorial supporting open access.  For the first, see Free Market Science, Nature Cell Biology, July 2007 (blogged here yesterday).

Scott Jaschik, New Model for University Presses, Inside Higher Ed, July 31, 2007.  Excerpt:

It’s the nightmare-come-true scenario for many an academic: You spend years writing a book in your field, send it off to a university press with an interest in your topic, the outside reviewers praise the work, the editors like it too, but the press can’t afford to publish it. The book is declared too long or too narrow or too dependent on expensive illustrations or too something else. But the bottom line is that the relevant press, with a limited budget, can’t afford to release it, and turns you down, while saying that the book deserves to be published.

That’s the situation scholars find themselves in increasingly these days, and press editors freely admit that they routinely review submissions that deserve to be books, but that can’t be, for financial reasons. The underlying economic bind university presses find themselves in is attracting increasing attention, including last week’s much awaited report from Ithaka, “University Publishing in a Digital Age,” which called for universities to consider entirely new models.

One such new model is about to start operations: The Rice University Press, which was eliminated in 1996, was revived last year with the idea that it would publish online only, using low-cost print-on-demand....

Rice is going to start printing books that have been through the peer review process elsewhere, been found to be in every way worthy, but impossible financially to publish....

Some of the books Rice will publish, after they went through peer review elsewhere, will be grouped together as “The Long Tail Press.” In addition, Rice University Press and Stanford University Press are planning an unusual collaboration in which Rice will be publishing a series of books reviewed by Stanford and both presses will be associated with the work….

Alan Harvey, editor in chief at Stanford, said he saw great potential not only to try a new model, but to test the economics of publishing in different formats. Stanford might pick some books with similar scholarly and economic potential, and publish some through Rice and some in the traditional way, and be able to compare total costs as well as scholarly impact. “We’d like to make this a public experiment and post the results,” he said.

Another part of the experiment, he said, might be to explore “hybrid models” of publishing. Stanford might publish most of a book in traditional form, but a particularly long bibliography might appear online….

 iCommons has launched its Open Business Guide.  Excerpt:

Giving away things for free seems an unlikely business strategy. But the fastest growing business of the last decades offers its primary services for free. Google was created without a revenue model in mind, and when it started had no way of making money.

Web 2.0, peer to peer, social networking, crowd sourcing, open innovation, peer production, non-monetary incentives, free culture, Creative Commons, Free and Open Source Software are all terms which have gained prominence in the debate surrounding the present and future of culture, film, radio, tv, education, many other fields and last but not least 'business' in general.

Against this background OpenBusiness.cc, an international project with partners in Brazil, South Africa and the UK, supported by the Open Society Institute, International Development Research Centre, Ford Foundation and Arts Council England, has collected examples of new business models and processes that focus on:

• lowering the costs of market entry for individuals by providing tools or services, that ‘open’ up traditional business boundaries using the Internet
• sharing information for free using alternative ‘open copyright models’ while exploring new revenue models
• giving substantial parts of content away for free while creating derivative revenue streams
• operate organizationally like Open Source software production, but translate the model to services (finance, or film or music production) ...

One of the guide’s examples is an OA publisher:

HSRC Press primarily publishes the output of [South Africa’s] Human Sciences Research Council. It has adopted an open access publishing model. HSRC adopted the model because the primary goal in publishing the research materials as opposed to seeking financial reward through the turnover from book sales.

Instead, the goal of HSRC to attract further research funding and contracts, and crucial avenues of dissemination, which can increase the overall size and influence of the HSRC organisation.

Printed books are offered via the website, and can be read on-screen, downloaded for printing or ordered on the website as a POD publication through an e-commerce engine (and supplied on a cost-recovery basis). Having adopted this model revenue has increased by 300%! …

Put it in the Depot! JISC Inform, July 23, 2007.  A podcast interview with Peter Burnhill, director of EDINA.  From the description:

All researchers and academic authors in the UK now have a repository in which to deposit their research papers under terms of open access. The Depot, a national JISC-funded repository based at EDINA in the University of Edinburgh, was launched last month to provide a range of services to support the self-archiving of research papers.

‘The principal purpose of the Depot,’ says Peter Burnhill, director of EDINA, is ‘to allow all UK academics to share in the benefits of open access. If they have an institutional repository, that’s to the good. But up to now they’ve been excluded unless they have an institutional or access to a subject repository.’

The Depot was first conceived solely as a national repository for those authors who did not yet have access to an institutional repository. But, as Peter Burnhill continues, while the Depot does include this function, the thinking developed to something altogether more ambitious: ‘The way we’ve designed the Depot at the reception area is that there’s a redirect service so that if there’s somebody from an institution which has an institutional repository we can redirect them to its front page, so they can take the necessary steps. So it generates content for all institutional repositories.’

This, he says, is the ‘Repository Junction’, a facility within the Depot that allows not only the re-routing of submissions of academic papers and journal articles (e-prints) but also of other educational and research content….

‘But what we’ve done with the Depot is to gear this for the researcher, the academic author who is now persuaded that open access is the way to go… After all, authors want people to read what they write; what they want is recognition. They want to be read, they write to be read and to be recognised.’

As part of his review of the access policies at different publishers, on July 15, Peter Murray-Rust reviewed the policies at OA publisher, Libertas Academica.  On July 28, he received this note from LA's Tom Hill:

Dear Dr Rust,

...I very much appreciate your critique on our OA policy. It appears that in our haste to develop our journals we have neglected to make our policy, particularly with respect to copyright, as transparent as it should be.

I have therefore made the following changes:

1. We now clearly apply the CC-BY licence.

2. I have asked our web developer to remove the obsolete copyright statement from the bottom of all web pages. Given that this is Saturday, this change will probably not take place until Monday NZ time....

Comment.  Congratulations to Peter MR for his initiative and to kudos to Tom Hill for his constructive response.

Update.  Peter MR continues his review series with several posts (first, second, third) on the data access policies at CODATA.

Steve Foerster, The Demise of Old-Fashioned Scholarly Journals?  iCommons, July 30, 2007.  Excerpt:

Recently I attended a debate called Intellectual Property Rights: Wrong for Developing Countries?" at the National Academies in Washington, D.C. The two speakers were Bruce Lehman, Chairman of the International Intellectual Property Institute, and John Wilbanks, Vice President of Science Commons….

Both, at one point or another, referred to scholarly journals as "content providers"….

Well, as someone working in higher education, I don't really think of scholarly journals as content providers. I think of the academics that research and write the articles as content producers, and the journals merely as distribution channels. Thus, if academics are passing articles around using the Internet, it's because the Internet is a superior distribution channel to the journals themselves -- even when those journals are themselves online unless they also offer open access….

There is one important aspect of subscription based scholarly journals that isn't addressed by simply replacing them with online open access alternatives, and that is the relative prestige that publication in different journals offers….At the same time, however, given the advantages of open access and online distribution, how long can this save subscription based journals?

In fairness to John Wilbanks, he was a passionate proponent of increasing access to knowledge, and he did remark that it seems like journal publishers are among those industries that have done a poor job finding new business models that work when faced with the Internet. But I wonder if it's merely a failure of their imagination. I'm hard pressed to think of a way they can add value when every aspect of scholarly articles from concept to peer review to distribution can now be handled without them. Could it be that they're simply dinosaurs in a world where it has begun to snow?

Dorothea Salo, Drive-by thoughts on the Ithaka report, Caveat Lector, July 30, 2007.  Excerpt:

The Ithaka folks put out a really sharp report on the state of university presses and libraries vis-a-vis scholarly publishing last week. This is excellent stuff; I highly recommend it. A few random thoughts on it....

The hits at institutional repositories are so good I’m going to quote them in [a forthcoming] article. Yes, we are dusty university attics. No, I don’t like it either. However… we’re not as well-funded as the uni presses think we are. Nor I don’t understand why some of these folks aren’t working with us, neither. Heaven forbid we should solve some of their preservation problems or give their backlist new distribution channels or rescue their out-of-print works or anything. But siloing and Not Invented Here is the heart of the difficulty, isn’t it? ...

I don’t mind the print-on-demand-for-pay models so much, but I do think trying to make direct money off e-publishing, especially of low-demand monographs, is a pipe dream. Bite the bullet and go open-access. The argument you then take to university brass is a cost-containment one: “This stuff needs to get published. It can get published at zero marginal cost and at the same time take advantage of greater reach from data-mining and web crawling, or it can get published in print at huge marginal cost and languish in warehouses because libraries can’t afford to buy it, or it can get published online with totally unnecessary (and possibly not recoupable) marginal costs of building and maintaining secure datacenters and fulfillment operations, or it can not get published at all and torpedo careers. You tell me what makes the most sense.” ...

Heather Morrison and three co-authors, E-LIS: The Open Archive for Library and Information Science, Charleston Advisor, July 2007.   Excerpt:

E-LIS is a service for authors, journals, and conference organizers. All documents in E-LIS are fully Open Access, reflecting the purpose of the E-LIS archive, to advance the Open Access philosophy by making available papers in LIS (library and information science) and related fields....

In summary, E-LIS is the largest of the Open Access archives for library and information science, and growing rapidly. All documents are Open Access, and more than half are peer reviewed. In addition to size, a key strength of E-LIS is its broad, global base and multilingual support....

Fernanda Peset and three co-authors, Use of OAI protocol and its impact in digital libraries: a case study in Spain, Portugal and Latin America, in ARD Prasad and Devika P. Madalli (eds.), Proceedings International Conference on Semantic Web and Digital Libraries (ICSD-2007), Bangalore, India, 2007, pp. 459-471.  Self-archived July 29, 2007.

Abstract:   The current communication approaches the situation of the development of repositories that use the Open Archives Initiative (OAI) protocol for data collection. These type of digital libraries are undergoing a worldwide boom. This work studies the current state of their [implementation] in Spain, Portugal and Latin America. In order to do so, the existing projects in the official records have been studied using a methodology beyond the existing records of repositories. It concludes that the situation in 2006 is fairly encouraging in so far as the number of projects, but that it is quite deficient as concerns the quantity of data stored.

Free Market Science, Nature Cell Biology, July 2007.  An editorial.  Excerpt:

...[T]he classical peer reviewed journal is not likely to be replaced anytime soon. However, that does not mean that a parallel internet based universe of information sharing (the market) cannot flourish. Over the past few years, Nature Publishing Group has set up a number of open access platforms for non-journal based information exchange. Databases such as the Molecule Pages and gateways (for example, [Signaling Gateway] and [Cell Migration]) aid human and bioinformatic navigation of published information. Blogs — be it subject centred ones such as Free Association, Action Potential and The Niche, our methods blog Methagora or newsblogs — aim to foster informal discussion, although involved online debates remain all too rare. Finally, our reference manager, Connotea, was described in our September 2005 editorial....

PLoS recently launched an innovative journal called PLoS ONE....

As this journal goes to press, the next step in web-based scientific exchange has set a number of science blogs abuzz: Nature Publishing Group is about to launch Nature Precedings, a platform that aims to facilitate sharing and discussing prepublication data....It is noteworthy that, similarly to PLoS one, the content carries a 'Creative Commons Attribution' licence, which requires only proper citation....

In essence, biologists will get a taste of what has been an integral part of the physical sciences community for decades in the form of preprint servers such as arXiv with its over 100,000 articles. The jury is out on how this service will be used....However, there is good cause to be optimistic, as even traditionally secretive research areas, such as pharma-research, are occasionally opening up with laudable open-access projects such as Synaptic Leap — a site that facilitates sharing data on neglected tropical diseases. We are keen to hear your views, perhaps via one of our blogs?

We hope that these parallel universes of information distribution will flourish side-by-side to aid navigation of the formidable knowledgebase accumulating in the biosciences....

Further reading [here].

Comment.  Also see my own list of Nature’s OA and near-OA projects, which is (interestingly) longer than the one in this editorial.  There is some controversy about how open some of these projects are.  But there is no doubt that some of the projects are full OA and that Nature is genuinely experimenting with different ways to widen access.  What’s new and encouraging here is that a Nature journal is editorializing its endorsement of OA, not just its willingness to experiment —even if it’s not an unqualified endorsement of OA but only of OA/TA coexistence. 

Update. On July 27 Nature launched an OA supplement on AIDS --too new to appear in the NCB editorial or in my earlier list.

ALPSP has launched an experimental hybrid OA program for its journal, Learned Publishing.  From today's announcement:

The Association of Learned and Professional Society Publishers (ALPSP), publisher of Learned Publishing...announces the launch of ‘ALPSP Author Choice’, an optional Open Access model whereby authors can choose to make the online version of their article freely available to all immediately on publication. The fee for this optional service is £1,250/$2,500 for members of ALPSP and the Society for Scholarly Publishing (SSP) and £1,500/$3,000 for non-members. ‘ALPSP Author Choice’ is being launched on a trial basis by ALPSP, the international association for non-profit publishers and those who work with them. The first article to be published under the new service appeared in the July 2007 issue of the journal  (Volume 20, No 3), and is entitled Going all the way: how Hindawi became an open access publisher by Paul Peters.

Learned Publishing already provides ‘Delayed Open Access’: all papers can be accessed free of charge 12 months after publication. The journal is also freely accessible to all ALPSP and SSP members, and to participants in the HINARI and AGORA projects.

The new open access option is being tested by ALPSP to see if it provides a viable way of sustaining the costs of peer review, editing and other aspects of journal publication.

ALPSP’s CEO, Ian Russell, said today: ‘Many of the over 350 members of ALPSP are trialling open access business models for their journals. We have always supported the need for serious debate backed by experimentation in order to help determine the effects, both positive and negative, of Open Access.  We see this initiative as a useful way of establishing if an author-side payment choice can be viable for a journal such as Learned Publishing, which currently involves a combination of subscription, advertising, and membership income to support its publication.’ ...

The ‘ALPSP Author Choice' service is being offered on a trial basis that will run for 12 months, before being reviewed by ALPSP Council, at which point the current subscription rates will also be considered.

Also see the ALPSP Author Choice page, which includes this new information:

Articles included in the 'ALPSP Author Choice' scheme will be made available under the Creative Commons 'Attribution-Noncommercial-No Derivative Works' 2.0 UK: England & Wales Licence.

The copyright in the article/s remains with the author/s, and ALPSP will acknowledge this in the copyright line which appears on the article. All authors are free to use the pre-publication version (after peer review, but not the published article/PDF) of their articles for the internal educational or other purposes of their own institution or company; mounted on their own or institutional website; posted to free public servers of preprints and/or articles in the relevant subject area; or in whole or in part, as the basis for further publications or spoken presentations. 'ALPSP Author Choice' further entitles authors to post the final PDF version of the article which may be posted as specified above, provided acknowledgement to the published original in standard bibliographic citation form is given, together with a link.

Comments. 

• This policy meets at least five of my nine criteria for hybrid OA journals.  It lets authors retain copyright, it uses a CC license, it provides OA to the published edition, and it allows self-archiving in repositories independent of the publisher.  In addition, ALPSP does not retreat its current greenish policy to allow even non-participating authors to self-archive, although self-archivers who don’t pay the Author Choice fee must still, as now, limit the use of the self-archived edition to the “internal educational or other purposes of their own institution or company”.  (I’m not endorsing this limitation; on the contrary, I criticized it in the June issue of SOAN and stand by my criticism.  I’m only saying that ALPSP has not retreated from the self-archiving policy that includes it.)
• On one point, the policy is confusing.  On the one hand, it wants to limit the use of self-archived articles by non-participating authors.  But on the other, it seems to apply the same limitation to participating authors.  (Participating authors may “post the final PDF version of the article which may be posted as specified above”; I take the word “above” to point to the terms for non-participating authors.)  That limitation is inconsistent with the policy to leave copyright in the hands of the author and inconsistent with the CC-NC-ND license.  It’s also just silly in light of the fact that the ALPSP's own copy of the Author Choice article is not subject to the same limitation.  Will ALPSP ask readers who learn something from an article whether they are affiliated with the author’s institution and whether they read the publisher’s copy or the self-archived copy?
• On one key issue, the policy is silent.  ALPSP doesn't say whether it wants to insert itself between authors and their funders by requiring authors to pay the Author Choice fee in order to comply with a prior and independent funding contract to provide OA to their peer-reviewed manuscript. 
• ALPSP does not promise to reduce the subscription price in proportion to author uptake.  Hence, it's adopting the "double charge" business model for Author Choice articles.

Ismael Peña-López, The personal research portal: web 2.0 driven individual commitment with open access, Knowledge Management for Development Journal, 3, 1 (2007) pp. 35-48. 

Abstract:   Researchers and research interests in developing countries are underrepresented in mainstream academic publishing systems. R