Open Access News

News from the open access movement

Saturday, January 08, 2005

OA collection of ELPUB conference papers

Bob Martens of Vienna University Of Technology has assembled an OA database of all the ELPUB conference papers since 1997. (Thanks to Gerry McKiernan for the link.) Charles W. Bailey points out that the database contains many papers about OA.

More on OA to drug trial data

Barry Meier, Drug Industry Plans Release of More Data About Studies, New York Times, January 7, 2005 (free registration required). Excerpt: 'Faced with pressure from lawmakers and editors of medical journals, four trade groups representing the world's biggest drug makers said yesterday that their members planned to release more data about clinical drug trials. In a joint statement, the groups said their member companies had committed themselves to disclose more information about drug studies, both when the studies are started and when results are released. The groups included the Pharmaceutical Research and Manufacturers Association in Washington and organizations in Europe and Japan....The industry is confronting two immediate problems. Drug makers are facing the prospect of federal legislation that would require them to register studies in a public database and post their results in it as a condition for running a trial. Separately, several prestigious medical journals have said they will soon stop publishing the results of clinical drug trials unless certain data about those studies are disclosed in a public database when a trial starts.'

Open-source drug project launches a wiki

The Tropical Disease Initiative in a project for the open-source development of drugs to treat tropical diseases. (For background, see the excellent article in last month's PLoS Medicine.) TDI has just launched a wiki. Quoting from the wiki: 'The Tropical Diseases Initiative (TDI) is... "...a decentralized, community-wide effort that (a) searches parasite genomes for new targets, (b) finds chemicals that bind to known targets, (c) evaluates each candidate drug's chances for success, and (d) selects the most promising candidates for further development." It's currently just an idea. The aim of this wiki is to see if we can turn it into more than that, starting with a website.' (PS: I can't recall seeing an earlier example of a wiki devoted to serious, original research on a topic in the natural sciences.)

Open source, open access, and open content in the humanities

Saul Fisher, The Open Source Movement and Higher Education: Consequences for the Humanities, a presentation at the Modern Languages Association Convention, December 30, 2004. Excerpt: 'Aside from such general expected consequences for higher education and its institutions, what, then, are specific ways in which 'open' tools and resources may shape the humanities? Here I mention two possibilities. First, one probable impact that may be traced to the character of developing 'open' structures (and the primary inspiration is the development of OS applications) is an intensification of collaborative processes. And one particular instance where this may be of fantastic potential is the promotion of a culture of collaborative development for given, highly specific domains of study, across institutions (and so independent of their contingent strengths or weaknesses in the domain) and as informed by discipline-wise needs (as for example, in joining few and dispersed forces to promote the study of early Provençal literature). Another way 'open' resources and tools may affect the humanities is by helping to encourage a greater collaborative culture at the core of practices in the humanities disciplines. This might take several forms: [1] Research habits may become less isolated....[2] Authoring may acquire more diffuse agency....[3] Teaching habits may become less individualistic....[4] Publishing may be more of a collective enterprise.' (Thanks to Ross Scaife.) (PS: See my analysis of why OA in the humanities isn't moving as quickly as OA in the sciences.)

Data accessibility for systems microbiology

Merry Buckley, Systems Microbiology: Beyond Microbial Genomics, American Society for Microbiology, 2004. Excerpt: 'Enormous quantities of biological data have been accumulated over the years, including genome sequences, annotations, biochemical information, microarray profiles, and other types of information. These data could serve as an invaluable resource for developing a systems understanding of microbes, however, many important data sets are unavailable to public databases and others are not amenable to storage or comparison in a database format (video images etc.). Ideally, these data sets should be stored in searchable, cross-referenced databases that allow researchers ready access to information pertaining to their individual research efforts. For example, with new microarray data in hand, a researcher could access a relevant database to discover the location and context of a gene of interest, its place on a metabolic map of that organism, its relationship with or within regulatory networks, and related genes or pathways in other organisms. In order to make the best use of archival data and to move forward in the field, data of use in systems microbiology must be publicly accessible and encoded in a format that can easily be cross referenced.'

ALA draft strategic plan

Here are some excerpts from the ALA Draft Strategic Plan (December 16, 2004): 'Mission: To provide leadership for the development, promotion and improvement of library and information services and the profession of librarianship in order to enhance learning and ensure access to information for all....ALA is the leading advocate for...[t]he public's right to a free and open information society....Desired Future:...There is permanent public access to government information....ALA contributes to public policy decision-making in all areas related to education, libraries, and access to information....Strategic Objectives:...Increase ALA's influence in promoting First Amendment rights, intellectual freedom, equity of access, fair use, and privacy.'

More on the Zwolle Principles

Julia Blixrud, Balancing Stakeholder Interests in Scholarship-Friendly Copyright Practices, ARL Bimonthly Report, December 2004. Excerpt: 'The premise for the [Zwolle] meetings [December 2002 and following] was the need for universities to rethink their strategic role in the dissemination of academic scholarship. New technologies make the creation and distribution of scholarly work easier. How universities might raise awareness and educate their administrators and faculty about copyright and how to address the allocation of rights among the key stakeholders were the major topics of discussion. A significant outcome of the meetings was a set of principles, "Balancing Stakeholder Interests in Scholarship-Friendly Copyright Practices" (see sidebar). These principles were to a great extent based on the Tempe principles, and the report, "Seizing the Moment --Scientists' Authorship Rights in the Digital Age," from the American Association for the Advancement of Science. In addition, the Zwolle group has collected and reviewed agreements between authors and publishers, institutional copyright ownership policies, and is creating a "copyright toolkit" that will help inform publication agreements and university policies.'

More on DPubS

Terry Ehling, The Development of an Open Source Publishing System at Cornell and Penn State Universities, ARL Bimonthly Report, December 2004. Excerpt: 'Five years ago, the Cornell University Library submitted a proposal to the Andrew W. Mellon Foundation for the support of the design and deployment of a mechanism and environment for the online distribution of serial literature in mathematics and statistics. The resulting Project Euclid was funded in 2000 and launched as a multi-model publishing service in early 2003. Today Euclid delivers nearly 40 journals to libraries and individuals under subscription, hosting, or open access delivery plans. Project Euclid's technology infrastructure is based on a modular digital library architecture and protocol developed at Cornell in the early 1990s. The model developed by the library from this early digital library instantiation is now known as DPubS (Digital Publishing System). DPubS was designed specifically to organize, navigate, access, and deliver both open access and subscription controlled scholarly publications. In spring 2004 Cornell University Library in partnership with the Pennsylvania State University Libraries and the Pennsylvania State University Press were awarded a $670,000 grant from the Mellon Foundation to generalize and enhance the DPubS system and release the resulting improved version of the software under an open source license.'

Friday, January 07, 2005


From Hugh Stimson's blog: "Whenever I need cheering up, I scan through the Open Access News blog. There is so much going on there, and it's so good."

French introduction to OA updated

The École nationale des ponts et chaussées has updated its Dossier : l'Open Access, a useful introduction OA. See the original French or Google's English.

Thursday, January 06, 2005

On the significance of Creative Commons

Rainer Kuhlen and Jochen Brüning, Creative Commons (CC) – für informationelle Selbstbestimmung, gegen den Trend des Urheberrechts/Copyright als Handelsrecht; oder: Chancen für einen innovativen Drei-Stufen-Test? A preprint. In German but with this English-language abstract: 'Creative commons (CC), together with the Open access and the Free and Open Source Software (FOSS) initiatives, has in a very short time become a signal that there are alternatives to the dominant commercialization of knowledge and information and to the exploitation of authors of creative work. More systematically formulated: CC aims at reversing the world-wide trend of understanding copyright (including the European legal tradition of authors rights) primarily as a trade law. CC's objective is to rebind the rights on intellectual works to the authors not to the content industry. CC is thus an important contribution for saving authors' information autonomy.' (Thanks to Klaus Graf.)

Controversial German digitization proposal

Berlin publisher Hans Heinrich has proposed a controversial plan to use public money to hire unemployed Germans to digitize images and manuscripts in German museums, libraries, and archives. The digital copies would not be OA and their use would require permission of the facilities housing the originals. Klaus Graf summarizes the controversy, offers some criticism of his own, and calls for OA to Germany's cultural heritage.

More on OA to drug trial data

Drug research openness promised, BBC News, January 6, 2005. An unsigned news story. Excerpt: 'Results of all industry clinical trials will be published on the internet later this year under plans drawn up by pharmaceutical trade associations. The database is voluntary but all the major pharmaceutical companies are said to have signed up to it. The move follows years of pressure on drug firms to publish negative results....Dr Richard Barker, director general of the ABPI, said: "The industry recognises that there are important public health benefits associated with making clinical trial information more widely available to healthcare practitioners, patients and others. "By publishing not just the results of trials that have taken place - whether positive or negative - but also those that are just starting, the industry has made a major step towards achieving greater transparency." Trade associations across Europe and in the US and Japan have signed up to the plan.' (Thanks to David Prosser.)

More on PLoS

PLoS has posted a press release with additional details about the three new journals to be introduced in 2005. PLoS Computational Biology - Fulltext forthcoming June 2005; Print ISSN: 1553-734X | Online ISSN: 1553-7358. PLoS Genetics - Fulltext forthcoming July 2005; Print ISSN: 1553-7390 | Online ISSN: 1553-7404. PLoS Pathogens - no start date or website yet at PLoS. Ulrich's indicates September 2005 -- Print ISSN: 1553-7366.

Potential revenue for OA journals

John Battelle, A New Idea for Publishing, Technology Review, January 2005. Excerpt: '[T]he Internet’s interactivity suggests an alternative economy in which the long-standing imbalance between publisher, audience, and advertiser could be corrected. A system of Internet-based marketing, which I'll call Publisher-Driven Advertising, or PDA, may be soon possible. In this system, publishers would pick and choose from a vast supply of advertisers. The first step toward building such a system has already been taken: the pay-per-click (PPC) network. If you have ever visited Google or any content site that runs Google's ads, you've seen it....Those text-based ads on the right side of the screen represent two shifts in the traditional relationship between publishers and advertisers. First, the advertiser pays only when the ad performs --when someone clicks on the ad itself. Second, paid search networks "disaggregate" advertisers from publishers --that is, advertisers no longer purchase space on the publisher's site but instead pay for keywords....Next, imagine that, instead of buying into PPC networks or specific sites, advertisers release their ads onto the Internet. Because an Internet-based ad is already a little piece of software, it can be tagged with information about its target audience, how much the advertiser is willing to spend to reach that audience (and how much each click will cost), what kind of websites are acceptable or forbidden (such as porn sites), and any number of other attributes. Most important, each ad could communicate with a "home" application that tracks its progress and status....Why is this model better than the current one? Because publishers know their audiences best. There's no incentive for publishers to place ads that don't perform or that offend their readers.'

(PS: This system is doesn't exist yet, so we can't tell whether it would work in any publishing sector. But if it ever gets off the ground, would it work for scholarly journals? Advertising needn't pay all the bills at an OA journal in order to generate helpful revenue.)

PLoS to launch 3 OA journals in 2005

Public Library of Science (PLoS) announced today that they will launch three new Open Access journals in 2005. The press release indicates that the forthcoming titles are: PLoS Genetics, PLoS Computational Biology, and PLoS Pathogens. (Thanks to Gary Price.)

The Google library project will help libraries and publishers

Emily Hagedorn, Google's plan to put books online will boost libraries' exposure, Tallahasee Democrat, January 6, 2004. Excerpt: 'Carol Pitts Diedrichs hopes that Google's new program to put thousands of texts online will drive readers back to where they once started: the library...."People don't sit at a computer and read a book much," Diedrichs said. "What we hope it will do is drive users to us to use our collections." ...Google users can also see which books are at 23,000 libraries through Online Computer Library Center's WorldCat catalog, the world's largest bibliographic database. That non-profit, computer library service turned WorldCat's entire database over to Google, said Wendy McGinnis, the center's director of communication and public relations. This means that with each book search, a tab will pop up, directing the user to find that book in a local library....Stephen Wrinn's expectations take Diedrichs's a step further. As director of the University Press of Kentucky, Wrinn is putting excerpts from some of the press's books online through Google, expecting that it will bump up sales. The catch: Googlers won't be able to print or copy and paste the information from their site. "The whole thing hinges on the fact they can't reproduce," said Wrinn. All of the press's 850 titles will be online at some point, said Leila Salisbury, University Press's marketing director.'

OA to UN documents

On December 31, 2004, the United Nations launched its Official Document Service, which offers open access to searchable, multilingual, full-text versions of UN documents. For more details, see the press release, training guide, or FAQ. (Thanks to ResourceShelf.)

Free online audio books for the blind

Unabridged, launched in November, is a free online lending library of audio books for the blind. For more detail, see the FAQ or yesterday's press release.

JISC announces funding for 5 OA journals

Today JISC made the announcement previewed yesterday by Saeed Shah in The Independent. From the JISC announcement: 'Following a remarkable year for the spread of open access ideas and the gathering of momentum for real change, the New Year begins with an announcement by JISC of the winners of funding under the second round of its Open Access programme. Following the success of the first year of the JISC programme, the decision has been made to award five publishers funds to support open access delivery for their journals. A total of £150,000 will be awarded to some of the key scholarly publications in their fields. These journals are: The New Journal of Physics (published by the Institute of Physics Publishing); Nucleic Acids Research (Oxford University Press); Journal of Medical Genetics (British Medical Journals); the journals of the International Union of Crystallography (IUCr); and The Journal of Experimental Botany (The Society for Experimental Biology). JISC funding will ensure the waiving of all or part of the submission/publication fees for all UK HE authors....[As a result of the first year of funding] the New Journal of Physics has seen UK submissions increase by 300% in the last six months, while access to articles from UK users has risen 71%. The journal’s impact factor has risen from 1.76 to 2.48....A further round of funding will be made available to the publishing community later in 2005.'

Update. Since the JISC announcement, I've seen follow-up press releases from Oxford University Press and the Institute of Physics.

More on how OA increases citation impact

Tim Brody, Citation Impact of Open Access Articles vs. Articles available only through subscription ("Toll-Access"), a preprint in progress. The best compilation of data to date on the effect of OA on citation impact in physics and mathematics for the decade 1992-2003. Excerpt: 'The data come from the Institute for Scientific Information (ISI) CD-ROM citation database, which covers the main journals in all fields, and from the OA Physics/Mathematics Archive where authors can self-archive their articles to make them Open Access (OA). The method was to take all the physics and mathematics articles indexed by ISI from 1992-2003 and first calculate how much each article is cited. Then all these articles are divided into those that are and are not in Arxiv, hence are or are not OA. The OA advantage is then calculated from a comparison of the citation counts for the OA versus the non-OA articles: 100(OA/non) - 100% (OA divided by non-OA citation counts, minus 100%). This gives the percentage by which citation impact is altered, positively or negatively, by making the article OA (by self-archiving it in Arxiv). As will be seen, virtually all of the OA impact effect (red) is positive: OA enhances citation impact substantially, sometimes by several hundred percent. This is to be expected, because increasing accessibility increases rather than decreases potential usage.'

Brody and the six other members of his project are extending their study beyond physics and mathematics. They are not only collecting and analyzing data from a large number of other fields. They are organizing the data behind an interactive interface allowing users to select any combination of research specializations and display graphs of their data on the same page. For example, here's the page on geriatrics, acoustics, and linguistics.

OA is the top library story of 2004

The editors of LIS News have compiled a list of the Ten [Library] Stories That Shaped 2004. Open access is number 1.
Open Access and the Economy

Viable alternatives to for-profit publishing gained steam this year with the popularity of Wikipedia, the successes of the Public Library of Science, a proposal by the National Institutes of Health, and the milestones reached by Project Gutenberg. Open Access publications holds great promise for addressing the hyper-inflating cost information.

Librarians are charged with spreading and preserving information. Despite advances in technology, copyright extensions and fair use limitations are opposing these tasks like never before. Librarians are also getting the squeeze from spiraling publishers' prices and budgetary constraints.

Being stifled by profiteering content providers and their legal campaigns against the freedom of information is the greatest obstacle facing libraries today.

(PS: This is exactly right. For more detail on the OA developments in 2004, see my timeline or 2004 review.)

Wednesday, January 05, 2005

Preview of JISC support for 5 OA journals

Saeed Shah, Reed Elsevier facing fresh threat to science journal profits, The Independent, January 6, 2005. Excerpt: 'Five more leading science journals are to partly or fully abandon charging subscriptions and take up the "open access" model, it has emerged, in a blow to traditional publishers in the sector such as Reed Elsevier. An influential government-funded organisation, the Joint Information Systems Committee (JISC), will announce later this week that it is providing funding to the journals in order to aid the transition to the "author-pays" or open access. Fred Friend, a consultant to the JISC and a leading advocate of open access, said: "Reed's problem is that it's had a very easy life for a number of years, based on secure funding from libraries. That gravy train's coming to an end because libraries cannot afford it any more." The publications involved in the JISC initiative are The New Journal of Physics (published by the Institute of Physics Publishing); Nucleic Acids Research (Oxford University Press); Journal of Medical Genetics (British Medical Journals); the journals of the International Union of Crystallography; and The Journal of Experimental Botany (The Society for Experimental Biology)....Martin Richardson, managing director of journals at Oxford University Press, said: "Open access has not so far been shown to be commercially viable. This JISC grant will ensure a sufficiently large sample to see how well it works." JISC's had previously backed a smaller trial, involving some of the same journals. It said yesterday that the results had been extremely encouraging. For instance, the New Journal of Physics saw a 300 per cent jump in author submissions, while the Journal of Experimental Biology saw access rise by 27 per cent.'

Two articles critical of OA and the NIH plan

Here are two articles from the December issue of BioScience. In both cases, not even an abstract is free online, at least so far. (Thanks to Donat Agosti.)
  1. Timothy M. Beardsley, Who Pays for Publication? An editorial. Excerpt: 'The immediate impetus to [Ellen Paul's] concern [see second article, below] (and that of [the American Institute of Biological Sciences]) is a startling proposal that was issued last September by Elias Zerhouni, director of the National Institutes of Health (NIH). In line with recommendations from the US House of Representatives Appropriations Committee, Zerhouni proposed that within six months of publication, articles resulting in whole or in part from NIH-funded research be made available online to the public at no cost. Copyright be damned, he might have added. [PS reply.] By mandating open-access publication in what would have to be a huge government-funded database, Zerhouni's scheme threatens the ability of not-for-profit, as well as commercial, publishers to cover the costs of peer review, editing, and production by the traditional method of charging libraries and individuals for subscriptions. [PS reply.] ...Scientists understandably like the idea of their work being made widely available, and many societies are studying methods for increasing access. It remains to be seen whether scientists will be as enthusiastic about paying the several thousand dollars per article that even not-for-profit publishers would have to charge, over the long term, for open-access publication. [PS reply.]'

  2. Ellen Paul, Warning: Open Access May Be Hazardous to the Health of Your Scientific Society. Excerpt: 'For most scientists, the open-access controversy has seemed to come out of the blue. All of a sudden, government policies about free online access to research publications are looming, catching scientific societies by surprise. In fact, the issue has been simmering for years. A timeline maintained by Peter Suber, an open-access advocate at Earlham College, shows the first open-access journal appearing in 1990. It is telling that Suber's timeline actually begins in the 1960s, with the development of the Internet. Call it open access, or call it free-and-easy access --it must be reckoned with. As NIH director Elias Zerhouni said in a meeting with publishers and scientific societies, "the status quo is not an option." Neither is a government-mandated, inflexible model that ignores the concerns of small, nonprofit scientific societies. An important issue with serious consequences requires a more thoughtful, nuanced approach that allows everyone --including authors, publishers, and nonprofits-- time to adapt to this radical change in scientific publishing.' (PS: I have only two very general replies to Ellen Paul's article. First, publishers have had time and will have more time to adapt to the NIH policy. Second, continuously rising subscription prices are hazardous to the health of a journal, the research niche it serves, and the scientific society that become dependent on the revenue.)

Removing IP barriers to knowledge sharing in developing countries

Kevin Outterson, Nonrival access to pharmaceutical knowledge, a preprint submitted to the WHO Commission on Intellectual Property Rights, Innovation & Public Health, January 3, 2005. From the abstract: 'On innovation grounds, pharmaceutical patents are unnecessary in low income populations, since such markets cannot do much to support global pharmaceutical profits. The public health needs of low income populations require patented drugs to be made produced at the marginal cost of production, without R&D cost recovery. Nonrival access to pharmaceutical knowledge achieves both goals simultaneously.'

From the body of the article: 'The "nonrival access" proposal is to permit unrestricted access to pharmaceutical knowledge for low income populations. IP rent extraction to support R&D would be limited solely to high income populations. Pharmaceutical goods (pills) are rival. Two people cannot share the same pill. Taking a rival good requires compensation. Pharmaceutical knowledge is nonrival, and can be shared without diminishing anyone else's knowledge. The only reason not to share pharmaceutical knowledge is to promote future innovation. Nonrival access proposals must account for retaining optimal innovation incentives....Nonrival access would greatly improve global human health, particularly among low income populations. Nonrival access would not harm global innovation incentives, since patent rent extraction would continue in high income markets. Several models for nonrival access are possible, but the mechanisms must actually result in pharmaceutical production at MCP [marginal cost production] in quantities sufficient to meet the clinical needs of low income populations. Anything less might be a step in the right direction, but is not nonrival access.'

Licensing genomic inventions

On November 19, the NIH published a draft of its document, Best Practices for the Licensing of Genomic Inventions, for 60 days of public comment. If you have an opinion, make sure to submit it before January 18.

A successful OA journal from a society publisher

SPARC has announced its partnership with Optics Express, an OA journal published by the Optical Society of America. From the December 7 press release (posted January 4): 'The partnership is intended to call attention to the potential for open access publishing in the society-publishing environment....Ranked in the top ten optics journals by ISI, Optics Express was among the first peer-reviewed open-access journals in the marketplace and has played an increasingly important role for OSA since the journal's founding in 1997....OSA elected to make access to articles free and recover costs through a publication fee. This has proven not to be a barrier to submission, and the journal never refuses a worthy article because the author cannot afford the fees. By 2002, Optics Express broke even, with revenue covering staffing, overhead and development costs, and this year, OSA will generate a modest net surplus. Optics Express receives its total revenue from publication charges, which are $450 for articles six pages and under, and $800 for articles over six pages.'

Tuesday, January 04, 2005

Skepticism about OA

Scientific literature: Who should pay - author or subscriber? DCL News, January 2005. An unsigned editorial. Excerpt: 'One of the biggest threats to the established order is the Public Library of Science (PLoS), which publishes two journals - Biology and Medicine - and exists on donations from charitable foundations. Its executive director, Vivian Siegel, says her organization's mission is nothing less than to democratize science. "We think of ourselves as a combination of scientific publisher and an advocacy group to create a change that is larger than ourselves."...As it stands, there is no proof that the author pays model is sustainable. In five years of operation BioMed Central, for example, is yet to break even. What's more, there is no consensus on how much scientists should pay to publish their work. PLoS charges around $1500 per article; BioMed Central half that sum.' (PS: Two quick replies: PLoS launched with the help of foundation money but its business model is to operate on article processing fees and institutional memberships. There needn't be a consensus on how high to see processing fees; different journals in different fields will have different expenses.)

Open publishing and the European Citation Index for the Humanities

Francesca Di Donato, Verso uno "European Citation Index for the Humanities": Che cosa possono fare i ricercatori per la comunicazione scientifica, Bollettino Telematico di Filosofia Politica, October 26, 2004. In Italian but with this English-language abstract: 'As a matter of principle, to open publish is a tautology, because making a text public means to maximize the access to texts and documents; but in practice, the equivalence doesn't work. Why? The answer depends on a twofold tension: the first tension is the one between Science and Technology, that is, between on the one hand the research process and the needs of scientists, and on the other, technological possibilities and limits, depending on publishing media (printed paper, computers, the Internet and the Web). The second is the tension between cataloguing (classification) and selection, that means the tension between the need to archive the results of human research, and to make them accessible; and, when quantity grows and several restrictions come out, the need of selection. This article is a discussion of a recent initiative of the ESF, the "European Citation Index of the Humanities"; it aims at providing some elements for the authors to consider, seeking an answer to the first question.'

Teaching future librarians about OA

Cheryl L. Davis and Barbara B. Moran, Preparing Tomorrow's Professionals: LIS Schools and Scholarly Communication, College & Research Libraries News, January 2005. Excerpt: 'Today's LIS (Library and Information Science) graduates will enter a work world transformed by the revolution in scholarly communication. These changes affect virtually all aspects of academic library operations. New librarians must confront challenges such as balancing and providing appropriate access to print and electronic serials collections and keeping abreast of not only current journal and database subscriptions, but also the growing number of accepted (and cited) open-access scholarly publications. They must wrestle with copyright issues and the implications of developing institutional repositories.'

Scholarly communication in the humanities

Richard K. Johnson, The Future of Scholarly Communication in the Humanities: Adaptation or Transformation? A presentation at the meeting of the Council of Editors of Learned Journals, December 30, 2004. Excerpt: 'The most compelling motivation for Congress and NIH to support open public access to NIH-funded research is to demonstrate to taxpayers the return on their investment in doubling the size of NIH is recent years. Perhaps there is a lesson here for the humanities. Expanded public exposure for scholarship in the humanities offers the potential for enhanced political and financial support. By reaching a broader audience beyond specialists in a single field, open global sharing of knowledge also will support interdisciplinary scholarly perspectives....What do these examples [of OA archiving and OA journals in the STM fields] have to do with the humanities? They simply suggest that powerful — if not unstoppable — forces are chipping away at the traditional journal. Will the outcome be adaptation or transformation? I think there will be both. There will be e-journals (and e-books) that look much like what is supplied in print today. But the foundation beneath these, the ways in which they are accessed and used, what they contain, and the profile of users is likely to be transformed. The toughest issues we face today revolve around business models – who pays the tab in a disaggregated environment? Perhaps toughest of all, how is the certification process supported? Publishers and libraries aren’t the only players asking themselves these questions. The costs associated with publishing are the least part of the overall research process. Since academic institutions, funders, and the public are key beneficiaries of research, I think we can expect them to play new, active roles in reshaping scholarly communication in the sciences, the social sciences, and, yes, the humanities.'

PubChem, from the folks who brought you PubMed

Eric Sayers, PubChem: An Entrez Database of Small Molecules, NLM Technical Bulletin, January-February 2005 (reprinted from NCBI News, Summer-Fall 2004). Excerpt: 'The NCBI has released three new Entrez databases that link small organic molecules to bioactivity assays, PubMed abstracts, and protein sequences and structures. The new databases compose the PubChem project at NCBI, a part of the NIH Roadmap Initiative. They are PubChem Substance, PubChem Compound, and PubChem Bioassay. PubChem Substance contains over 800,000 chemical samples imported from 14 public sources including ChemIDplus, the Developmental Therapeutics Program at the National Cancer Institute (NCI), KEGG, NCBI Molecular Modeling Database (MMDB), and the NIST Chemistry WebBook. Chemical entities in PubChem Substance records that have known structures are validated, converted to a standardized form, and imported into PubChem Compound. This standardizing allows NCBI to compute chemical parameters and similarity relationships between compounds....PubChem Compound also indexes these chemicals using 34 fields, many of which represent computed chemical properties such as the number of chiral centers, the number of hydrogen bond donors/acceptors, molecular formula and weight, total formal charge, and octanol-water partition coefficients (XlogP). These groups are provided as Entrez links that allow similar compounds to be retrieved quickly....PubChem Bioassay allows one to search for bioactivity. For instance, the query "leukemia AND lc50[tid description]" in PubChem Bioassay retrieves eight growth inhibition assays with measured LC50 values in various leukemia cell lines. Links are then provided to PubChem Substance and PubChem Compound for these chemicals so that they may be further explored.'

Conference presentations

The presentations from the ALPSP-SSP meeting, Open Access Publishing: Does it really work in practice? (Washington D.C., November 8, 2004), are now online.

Sorghum genome sequence in the public domain

Orion Genomics has sequenced the sorghum genome and assigned its work to the public domain. From today's press release: 'Orion Genomics, a Second Code biotechnology company, announced today that it is donating to public researchers all of its proprietary gene-enriched DNA sequence from the sorghum plant, a close relative of corn and one of the most important cereal crops worldwide....A paper authored by Orion researchers appears online today in The Public Library of Science [PLoS Biology] and describes the way in which Orion's GeneThresher(TM) technology was used to quickly and cost effectively elucidate for the first time more than 95 percent of the genes in sorghum. Previously, using traditional technologies, the sorghum sequence was too large to be cost-effectively determined. The sorghum sequence is available at Genbank of the National Center for Biotechnology Information, a division of the National Library of Medicine (NLM) at the National Institutes of Health (NIH).'

More on the launch of Science Commons

Michelle Keller, Profit, patents and progress, The Stanford Daily, January 4, 2005. Excerpt: 'On Saturday, Creative Commons, a nonprofit dedicated to offering flexible copyrights for creative works, launched Science Commons, designed to ease the sharing of scientific research and datasets....Science Commons will help authors publish work online with licenses based on the Creative Commons copyright licenses, allowing researchers to publish in multiple journals, post up their work on their own Web site and share raw datasets....[While patents and copyrights can encourage innovation, they] can also hinder innovation, making it difficult for other researchers to access articles and utilize data....Science Commons offers an alternative to completely dropping journals, offering researchers an opportunity to publish Open Access material, which has more flexible copyrights, and is often free and available online. "I'd expect our involvement in this area to mirror our work elsewhere," [John] Wilbanks [new director of Science Commons] explained. "When a group in the community — be they an Open Access journal or a major publisher, needs to share a document — we want to make sure there's a Science Commons license that lets them share." '

OA to Neuropsychopharmacology back run

The Nature Publishing Group has announced that Neuropsychopharmacology now provides open access its archive of issues more than 12 months old. (Thanks to Péter Jacsó.)

Monday, January 03, 2005

Measuring the impact of an OA resource

Michael J. Kurtz and five co-authors, Worldwide use and impact of the NASA Astrophysics Data System digital library, Journal of the American Society for Information Science and Technology, September 20, 2004. Only this abstract is free online, at least so far: 'The NASA Astrophysics Data System (ADS), along with astronomy's journals and data centers (a collaboration dubbed URANIA), has developed a distributed online digital library which has become the dominant means by which astronomers search, access, and read their technical literature. Digital libraries permit the easy accumulation of a new type of bibliometric measure: the number of electronic accesses ("reads") of individual articles. By combining data from the text, citation, and reference databases with data from the ADS readership logs we have been able to create second-order bibliometric operators, a customizable class of collaborative filters that permits substantially improved accuracy in literature queries. Using the ADS usage logs along with membership statistics from the International Astronomical Union and data on the population and gross domestic product (GDP), we have developed an accurate model for worldwide basic research where the number of scientists in a country is proportional to the GDP of that country, and the amount of basic research done by a country is proportional to the number of scientists in that country times that country's per capita GDP. We introduce the concept of utility time to measure the impact of the ADS/URANIA and the electronic astronomical library on astronomical research. We find that in 2002 it amounted to the equivalent of 736 full-time researchers, or $250 million, or the astronomical research done in France.' (Thanks to Charles W. Bailey, Jr.)

Many roads to OA

Dick Kaser and Marydee Ojala, Open Access Forum: Many Roads to Open Access, Information Today, January 3, 2005. Not even an abstract is free online, at least so far. (Thanks to Charles W. Bailey, Jr.)

Update. I just got access to the text, thanks to Marydee Ojala and Stevan Harnad. Excerpt: 'Two parallel Open Access Forums, one at Internet Librarian International in London, U.K., in October 2004, and the second at Internet Librarian in Monterey, Calif., in November 2004, showcased the issues involved in open access....Both Forums featured an interview with OA advocate Stevan Harnad, professor of cognitive science at the University of Southampton....As Harnad explains it, open access is toll-free online access to the full text of scholarly, peer-reviewed journals. He notes that of the 24,000 such journals, 23,000 of them hold to the traditional subscription-based model. That’s the toll road. The green road is self-archiving. Harnad insists that self-archiving moves the costs from the user's institution to the author's institution. He also stresses that it should be the author's institution, not the author, paying those costs. The gold road is open access journals, such as those from BioMedCentral and the Public Library of Science.'

More on the NIH plan

Lila Guterman, Critics and Proponents Debate NIH's Plan to Free Access to Scientific Materials, Chronicle of Higher Education, January 7, 2005 (accessible only to subscribers). Excerpt: 'Proponents and critics of open access have had a lot to talk about these days as they anxiously await the U.S. government's final plan to make large swaths of scientific literature freely available....Dr. Zerhouni characterized the comments, a fraction of which the agency has posted on its Web site, as "overwhelmingly supportive." Indeed, Richard K. Johnson, director of the Scholarly Publishing and Academic Resources Coalition, or Sparc, called the draft plan "a brilliant compromise."...One scientific-society executive who requested anonymity said that many publishers object to any new government intrusion into the process. They fear that other agencies that finance research will adopt the NIH approach and go even further. "It ain't going to stop with six months," the executive said. The second element of compromise is that the NIH will only request, not require, that researchers send them copies of their papers. Dr. Zerhouni told The Chronicle that that provision was included so that members of scientific societies who might be hurt by the public archive could decline to participate. Patricia S. Schroeder, a former congresswoman who is president of the Association of American Publishers, doubts the efficacy of that step. "The NIH is this two-ton gorilla," she said, because it is the country's largest provider of research grants. "You don't dare not comply with it, really."'

Searching handwritten manuscripts

Ian Austen, A New Script for Searching Texts Written by Hand, New York Times, December 30, 2004. Excerpt: '"There is an enormous amount of handwritten stuff locked away in many archives, libraries and museums," said R. Manmatha, a research assistant professor with the Center for Intelligent Information Retrieval at the University of Massachusetts, Amherst. "Most of the time when people do research they just ignore this stuff because it's not accessible."...To develop their system, Dr. Manmatha and his students obtained about 1,000 pages of George Washington's correspondence that had been scanned from microfilm by the Library of Congress....The breakthrough came from looking at research into how people read, Dr. Manmatha said. Rather than analyzing individual letters, he said, people look at words and even parts of sentences as whole units....Even after training, the resulting software lacks the accuracy of programs used to read and digitize printed books, Dr. Manmatha said. But that it is not a significant problem. "That's the difference between having to recognize a thing and having to search it," he said. "You don't have to get every word right." Right now, Dr. Manmatha believes that the system is about 65 percent accurate....Though no library or archive has yet approached Dr. Manmatha about the system, he will brief Google about it early next year. With sufficient funds for software development and document scanning, Dr. Manmatha said, it may be possible within a decade for people to search historical manuscripts from home as easily as they now locate anything else on the Web.'

More on Google Scholar

Francis C. Assisi, Anurag Acharya Helped Google's Scholarly Leap, IndoLink, January 3, 2005. A profile of Anurag Acharya, the Google engineer behind Google Scholar. Excerpt: 'To rank the results, Google Scholar applies the same criteria that scientists use when deciding which papers to read, says Acharya, including the importance of the journal and how often the work has been cited. Although the tool obtains abstracts for most articles, one will need a subscription to download the full text of some publications. Acharya says upcoming features will include limiting searches by date. According to Acharya, a former faculty member at UCSB, the project was also an effort to address a problem he confronted while enrolled in his B.Tech at IIT Kharagpur. As a student he found materials in his college library, at times, to be significantly out of date. Acharya, who earned his Ph.D. from Carnegie Mellon in 1997, expects Google Scholar will make the world's scientific literature universally accessible....What is the secret of Google’s spectacular success over the past six years? Says Krishna Bharat [the engineeer behind Google News]: "At Google we have a broad charter - to organize the world´s information and make it universally accessible and useful. The mission puts people before profits, so our focus is locked on to a stable target - meeting people's expectations, rather than the whims of the marketplace."'

Google and Vannevar Bush

Google's New Deals Promise to Realize a 60-Year-Old Vision, Chronicle of Higher Education, January 7, 2005 (accessible only to subscribers). An unsigned essay. On how Google will realize the vision of Vannevar Bush for associative indexing. Excerpt: 'To Mr. Bush, the challenge was not storage. Books already did that job marvelously. The looming crisis, according to Mr. Bush, was a breakdown in the system for indexing and retrieving ideas...."Mendel's concept of the laws of genetics was lost to the world for a generation because his publication did not reach the few who were capable of grasping and extending it," Mr. Bush wrote. "And this sort of catastrophe is undoubtedly being repeated all about us, as truly significant attainments become lost in the mass of the inconsequential."...What was needed, according to Mr. Bush, was a new kind of indexing to create an information revolution. He called it "associative indexing" -- "the basic idea of which is a provision whereby any item may be caused at will to select immediately and automatically another. ... The process of tying two items together is the important thing."...So the Google deals are revolutionary....With its focus on providing simple ways for users to snatch useful information out of billions of pages of data, Google could make something like Mr. Bush's vision of "associative indexing" a reality....Andries van Dam, a computer-science professor at Brown University who was involved in the early work on hypertext systems in the 1960s, says that search engines are already more sophisticated than Mr. Bush envisioned because he imagined that associative indexing would need to be done by hand, as researchers noticed connections among concepts.'

More on the Google library project

Scott Carlson and Jeffrey Young, Google Will Digitize and Search Millions of Books From 5 Top Research Libraries, Chronicle of Higher Education, January 7, 2005 (accessible only to subscribers). Excerpt: 'Just how much access to copyrighted works will be allowed is still open to question, he said. "It's going to begin a dialogue between Google and the publishers, and the libraries and the publishers. We don't know the outcome of those discussions yet."...Paul N. Courant, provost and executive vice president for academic affairs, said the digital collection at Michigan would be used "to the maximum extent permitted by law." He envisions students' and researchers' getting access to works in the public domain from their home computers. He also sees the university library setting up a catalog in which the entire collection is searchable down to the level of words and phrases. A project like this is worth "hundreds of millions" of dollars to the university, he said. "This is an important moment in the history of libraries, and an important moment in the history of scholarship."...Brewster Kahle, librarian for the Internet Archive, appreciates Google's commitment to putting books online. "I think Google will do a great job of that," he said, "as well as other search companies" that will very likely follow suit. But Mr. Kahle said he hoped the libraries involved would also place copies of their scanned books in open-access archives. Otherwise, he said, the result will effectively "commercialize the public domain."...It is unclear whether there will be such open access to the books that Google scans, however. Under the terms of the libraries' deals with Google, each university will be given a digital copy of every book scanned and will be able to use those copies in almost any way it wants. One restriction, however, is that the libraries cannot "give it all to Yahoo or the other search companies," noted Oxford's Mr. Milne. Mr. Milne said he would be "happy to talk to anybody about any sensible idea" to add the university's digital copies to open archives, as long as doing so stayed within the bounds of the university's agreement with Google. "We as librarians are quite used to cooperating with our peers at other institutions," he added.'

OA resource for cancer therapy decisions

Cancer Monthly is a new open-access compendium of information on cancer therapies, launched by a group of families to provide the service they wished had been available when they had to make therapy decisions for relatives. From the site: 'Cancer Monthly is the result of the efforts of volunteers whose lives have been forever changed by cancer. When we needed treatment results, they were not available to us. We have invested three years of time and considerable resources to make Cancer Monthly a reality so that this information would be available to other patients. While there are many sites that provide treatment options, this is the only resource that reports the actual results of these therapies. You should use this information to help make informed treatment decisions with your professional healthcare provider.' For more background, see Kristen Philipkoski's story on the launch, Posting Straight Facts on Cancer in today's Wired News.

Best free reference sites of 2004

Machine-readable Project Gutenberg catalogue

Project Gutenberg now provides its complete catalogue in RDF/XML format. Librarians might also want the MARC21 records in a zip or bz2 file. (Thanks to pamplemousse via LIS News.)

Interview with Vitek Tracz

Richard Poynder interviews Vitek Tracz in the January 3 issue of Information Today. Excerpt: 'A serial entrepreneur remarkable for being one of the few remaining innovators in the STM publishing industry, Vitek Tracz, chairman of the London-based Current Science Group, has, over the years, created a series of mold-breaking businesses under the Current Science Group umbrella, including Gower Medical Publishing, Current Drugs, and the Current Opinion series of journals. Convinced that all research must ultimately be freely available on the Web, Tracz has become a powerful advocate for open access. He was a key player in the development of PubMed Central, NIH's free literature repository, and, in 1998, he founded the first open access publisher, BioMed Central....[Quoting Tracz:] Biomedical science simply can't function efficiently anymore without open, unrestricted access to research results....We have seen how important this is with the genome. As a consequence, it is important to completely rethink the way science reports its findings, and this is a big challenge to science publishers as well as to scientists....[At BioMed Central] we need about 2,000 to 2,500 papers a month to break even. We estimate that we will have around 2,000 by the end of next year. While open access publishing will never be as profitable as the current system of selling subscriptions, we are confident it can and will be profitable....Submissions to our journals are now running at more than 700 papers a month. A year ago, this figure was 300; 2 years ago, it was about 120. So it is more than doubling each year. We know that authors who have published open access once publish that way again. And they tell others. Today, around 1 percent of papers are published open access. I believe that when this becomes more like 5 percent, we will reach a tipping point. Suddenly everyone will start knowing someone who has done it and for whom it worked well, and at that point the rate of growth will increase rapidly....Self-archiving is, of course, very desirable, but the issue is quite simple: Publishers are not really going to allow authors to self-archive in an easy way, and authors are not going to do it unless it is completely painless....However, we publishers must remember that the issue is not what is good for publishers, but what is good for science. It is neither in the interests of funders nor of authors not to embrace open access. It is only in the interests of traditional publishers to continue the status quo. If some publishers find that there is no money in publishing, they will do something else. The central point in the open access debate is that it is essential for science and beneficial for society. That is what makes it inevitable.'

OA one of the hot stories of 2004

Paula J. Hane, Wrapping Up 2004; Looking Forward, Information Today, January 3, 2005. On the information industry as a whole, but picking out OA as one of the hot stories of 2004. Excerpt: 'Open Access initiatives exploded. We posted eight NewsBreaks over the year that covered the major developments and the controversies concerning scholarly publishing and open access. There were also several conference forums on the issues, plus columns, features, and commentaries in Information Today, including Richard Poynder’s two-part series on the OA movement in the October and November issues, which included his widely cited interview with OA proponent Stevan Harnad....Open access is an ongoing story. The consensus seems to be that multiple publishing models will co-exist while things settle down.'

Sunday, January 02, 2005

Spreadsheet on article costs

Philip Davis, Calculating the Cost per Article in the Current Subscription Model, a preprint. Abstract: 'This spreadsheet calculates the cost per article published in the current subscription model for 113 institutions designated under the Association of Research Libraries. It graphs these institutions by FTE (full time equivalent enrollment) and compares the results to a range of costs postulated in the producer-pays open access model. This spreadsheet uses publicly-available information and the author regrets any errors within. It was designed to promote dialog and additional analysis -- not to advocate a particular position. Modifying the starting assumptions will recalculate the values in the spreadsheet and update the graph. Readers are encouraged to change the assumptions based on more accurate information or alternative scenarios.'

Update. Davis' spreadsheet has sparked a good discussion thread on LibLicense.

January issue of SOAN

I just mailed the January issue of the SPARC Open Access Newsletter. In addition to the usual round-up of news from the past month, it takes a closer look at the Google library project, reviews OA developments in 2004, and offers some predictions for 2005.