Open Access News

News from the open access movement

Saturday, March 08, 2008

Rebalancing fair use and anti-circumvention

Pamela Samuelson, A Reverse Notice and Takedown Regime to Enable Public Interest Uses of Technically Protected Copyrighted Works, a one-hour MIT World webcast of a talk recorded on November 6, 2007.  (Thanks to Gary Price.)  From the blurb:

...[In pushing for anti-circumvention legislation,]industries’ starting contention was that “you don’t have a right to make a fair use of something you don’t have lawful access to.” So they outlawed the tools for circumventing technical protections. But while breaking a DVD’s code is a violation of the law, Samuelson believes “you have lawful access to a DVD you bought, and you ought to be able to bypass it to make fair use.” So it should be OK to bypass TPMs to gain fair use, she says, and that’s what the debate is about.

Through recent court cases, fair use claims are nibbling away at prohibited circumventions. And a group led by Samuelson has come up with a remedy she calls “reverse notice and take down.” Through this, someone seeking fair use gives notice to a copyright holder that uses a TPM, and asks to make fair use of desired material. The copyright holder then has an obligation to either take down the TPM or explain why not. If the owner doesn’t respond at all, “the fair user can go ahead and hack as they want.” If the copyright owner objects, the fair user can seek declaratory judgment to enable fair use.

This puts a burden on the prospective fair user, acknowledges Samuelson, but over time, case by case adjudication “could establish principles to establish balance in anticircumvention rules.” ...

Lancet editorial on OA

Clinical knowledge: from access to action, The Lancet, editorial, March 8, 2008. (Thanks to Dave Chokshi.) Free registration is required for access to the full text.

When the Harvard Faculty of Arts and Sciences recently voted for a motion on open access, a cold shudder ran through the spine of the traditional publishing community. ...

The widespread interpretation of this policy is dramatic, even revolutionary. ... Advocates of open access have welcomed Harvard's policy. We too see great merit in a university collecting, archiving, and sharing the products of its intellectual endeavour directly with a wider audience. ... The Lancet understands that several leading universities are now preparing to follow Harvard's example.

Meanwhile, the open-access movement is progressing, although more slowly than many of its most zealous advocates would wish. Although BioMed Central has grown substantially during the past 3 years, it has yet to capture the quality end of the research sector. The Public Library of Science has been more successful. ... But open archiving has been less successful, although government mandates are likely to increase future publication on internet repositories.

How have traditional publishers responded to the research community's interest in wider access to medical science? With too little imagination, according to some critics. The priority for a few medical publishers has been cost-cutting and job losses. This strategy is unlikely to send a positive signal to the medical research community. ...

What should editors and publishers do? They need to cast dullness to one side, and become leaders instead of followers. They need to start shaping the physician's information world, instead of reacting to it. They need to pay less attention to their financial bottom line, and commit themselves to a larger, more inspiring mission—to join doctors in working to achieve the highest attainable standards of health for the communities they serve. Most medical publishers have forgotten that mission. It is time they returned to it.

Update. See also my comments at

Update. Also see the comments from Lancet readers on this editorial.

OA is socially responsible research

Stian Haklev, A “Fair Trade” logo for academic research?, Random Stuff that Matters, March 7, 2008.
... I have come up with a few [ethical] points that I would like to commit myself to, and which I think are important and decent in terms of doing [anthropological] research in developing countries.
  • All research output should be published through open-access channels, whether open-access journals, or journals that allow self-archiving. ...
The title of this blog post comes from the flippant idea I had this morning in conversation with my flat mates that perhaps some kind of a “Fair Research” designation should be developed, with a logo that could be applied to research materials, certifying that they had followed a certain number of practices. I realize that this would probably be very inflexible, as researchers are continually re-evaluating what practices are appropriate in any given situation. Yet, I would like to see a much stronger movement to force people to consider these ideas.

Limitations and exceptions for international copyright

P. Bernt Hugenholtz and Ruth L. Okediji, Conceiving and International Instrument on Limitations and Exceptions to Copyright, a report sponsored by the Open Society Institute, March 6, 2008.

The task of developing a global approach to limitations and exceptions (“L&E’s”) is one of the major challenges facing the international copyright system today. As mechanisms of access, L&E’s contribute to the dissemination of knowledge, which in turn is essential for a variety of human activities and values, including liberty, the exercise of political power, and economic, social and personal advancement. Appropriately designed L&E’s may alleviate the needs of people around the world who still lack access to books and other educational materials, and also open up rapid advances in information and communication technologies that are fundamentally transforming the processes of production, dissemination and storage of information. ...

A new international instrument on L&E’s offers a unique opportunity to coordinate, harmonize and balance the heightened (and new) standards of protection set forth in the successive Berne Convention Revisions, the TRIPS Agreement and the WIPO Internet Treaties. ... A global approach to L&E’s would further help: ... ii) to alleviate institutional weakness of States who need diffusion most ([developing countries] and [least developed countries]); iii) to counteract the recent shift to bilateralism and regionalism in international copyright policymaking and; iv) to constrain unilateral ratcheting up of global standards. ...

The minimum goals of an international approach to L&E’s would include: ... ii) facilitation of access to tangible information products; iii) promotion of innovation and competition; iv) support of mechanisms to promote/reinforce fundamental freedoms; and v) provision of consistency and stability in the international copyright framework by the explicit promotion of the normative balance necessary to support knowledge diffusion. ...

Comment. Copyright limitations and exceptions (such as fair use) are not necessary for OA. But limitations and exceptions facilitate access and re-use of non-OA materials in appropriate contexts, particularly (for our purposes) research and education.

Closed journals are data silos

David Wiley, On fully distributing the social network, Iterating Toward Openness, March 6, 2008.
... Facebook’s approach is a classic old-fashioned business model propped up by creating artificial scarcity where none actually exists. It’s much like the problems with the academic publishing businesses right now. The journal publishers want me to come up with a great research idea, go find funding for the work, do the work, write up the work, and then completely sign over all the rights to my work to them - so that I have to pay a license fee to use my own writing with my own students in my own classroom. Facebook wants me to have meet lots of people, make friends with many of them, spend my time connecting the dots between myself and my friends online, and label our relationships, so that Facebook can tell me I don’t have permission to use my own work. Springer, Elsevier, and Facebook… just another couple of data silos. ...
Comment. See this post for another comparison of Facebook to OA.

OA dictionary file for chemistry

Open Source Chemistry Dictionary is a dictionary file of chemistry terms, apparently released on February 8. It includes instructions for installing the file on Microsoft Word or The file is licensed under the Creative Commons Attribution License.

OA to criminology

Allan Scherlen and Matthew Robinson, Open Access to Criminal Justice Scholarship: A Matter of Social Justice, Journal of Criminal Justice Education, March 2008. Abstract:
The paper argues that criminal justice scholarship disseminated through the traditional journal subscription model is not consistent with social justice. Adoption of "open access" principles in publishing benefits both authors and readers through broader and more egalitarian dissemination of criminal justice literature. Moreover, when viewed in light of social justice theory, open access is a more just method of scholarly communication. After providing a brief outline of the history and basic aspects of open access, the paper uses the framework of the social justice theories of John Rawls and David Miller to argue why open access is more just than traditional subscription models of publishing and why criminal justice scholars and their associations must consider the importance of supporting open access initiatives and promoting the dissemination of scholarship as widely as possible if they are concerned about attaining justice for criminal justice scholarly literature.

Why IRs are important for smaller institutions

Allan Scherlen, Institutional Repositories: A Good Idea for North Carolina, North Carolina Libraries, Fall/Winter 2007. Abstract:
Librarians at universities in North Carolina are beginning to consider whether to establish electronic repositories where faculty and students can deposit copies of their scholarship for preservation and world-wide access. This article addresses a number of questions and concerns that arise, especially for librarians at smaller institutions, as they consider implementing an institutional repository (IR) program. Does a given institution have enough scholarly content to warrant building an IR? What does an IR provide that is not already available from publishers and database providers? Why would anyone search an IR? Is an IR too costly for a small institution with a limited budget to set up and maintain? The author argues that while building an IR collection requires a significant commitment in staff resources, the outcome of making the collective scholarship of North Carolina open access through IRs will be immensely beneficial to scholars, hosting institutions, students, and citizens of North Carolina and beyond.

Major book on OA and German copyright

Rainer Kuhlen, Erfolgreiches Scheitern - eine Götterdämmerung des Urheberrechts?  [Successful failure - a Götterdämmerung of copyright?] Verlag Werner Hülsbusch, 2008.  (Thanks to Klaus Graf.)  A new 644 page book, published in a priced/print edition, an OA edition in PDF (2.61 MB), and an OA edition in HTML (still under construction).   See especially:

  • Chapter 8, Open Access — kopernikanische Wende
    für die Öffentlichmachung und die freie Nutzung von Wissen [Open access - Copernican revolution for publishing (or making-public) and the free use of knowledge], pp. 457 - 552.
  • Chapter 9, Geschäfts- und Organisationsmodelle
    für Open Access [Business and organization models for open access], pp. 553 - 580.

PS:  Kuhlen holds the UNESCO Chair of Communications at the University of Konstanz.  For more background, see my past posts on him and his organization, Aktionsbündnis - Urheberrecht für Bildung und Wissenschaft [Coalition for Action - Copyright for Education and Research].

The book, BTW, is published under two different CC licenses:  the international version of the CC-BY license and the German version of the CC-BY-NC-SA license. 

More on OA for ETDs

Richard Fyffe and William C. Welburn, ETDs, scholarly communication, and campus collaboration: Opportunities for libraries, C&RL News, March 2008.  Excerpt:

For many libraries, ETDs (Electronic Theses and Dissertations) are the first targets for an institutional repository program, and represent an opportunity to engage graduate students and their faculty advisors in broader conversation about open access, intellectual property management, long-term management of digital content, and other scholarly communication issues....

Potential benefits for students and universities

  • Expressiveness. ETDs can incorporate a wider range of media than printed dissertations, allowing students to express their interpretations and research findings through color imagery, audio, video, and interactive media.
  • Visibility. ETDs increase the visibility of students and their advisors, potentially leading to improved job prospects or graduate school placement for students and better recruitment for colleges and universities.
  • Operational efficiency. Theses and dissertations typically begin life as digital documents. Accepting and storing them digitally can be more efficient for students and the institution alike. Students are relieved of the expense of printing multiple copies of lengthy documents, and university units are relieved of the inefficiencies of interoffice routing, collating, and storage of multiple copies.
  • Knowledge-sharing. Most institutions find that ETDs are being downloaded hundreds if not thousands of times. By comparison, most printed theses and dissertations are seldom used. ETDs appear to be an effective way of sharing original research both across and beyond the academy....

PS:  Also see my own argument for OA to ETDs (in SOAN for July 2006).

ACS blocks use of industry-standard chemical numbers in Wikipedia

Antony Williams reports that Chemical Abstracts Service (CAS, a division of the American Chemical Society, ACS) will  not allow the industry-standard but proprietary CAS Registry Numbers to organize the growing body of chemical information on Wikipedia.  Excerpt:

...A comment from Eric Shively at CAS can be found here online at Wikipedia. He comments:

Chemical Abstracts Service (CAS) objects to anyone encouraging the use of SciFinder and STN to curate third-party databases or chemical substance collections, including the one found in Wikipedia.  SciFinder and STN are provided to researchers under formal license agreements, under which the researchers agree to refrain from using these tools to build databases....

It’s an interesting stance. This at a time when there is more focus on facilitating information exchange. In an environment where people are using resources such as Wikipedia to source information one would assume that the availability of CAS numbers would actually be encouraged rather than so blatantly discouraged. It’s been said before that CAS numbers are like the phone numbers of the chemistry world....

Also see Peter Murray-Rust's first comment:

...Here the issue is that CAS identifiers have come to be accepted as a primary identifier system for chemistry - thus caffeine has the CAS number [58-08-2]....

CAS numbers are copyright CAS/ACS who have the legal right to regulate their use - as above. They would make excellent identifiers for the semantic web, except that they are closed. If I want to find out what [67-64-1] is I can only do this by paying CAS - about 6 USD for each lookup (e.g. on STN Easy). This immediately rules it out for any semantic web application which assumes that resolving links is free. Wikpedia tells me that this number corresponds to acetone (nail varnish remover) but they now do not have the freedom to do this....

An open system of identifiers would be highly valuable in developing the chemical semantic web and increasing quality. The closed and restrictive practices of CAS make it more difficult to create Web 2.0 applications in chemistry....

[Robert Massie, President of CAS] has already hinted that there is systematic stealing of CAS material. I do not condone this, but neither do I condone the closed control of a valuable system of identifiers....

And PMR's second comment:

Wikipedia has between 1000 and 2000 chemical substances (ca 0.01% of the total number of substances in CAS)....

The American Chemical Society - hitherto a respected learned society - is now telling a voluntary community of scholars that it forbids them to check their facts. It is preventing them disseminating chemistry.

I wonder if there is anything in the history of learned societies that matches this action....There are so many positive things they could have done.

As it is they have done the following:

  • re-asserted their position that they care for revenue more than supporting the wider chemical community
  • re-advertised themselves as one of the least progressive learned societies
  • alienated a growing number of young scientists who look to the Web as a critical part of the future of chemistry...

The use of CAS numbers has been abandoned by organisations such as PubChem for exactly this reason. PubChem now has nearly 20 million substances....It’s highly respected (although ACS lobbied the US government to limit Pubchem’s activities). It is part of the NIH and now - with the NIH mandate - effectively safe from the ACS. It provides a credible alternative.

We (including Wikipedia) should now switch from using CAS numbers to using PubChem IDs wherever possible....

Update.  Also see Glyn Moody's comment, The World's Leading Anti-Scientific Society.

Update.  Also see the follow-up posts from Cameron Neylon and Antony Williams on the specific problem of shifting from the closed CAS numbers to some open alternative.

Slow progress under U of Zurich's OA mandate

Klaus Graf has done a new review of the OA mandate at the University of Zurich.  When he first reviewed its progress last year (March 2007), he found that the compliance rate was very low.  In his new review, he finds that only 252 documents were deposited in ZORA, the UZ repository, during 2007, and only 25 so far in 2008.   By contrast, the U of Freiburg repository added about 1,100 documents without a mandate.  Read his new review in the original German or Google's English.

OA mandate at the U of Tasmania

The University of Tasmania is preparing to implement an OA mandate recommended by its Research College Board.  (Thanks to Arthur Sale.)  Yesterday Jo Laybourn-Parry, the UT Pro Vice-Chancellor for Research, sent this message to the UT community: 

The Research College Board has recommended that all publications from 2007 onwards be mandated for entry into a UTAS digital repository such as ePrints.  I am keen for this to happen.

We are aware that the Labor Government's proposed Excellence in Research for Australia (ERA) will concentrate on metrics such as citations, and ensuring that our publications are publicly available through the repository will help position us positively. The earlier the articles are in the repository, the more citations they will attract, especially in the first few months after publication.

Many of you have already placed all or some of your publications into ePrints.

I am particularly concerned that you are not put in the position of entering data twice, and I am aware that you will soon have completed entering your 2007 publications into PES [Publication Entry System].  Therefore I have asked our technical staff to work on an automatic upload of all 2007 PES entries to ePrints. This will take place over the next month....

Comment.  Kudos to all involved at UT.  The UT School of Computing has had its own OA mandate since at least August 2006.  The new university-wide mandate would be Australia's third, after mandates at the Queensland U of Technology (January 2004) and Charles Sturt University (circa January 2008).

More on the February DFG-DINI conference

Ulrich Herb, Vernetzung tut not: Open Access 2.0?  Telepolis, March 8, 2008.  A report on the DFG-DINI conference, Förderung der wissenschaftlichen Informationslandschaft in Deutschland: Chancen und Strategien beim Aufbau vernetzter Repositorien (Berlin, February 26-27, 2008).  Read the German original or Google's English.

Friday, March 07, 2008

American U. of Rome launches IR

The American University of Rome has opened an institutional repository, as announced yesterday (short version, long version).

Acta Crystallographica E converts to OA

According to a post yesterday by Peter Murray-Rust, Acta Crystallographica Section E: Structure Reports Online has converted to OA. The journal is published by the International Union of Crystallography and is peer-reviewed, with monthly issues. Apparently the journal previously offered hybrid OA, as do several other IUCr journals. The publication fee is $150, as reported here; waivers are available for authors from developing countries, and discounts are available for authors with an institutional subscription to Acta Crystallographica C. Articles will be published under the Creative Commons Attribution License, and authors do not transfer copyright to the journal.

I haven't seen any statement from the journal or publisher about the conversion, but we'll add them here is they surface later.

Wall Street Journal on OA: access barriers are "bad for capitalism"

Daniel Akst, Information Liberation, Wall Street Journal, March 7, 2008.  Excerpt:

If your child has a life-threatening disease and you're desperate to read the latest research, you'll be dismayed to learn that you can't -- at least not without hugely expensive subscriptions to a bevy of specialized journals or access to a major research library.

Your dismay might turn to anger when you realize that you paid for this research. Through the National Institutes of Health alone, American taxpayers funnel more than $28 billion annually into medical research. That's leaving aside the billions more in public spending on state universities or the tax exemptions granted for gifts to private campuses.

American institutions of higher education are knowledge machines of unprecedented fecundity, but much of the knowledge they produce is locked up in high-priced scholarly journals that most people can't easily get. Citizens thus find themselves in the position of paying for research and then paying again to buy it back from academic journals whose prices have been spiraling upward....

But change is on the horizon. Congress has mandated that by April 7 papers arising from NIH-sponsored research -- roughly 80,000 of them a year -- be made freely available in the federal PubMed [Central] database....

Another blow for open access to scholarly research was struck recently by Harvard's arts and sciences faculty, whose members voted to publish on the Internet for all to see -- gratis....The faculty members will still publish in expensive journals, but the move to put the same materials on the Internet is a stake poised at the heart of a vampire that has been sucking dollars out of academic institutions for years through the ever-sharper bite of subscription prices....

Other than in the realm of life-saving medicine, why should any of this matter to nonacademics? Well, for one thing, barriers to the spread of information are bad for capitalism. The dissemination of knowledge is almost as crucial as the production of it for the creation of wealth, and knowledge (like people) can't reproduce in isolation....

Keeping knowledge bottled up is also bad for the world's poor; indeed, opening up the research produced on America's campuses via the Internet is probably among the most cost-effective ways of helping underdeveloped countries rise from poverty....

Microsoft to digitize Princeton seminary books

Princeton Theological Seminary and Microsoft yesterday announced a partnership to digitize the school's public domain library holdings. The digital editions will be OA through Microsoft's Live Search Books service. The collection includes "religious texts from the early history of printing, editions of John Calvin and John Knox, writings of the Puritans, and hymn verses of Isaac Watts." See the announcement from Microsoft or Princeton.
Microsoft will give the Seminary digital copies of all the materials and allow them to be shared with noncommercial institutions and nonprofit organizations ...

The digitization will be performed by the Internet Archive ...

FWF strengthens its OA policy from a request to a requirement

Austria's Förderung der wissenschaftlichen Forschung (Fund to Promote Scientific Research, or FWF) has strengthened its OA policy.  (Thanks to the Informationsplattform Open Access and Daniel Mietchen.) 

The older policy, adopted in October 2006, applied only to project leaders and merely requested OA for FWF-funded research.  The new policy applies to all employees in FWF-funded research projects and requires OA.  FWF will grant exemptions only when compliance would be unlawful --which may be whenever the publisher does not allow OA archiving. 

Like other funder policies, this one is strictly about green OA.  But FWF also supports gold OA, or OA journals.  It encourages grantees to publish in OA journals and allows them to use grant funds to pay publication fees at fee-based OA journals.

Read the new FWF policy in German or Google's English.  Also read the March 6 press release in German or Google's English.

Jan Velterop leaves Springer for KnewCo

Jan Velterop is leaving his position as Open Access Director at Springer to become the CEO of KnewCo.  From Springer's announcement yesterday:

Jan Velterop, Springer’s Director of Open Access, and a driving force behind Springer Open Choice, will be leaving Springer to pursue a new career as CEO of KnewCo Inc....

Velterop is one of the most prominent figures of the open access community. He joined Springer in August 2005 from BioMedCentral, an established open access biomedical research publisher, where he was Publishing Director.

Over the past years at Springer, Velterop was instrumental in both outreach to the research community and also in familiarizing Springer’s publishing professionals with the possibilities that open access can deliver for the company.

“When I joined Springer to promote Open Choice, I did so knowing that it would not be enough to simply promote this service to authors in the scientific community. I realized that a large part of my role would be to convince publishers that open access was not a threat to established publishing companies, but rather an opportunity. I am happy to say that the reaction from authors and institutions was positive and that my colleagues have come to accept that Open Choice can be a valid alternative to the subscription model, especially in some disciplines,” said Velterop.

Derk Haank, Springer’s CEO said, “Jan was a key component of our approach to open access. Our belief was that if the community wanted the option to publish using open access, we should, at the very least, enable them to do so. During his time with us, Jan has used his considerable publishing know-how and his standing in the community to help make Springer Open Choice a robust and well-known service. We wish him well in his new endeavors.”

Springer will continue to develop Open Choice and remains committed to growing the share of articles published using open access....

KnewCo is the company behind the OA WikiProfessional project, which has already launched WikiProteins.  For some background, see this February 2007 Nature article on the project and my blogged excerpt

From the KnewCo mission page:

Knewco has a radically different response to the unprecedented challenge of managing the exponential growth of knowledge....A company founded by scientists for scientists, Knewco's mission is to deploy its advanced semantic technology to accelerate key elements of the scientific process, and specifically semantic enrichment of web-published content, to support on-line knowledge discovery....

Knewco believes that knowledge is more than what is contained in publications in that it includes the associative power of the human mind of the scientist. This associative power will be accelerated when scientists and knowledge users are empowered to invent based upon knowledge that has been mined and moved along the following continuum:

  • Simple flat text is converted into semantically enriched pages;
  • Reading documents is transformed to meta analysis (added value on top of just information;
  • Textual research time is maximized when mined information allows one to go from reading to consulting....[or] from 'mined to mind.' ...

Thus, this Knewco mined data would no longer be (only) text per se, but rather the first nuggets of embryonic knowledge, i.e., Knowlets™, which is computer readable and is associated with the relevant experts as a stepping stone to new knowledge. Helicopter views on knowledge domains are an essential and long overdue element of the scientific process....

Comment.  Jan was one of the framers of the Budapest Open Access Initiative, the first publisher of BioMed Central, and the first Open Access Director at Springer --or for that matter, at any major, predominantly TA publisher.  He's a pioneer of OA and will take that seasoned perspective to KnewCo.  I wish him well.

Thursday, March 06, 2008

State of open bibliographic data

Rufus Pollock, Open Bibliographic Data: The State of Play, Open Knowledge Foundation Weblog, March 6, 2008.

Given the public role of libraries and the fact that bibliographic metadata (i.e. the material in library catalogues) doesn’t seem that exciting from a commercial point of view you might think that, of all the types of data out there, it would be bibliographic data that would be the most open. You might even think, given the public-spiritedness of librarians, that this is the kind of area where not only could it be openly available but it would be openly available (in nice little bzip or gzipped dumps …).

In fact the situation is quite the opposite. Most libraries appear to implicitly or explicitly exert rights over their data with some libraries licensing access to their catalogue data for substantial sums of money. The following lists some of the examples (both closed and open) that we know of ...

See the post for the list.

OA for improving reference service

Steve Lawson, Open Access and the reference librarian, See Also..., March 4, 2008.

... The stereotype around librarians and Open Access is that librarians are on board mostly because we think that we’ll end up getting to ax expensive journals and thus solve our “serials crisis.” (Can a “crisis” last twenty years?)

I’m sure a lot of librarians do think that, especially directors and heads of collection development and others who have to write checks to Elsevier and similar corporations. But for the reference librarian, I think the thought process is a little different.

Instead of thinking of the up-front cost of the journal, we reference librarians are thinking more about helping people one-on-one. ...

So it is a big drag if instead of being able to give someone the perfect source, we instead end up with just a citation and not the full text in hand or online. It is no fun at all if instead of a full text PDF we find a web page demanding a credit card number to buy the three-page article for thirty bucks. Where is the satisfaction in telling someone to go to ILL? That is an itch unscratched. ...

Report from Open Access Collections workshop

New OA journal on tropical conservation

Tropical Conservation Science is a new peer-reviewed OA journal publishing "research relating to conservation of tropical forests and of other tropical ecosystems". The inaugural issue was released in March 2008. See the March 3 press release.

The journal is published by, an environmental science news site, and will be published quarterly. Submissions are accepted in English, Spanish, Portuguese, French, German and Chinese; submissions in a language other than English will be published alongside an author-supplied English translation. The submission guidelines ask authors to agree to the Creative Common Attribution License, but I don't see the license tagged on the first issue. (Thanks to Bio-Medicine.)

Parkinsons genome data added to NIH database

Genome-wide association study on Parkinson's disease finds public home at NIH, press release, March 4, 2008.

Data from one of the first genome-wide association studies (GWAS), which focused on Parkinson’s diseases and was funded in part by The Michael J. Fox Foundation for Parkinson’s Research (MJFF), is now being made available to researchers through the National Human Genome Research Institute (NHGRI) and the National Center for Biotechnology Information (NCBI), both of the National Institutes of Health (NIH). NHGRI hopes to speed up research by making previously unavailable GWAS data sets publicly available to the research community. ...

[The] study will be added to dbGaP, the database of Genotypes and Phenotypes operated by the National Library of Medicine’s National Center for Biotechnology Information. The dbGaP database contains individual-level data on genotype (an individual’s genetic makeup), and phenotype (observable traits and characteristics). ...

For researchers who want to view the ... data, dbGaP offers two levels of access. The first is open access, where certain data are available without restriction, and the second is controlled access, which requires authorization. The open-access section allows users to view study documents that do not risk identifying individual participants, such as protocols and summaries of genotype and phenotype data. The controlled-access portion of the database allows approved researchers to download individual-level genotype and phenotype data from which the study participants’ personal identifiers, such as names, have been removed. ...

Although personally identifying information is not included in the database, concern remains that it may someday be possible to identify someone based on their genetic profile. For this reason only researchers agreeing not to attempt to identify individuals in the database will be given access to the data, as outlined in NIH's Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies (GWAS) ...

See also past OAN posts on dbGaP.

Update. See also Jim Till's comments.

On OA for publicly-funded research in history

Tom Scheinfeldt, Federal Funding for the Humanities, Found History, March 4, 2008.
... [F]ederal funding allows—and increasingly demands—us to give all of our resources away at no cost. While our society is getting increasingly closer to eliminating the first digital divide, where network access was determined by demography, we are nevertheless seeing a second digital divide, where many of the best sources of networked information are available only by paid subscription. Small school districts, home schoolers, small businesses, and ordinary taxpayers without a university or corporate affiliation usually cannot afford access to important information resources like LexisNexis and ProQuest. By freeing us from the burdens of cost recovery that private information providers face and private foundations increasingly impose, federal funding helps us provide pertinent, high quality, open access information resources that reach not only the well heeled and well connected, but ordinary Americans. ...

OA repositories for scientific data

Peter Murray-Rust, Repositories for Scientific Data (at OR08), A Scientist and the Web, March 4, 2008. An abstract of a forthcoming keynote address at Open Repositories 2008 (April 1-4, 2008, Southampton).

Scientists are producing data at an ever increasing rate (”the data deluge”) due to automated instruments, image capture and simulation tools. This holds the promise of “data-driven science” where scientific discovery can be made by linking or mining existing data. The reality is, unfortunately, that almost all this data is lost. Although some publishers welcome data as an adjunct to “fulltext”, many do not and most do not have the domain expertise to store and curate the data. And although “big science” (such as high energy physics, geospatial imaging, genomics and structural biology) can often provide domain repositories (e.g. in bioinformatics) most science (”the long tail”) cannot.

There is an urgent need to address this problem. Current Institutional Repositories (IRs) are geared to storing and disseminating scholarly manuscripts and while some are prepared to accept other digital artefacts the practice is fragmented and does not scale. We need to define “Data Repositories” (DRs) which serve the interests of the scientists directly. This is highly domain-dependent and there is no one-size-fits-all solution. ...

Wednesday, March 05, 2008

Leaving your literary estate to the public domain

In the U.S., copyright on works of individual authorship (as opposed to corporate authorship; includes joint authorship by more than one individual) lasts for 70 years after the author's death. In some other jurisdictions, it lasts for life + 50. This copyright, if not opened such as by a Creative Commons license, will act as a barrier to the use rights which form the BBB definition of OA. That's a long period to wait for OA. Plus, the author's death makes it harder to locate the rightsholder (who inherited the copyright), making it more difficult to secure permissions and increasing the likelihood the author's work will become orphaned.

This page has been circulating around the Web in recent days (apparently since February 26 or later). It depicts a sticker which an individual can apply to her ID card, in the manner of an organ donor sticker, indicating the individual wishes her copyrights to be released to the public domain upon her death.

Tuesday, March 04, 2008

OA collection of Audubon illustrations

The University of Pittsburgh library on March 3 released an OA collection of bird illustrations by John James Audubon. Audubon is the noted naturalist for whom the Audubon Society is named. The illustrations are from Birds of America and Ornithological Biography. (Thanks to Wired Campus.)

Google to expand OA book digitization

Jeffrey R. Young, Google Plans to Expand Book-Scanning Partnerships, Wired Campus blog, March 4, 2008.

The news from Marissa Mayer, Google's vice president for search products and user experience: Google will expand its Book Search project, which has scanned more than a million books to date with partner libraries and other institutions. The post is short on details, but there may be more in the podcast.

3 PLoS journals move to Topaz platform

At some point since February 26, PLoS Computational Biology, PLoS Genetics and PLoS Pathogens -- OA journals published by the Public Library of Science -- began their move to the Topaz software platform, as announced here by Mark Patterson. PLoS ONE and PLoS Neglected Tropical Diseases already use the Topaz platform.

... [T]he Topaz platform will bring some valuable additional benefits. Authors of research articles, for example, will see an increase in publication speed, as a result of a streamlined publication process. ... We are also introducing a workflow that will help authors who use Latex. Finally, we have a mechanism for highlighting any corrections that need to be made to published articles – this can take place within days, instead of the usual lag of several months ... Once these new processes are bedded in, we hope to shave at least two-three weeks off the time to publication.

Readers will notice some more options when they are looking at the articles – notes can be added, a discussion can be started or joined, and the article can be rated. ...

One final point about these changes concerns the finances of the journals. The streamlined production and web hosting via Topaz brings cost savings too, which will take the journals very close to economic self-sufficiency. If they continue to grow at their current trajectories, one or two of the community journals will be supporting themselves by the end of this year. ...

The migration of PLoS Computational Biology, PLoS Genetics, and PLoS Pathogens places five of our journals on the open source publishing platform called Topaz. PLoS Biology and PLoS Medicine will follow later this year. ...

As announced yesterday, they're still working out some software troubles with the new platform, so you may encounter errors if you visit the sites at this time.

WIPO Committee on Development meeting in Geneva

The World Intellectual Property Organization's Committee on Development and Intellectual Property is meeting in Geneva from March 3-7, 2008.

WIPO is a UN agency which administers major treaties regarding international copyright and related policies, and therefore somewhat of a policy-making body for member states. In addition to member states, numerous NGOs are accredited to WIPO as observers, including OA proponents such as the Library Copyright Alliance, the Open Knowledge Foundation, and Electronic Information for Librairies.

This is the first meeting of the Development Committee, created to oversee implementation of WIPO's new Development Agenda (i.e., to explicitly acknowledge and promote the goal of development through WIPO's policies and activities). The committee will discuss how to implement a list of 45 proposals, agreed upon in 2007. Topics include access to knowledge.

For more information, see coverage at Intellectual Property Watch and by Knowledge Ecology International. The Electronic Frontier Foundation has posted the list of proposals, with proposals to be considered for "immediate" implementation highlighted in yellow.

Update. See also past OAN posts on the Development Agenda.

Toolkit for authors, researchers, and repository staff

On February 28, VERSIONS (Versions of Eprints – a user Requirements Study and Investigation Of the Need for Standards) released its toolkit for authors, researchers, and repository staff. Among its "top hints":
  • ... Consider carefully how you will disseminate your work before signing any agreements with publishers and keep a copy of your signed agreements
  • Deposit your work in an open access repository and think of your readers by guiding them to your latest and published versions ...

On the variance in Hindawi's publication charges

Heather Morrison, Hindawi Article Processing Charges: Range, Median / Mode, Average, The Imaginary Journal of Poetic Economics, March 2, 2008. Of 102 journals by OA publisher Hindawi, processing fees range from free (3 journals) to €1,000, with a median and mode of €400 and a mean of €476.

Less than 10% of OA psychology journals charge a publication fee

Heather Morrison, Less than 10% of Open Access journals in psychology charge a publication fee , The Imaginary Journal of Poetic Economics, March 2, 2008. Out of 84 psychology journals listed in the Directory of Open Access Journals, only 8 charge a publication fee.

For more on no-fee journals, see:

On damage from the lack of OA

Heather Morrison, The Access Gap in British Columbia, The Imaginary Journal of Poetic Economics, March 1, 2008.
Abstract: This post illustrates the gap in access when we rely on subscriptions, a gap that is huge even in a have province like British Columbia, in a wealthy country like Canada. A researcher who does not see the costs of the subscriptions, may never see the gap. A student, while at a research university, has ready access to tens of thousands of scholarly journals, backed up by a document delivery department that can fill any remaining gaps. A student who graduates and moves to a smaller town or rural area will still have better access than many of the people in the world, thanks to BC's excellent public library system; however, this is still less than 5% of what the alumnus had access to as a student. A small public library cannot begin to dream of providing an equivalent service to the university, with much fewer staff and a much greater gap to fill.
See a reaction post by Ryan Deschamps, Does a Fish Know It’s Wet? : Access to Scholarly Journals in Public Libraries, The Other Librarian, March 3, 2008.

... Morrison ... uses the example of typical alumnus who, as a student, has access to just about everything under the sun, research-wise, but who has their access reduced to less than 5% of they had before. Considering many of these alumni will be professionals — working as public servants, lawyers, doctors, or whatnot — this is a great concern. One that, clearly, public libraries ought to address if they were not so busy keeping up with all their other services.

The group Morrison does not mention, however, is the group that most concerns me — those who do not know scholarly journals exist in the first place, or who, for one reason or another do not care. ... [I]t is hard to say what choices people would make if they had a choice among the blogosphere, wikipedia, mainstream news and scholarly literature and full awareness of latter’s role in understanding the truth.

A good example is the pseudo-myth of the online predator. As Bruce Schneier has uncovered, most parents’ fears of online predators lurking after their children are unfounded. The mainstream news, and even Google for a good while, would suggest differently — it is the scholarly literature that is best able to handle such a question without blurring the issue behind sensationalism and fear. If parents were more easily able to access and evaluate such literature, there could be a lot of headaches saved all over the world on this issue. Climate change is another obvious issue that comes to mind as well. Ditto most health scares. ...

Alpha release of CiteSeerX

The alpha release of CiteSeerX, the "Next Generation CiteSeer", was announced on March 3.

New version of Charles Bailey's e-publishing bibliography

On March 3, Charles Bailey announced Version 71 of the Scholarly Electronic Publishing Bibliography. See the announcement for a description of changes.

OA database for structural biology

Proteopedia is a new OA database for "making structural biology clearer for chemists and biologists by linking textual content to 3D structures". (Thanks to Peter Murray-Rust.)

Book prospectus from John Willinsky

John Willinsky, Could Locke Still Be the Key? Part I, Slaw, March 2, 2008. Willinsky is the author of The Access Principle and director of the Public Knowledge Project.

What follows is the opening of a book prospectus I am in the midst of developing for a work on John Locke and what I refer to as the “intellectual properties of learning.” ... Putting this in Slaw follows on recent Web 2.0 data-mashups that would drag the book-in-progress into the network, setting it adrift in the blogosphere and giving readers a chance to peer and prod. ...

[T]he root of the problem lies in treating both a study of the American revolution and a song by Justin Timberlake as indistinguishable forms of intellectual property over which the copyright holder can exercise monopoly rights for decades. Lumping all intellectual properties together like this is simply not the best thing for what John Locke referred to as “the common-wealth of learning,” ... The book will set out how Locke is the source of both problem and resolution within learning’s oddly mixed knowledge economy. After all, no one has had a greater influence over the prevailing theory of property. And yet within his theory, this book will show, is an overlooked place for the distinct intellectual properties of learning.

This book will use the place of learning within this theory of property to work out a series of principles for sorting out the current contradictions afflicting the economics of research and scholarship. ...

Feb/March issue of Research Information available

The February/March 2008 issue of Research Information is now available. OA-related articles include:

Integrating institutional and funder mandates

Stevan Harnad, How To Integrate University and Funder Open Access Mandates, Open Access Archivangelism, March 2, 2008.
SUMMARY: Research funder open-access mandates (such as NIH's) and university open-access mandates (such as Harvard's) are complementary. There is a simple way to integrate them to make them synergistic and mutually reinforcing:

Universities' own Institutional Repositories (IRs) are the natural locus for the direct deposit of their own research output: Universities are the research providers and have a direct interest in archiving, monitoring, measuring, evaluating, and showcasing their own research assets -- as well as in maximizing their uptake, usage and impact.

Both universities and funders should accordingly mandate deposit of all peer-reviewed final drafts (postprints), in each author's own university IR, immediately upon acceptance for publication, for institutional and funder record-keeping purposes. Access to that immediate postprint deposit in the author's university IR may be set immediately as Open Access if copyright conditions allow; otherwise access can be set as Closed Access, pending copyright negotiations or embargoes. All the rest of the conditions described by universities and funders should accordingly apply only to the timing and copyright conditions for setting open access to those deposits, not to the depositing itself, its locus or its timing.

As a result, (1) there will be a common deposit locus for all research output worldwide; (2) university mandates will reinforce and monitor compliance with funder mandates; (3) funder mandates will reinforce university mandates; (4) legal details concerning open-access provision, copyright and embargoes will be applied independently of deposit itself, on a case by case basis, according to the conditions of each mandate; (5) opt-outs will apply only to copyright negotiations, not to deposit itself, nor its timing; and (6) any central OA repositories can then harvest the postprints from the authors' IRs under the agreed conditions at the agreed time, if they wish.

University of Bergen drafting an OA policy

Kjerstin Gjengedal, Harvard makes Open Access compulsory, På Høyden, March 3, 2008. In light of recent move by Harvard, Norway's University of Bergen is considering an OA policy:
... Vice-Chancellor Sigmund Grønmo maintains that [University of Bergen] wishes to increase the use of open access, and informs that a case is being prepared which will be presented to the board shortly. ...

Monday, March 03, 2008

Open Knowledge Definition in Spanish and Catalan

The Open Knowledge Foundation today announced that its Open Knowledge Definition has been translated into Spanish and Catalan.

Interview on OA to health statistics

An interview with Sally Stansfield - Who owns the information? Who has the power?, Bulletin of the World Health Organization, March 2008. Stansfield is executive secretary of the Health Metrics Network.

... Q: Are people in the developing world aware that they are missing out on the kind of information that is taken for granted in industrialized countries?

A: No, in general the statistical services in countries are managed by governments and they are used to serve the needs of government officials, so it is rare that those statistics are systematically disseminated to citizens. It is rare [also] that citizens see it as their right to be able to hold their government accountable using those statistics. ...

Sunday, March 02, 2008

February update from RePEc

The February 2008 report from the Research Papers in Economics project, released today, includes the news that its IDEAS service moved to a new server with a faster Internet connection. The post also reports a significant increase in traffic over the previous February, and other milestones passed.

CC blog aggregator launches

Creative Commons today launched Planet Creative Commons to aggregate posts from the official CC blog, blogs of national jurisdictions, and CC community members. Announcement here.

Lessons from an OA book experiment

The main lesson, apparently: give readers the book in a useful format, not a crippled one. The experiment in question is a free download of Neil Gaiman's novel American Gods.

See commentary at Free Government Information and Boing Boing, both dated March 2.

See also Gaiman's comments on why free reading is important (to fiction, but echoing Heather Morrison's comments about aiming for obscurity).


I'll be on the road Monday-Thursday with few opportunities for blogging or email.  But Gavin will be on the job and I'll start to catch up myself on Friday.

March SOAN

I just mailed the March issue of the SPARC Open Access Newsletter.  This issue takes a close look at the new OA mandate adopted by a unanimous vote of Harvard's Faculty of Arts and Sciences.  The round-up section briefly notes 109 OA developments from February.

Update.  I'm having trouble getting the email edition out to all subscribers, and unfortunately I may have to leave town before I can solve this problem.  If I do, remember that the web edition is online and unaffected.