Open Access News

News from the open access movement

Saturday, December 22, 2007

Linking from a PubMed abstract to OA full-text on Michigan's IR

Sandy Swanson, University of Michigan’s digital repository now available through PubMed, MHSLA blog, December 21, 2007.  (Thanks to Charles Bailey.)  Excerpt:

From MLA Focus:

Deep Blue and PubMed LinkOut: A Higher Profile for University of Michigan Research

Researchers who find articles by University of Michigan (UM) authors in PubMed can now directly-and for free-link to the full text using Deep Blue, UM’s digital repository, via PubMed’s LinkOut feature. Deep Blue is an online archive that preserves and provides access to UM intellectual and creative work. It is the first institutional repository to provide such links.

To see all the items in Deep Blue that are in PubMed, enter “loprovdeepblue [sb]” in the PubMed search box. At this posting, there are over 8,800 articles.

I don’t find a way to add the Deep Blue collection in the LinkOut submission utility, and I don’t see a “free full text” button on the abstracts. However, Deep Blue’s link icon can be added to a library’s shared MyNCBI account; use Configure > PubMed > LinkOut > Miscellaneous > MLibrary (Deep Blue) (DeepBlue).

Update.  See Stevan Harnad's comment, Deposit institutionally, harvest centrally, Open Access Archivangelism, December 23, 2007.  Excerpt:

...Congratulations to the University of Michigan and PubMed for adding this excellent and timely feature (to both PubMed and Michigan's Institutional Repository [IR], Deep Blue)! But why stop there?

The implications are obvious: Central Repositories [CRs] (like PubMed Central and Arxiv and CogPrints) should not be deposited in directly, because that merely complicates and competes with a systematic worldwide policy of depositing all institutional research output in each institution's own, OAI-compliant IR. Institutions are the primary research providers. They have the greatest stake in ensuring that all their own research output is maximally visible, accessible, and usable, thereby maximizing the institution's research impact. Institutions are also the best placed to showcase, monitor and reward the self-archiving of their own research output.

All institutions should mandate that all their research article output must be deposited in their own IR. Research funders (like NIH) should also mandate that all the research article output from the research they fund must be deposited in the fundee's own institution's IR.
Then CRs like PubMed Central as well as indexers like PubMed (or Thompson ISI or Scopus or Google Scholar) can either link to or harvest from the network of interoperable, OAI-compliant IRs....

And remember that the Web era means distributed content provision and central harvesting, Google-style. It is not, as in paper days, that all the content needs to go in one central physical space.

Swan, A., Needham, P., Probets, S., Muir, A., Oppenheim, C., O’Brien, A., Hardy, R., Rowland, F. and Brown, S. (2005) Developing a model for e-prints and open access journal content in UK further and higher education. Learned Publishing 18 (1). pp. 25-40.

Abstract: A study carried out for the UK Joint Information Systems Committee examined models for the provision of access to material in institutional and subject-based archives and in open access journals....A "harvesting" model is recommended....

First beta of Fedora 3.0

The Fedora Commons has released the Fedora 3.0 Beta 1 for testing.  For details, see Thursday's announcement.

More on the People's Open Access Education Initiative

Richard F. Heller and six co-authors, Capacity-building for public health, Bulletin of the World Health Organization, December 2007.  Excerpt:

...The free and open-source software (FOSS) movement provides inspiration for an affordable and credible solution [to the problem of inadequate medical training in low and middle income countries]....

In the education field, there are now parallel developments of Open Educational Resources (OERs) with an ever-expanding range of high-quality online resources that are freely available through the Internet. There is major international interest and commitment in the use of OERs, as demonstrated by the UNESCO International Institute for Educational Planning’s Open Educational Resources Community....

Web 2.0 refers to the evolution of Internet use from the one-way transfer of information (Web 1.0) to collaboration and participation among users. In the context of education, students are not just recipients of education but are involved in collaboration in learning activities, expressed as eLearning 2.0 or Education 2.0. Education 3.0 is considered to be the extension to this, where open-access materials are created and adapted by various collaborating groups and individuals including the students....

Building on these needs and inspirations, we have proposed an educational initiative based on the open education resources available on the Internet. If we can develop an educational context around the open resources that are freely available, this might provide a low-cost solution to capacity-building in developing countries. This added context would include:  a gateway or repository for accessing materials that are linked to identified competence development and can be modified to reflect local settings; the teaching or facilitation of learning through online-focused discussions; a system for accrediting learned competences.  We have termed this the People’s Open Access Education Initiative (Peoples-uni)....

PS:  Thanks to Gavin Yamey for the alert and for background on how PLoS is supporting the POAE.

Scientific breakthroughs of 2007

Science Magazine is providing free online access to its series of articles on Breakthroughs of the Year 2007.

ETD collections in Italy

Paola Galimberti and Marialaura Vignocchi, Time for a change: the Italian CRUI-Open Access Working Group’s action for a national e-theses provision service, in Proceedings ETD 2007 - Added Value to e-theses, Uppsala 2007.  Self-archived December 22, 2007.

Abstract:   The paper intends to present the status of e-theses collections in Italy, focusing on the major drivers for change that can contribute to create the basis of a national e-theses provision service able to collaborate with other international services. Finally, it illustrates the e-theses project of Bologna University as a case study of a viable integrated system offering added-value services.

Update.  Also see the CRUI guidelines themselves (in Italian) and this short summary in English.

Podcast on launch of a new OA journal

MIT linguistics professor Kai von Fintel has made an 11 minute podcast on the founding the new OA journal, Semantics and PragmaticsFrom MIT's blurb:

The fourth episode in a new series of podcasts on various aspects of scholarly publishing & copyright is now available.

In this episode, we hear from Professor Kai von Fintel, Professor of Linguistics at MIT, whose research areas are in semantics, pragmatics, and philosophy of language, and the intersections among them.

Professor von Fintel discusses the launch of a new open access journal, Semantics and Pragmatics, with co-editor David Beaver of the University of Texas at Austin. The podcast was recorded at a critical moment in the journal’s history, a few weeks after its website was launched and opened for submissions, and a few months before the first papers are expected to appear there, in early 2008....

PS:  For background, see my blog posts on Fintel's work in launching S&P.

After the NIH mandate

Stevan Harnad, After the NIH Green OA Self-Archiving Mandate, Open Access Archivangelism, December 21, 2007.  Excerpt:

This is from your greedy, never-satisfied Archivangelist:

Now that the NIH Green OA Self-Archiving Mandate looks as if it will shortly be signed into Law:

  1. There is no need to wait to implement the NIH mandate
  2. There is no need to ape it: It can easily be optimised
  3. There is no need to reserve Green OA self-archiving for NIH-funded biomedical research
  4. All universities should mandate that all their research articles in all their disciplines are self-archived
  5. There is no need to self-archive all those articles in PubMed Central: They should be self-archived in each university's own Institutional Repository
  6. There is no need to allow deposit to be embargoed for 12 months: Deposit should be mandated immediately upon acceptance for publication
  7. Embargoed articles can be set as Closed Access during any embargo
  8. Meanwhile the Institutional Repository will allow users webwide to email the author a semi-automatic request for an eprint for individual use immediately for any deposit that is not yet OA.

This will provide either immediate OA (62%) or almost-immediate, almost-OA (38%) for all research articles in all disciplines, worldwide. It will also ensure the natural and well-deserved death of research access embargoes soon thereafter.

Summary of how to optimize the Green OA Self-Archiving Mandate:
I. Universities mandate deposit in their own Institutional Repositories.
II. Deposit is mandated immediately upon acceptance for publication.
III. The permissible embargo is on the date the deposit is set as OA, not on the day the deposit is made.

"Optimizing OA Self-Archiving Mandates: What? Where? When? Why? How?"

Comment.  I agree with all of Stevan's points.  On the other side, I'm sure he agrees that when the NIH mandate finally becomes law, it will be a  major victory.  There's no contradiction in celebrating the victory while remembering that there's still more to do.  If there were, nobody could celebrate anything.

Citizendium picks CC-BY-SA license

The Citizendium encyclopedia project picks a Creative Commons license, a press release from Citizendium, December 21, 2007.  Excerpt:

In a much-awaited move, the non-profit Citizendium encyclopedia project announced that it has adopted the Creative Commons Attribution-ShareAlike 3.0 Unported License (CC-by-sa) as the license for its own original collaborative content. The license permits anyone to copy and redevelop the thousands of articles that the Citizendium has created within its successful first year.

The license allows the Citizendium to join the large informal club of free resources associated especially with Creative Commons and the Free Software Foundation. Wikipedia uses the FSF’s GNU Free Documentation License (GFDL), which is expected to be made fully compatible with CC-by-sa in coming months. Therefore, Wikipedia and the Citizendium will be able to exchange content easily....

To explain the choice of license to present and future contributors, [Citizendium founder and editor in chief Larry Sanger] released a 22,000-word essay: “An explanation of the Citizendium license.” The project underwent a very lengthy deliberation process in multiple groups and venues, beginning last spring....

The project rejected a license (CC-by-nc-sa) that would forbid commercial reuse, an issue on which “Citizens” were evenly divided....

PS:  If you remember, Larry Sanger kicked off the discussion back in September by calling for "well-reasoned position statements, from anyone...about what licensing scheme" Citizendium should use.

Six finalists for 2008 Ben Frankllin award

Bioinformatics has named the six champions of open access and open source on the short list for its 2008 Ben Franklin Award.  From Kevin Davies' article in Bio-IT World:

  1. Philip E. Bourne (co-director, Protein Data Bank, University of California San Diego) –- Bourne is the founding editor-in-chief of PLoS Computational Biology, an open access journal published by the Public Library of Science. As co-director of the Protein Data Bank, he is responsible for continued free access to structural biology data and software distributed through the San Diego Supercomputer Center. He continues to develop widely used software tools including SciVee, a free scientific video delivery site in which video can be integrated with the open access literature to create a new learning experience.
  2. James L. Edwards (Encyclopedia of Life, Smithsonian Institution) -- Edwards has been an advocate for the development and sharing of biodiversity data since the early 1980s. As program director of the National Science Foundation's (NSF) Biological Research Resources Program, he advocated data standards for museum collections and for aggressive programs of database construction. As deputy assistant director for biological sciences at NSF, he helped develop blueprints for the Global Biodiversity Information Facility (GBIF). His latest project is the construction of an open-access Encyclopedia of Life
  3. Robert Gentleman (Fred Hutchinson Cancer Research Center) -- Gentleman is one of the minds behind the R Project, a powerful and increasingly popular suite of statistical tools. He co-founded and developed BioConductor, an open-source/open-development software project for the genomic data analysis. Gentleman espouses strong ethical views on the meaning of publishing data, with an emphasis on sharing data-transformation methods as well as the underlying data.
  4. Michael Hucka (California Institute of Technology) -- Hucka is the head of the Systems Biology Markup Language team ( and the coordinator of the development of SBML. SBML is one of the first XML language widely used in biosciences. Hucka has also pushed for more openness, whether in the language development, distribution or software support. Hucka is also the lead developer of the open-source Systems Biology Workbench.
  5. Francis Ouellette (Ontario Institute for Cancer Research) – Ouellette has been a tireless promoter of open-source access (read his top 10 things you can do to support open access). He was an early supporter of the PLoS community and has been a proponent of open access for work derived from public funding, e.g., Genome Canada.
  6. Steven Salzberg (University of Maryland, College Park) – Formerly with The Institute of Genomic Research, Salzberg has promoted open access and data sharing in several areas, producing several popular open-source bioinformatics tools (MUMmer, Glimmer, TransTerm, Jigsaw, etc.). Salzberg helped start the Influenza Genome Sequencing project and has lobbied for the data’s immediate release, publicly calling on other influenza researchers to follow his lead.

Bioinformatics will name the winner at the Bio-IT World Conference & Expo, on April 29, 2008.

Friday, December 21, 2007

Write publicly, act locally

Nick Montfort, Digital Media, Games, and Open Access, Grand Text Auto, December 21, 2007.  Excerpt:

With regard to your request, I cannot agree to review for your journal right now. If [it] becomes an open access journal, I will be very glad to review articles for the journal.

Having written this in an email recently, I wanted to post about my reasoning and ask what Grand Text Auto readers, commenters, and bloggers think about this issue. Open access journals and other scholarly publishing issues are classic ivory tower matters, but my concern about restricting access to Grand-Text-Auto-like subjects has a lot to do with my concern for non-academic readers and commenters here, as well as academics who aren’t at major research universities with full access to journals. This includes people at small liberal arts colleges, even if they write award-winning papers, and independent scholars, even if they regularly keynote conferences and contribute authored and edited volumes to the academic discourse....

I think there must be a few things that those of us who are part of the scholarly publishing process can do to foster an open-access future. The easiest thing that I’m able to think of is simply not volunteering our labor to lock academic writing away from the public....

In the case of pay-for-access journals, the same institutions that indirectly pay for important labor on a journal [by authors and referees] also must pay the for-profit company that runs the journal in order to the final outcome....

This process is one that I characterize as anti-publication. It may serve some credentialing purposes and help universities assess tenure and promotion cases, but it ends up restricting access to scholarly work rather than helping to publish that work, that is, helping to make it available to the public.

The may be several reasons that people choose to anti-publish their work, although bad faith must be the major one. In some fields there are few options for true publication that also contextualize one’s work and bring it to the attention of one’s colleagues. The best way to get word out about recent research to the subscribing elite may be, in these cases, through entrenched, well-known avenues for anti-publication. One could even argue that for esoteric, specialized fields that have no connection to the public (if there are such things), the lack of public access doesn’t matter.

This is hardly the case in digital media, where non-academics ranging from poets and artists to game-makers are working with academics to determine what the creative possibilities for computing can be....

When I made this rather easy decision, refusing to review an article for a for-profit, non-public journal,...I was...thinking that those of us who are academics dealing with digital media have the chance now to determine whether we’re going to become one of those public-irrelevant fields where anti-publication is the norm and we speak only to ourselves, or whether we want to speak to and learn from those creating and encountering poems, games, art, drama, writing, and other sorts of digital work outside the university.

Moving toward OA data in archaeology

Stefano Costa, Open Access Data in Archaeology: a brief roadmap, Open Archaeology, December 21, 2007.  Excerpt:

Following my previous post about the first draft of a Protocol for Implementing Open Access Data, which has been also discussed on some other archaeoblogs, I'd like to give here my idea for a brief roadmap of what should be done by archaeologists to make Open Access Archaeology really possible.

The first part deals with the legal and bureaucratic status of archaeological data, which is varying from country to country. In some (rare) cases, this is not an issue at all...In Italy, at the opposite, archaeological research is limited and controlled by the state, through the Ministry of Cultural Heritage...

The status of archaeological data obtained by research is not very clear in this sense, and in many cases contract archaeology professionals are excluded from the scientific publication of data.

The second part is represented by copyrights and diritto d'autore/droit d'auteur (depending on where you are based). Once legal and bureaucratic issues are cleared, possibly directly involving Ministry officers in the discussion, it should be clear at least who is the owner of any rights upon data....

But before choosing a license and abiding your rights, it's necessary to know your rights. A clear statement about which rights you, as archaeologist, own on “your” data, and which you don't, would be a landmark. Rights you don't own are best summarised by the “Facts are free” motto, that is also a part of database copyright laws.

The third part should be easier to undertake: what is the best “license” that one should choose for data, if (s)he wants them to be Open Access Data? ...

Once these three points have been cleared, the necessary last step is to develop best practices, because a very short number of people has the time and will to go into the details of copyright law. Here are some example cases that hopefully are going to be very common:

  1. Alice is an archaeologist. She has worked for 2 years on her research project studying roman coins, collecting information from published excavation reports and museum catalogues, and now she has compiled a quite large database that she wants to publish as open access data. What should Alice do?
  2. Bob is an archaeologist, too. At some point Bob discovers Alice's database, which has been published as OA. Alice's data would be very useful for his research about trade in ancient Mediterranean. Can Bob get the whole database and reuse its contents without contacting Alice?
  3. Xavier is a student, and he's preparing his master's thesis about lithic tools in Southern France. He finds that a few years ago someone else created a database containing object counts and tipologies from a good number of archaeological sites. This database can be queried through a website, but it is not released as OA, and a copyright statement on the website says that all rights are reserved. Can Xavier reuse some of the data in the database without breaking any existing right of the original author?

There are other possible everyday use cases that should be added to the above list, and I think it would be a very good idea to collect them and try to write a public best practices document that is suitable for the needs and habits of archaeologists.

Swan on Esposito

Alma Swan, The science and the say-so, Optimal Scholarship, December 21, 2007.  Excerpt:

...In a new blog posting pleading for a more scientific approach to studies on science publishing (subtext: Open Access proponents cook the books), Joe Esposito takes issue with a number of studies on Open Access on the grounds that they are not what he terms ‘scientific’. He also suggests that I am ‘behind’ these things, thus according me far more credit than I warrant, but since I am mentioned (twice, indeed) and a lot of people seem to be somewhat confused about the issues Mr Esposito raises, I thought it might help to clarify the situation.

The first contention is that OA proponents imply that librarians are stupid. The reason we must think them stupid, apparently, is that we say they won’t necessarily cancel subscriptions to journals whose contents can be obtained for free in Open Access form on the Web. But that misses the point: we say that cancellations won’t necessarily occur because that is what we observe, in real life....

This is the one experiment that has actually been conducted so far – by the community itself, by way of everyday practice – on the effect of Open Access on journal cancellations. (Oh, and just to forestall the “Ah, but arXiv only contains preprints” chorus, the data show that more than half of the articles in arXiv are postprints, i.e. the peer-reviewed version.) ...

There are a number of straightforward reasons, listed here and here, for preferring to continue to subscribe to journals – journals are more than just articles and contain other types of content that people want to read; they contain the final polished-up versions of articles whereas OA versions are simply the author’s final product; there is no guarantee that every article from a journal will be made OA by its author. Some of these may not hold up forever. We will start to see which journals have true added value – that is, something that customers will pay for – and which are just a collection of articles: the marketplace will reveal that. There are also other reasons, ones not so straightforward and certainly not so easy to describe. They are to do with allegiances to certain publishers, particularly specific society publishers who are viewed as ‘the good guys’ and thus worthy of loyalty; they are to do, partly, with the sorts of deals that publishers are prepared to offer in every individual case; and then they are very much to do with the views of faculty, without which no librarian makes a final decision on what to cut and what to reprieve....

The second point at issue is about a statistic. I was responsible for collecting the data behind this statistic....

The question was ‘What would be your response if your employer or research funder required you to make your work Open Access’, and respondents were offered three options:

  • I would comply willingly
  • I would comply reluctantly
  • I would not comply

The result was that 81% of respondents agreed with the first statement – they would comply willingly. 14% agreed with the second, and 5% agreed with the third.

Back to the present, and Mr Esposito’s argument....He says: “it was found that 81% of researchers say that they would comply with mandates. Now, what does this prove exactly? More than 81% of Americans comply for the most part with the U.S. Tax Code, but that is hardly indicative of support for the current administration or the way tax monies are spent. What it does reveal is a healthy respect for the punitive powers of The Man....

Bong! What was actually found was that 81% of researchers say they would comply willingly with mandates....

Now to the third point. Here it is: “A more complicated item, and one that is more susceptible to reasoned argument, is what is called the Open Access Advantage. No, this is not a frequent flier program but the notion that authors who work in OA formats are more likely to be cited than authors who work in proprietary or “toll-access” media. Superficially, this may appear to make sense; after all, if everyone can read an OA article, surely it has a better chance of getting cited than an article that has more limited distribution by virtue of the constraints imposed by subscription barriers. On the other hand, an article in the toll-access Lancet is much more likely to be cited than an article deposited in a no-name repository, with only Google keyword searching enabling the poor, already overburdened reader. Once again we find Alma Swan behind this [sic - AS]. The problem with the alleged Open Access Advantage is, first, it entirely ignores the overall marketing context of any particular work. The fact is that some OA venues are brilliantly marketed; I would point to the Public Library of Science in particular. But marketing is not a constant; it varies journal by journal, issue by issue, and article by article. Swan’s analysis does not take these variables into account.”

Oh dear. What a mix-up....Unfortunately, Mr Esposito comes to his own conclusions about the Open Access Advantage without seemingly having read the studies that demonstrate it. He also appears misinformed about the authorship of studies in this area, by the way. I am flattered by the attention and attribution, but none of the studies were my work. Anyway, his thesis seems to be that the OA Advantage – the increase in citations that OA articles in general enjoy over those that are not Open Access – is all to do with which journal they are published in, and the marketing success thereof.

Another bit of say-so, I’m afraid. I am not aware of any studies that have been guilty of such sloppy design, and would be very surprised if anyone could point me at one that is. There have been several studies that have used good methodologies, including those by Kristin Antelman and Michael Kurtz and co-workers. But the one I normally use to support the statement that OA enhances citations is that done by Stevan Harnad and his groups in Montreal and Southampton, whose methodology is utterly sound. It is here for those who wish to make a proper critical appraisal of the work....

Two articles from the same issue of the same journal are as near-identical in characteristics as is possible to be, so this is a highly controlled experiment. The citations to such paired articles were compared and measured. The aggregated results for different scholarly disciplines showed that in every discipline there is an increase in citations for OA articles compared with citations for non-OA articles. The graph that illustrates the findings is in this article. They have to be explained by Open Access. There is no ‘marketing’ issue involved at all; and no comparing different journals, different fields...or different publishers....

Another study of author attitudes toward OA journals

Thomas Hess and three co-authors, Open Access & Science Publishing:  Results of a Study on Researchers’ Acceptance and Use of Open Access Publishing, in Management Reports of the Institute for Information Systems and New Media, LMU München, 2007. 

Executive Summary:  This Management Report summarizes the main descriptive results of a study on researcher’s acceptance of Open Access publishing. The study was conducted in 2006 by the Ludwig-Maximilans-University Munich, Germany, in cooperation with the University of Arkansas at Little Rock. The main focus is centered on the question if and why scientists decide or do not decide to publish their work according to the Open Access principle without access barriers and free of cost to readers. With the responses from 688 publishing scientists it could be demonstrated that the general attitude toward the Open Access principle is extremely positive. However, many seem to be rather reluctant to publish their own research work in Open Access outlets. Advantages like increased speed, reach and potentially higher citation rates of Open Access publications are seen alongside insufficient impact factors, lacking long-term availability and the inferior ability to reach the specific target audience of scientists within one’s own discipline. Moreover the low level of use among close colleagues seems to be a barrier towards Open Access publishing.

OA in the GeWiF 2007 yearbook

Frank Havemann, Heinrich Parthey, and Walther Umstätter (eds.), Integrität wissenschaftlicher Publikationen in der Digitalen Bibliothek:  Wissenschaftsforschung Jahrbuch 2007, Gesellschaft für
Wissenschaftsforschung, 2007.  (Thanks to the Open Access Informationsplattform.)  The whole volume is OA and includes these articles on OA:

  • Stefan Gradmann, Verbreitung vs. Verwertung. Anmerkungen zu Open Access, zum Warencharakter wissenschaftlicher Informationen und zur Zukunft des elektronischen Publizierens (p. 93)
  • Uta Siebeky, Auf der Green Road to Open Access. Ein Praxisbericht aus dem Fritz-Haber-Institut der Max-Planck-Gesellschaft (p. 121)
  • Bettina Berendt and Frank Havemann, Beschleunigung der Wissenschaftskommunikation durch Open Access und neue Möglichkeiten der Qualitätssicherung (p. 137)
  • Rubina Vock, Die Bedeutung von Wissenschaftlerinnen und Wissenschaftlern beim Aufbau der Informationsplattform (p. 179)

German intro to OA

Steffen Bernius and Matthias Hanauske, Open Access, Wirtschaftsinformatik, 6 (2007).  A general introduction to OA, in German.  Because it's a PDF, I can't link to a machine translation.  (Thanks to the Open Access Informationsplattform.)

National OA project in Armenia

The National Academy of Sciences of Armenia will develop an OA communication system for Armenian research, thanks to a grant from the Open Society Institute Assistance Foundation in Armenia.  From Monday's announcement:

The Open Society Institute Assistance Foundation in Armenia has granted the Fundamental Scientific Library of the National Academy of Sciences (NAS) with a one year grant to develop an Open Access based scholarly communication system for the national academic community.

The Fundamental Scientific Library of the National Academy of Sciences is the main and largest repository of scholarly publication in the Republic of Armenia. The National Academy of Sciences houses 29 research institutions and is an overall leading producer of scientific content. Eighteen NAS libraries are members of the eIFL-supported Electronic [Library] Consortium of Armenia ELCA, whose main objective is to ensure and enhance access to online scientific journals to libraries, universities, research and other non-commercial organizations. However the National Academy of Sciences publishes 13 peer-reviewed journals with an international reputation, partners in different EU and US funded research projects, and a supercomputing GRID infrastructure is operating, academic institutions are not yet well prepared for the challenges of the knowledge society and scientists are not familiar with the modern trends on scholarly communication.

The Open Society Institute has been supporting the implementation of digital technologies in Armenia in the last years and this new project will seek to raise awareness and encourage alternative solutions to the traditional system of scholarly communication  based on peer reviewed academic journals by commercial publishers. The grant period will run through the whole 2008 and will look into Open Access publishing procedures, institutional repositories and self-archiving toolsets for the local research community. In addition, the project will publish 12 issues of an electronic journal mainly focused on Mathematics and Physics. Tigran Zargaryan, director of the Fundamental Scientific Library of the National Academy of Sciences, will coordinate the project.

OA math textbooks opening wider

David Santos is making even more open by permitting rather than blocking commercial use.  According to Open Text Book:

...[H]e’s agreed to gradually phase out use of the Open Publication License with the noncommercial option, and to start using a license compatible with the Open Knowledge Definition.

Several of the books on the site’s download site are now available under the GFDL, including:

  • Elementary Algebra Lecture Notes
  • Precalculus I and II Lecture Notes
  • Linear Algebra Notes
  • Number Theory Notes...

More on society journals moving to OA and BMC

Stefan Busch, Society journals take a fresh look at open access publishing, BioMed Central Blog, December 21, 2007.  Excerpt:

A notable trend at BioMed Central during 2007 has been the increasing number of inquiries from scientific societies interested in starting new open access journals or transferring their existing journals to BioMed Central, in many cases converting to open access from a previous subscriber-only model.

Society journals that have recently signed transfer agreements with BioMed Central include Journal of the International Society of Sports Nutrition and the Journal of Cardiovascular Magnetic Resonance. Several further such transfers are in the pipeline.

This surge in interest seems to result from a combination of factors. Firstly, the so-called 'serials crisis' continues to bite, in that subscription costs are rising faster than library budgets, and so many libraries find they need to cancel journal subscriptions each year. This has hit smaller society journals hard – especially those which do not form part of one of the major commercial publisher 'Big Deal' arrangements.

Secondly, open access publishing has now established itself as a viable and attractive alternative to the traditional model – it is no longer a new-fangled experiment. Learned societies are rightly cautious about change, and wish to avoid risk, but the risk of moving to the open access model now seems more and more attractive compared to risks of sticking to what is in many cases the increasingly unsustainable subscription-based model.

Lastly, but not least, there is the underlying mission of scientific societies, which is typically to support and promote research and researchers in a given field. As the open access publishing model becomes more familiar, it is more and more widely recognized that open access journals can provide a natural and financially sustainable means for societies to achieve their objectives, and increasing numbers of societies are seizing that opportunity.

Of course, change does not happen overnight, not least because societies are often signed-up to multi-year publishing arrangements with their existing publishers. But a recent study by Peter Suber and Caroline [Sutton]has revealed the surprisingly large number of scientific society journals (collated here as a spreadsheet) that already operate on an open access or hybrid open access model....

New publisher of OA journals

Merlien is a new publisher of OA journals.  It has one journal already on its feet, The Journal of E-Working, now in its second issue, and plans for two more:  The Journal of Open Innovation and Virtual Worlds Business Review

Update (1/4/08). Merlien has adopted the CC-BY license for The Journal of E-Working. An excellent move!

Tranche project adopts OA data protocol

The Tranche Project (from Proteome Commons) is the first I've seen to adopt the Protocol for Implementing Open Access Data from Science Commons.  (Thanks to bbgm.) 

The Tranche Project uses hashes to insure that a dataset to which you link hasn't changed since you last consulted it.

More on the imminent OA mandate at the NIH

Rick Weiss, Measure Would Require Free Access To Results of NIH-Funded Research, Washington Post, December 21, 2007.  Excerpt:

It is barely a drop of ink in the gargantuan omnibus spending bill that Congress just passed. But a provision that would give the public free access to the results of federally funded biomedical research represents a sweet victory for a coalition of researchers and activists who lobbied for the language for years.

Under the bill's terms, scientists getting grant money from the National Institutes of Health would now have to submit to the NIH a final copy of their research papers when those papers are accepted for publication in a journal. An NIH database would then post those papers, free to the public, within 12 months after publication.

The idea is that taxpayers, who have already paid for the research, should not have to subscribe to expensive scientific journals to read about the results.

That populist line -- spearheaded by patient advocacy groups seeking easier access to the latest medical findings and supported by libraries whose budgets have had trouble keeping up with rising journal subscription costs -- ultimately overwhelmed objections from journal publishers....

Among the publishers' concerns are that they would lose income from paid subscriptions, which would undermine their ability to sponsor educational activities and peer reviews. Of equal concern, they say, the policy may violate copyright law, a potential legal tangle that some hinted yesterday might have to get sorted out in court.

"The issue isn't finished yet," said Allan R. Adler, vice president for legal and governmental affairs at the Association of American Publishers, which lobbied hard against passage. "It's not as simple as some have made this out to be."

That attitude sounded Grinch-like to Heather Joseph, executive director of the Scholarly Publishing and Academic Resources Coalition, which led the fight for the open-access language.

"The basic reason we went to bat so hard for this was because we thought it was the right thing to do with taxpayers' science," Joseph said. "Now there will be $29 billion in taxpayer investments freely available to the public," she said, referring to the NIH medical research budget....

The NIH will now start working out how to implement the legislation, a process that could take six months, said John Burklow, NIH communications director. "Our main goal right now is to make sure everyone understands the policy and knows how to follow it" once it comes into effect, he said.

PS:  Remember that the OA mandate is not yet law.  The funding bill containing it must still be signed by the President.

Thursday, December 20, 2007

IEEE-SPS partners with Connexions on open ed modules

SPS Partnering with Connexions for Open-Access Educational Repository, Inside Signal Processing E-Newsletter, December 2007.  (Thanks to Ahmed Hindawi.)  Excerpt:

IEEE is partnering with open-access educational repository Connexions on a major initiative to develop a critical mass of signal processing educational modules and courses that will be available for free access by anyone, anywhere, at any time.  This is one of the latest education and outreach effort by the IEEE Signal Processing Society (SPS), as announced by the SPS President Alfred O. Hero in the November 2007 issue of IEEE Signal Processing Magazine [PS: and blogged on OAN at the time].

The materials will pass through a careful IEEE-SPS peer review that will earn them the imprimatur of the IEEE brand for quality and eventually will be available not just in English but also in a number of languages, including Spanish and Chinese.

The project will begin accepting submissions of content for conversion and reviewing in January 2008. If you would like to get started early contributing your own content, please visit the Connexions Author’s Guide. For more information, read more from this SPM article and visit the project website.

Update (1/31/08). Also see the home page for this project. (Thanks to Mel DeSart.)

Free and open source alternatives to Adobe Acrobat

Codswallop has put together a list of 50+ open source/free alternatives to Adobe Acrobat

PS:  I'm not blogging these tools because they can put texts into PDF format, but because they can get them out.

NEEO survey of economists

Nereus is conducting a survey of economists in order to strengthen NEEO (Network of European Economists Online), its portal of OA economics research.  From the survey site:

NEEO (Network of European Economists Online) is an EU-funded project which will address the lack of integration of academic output amongst premier European economists institutions by creating a powerful new research tool call Economists Online. The survey is intended to identify the needs of the end users and will be used as a basis for the content acquisition and dissemination plan and design of the project’s information services.

Specifically the survey will help us to identify:

  • authors’ requirements for storing and disseminating full text documents they have produced
  • authors’ requirements for storing and disseminating statistical datasets they have produced
  • researchers’ requirements for access to documents and datasets
  • need for value-added services ...

Case study: self-archiving is easy

Alex Golub, An open access case study, Savage Minds, December 19, 2007.  Excerpt:

The current issue of the journal Games and Culture is running an article I’ve written with the scarily erudite Kate Lingley....If you want to read the other articles in the journal and your library doesn’t subscribe to Games and Culture, you will have to ILL them or pay US$15 to download a PDF. If you want to read my article, however, you can download it for free or even check out the preprint on Mana’o. Let me take this as a case study in open access…

When Lingley and I started working on the article, I began looking at open access possibilities. The first thing I asked was: what are this journal’s policies on open access? I found the answer to this question at RoMEO...[which is] incredibly easy to use—all you do is type in the name of the journal you are publishing in, and they tell you what its policies are....

So Romeo told me that Games and Culture would allow me post my pre-print (i.e. my page proofs) but that I had to wait 1 year before I could archive my post-print. Now for most people this is fine, since page proofs are pretty much finished projects. But because I am an open access nut I wanted to do more—I wanted to make sure the final version of our article was available to everyone.
What I had to do was change the author’s agreement—the contract that you sign before a publisher publishes your stuff. But how to deal with all that legalese when you’re not a lawyer? Easy—SPARC, another open access organization...[has developed] the SPARC author’s addendum. You just print this out, fill it out, and attach it with your author’s agreement —it keeps you from signing away your right to post PDFs of your work (for nonprofit purposes).

Most publishers I’ve encountered don’t have any problem with the SPARC addendum, but Games and Culture did....So in due course I got an email from the publisher saying that they wouldn’t accept my addendum, but would be willing to work with me to find other solutions to my concerns.

I told them that I wanted the article to be open, since many anthropologists didn’t read Games and Culture and the subscriber base was still relatively small. They agreed to make my article free for download for the first three month it appeared, and then to also open it up over the course of the periodic ‘free trials’ that they offer—roughly three months out of the year. The result is that my article will be available for download 6 out of the 12 months before I get control back over the post-print.

The end result: success! Using simple tools like RoMEO and the SPARC author’s addendum my work is now (mostly) open. Readers benefit from access to my research, I benefit from increased publicity for my work, Games and Culture gets a lengthy plug on my blog, and Sage gets a positive write up as well.

The moral of this story are simple: open accessing your work is incredibly easy if you use the tools that others have made for you, and journals are willing to compromise. If anything, anthropologists fixated on the belief that the only possible business model for journals is closed access, pay for content underestimate the flexibility and innovation of the publishing industry. And visions of punitive publishers take you to court for insisting on retaining the rights that you as an author have are vastly over estimated.

So go for it—the next time you publish something, try taking these simple steps. And then email your postprint or preprint to and we’ll help make your work available for all.

Intro to OA for ESRC grantees

The UK Economic & Social Research Council has released An Introduction to Open Access for ESRC Grant Holders.  It offers a general introduction to OA and a restatement of the ESRC's OA mandate from October 2006.  (The intro relies in several places on my Open Access Overview.)

For some OAN readers, this glimpse into the future may be new:

There have been a number of developments since the ESRC Open Access mandate came into effect (in October 2006), including strong interest from within the community in scoping and developing open access repositories, predominantly institutional.

The second phase of ESRC Society Today provided proof of concept for interoperation with other repositories, allowing automated harvesting and linkage of ESRC funded output records, and extending the awards and outputs database as an ESRC Social Sciences Repository (a subject repository). Users within the community are also utilising the technology to harvest ESRC materials from the repository for their own purposes.

Research Councils UK has commissioned a Study on Open Access to Research Outputs, aimed at reviewing the impact of the RCUK position statements on Open Access, which is scheduled to deliver its findings in autumn 2008.

OpenMED self-archiving tutorial updated

OpenMED@NIC updated its OpenMED self-help tutorial in April 2007 and then again yesterday.  Naina Pandita tells me that it is used at India's Government Siddha Medical College to educate doctors and teachers about self-archiving.

Wednesday, December 19, 2007

Congress sends revised spending bill, and OA mandate for NIH, to President

This evening the House of Representatives passed an omnibus spending bill containing language requiring the NIH to adopt an OA mandate.  The Senate passed the bill on Tuesday. 

Because it cuts spending to the levels President Bush requested, and gives him $70 billion for the war in Iraq and Afghanistan, he is expected to sign it. 

The OA mandate for the NIH isn't law yet, but it's very, very close. Watch this space.

IRs coming to all Irish universities

UCD Library Implements Institutional Repository with the help of Enovation Solutions, Irish University Association News, December 2007.  Excerpt:

UCD [University College Dublin] Library and Enovation Solutions have completed the development of an open access institutional repository to collect, preserve and disseminate the full-text research outputs of researchers at University College Dublin.

The repository, which was built on the DSpace technology platform, was chosen by UCD Library because of its open source flexibility, successful use by other Irish universities, and the availability of local support from Enovation Solutions....

Enovation's development work included considerable changes to the main DSpace data fields and some specific enhancements to the DSpace website.

The Library is currently piloting the repository with the Schools of Economics, Geography Planning and Environmental Policy and the Geary Institute. They plan to officially launch it as a university-wide service later in 2008. Further application developments, which are scheduled to start in the New Year, will involve integrating the repository with the existing research management system at the library to allow for full data flow between the two.

This innovative development is part of a 3-year project initiated by the IUA Librarians' Group and part-funded through the Higher Education Authority Strategic Innovation Fund. The project will establish open access institutional repositories in all Irish universities by 2008, augmented by an Irish portal to discover and access Irish research outputs....

New OA journal of late antique culture

The Journal for Late Antique Religion and Culture is a new peer-reviewed OA journal from Cardiff University.  The inaugural issue is now online.  (Thanks to Klaus Graf.)

Intro to OA for non-academic information professional

The December issue of AccessInformation is now online.  This is a newsletter for non-academic information professionals.  The December issue includes an introduction to OA.  Excerpt:

As knowledge workers, you are aware of the widening availability of peer-reviewed and scholarly literature accessible from the Web. Google was a catalyst in this content explosion when it gained the permission of database companies and individual publishers to crawl and index publications contained in commercial databases such as JSTOR. Frequently, however, Google links to an abstract of an article with an option for purchasing the full article (pay-per-view). While we applaud this increased awareness and access to scholarly publications, we are also concerned about the rising costs involved. Many fees are $30 or more for a single article and some have risen as high as $50 per article in recent months. When trying to acquire a list of 150 articles necessary for a court case, this can add up to a very high price tag!

While we recognize the convenience of purchasing specific articles on demand and understand that most publishers are commercial enterprises, we strive to search for alternative, price-sensitive sources of authoritative information. One such alternative is the growing number of open access journals available on the Web.

Peter Suber, a policy strategist who specializes in open access to scientific and scholarly research literature, firmly believes that increased prices for subscriptions and pay-per-view options will continue to be obstacles for some time. “The best hope is open access, not decreasing prices,” states Suber. Open access will continue to expand as more and more taxpayers demand access to the results of federally sponsored research....

Following we have provided some background information on the open-access movement as well as a brief list of some open access sources available....

Reminding faculty of the benefits of self-archiving

Librarians at Sheffield Hallam University are reminding faculty of the benefits of depositing their peer-reviewed postprints in the institutional repository, SHURA (Sheffield Hallam University Research Archive).  Excerpt:

...[SHURA] is a long-term project begun this year that makes peer-reviewed research from Sheffield Hallam University available online for free to everyone . It is intended to be a secure and permanent home for articles from all the disciplines at the university.

The open access movement is one that is becoming increasingly prominent and mainstream within academic publishing. Such archives greatly increase the visibility and impact of research: articles can now be easily found and accessed by researchers worldwide through Google Scholar and other search tools. Likewise, open access archives make it possible for you to access articles without being restricted to the contents of only those journals to which we subscribe. And as more institutions create their own open access archives, the publishing world is increasingly accepting it. Publishing in an archive is usually supplementary to publishing in a journal and many journals are happy for articles submitted to them to also be published in online archives, although within certain provisos....

Open culture in Montreal

The theme of La Biennale de Montréal 2009 will be open culture.  For details see the director's announcement.

Costs of for-profit and non-profit journal publishing

Roger Clarke, The cost profiles of alternative approaches to journal publishing, First Monday, December 2007. 

Abstract:   The digital era is having a substantial impact on journal publishing. In order to assist in analysing this impact, a model is developed of the costs incurred in operating a refereed journal. Published information and estimates are used to apply the model to a computation of the total costs and per–article costs of various forms of journal publishing. Particular attention is paid to the differences between print and electronic forms of journals, to the various forms of open access, and to the differences between not–for–profit and for–profit publishing undertakings.

Insight is provided into why for–profit publishing is considerably more expensive than equivalent activities undertaken by unincorporated mutuals and not–for–profit associations. Conclusions are drawn concerning the current debates among conventional approaches and the various open alternatives.

From the body of the paper:

[I]t would appear that open access journal publishing is achievable through not–for–profit channels far more cheaply and efficiently than through for–profit organisations....

For–profit publishers have higher cost–profiles than not–for–profit associations, because of the additional functions that they perform, in particular their much greater investment in branding, customer relationship management and content protection....

The distinctive differences that remain in for–profit publishing are:  [1] higher–quality branding; [2] more active marketing; [3] more aggressive customer management; and, [4] content protection.

But the primary beneficiaries of these features are the publisher and its owners. Only in the case of for–profit business units within not–for–profit associations are the owners closely associated with an academic community. Academic communities have little incentive to contribute to the funding of sophisticated technical features that are designed to support organistions’ strategic and marketing objectives rather than community service. In short, the ‘value–add’ that for–profit publishers offer appears to be of little or no benefit to academic communities....

Curriki wins open education prize from UNESCO

Curriki is one of two winners of this year's King Hamad Bin Isa Al-Khalifa Prize.  From today's announcement: announced that it has been awarded the King Hamad Bin Isa Al-Khalifa Prize for the use of Information and Communications Technology (ICT) in education at the UNESCO Headquarters in Paris. Curriki was one of two winners chosen from among 68 projects from 51 countries and one international nongovernmental organization focusing on the theme of open access to education....In addition to the UNESCO honor, Curriki also unveiled a series of significant international partnerships with organizations in the United Kingdom, Canada and South Africa.

Curriki's open source model allows the education community to share, improve and collaborate on the development of curriculum and curricular resources....

"Over 400 million kids, worldwide, do not have access to a primary education. Curriki is all about eliminating this education divide working in conjunction with governments, educators, the private sector, students and the community at large," said Scott McNealy, the founder of Curriki and the Chairman and Co-Founder of Sun Microsystems. "Winning the UNESCO prize as well as these and other forthcoming international partnerships are important steps to making sure that every child has access to high quality curriculum at no charge."

PS:  Congratulations to Curriki.  Does anyone know who the other winner is?  I only had time to run a quick search and couldn't turn up the name.

Tuesday, December 18, 2007

Update to Bailey bibliography

Charles W. Bailey Jr. has released version 70 of his monumental Scholarly Electronic Publishing Bibliography. The new version cites and organizes over 3,195 print and online articles, books, and other sources on scholarly electronic publishing.

Scientific American recognizes two OA leaders

Today Scientific American announced this year's SciAm 50.  Two of the winners have an OA connection.

  • The first place award, Research leader of the year, went to the Wellcome Trust Case Control Consortium (WTCCC) for its work on "the mammoth challenge of ferreting out the causes of diseases in which multiple genes are implicated."  The SciAm citation doesn't mention that WTCCC freely shares its data, summary statistics, and software.
  • Ilaria Capua was recognized for her work on OA for avian flu data.  From the citation:  "Until recently, laboratories doing bird flu research often kept their findings private, with access to many avian influenza gene sequences confined to just 15 facilities globally....Instead of entering her avian influenza findings into this database, Ilaria Capua of Vialle University in Padua, Italy, disclosed the results of her studies in the publicly accessible GenBank and boldly rallied her colleagues to follow.  Her efforts helped to pave the way for the Global Initiative on Sharing Avian Influenza Data, a consortium through which findings can be freely shared while giving credit to researchers involved."  Also see my blog posts on her OA work.

PS:  Congratulations to Ilaria Capua and everyone at the WTCCC.

CC launches two new licensing projects

Creative Commons Launches CC0 and CC+ Programs, Creative Commons blog, December 17, 2007.  Excerpt:

Today, Creative Commons announced the launch of CC0 (aka CC Zero) and CC+ (aka CC Plus). These programs are major additions to CC’s array of free legal tools.


CC+ is a protocol to enable a simple way for users to get rights beyond the rights granted by a CC license. For example, a Creative Commons license might offer noncommercial rights. With CC+, the license can also provide a link to enter into transactions beyond access to noncommercial rights — most obviously commercial rights, but also services of use such as warranty and ability to use without attribution, or even access to physical media.

“Imagine you have all of your photos on Flickr, offered to the world under the CC Attribution-NonCommercial license,” said Lawrence Lessig, CEO of Creative Commons. “CC+ will enable you to continue offering your work to the public for noncommercial use, but will also give you an easy way to sell commercial licensing rights to those who want to use your work for profit.” ...


CC0 is a protocol that enables people to either (a) ASSERT that a work has no legal restrictions attached to it, or (b) WAIVE any rights associated with a work so it has no legal restrictions attached to it, and (c) SIGN the assertion or waiver.

“In some ways, CC0 is similar to what our public domain dedication does now,” said Lessig. “But with CC0, the waiver of rights will be more robust internationally, and both the waiver and assertion will be vouched for, so that there is a platform for reputation systems to develop. People will then be able to judge the reliability of content’s copyright status based on who has done the certifying.”

CC0 was previewed at Creative Commons’ 5th birthday event this past weekend in San Francisco. A beta version of the protocol will be released for public discussion on January 15, 2008. This will include the traditional components of the CC architecture — legal code, human-readable explanation, machine-readable metadata, and tools. The Berkman Center for Internet & Society at Harvard Law School will collaborate with Creative Commons on drafting the legal code for CC0....

Update.  Gavin Baker wrote to make clear that CC+ is not a new license but a way to extend existing CC licenses.  CC0 will be a new license, but is still being drafted.  (Thanks, Gavin.)

Printing and exporting wiki text

Wikis go printable, a press release from the Wikimedia Foundation, December 13, 2007.  Excerpt:

The Wikimedia Foundation today announced a partnership that will make it possible to obtain high quality print and word processor copies of articles from Wikipedia and other wiki educational resources. The development of the underlying open source software is supported by the Open Society Institute and the Commonwealth of Learning, and led by, a start-up company based in Germany....

Deployment of the technology will happen in three stages. The first stage, launched today, is a public beta test running on of functionality for remixing collections of wiki pages and downloading them in the PDF format....

The second stage, planned for early 2008, will be the deployment of the technology on the projects hosted by the Wikimedia Foundation, including Wikipedia. At this point, users will also be given the option to order printed copies of wiki content directly from "The integration into Wikipedia will be a milestone for print-on-demand technology. Users will literally be empowered to print their own encyclopedias", according to Heiko Hees, product manager at

The third stage, planned for mid-2008, will be the addition of the OpenDocument format for word processors to the list of export formats. "Imagine that you want to use a set of wiki articles in the classroom. By supporting the OpenDocument format, we will make it easy for educators to customize and remix content before printing and distributing it from any desktop computer," Sue Gardner explained. This work is funded through a US$40,000 grant by the Open Society Institute.

The technology developed through this cooperation will be available under an open source license, free for anyone to use for any purpose. It ties into the MediaWiki platform, the open source technology that runs Wikipedia. As a result, thousands of wiki platforms around the world will have the option of providing the same services to their users.

2007 Horizon Report

The New Media Consortium and EDUCAUSE Learning Initiative have published the 2007 edition of the Horizon Report.  Excerpt:

The annual Horizon Report...seeks to identify and describe emerging technologies likely to have a large impact on teaching, learning, or creative expression within higher education....

As it does each year, the Horizon Advisory Board again reviewed key trends in the practice of teaching, learning, and creativity, and ranked those it considered most important for campuses to watch....

  • Academic review and faculty rewards are increasingly out of sync with new forms of scholarship. The trends toward digital expressions of scholarship and more interdisciplinary and collaborative work continue to move away from the standards of traditional peer-reviewed paper publication. New forms of peer review are emerging, but existing academic practices of specialization and long-honored notions of academic status are persistent barriers to the adoption of new approaches. Given the pace of change, the academy will grow more out of step with how scholarship is actually conducted until constraints imposed by traditional tenure and promotion processes are eased....
  • The notions of collective intelligence and mass amateurization are pushing the boundaries of scholarship. Amateur scholars are weighing in on scholarly debates with reasoned if not always expert opinions, and websites like the Wikipedia have caused the very notion of what an expert is to be reconsidered. Hobbyists and enthusiasts are engaged in data collection and field studies that are making real contributions in a great many fields at the same time that they are encouraging debate on what constitutes scholarly work—and who should be doing it. Still to be resolved is the question of how compatible the consensus sapientum and the wisdom of the academy will be....

The 2007 Horizon Project Advisory Board also considered critical challenges facing higher education over the five-year time period described in this report....

  • There are significant shifts taking place in scholarship, research, creative expression, and learning, and a profound need for leadership at the highest levels of the academy that can see the opportunities in these shifts and carry them forward. At few points in the history of the academy has there been an opportunity to really impact the ways in which learners and scholars interact. We are seeing the convergence of many new ideas on how we work, learn and interact, and it will take visionary leadership to see and capitalize on these shifts. At the same time, few leaders are following critical trends such as those listed in the previous section, and fewer still are speaking out on the issues that accompany them. The thoughtful perspectives of university presidents, provosts, and other learning-focused leaders, for example, could temper the moral panics that hamper effective conversations on critical topics such as digital rights, online safety, and access....

PS:  The report does not identify OA as one of the trends or challenges worth watching.  It only mentions OA explicitly once, in an innocuous sentence on p. 21:  "The proliferation of audience-generated content combined with open-access content models is changing the way we think about scholarship and publication—and the way these activities are conducted."

Bruce Alberts named ed-in-chief of Science

The new editor-in-chief of Science Magazine is Bruce Alberts, a friend of OA who has defended the principle in public.  As President of the National Academy of Sciences, he tried to shorten the embargo on PNAS to two months, though he eventually moved it back to six months.  I suspect he will try OA experiments at Science.

Monday, December 17, 2007

Why we need OA to citation data

Mike Rossner, Heather Van Epps, and Emma Hill, Show me the data, Journal of Cell Biology, December 17, 2007.  An editorial.  Excerpt:

The integrity of data, and transparency about their acquisition, are vital to science. The impact factor data that are gathered and sold by Thomson Scientific (formerly the Institute of Scientific Information, or ISI) have a strong influence on the scientific community, affecting decisions on where to publish, whom to promote or hire, the success of grant applications, and even salary bonuses. our knowledge, no one has independently audited the underlying data to validate their reliability....

Thomson Scientific makes its data for individual journals available for purchase. With the aim of dissecting the data to determine which topics were being highly cited and which were not, we decided to buy the data for our three journals [at Rockefeller University Press] (The Journal of Experimental Medicine, The Journal of Cell Biology, and The Journal of General Physiology) and for some of our direct competitor journals. Our intention was not to question the integrity of their data.

When we examined the data in the Thomson Scientific database, two things quickly became evident: first, there were numerous incorrect article-type designations. Many articles that we consider "front matter" were included in the denominator. This was true for all the journals we examined. Second, the numbers did not add up. The total number of citations for each journal was substantially fewer than the number published on the Thomson Scientific, Journal Citation Reports (JCR) website (subscription required). The difference in citation numbers was as high as 19% for a given journal, and the impact factor rankings of several journals were affected when the calculation was done using the purchased data (data not shown due to restrictions of the license agreement with Thomson Scientific)....

When queried about the discrepancy, Thomson Scientific explained that they have two separate databases—one for their "Research Group" and one used for the published impact factors (the JCR). We had been sold the database from the "Research Group", which has fewer citations in it because the data have been vetted for erroneous records. "The JCR staff matches citations to journal titles, whereas the Research Services Group matches citations to individual articles", explained a Thomson Scientific representative. "Because some cited references are in error in terms of volume or page number, name of first author, and other data, these are missed by the Research Services Group."

When we requested the database used to calculate the published impact factors (i.e., including the erroneous records), Thomson Scientific sent us a second database. But these data still did not match the published impact factor data. This database appeared to have been assembled in an ad hoc manner to create a facsimile of the published data that might appease us. It did not....

It became clear that Thomson Scientific could not or (for some as yet unexplained reason) would not sell us the data used to calculate their published impact factor. If an author is unable to produce original data to verify a figure in one of our papers, we revoke the acceptance of the paper....

Just as scientists would not accept the findings in a scientific paper without seeing the primary data, so should they not rely on Thomson Scientific's impact factor, which is based on hidden data. As more publication and citation data become available to the public through services like PubMed, PubMed Central, and Google Scholar®, we hope that people will begin to develop their own metrics for assessing scientific quality rather than rely on an ill-defined and manifestly unscientific number.

Update.  Also see Stevan Harnad's comments.  Excerpt:

Rossner et al are quite right, and the optimal, inevitable solution is at hand:

  1. All research institutions and research funders will mandate that all research journal articles published by their staff must be self-archived in their Open Access (OA) Institutional Repository.
  2. This will allow scientometric search engines such as Citebase (and others) to harvest their metadata, including their reference lists, and to calculate open, transparent research impact metrics....

Update. Also see Thomson's response to the editorial.

Update (1/10/08). Rossner, Van Epps, and Hill have written a second editorial in response to Thomson's response.

Petition for OA to bibliographic data

Response to Working Group on the Future of Bibliographic Control (Library of Congress), a petition drafted and organized by the Open Knowledge Foundation:

The draft report of the Library of Congress's Working Group on the Future of Bibliographic Control features many interesting suggestions. In particular we wholeheartedly endorse the vision of a bibliographic ecosystem which is "collaborative, decentralized, international in scope and web-based". However, we are concerned that the report lacks any discussion of a key component for any future of bibliographic data: open licensing and access.

Over the past few years, open licensing has facilitated the explosive growth of a 'knowledge commons'. To give a few prominent examples: Open Access journals, Open Educational Resources and Open Data in scientific research have all been enabled by licenses which permit material to be freely re-used and re-distributed. And a recent meeting of open government advocates, including people from Yahoo, Google, Stanford, and Berkeley, called for government agencies to follow eight principles of Open Data. This outpouring of support for openness has led to an incredible rise in community-led development and innovative uses.

Bibliographic records are a key part of our shared cultural heritage. They too should therefore be made available to the public for access and re-use without restriction. Not only will this allow libraries to share records more efficiently and improve quality more rapidly through better, easier feedback, but will also make possible more advanced online sites for book-lovers, easier analysis by social scientists, interesting visualizations and summary statistics by journalists and others, as well as many other possibilities we cannot predict in advance.

Government agencies and public institutions are increasingly making data open. We strongly encourage the Library of Congress to join this movement by recommending that more bibliographic data is made available for access, re-use and re-distribution without restriction.

PS:  Please consider adding your name.  Although I was an early signatory to this petition, I'm late in blogging it because I didn't realize it was ready for public disclosure.  Sorry for the delay.

Open images for medical research

David R. Holmes III and Richard A. Robb, Data, data everywhere, nor an image to read - Finding open image databases, Insight Journal, July 15, 2007.  (Thanks to Jim Till.)

Abstract:   Open Science includes access to both open source software/methodologies and open data. While there has been progress in open image databases, the results of these efforts are under-reported. As such, imaging scientists are unaware of the available data. In addition, many researchers are interested in providing their data to the greater research community, but may be unaware of the process to release the data. The purpose of this paper is to describe our efforts in developing an open website which includes information on accessible medical image databases as well as some of the logistics for providing an open image database. Most importantly, the authors are requesting participation from the community to contribute to the Medical Image Database Repository in order to consolidate the collect knowledge of the community.

The future of institutional repositories

Greg Crane, Open Access and Institutional Repositories: The Future of Scholarly Communications, Academic Commons, December 16, 2007.  Excerpt:

Institutional repositories were the stated topic for a workshop convened in Phoenix, Arizona earlier this year (April 17-19, 2007) by the National Science Foundation (NSF) and the United Kingdom's Joint Information Systems Committee (JISC). While in their report on the workshop, The Future of Scholarly Communication: Building the Infrastructure for Cyberscholarship, Bill Arms and Ron Larsen build out a larger landscape of concern, institutional repositories remain a crucial topic, which, without institutional cyberscholarship, will never approach their full potential.

Repositories...extend the core missions of libraries into the digital environment by providing reliable, scalable, comprehensible, and free access to libraries' holdings for the world as a whole. In some measure, repositories constitute a reaction against those publishers that create monopolies, charging for access to publications on research they have not conducted, funded, or supported. In the long run, many hope faculty will place the results of their scholarship into institutional repositories with open access to all. Libraries could then shift their business model away from paying publishers for exclusive access....

Repositories offer one model of a sustainable future for libraries, faculty, academic institutions and disciplines. In effect, they reverse the polarity of libraries. Rather than import and aggregate physical content from many sources for local use, as their libraries have traditionally done, universities can, by expanding access to the digital content of their own faculty through repositories, effectively export their faculty's scholarship....

The repository movement has, as yet, failed to exert a significant impact upon intellectual life. Libraries have failed to articulate what they can provide and, far more often, have failed to provide repository services of compelling interest. Repository efforts remain fragmented: small, locally customized projects that are not interoperable--insofar as they operate at all. Administrations have failed to show leadership. Happy to complain about exorbitant prices charged by publishers, they have not done the one thing that would lead to serious change: implement a transitional period by the end of which only publications deposited within the institutional repository under an open access license will count for tenure, promotion, and yearly reviews....

The published NSF/JISC report wisely skips past the repository impasse to describe the broader intellectual environment that we could now develop....[I]ntellectual life increasingly depends upon open access to large bodies of machine actionable data....

To accomplish this goal [of green OA to publicly-funded research], the report proposes a detailed seven-year plan....

Science Commons protocol for open data

Announcing the Protocol for Implementing Open Access Data, Science Commons blog, December 16, 2007. 

Today, in conjunction with the Creative Commons 5th Birthday celebration, Science Commons announces the Protocol for Implementing Open Access Data (”the Protocol”).

The Protocol is a method for ensuring that scientific databases can be legally integrated with one another. The Protocol is built on the public domain status of data in many countries (including the United States) and provides legal certainty to both data deposit and data use. The protocol is not a license or legal tool in itself, but instead a methodology for a) creating such legal tools and b) marking data already in the public domain for machine-assisted discovery.

You can read the Protocol here.

We built the Protocol after a year- long process of meetings and consultations with a broad set of stakeholders, including representatives of the geospatial and biodiversity science communities. We solicited input from international representatives from China, Uganda, Brazil, Japan, France, Netherlands, Germany, Italy, the United Kingdom, Colombi, Peru, Belgium, Catalonia and Spain.

We expect to convert this work into a working group with founding members from our existing communities of practice. However, the world is moving very quickly in terms of data production, and as such we created the Protocol as a guide and as a tool to bring together the existing data licensing regimes into a single space.

As part of that decision, Science Commons has worked with data licensing thought leaders and is pleased to announce partnerships with Jordan Hatcher, the lawyer behind the Open Database License; Talis, the company behind the Open Database License process; and the Open Knowledge Foundation, creators of the Open Knowledge Definition.

Jordan has drafted the Open Data Commons Public Domain Dedication and License - the first legal tool to fully implement the Protocol. It is available at his Web site. This draft is remarkable not just for the Public Domain Dedication but for the encoding of scholarly and scientific norms into a standalone, non-legal document. This is a key element of the Protocol and a major milestone in the fight for Open Access data. Talis, a company with a strong history in the open science data movement, played a key role in birthing Jordan’s work, and we’re pleased to work with them as well.

We are also pleased to announce that the Open Knowledge Foundation has certified the Protocol as conforming to the Open Knowledge Definition. We think it’s important to avoid legal fragmentation at the early stages, and that one way to avoid that fragmentation is to work with the existing thought leaders like the OKF.

We will be launching a wiki for comments on the Protocol soon, and will announce a strategy for versioning the Protocol in 2008.

From the protocol itself:

This memo provides information for the Internet community interested in distributing data or databases under an “open access” structure. There are several definitions of “open” and “open access” on the Internet, including the Open Knowledge Definition and the Budapest Declaration on Open Access; the protocol laid out herein is intended to conform to the Open Knowledge Definition and extend the ideas of the Budapest Declaration to data and databases....

This memo...will be submitted to the World Wide Web Consortium for consideration....

The motivation behind this memorandum is interoperability of scientific data....


  • This protocol is much needed and well conceived.  It's a very good sign that so many key stakeholders are already part of the process and support it.  (There's little chance of interoperable data without cooperating stakeholders.)  Kudos to John Wilbanks and Science Commons for this feat of coordination and problem-solving.
  • It's also persuasive.  For example, I've been thinking that any open data standard would probably have to require attribution, if only to recruit participating researchers.  But the protocol cogently argues that such a requirement would result in "attribution stacking" (e.g. crediting "40,000 data depositors in the event of a query across 40,000 data sets") and violate the "principle of low transaction costs."  It's equally cogent in arguing that open data should not limit re-use with "share-alike" and similar contractual restrictions.

Update.  Here's a related announcement from Jordan Hatcher, mentioned in the Science Commons post above:  "We’ve created a site [a blog, Open Data Commons] solely for the Open Data Commons project."  From the inaugural post on the new blog:

The new Open Data Commons set of legal tools are now available for comment. There are two documents for you to review:

Public Domain Dedication & Licence (PDDL)

Community Norms

We’ve created a FAQ for some of the initial questions here. A FAQ addressing some of the in-depth legal issues of the PDDL will be forthcoming.

The current draft PDDL is compliant with the newly released Science Commons draft protocol for the “Open Access Data Mark” and with the Open Knowledge Foundation’s Open Definition....

Update. Also see John Wilbanks' blog post on "the personal story that led us [at Science Commons] to the position that we reached."

Update (12/20/07). Also see the new Database Protocol FAQ.

Sunday, December 16, 2007

Using OA resources for biomedical research

Sukhdev Singh, Bio-Medical Information Retrieval from Net, a slide presentation at Lady Irwin College (New Delhi, December 11, 2007).  Focusing on OA resources.

UK experiment with non-commercial reuse of public mapping data

Charles Arthur, Finally! Ordnance Survey lets people do mashups with its maps, The Guardian, December 13, 2007.  Excerpt:

Normally we keep stuff about the Free Our Data campaign to its own blog, but some things are worth mentioning here too. Such as Ordnance Survey, the UK's mapping agency, which today announced that it is launching its OpenSpace project for wider use.

This ties in with our story in today's Technology section - though the key thing is, of course, that mashups in this way will only be available to nonprofit organisations.

From the press release:

OS OpenSpace enables web-savvy users to build mash-ups with a range of Ordnance Survey data in line with government aims to make public sector information more accessible.
Under an application programming interface (API) developers will register for a feed of data to experiment with non-commercially. It includes a range of mapping scales covering the whole of Great Britain down to street level.

But before you hang out all the bunting, it's only for some just now:

This week’s stage involves a hands-on preview to a dedicated group of developers who will have exclusive access to test functionality and build applications ahead of a public launch early in the new year....

The point of the Free Our Data campaign (in case it's new to you) is that we argue that data like the OS maps should be available for free commercial reuse (at present it's charged-for, and can be very expensive), and the cost of providing their services funded directly out of taxes. Then, commercial companies could thrive and compete without the drag of the data cost. (As an example, consider the multiplier effect of GPS - which I wrote about here.) ...

Bill to mandate OA for CRS Reports

Steven Aftergood, A Resolution on Internet Access to CRS Reports, Secrecy News, December 12, 2007.  Excerpt:

A bipartisan resolution to provide online public access to Congressional Research Service reports was introduced in the Senate yesterday.

"The Sergeant-at-Arms of the Senate, in consultation with the Director of the Congressional Research Service, shall make available through a centralized electronic system, for purposes of access and retrieval by the public ... all information described in paragraph (2) that is available through the Congressional Research Service website," the Resolution states.

Exemptions from disclosure are included for copyrighted and personal information, and for reports that are prepared confidentially for an individual member or committee.

The resolution, S. Res. 401, was jointly introduced by Senators Joe Lieberman, John McCain, Susan Collins, Patrick Leahy, John Cornyn and Tom Harkin....

Comment.  This is very good news.  I've been one (among many others) arguing for OA to CRS Reports for years.  CRS Reports form a small patch of the mosaic, compared to publicly-funded scientific research.  But I'm delighted to see Senate supporters of OA finally turn their attention to them.

Getting scientific about the merits of OA

Joe Esposito, Putting Science into Science Publishing, Publishing Frontier, December 11, 2007.  Excerpt:

...I am myself an advocate of many forms of OA publishing, so in criticizing some aspects of the OA agenda, I am not attempting to argue the other side, that is, the side of traditional publishing, especially by practitioners in the commercial sector. What I do not advocate is using baseless or incomplete arguments in support of anything, whether OA, WMD, or steroids in baseball....

There is a lot that is right (meaning well-argued, credible, and substantiated) about OA, but here is a partial list of what is not. For starters, there is the repeated insistence that librarians are stupid. The form this assertion takes is to argue that librarians will continue to pay for something that they can get for free....

[I]n a survey conducted by Alma Swan et al, it was found that 81% of researchers say that they would comply with mandates. Now, what does this prove exactly? More than 81% of Americans comply for the most part with the U.S. Tax Code, but that is hardly indicative of support for the current administration or the way tax monies are spent. What it does reveal is a healthy respect for the punitive powers of The Man. In OA circles, however, a forecast compliance with a mandate is viewed as the equivalent of democratic support.

A more complicated item, and one that is more susceptible to reasoned argument, is what is called the Open Access Advantage. No, this is not a frequent flier program but the notion that authors who work in OA formats are more likely to be cited than authors who work in proprietary or “toll-access” media. Superficially, this may appear to make sense; after all, if everyone can read an OA article, surely it has a better chance of getting cited than an article that has more limited distribution by virtue of the constraints imposed by subscription barriers. On the other hand, an article in the toll-access Lancet is much more likely to be cited than an article deposited in a no-name repository, with only Google keyword searching enabling the poor, already overburdened reader. Once again we find Alma Swan behind this.

The problem with the alleged Open Access Advantage is, first, it entirely ignores the overall marketing context of any particular work. The fact is that some OA venues are brilliantly marketed; I would point to the Public Library of Science in particular. But marketing is not a constant; it varies journal by journal, issue by issue, and article by article. Swan’s analysis does not take these variables into account.

More fundamentally, though, we have here the common but huge mistake of many people...[to believe] that the Internet has arrived, that its current state pretty much resembles its future state....Better to think of the current stage of the Internet (switching metaphors) as the second inning of a nine-inning ballgame. Before this game is over, entirely new and as-yet undreamed-of ways to call attention to content on the Internet will arise, and whatever advantage OA may hold today (in some circumstances for some articles) will be handed off to other publishing forms–which may, in time, hand them back to OA. The wheel goes ’round; where it stops, nobody knows.

Advocates of toll-access or traditional publishing should take no comfort from this. While many of the arguments for OA are offered in bad faith or with the best of intentions but the worst of reasoning, there is one stubborn fact about the Internet and OA, and that is that it is very, very easy for someone to connect to the Internet and upload content. OA is thus at a minimum an inevitable and unstoppable phenomenon. The justifications for it may be doubtful, but the fact of it is indisputable.

PS:  Before responding myself, I can save a lot of time by quoting Stevan Harnad's comments:  Putting Science Publishing Into Perspective, Open Access Archivangelism, December 15, 2007.  Excerpt:

Commentary on: "Putting Science into Science Publishing" by Joseph Esposito, Publishing Frontier (blog) December 11 2007.

The posting contains the by now familiar litany of lapses:

(1) Open Access is not only or even primarily about Open Access Publishing (Gold OA): It is about OA itself, which includes Green OA, the far bigger and faster-growing form of OA: Authors making their own published, peer-reviewed non-OA journal articles (not only or primarily their unpublished preprints) OA by self-archiving them in their own OA Institutional Repositories. Only 10% of journals are Gold OA, but over 90% of journals endorse immediate Green OA self-archiving by their authors -- with over 60% endorsing the immediate self-archiving of the author's final peer-reviewed draft.

(2) The question of whether librarians will cancel journals is not about Gold OA: It is about Green OA. Joseph Esposito contemplates whole-journal cancellations of subscriptions to Gold OA journals, whereas the speculations have been about whether and when librarians would cancel non-OA journals as Green OA self-archiving grows. Green OA self-archiving grows anarchically, not journal by journal. So not only is it hard for a librarian to determine whether and when all the articles in a given journal have become OA, but all the evidence (from the publishers) to date in the few areas (of physics) where Green OA self-archiving is already at or near 100% is that there are as yet no detectable cancellations as a result of 100% Green OA. (Rather, the publishers themselves seem to be adopting Gold OA in these areas: SCOAP3.)

(3) The OA citation impact advantage is not about unpublished or low-impact Gold OA journal articles versus high-impact non-OA journal articles: It is about the additional citation impact provided by OA, for any non-OA article, including those articles published in high impact journals! They don't lose their non-OA citations: they just gain further OA citations....  [PS:  Here omitting a chart.]

(4) The international, interdisciplinary survey evidence of Swan and Associates did not just tautologically confirm that people comply with requirements if required: The point was that over 95% of researchers report that they would comply with a Green OA self-archiving mandate from their employers or funders and 81% report they would do so willingly. (Only 14% said they would comply unwillingly, and 5% said they would not comply.) Arthur Sale's comparisons of actual mandates and compliance rates confirmed these findings, with spontaneous (unmandated) self-archiving rates hovering around 15%, encouraged self-archiving rates rising to about 30% and mandated, incentivized self-archiving rates approaching 100% within two years. (Not surprising, since academics are busy, and would be publishing much less too, if it were not for the existing universal publish-or-perish mandate.) Self-archiving is rewarded by the resulting enhanced research impact metrics, which their institutions also collect and credit, if researchers self-archive....  [PS:  Here omitting a chart.]

Comments. I support Stevan's responses and would only add a couple of my own.  Joe claims that OA advocates believe "that librarians are stupid. The form this assertion takes is to argue that librarians will continue to pay for something that they can get for free."

  • This is a careless reading of OA advocates.  First, let's separate predictions about what librarians will do from facts about what they are doing now.  Physics is the field with the highest levels and longest history of OA archiving.  If high-volume OA archiving causes librarians to cancel journals, we'll see it first in physics.  But after 16 years of phenomenal growth at the physics arXiv, the American Physical Society (APS) and Institute of Physics (IOP), have publicly acknowledged that they cannot identify any cancellations attributable to OA archiving.  In fact, both the APS and IOP even host their own arXiv mirrors. 
  • Joe must believe that librarians are stupid for not cancelling physics journals (and that APS and IOP are stupid for hosting mirrors of arXiv).  I don't pretend to know all the variables explaining the absence of cancellations in physics.  I've repeatedly called for a study of them, in part to help us predict whether other fields will or will not be like physics.
  • But there are good reasons why smart librarians might not cancel journals even after funder OA mandates raise the levels of OA archiving to the high levels we now see in physics.  I outlined four of them in an article in September 2007:

    First, all OA mandates include an embargo period to protect publishers....Libraries that want to provide immediate access will still have an incentive to subscribe.

    Second, OA mandates only apply to the final version of the author's peer-reviewed manuscript, not to the published version....Libraries that want to provide access to published edition, or the published version of the text, will still have an incentive to subscribe....

    Third, OA mandates only apply to research articles, not to the many other kinds of content published in scholarly journals, such as letters, editorials, review articles, book reviews, announcements, news, conference information, and so on.  Libraries that want to provide access to these other contents will still have an incentive to subscribe.

    Fourth, funder OA mandates only apply to articles arising from research funded by the mandating agency.  Very few journals publish nothing but articles from a single funder or even from a set of funders all of whom have OA mandates.  Libraries that want to provide access to all the research articles in a journal, regardless of the source of funding, will still have an incentive to subscribe.  (This incentive will weaken as more and more funders adopt OA mandates; but we're very far from universal funder mandates; unfunded research, which predominates in many fields, will still fall outside this category; and the other incentives above will still stand.)

  • Publishers who oppose OA mandates like to predict that mandates will cause journal cancellations.  But they invariably disregard the counter-evidence from physics and the four factors I've listed above.  Joe does too.  My own position is that other fields may or may not turn out to be like physics.  That is, I don't predict that rising levels of OA archiving will or will not cause cancellations in fields outside physics.  Stevan's position is virtually the same.  Instead of making a prediction, as I put it in the same September article, I prefer to "(a) point out that high-volume OA archiving has not caused cancellations in physics; (b) acknowledge that other fields may not turn out to be like physics in this respect; and (c) argue that if other fields do turn out to differ from physics in this respect, then mandated OA archiving is still justified."

Presentations from OA day at U of Konstanz

The presentations from the University of Konstanz Open-Access-Tage (Konstanz, December 6-7, 2007) are now online.  (Thanks to the Open Access Informationsplattform.)

OJS 2.2

The Public Knowledge Project has released version 2.2 of Open Journal Systems, the free and open source journal management package optimized for OA journals.  From the site:

OJS 2.2 includes an enormous number of new features, tune-ups, and bug fixes, including:

  • Complete overhaul of metadata storage, including site, journal, and article data, for full multilingual support
  • Support for numerous external packages and services such as OpenAds, phpMyVisites, and Google Analytics
  • Payment support
  • New plugin categories

...and much, much more.

Another free online Nature supplement

Nature has created another free online supplement, this time Proteins to Proteomes, sponsored by Pfizer.