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Ceri Binding and Douglas Tudhope, KOS at your Service: Programmatic Access to Knowledge Organisation Systems, Journal of Digital Information, February 5, 2004. From the abstract: "The lack of standardised access and interchange formats for knowledge organisation systems (KOS) are a barrier to their interoperability and wider use in automated Web and retrieval applications. Programmatic access to thesaurus (and other types of KOS) resources requires a commonly agreed distributed service protocol, building on lower-level standards, such as Web services. This paper reflects on our experiences in building a Web demonstrator of some novel thesaurus browsing and search tools, developed as part of a research project on the role of the thesaurus in controlled vocabulary retrieval applications....This leads to a proposal for a novel, unified semantic expansion service, which can be used both for specifying composite display formats and for query expansion services. Thesaurus (KOS) representations and service protocols for retrieval are closely linked. A service protocol should be explicitly expressed in terms of a well defined but extensible set of KOS data elements and relationships."
Michael Miller, Fac Sen discusses journal fees, The Stanford Daily, February 6, 2004. Excerpt: "A 'serials crisis' consumed the Faculty Senate yesterday afternoon as senate members debated a set of recommendations dealing with the high and rapidly increasing subscription costs for academic journals. With journal subscription costs having risen as much as 50 percent in the past five years and set to rise another 12 percent this year, the Committee on Libraries recommended in a report that the senate set guidelines aimed at reducing the Universityís reliance on the most expensive journals. 'The cost of journals has crippled University budgets,' said Biochemistry Prof. Doug Brutlag, who presented the report. After more than an hour of discussion, the motion was put off for debate at another session....[Michael] Keller [pointed] out that for-profit publishers have been known to target articles that are in course packets, increasing costs from $15 up to $60 when they determine that a journal article is in a course reader. The proposed resolution would have said, among its four points, 'Libraries are encouraged to systematically drop journals that are unconscionably or disproportionately expensive or inflationary. Special attention should be paid to Elsevier.' It would also have encouraged faculty to withhold articles from exploitative journals....'Digital repositories are going to be the infrastructure of the future,' Keller said. 'Itís very important that we invest as a university.'"
The MIT Libraries have written a public statement on their decision not to accept the three-year renewal packages on offer from Wiley and Elsevier. The librarians: "These actions ensure that if the Libraries need to reduce spending in the next year or two, we can make those decisions based solely on the specific needs of the MIT user community, without giving unfair advantage to certain publishers." They quote MIT Professor Marcus Zahn, chair of the Faculty Committee on the Library System: "[W]e are concerned about the pressures exerted on the scholarly publishing system by a small number of highly profitable commercial publishers concentrating in science and technology journals. These publishers lock libraries into high-priced packages for combined print/electronic output, and contractually constrain librariesí ability to manage expenditures. Libraries must invest a continually larger percentage of their budgets in providing access to these publications." (Thanks to LIS News.)
Niels Boeing, Journale zu Servern, Freitag, February 6, 2004. A short history of the serials pricing crisis and the rise of the OA movement. Boeing argues that OA will benefit scientists and scholars in all fields. (Thanks to Stefan Busch.)
Catherine D. DeAngelis and Robert A. Musacchio, Access to JAMA, JAMA: the Journal of the American Medical Association, 291, 370-371 (January 21, 2004). The editor-in chief of JAMA and her colleague state their views on what constitutes responsible medical publishing and the considerable time and effort required for cooperation with authors, peer review, and the production of a readable and useful journal for medical professionals and general readers. Further, they discuss production costs, especially in consideration of open access models such as PLoS, author charges, and foundation support, stating that it is unclear if such a model is viable, and from their point of view, not workable for their authors. Alternatively, JAMA proposes:
At least for the present, our plan for free access is as follows: (1) free online access for one major article published in the most recent issue; (2) by the end of February 2004, free online access for all major articles and editorials beginning 6 months after publication and up to 5 years after publication; (3) unlocked online articles (ie, PDF files) to facilitate readers' personal uses of articles including highlighting and annotating; (4) 25 free online accesses to each corresponding author's article for distribution to colleagues as soon as the article is published; and (5) free online access to countries in the developing world by our participation in the World Health Organization's HINARI (Health InterNetwork to Research Initiative) Project. We will continue to keep our subscription price as low as possible by offsetting cost with advertisements that follow our rules of professionalism.The authors conclude that this policy will stay in place while other OA models are tested in the marketplace.
Kenneth Olden and Thomas J. Goehl, EHP Moves to Open Access, Environmental Health Perspectives 112, A13-A14 (Jan. 2003). Peter noted EHP's move to open access last month. In a column the editors reflect on the history of open access initiatives and what influenced their decision to make EHP an open access journal. They write: "After carefully considering various scientific publishing models, we have concluded that the rationale behind the open access philosophy--that science best benefits society when it is freely and immediately available to all--is too compelling to ignore. As part of the U.S. government, we feel it is incumbent on us to take a leadership role in this area."
The Georgia State University Library has created a website Issues in Scholarly Communication, which includes a news blog, a section of internet resources, links to papers on scholarly publishing economics and journal cost-effectiveness studies, a discussion of open access, and information on library initiatives and how individuals can participate. Unfortunately some of the links are restricted to GSU affiliates. Nevertheless, it's an impressive collection of resources and bibliography, thorough and quite up-to-date. I like that GSU references the late Henry Barschall's studies of journal prices which pointed out the considerable cost differential between society and commercial publishers and raised the litigious ire of Gordon and Breach.
eclectic librarian, open access publications in library science, February 04, 2004. The eclectic librarian reports on open access activities among library associations; the American Library Association hasn't jumped in but a couple others have made publications openly available, and a link to a DOAJ listing of open access library science journals is provided.
David Ozonoff, The World of Open Access Journals Journal of Urban Health 80, 529-531 (Dec. 2003). (Access restricted to subscribers.) In a literature briefing column, Ozonoff provides summaries of three articles from open access journals. By way of introduction, the writer remarks "the availability of articles to anyone with an Internet connection is an important resource, especially for the developing world." He also notes the referenced articles' availability in PubMedCentral and bids "readers to sample the rich offerings of this new type of journal," while at the same time revealing that he is "Co-Editor in Chief of Environmental Health: An Open Access Science Source."
The December 2004 issue of Briefings in Bioinformatics features two articles that mention open access resources for the bioinformatics community. Unfortunately, the articles are not open access, but available with a subscription or per-article purchase through Ingenta. Mauro Vihinen, in Signal transduction-related bioinformatics services (pp.325-331,) reviews "open-access databases and software" available to the cellular signalling research community. And Rodrigo Lopez et al, in Public services from the European Bioinformatics Institute (pp.332-340), review the EBI's free services to the scientific community, especially database searches and software, all of which are available on the Institute's website.
Libraries take a stand, Harvard University Gazette, Feburary 5, 2004, p.10-11. An article in the Harvard University Gazette summarizes recent cancellations of Elsevier titles in the Harvard libraries, the efforts of the university library community to negotiate access terms, and the faculty response. Markus Meister, Harvard professor and a PLoS editorial board member, "was not surprised" at the Elsevier cancellations, and remarked on the necessity for "change in the structure of scholarly communications. The authors that rely on these Elsevier journals as a channel for publishing should be encouraged to find another channel." And Stuart Shieber noted that faculty members are recognizing "that the current system for dissemination of scholarly information is unsustainable," and are open to alternative publishing channels such as open access journals. (Source: Jessica Baumgart, j's scratchpad)
The presentations from the ICSTI Technical Meeting: Economic Models for Scientific Information, Production and Distribution (Paris, January 15-16, 2004) are now online. However, they will only be freely accessible to non-members, at least on the ICSTI site, until February 12. All six are explicitly about OA, some pro and some con. (PS: If you visit and view them now, the PPT slides will stay on your hard drive past February 12.) (Thanks to Jill O'Neill.)
Update. I just learned that the conference organizers have posted a brief summary of the issues raised at the meeting.
Into Africa, NewScientist, February 5, 2004. An interview with James K. Tumwine, founder of African Health Sciences, a peer-reviewed medical journal publishing African science for African readers. It's not free but affordable ($45/year). Why launch an African medical journal? One reason: "I wrote an article about health and education in Zimbabwe....[and] submitted it from a Harare address. The journal rejected it. Later, I went to work in the UK. I waited a couple of months and then resubmitted it to the same journal, from an Oxford address. It was published!" Are online resources useful in Africa? "You might search the MedLine database for abstracts - but when you want to see the full articles they want your credit card number. In Uganda the vast majority of the population don't have credit cards. In the end the full articles had to be faxed to us. Kofi Annan, the United Nations secretary general, recently initiated a programme to make 3000 electronic journals accessible to developing countries. But in Uganda you would have to go to one of the big libraries in Kampala to get them. Just accessing your email through the medical school connection can take up to three hours. So recently I installed a satellite dish outside my office. I'm paying 500,000 Ugandan shillings (£160) a month, which is more than my salary. Then there are technical problems like computers breaking down. For some the internet is just another part of life but for us it is part of a bigger struggle." (Thanks to Darius Cuplinskas.)
Henk Ellermann is on the team with folks from KNAW and DARE to extend the OAI protocol. He's written a brief introduction to the extended protocol, which allows for the exchange of object files, not just metadata. This is the key to supporting full-text searching, presenting thumbnails of image files, and creating new data providers that pull selected objects from other providers. It also standardizes the ingest procedure, which could be used to automate journal submissions or harvest papers from personal web sites for an institutional repository.
A new peer-reviewed, OA journal launched in January: Preventing Chronic Disease: Public Health Research, Practice, and Policy. What's unusual is that it's published by the National Center for Chronic Disease Prevention and Health Promotion, one of eight centers within the Centers for Disease Control and Prevention, a division of the Department of Health and Human Services, a branch of the U.S. federal government. The journal charges no processing fees. Nothing on the web site or in the inaugural issue says that the journal is OA --except a letter to the editor from Tommy G. Thompson, Secretary of the Department of Health and Human Services: "I commend the staff of Preventing Chronic Disease: Public Health Research, Practice, and Policy on producing a journal that reaches a broad public health audience and presents research in electronic form on the Web, available free to the public." (Thanks to Debra Lappin.)
Potter Wickware, US pressures publishers to honor trade embargoes , Nature Medicine 10, 109 (February 2004). (Access restricted to subscribers.) The American Society for Microbiology (ASM) is another agency that has responded to the trade embargo ruling by the Office of Foreign Assets Control (OFAC) of the U.S. Treasury Department and will not accept papers from Sudan, Libya and Iran and Cuba. The article quotes ASM editors who are unhappy with the policy, one of whom remarks on the potentially negative effects upon science as a whole, and another who calls the policy discriminatory. A Nature editorial in the same issue, Trading Scientific Freedom, reviews several objections against the policy and urges that scientists make their legislators aware of the "inconsistencies and ambiguities of the current regulations" and strive towards "the preservation of the freedom of scientific communication."
Tori DeAngelis, Data sharing: a different animal, APA Monitor on Psychology, February 2004. On OA to data in psychology, a disscussion meant to accompany a companion piece by DeAngelis that I blogged the other day. Mary Bullock is the associate director for science at the American Psychological Association. She thinks there are three reasons why open data sharing is not used as widely in psychology as it is in the natural sciences. "That said, the potential benefits of large-scale data sharing far outweigh the costs, Bullock believes. Pluses include increasing the power and generalizability of psychological findings by increasing effective sample sizes, getting more value from costly research investments and encouraging research across investigators and institutions." To help members learn the ropes, the APA will (1) offer training sessions "to help researchers learn secondary analysis of large databases" and (2) host a web page on data archiving and data sharing in psychology. (Thanks to Howard Kurtzman.)
Nicholas R. Cozzarelli, Kenneth R. Fulton, and Diane M. Sullenberger, Results of a PNAS author survey on an open access option for publication, Proceedings of the National Academy of Sciences, 101, 5 (February 3, 2004) p. 1111. I'd love to see this, but it's accessible only to subscribers.
Update. A generous reader just sent me the text. The survey found that about half the respondents (authors of accepted papers in PNAS) were willing to pay an extra fee for immediate open access to their work and half were not. The article includes anonymized quotes from some respondents. All those saying they oppose OA processing fees misunderstood the proposition. Three thought that OA and the fees to cover it would be mandatory, not optional. One thought that institutionally paid access made OA unnecessary. One thought that OA was not very important if "most of my colleagues" already subscribe. Most (including the journal editors) seemed to think the fees would be paid out of authors' pockets rather than by employers, funders, or governments.
Barbara Quint, The Great Divide, Searcher, February 4, 2004. Acknowledging the benefits of OA but also the drawback for libraries --in this sense remarkably similar to Scott Plutchak's editorial in JMLA, which also appeared today. Excerpt from Quint: "The 'Open Access' movement for freeing scholarship from commercial control has now spread across continents. It has moved from the offices of angry librarians to the laboratories of indignant scientists....Legislators have joined the fray...From sea to shining sea, librarians raging against publisher prices and contractual rigidities constitute a major lobbying force in these developments. But let's look down the road a bit, shall we?...The economic justification underlying the existence and continuance of most libraries lies in the expense of information." (Thanks to Jill O'Neill.)
Donald E. Knuth, David S. Johnson, and Zvi Galil, the former editors of the Journal of Algorithms, have written a public statement explaining their decision to resign from the Elsevier journal and launch a new journal with the ACM. Their letter is online now and will be published in March 2004 issue of SIGACT News. For most of the details on their reasons, they cite Donald Knuth's public letter of October 2003.
The presentations from the recent meeting in Chile, Strengthening Editors and Scientists Capabilities in Electronic Publishing (Valparaiso, January 14-15, 2004) are now online.
During the conference, the 120 participants from 15 countries drafted the Valparaiso Declaration for Improved Scientific Communication in the Electronic Medium, which was released today. Excerpt: "Journals must improve their production processes by using online technologies in order to reduce their publication times....Assessments of reading habits and analyses of the market for electronic journals clearly confirm the fact that the Internet is already a place of convergence and the preferred medium for the transmission of scientific knowledge....Managers of scientific journals are responsible for achieving their maximal dissemination, bringing with it greater visibility and accessibility. They should not only ensure that their contents and format are standardized but also that they are indexed in the greatest possible number of data bases and indexes, and that the complete texts are immediately available in multiple repositories....The gradual reduction in publishing costs as a result of electronic publication (given the fact that the costs of the production process are more and more being borne by the authors and readers) must inexorably lead to systems of communicating science that are open and managed by the scientific community itself." (PS: I've linked to an email copy of the declaration in our forum archive. If the conference posts an official version online, I'll blog the URL.)
T. Scott Plutchak, Embracing open access, Journal of the Medical Library Association, January 2004 (an editorial). Excerpt: "The reason to embrace the open access movement is that it promises to be a very good thing for society, not that it will be a good thing for libraries....I do not worry as much about the general public's access as I do about the doctor in rural northwest Alabama who is running a hospital on a shoestring....Some of the society publishers respond to this by pointing out that they already make their publications freely available after six months or a year....But too much of the literature is still controlled by the big for-profit companies, and they are not giving anything away. And, to tell you the truth, I am not satisfied with a year or six months anyway. Do you want your mother being treated by a clinician who is always six months out of date? Or is that just the price she has to pay for not living in a city with a major academic medical center? So, as a member of the public, I embrace the open access movement, because I think it will improve the quality of health care to the same degree that it turns out to be successful....As I write this, the major library organizations, along with a number of other public interest groups, are about to issue a public statement of strong support for PLoS and the open access movement. The Howard Hughes Medical Institute and the Wellcome Trust have already done so. The movement is gathering steam, and, for this, librarians should rejoice. The impacts of the open access movement will be very profound and will fundamentally alter the way we manage our libraries and the role that we as librarians play in our institutions. I do not think we can underestimate how radical these shifts will be."
Cindy Yee, Open-access journals debated, The Duke University Chronicle, February 4, 2004. Excerpt: "Although Duke administrators are wary of endorsing the open-access publishing movement, they agree that a drastic change is in order.... 'The industry needs to rethink its cost structure and find more cost-effective way of delivering services and processing their publications,' [Patricia] Thibodeau [associate dean for library services at the Duke Medical Center] said. She cited open-access models as possibilities, such as those used by the nonprofit Public Library of Science and for-profit BioMed Central....Duke administrators said a number of other concerns surround the open-access publishing debate. [Provost Peter] Lange, for example, said he was concerned that the fee structure could have a discriminatory effect across scholars working at different kinds of institutions, doing different kinds of research. 'Unintended consequences can be substantial, so it's a situation we need to analyze carefully,' he said. Lange said there is also the issue of a transition period, which could be problematic if universities are stuck paying both traditional subscription fees and helping out with authors' fees to open-access journals. Open-access agitators claim the transition period will not last long, saying that open-access journals will continue to grow in prestige and popularity, forcing traditional publishers to decrease prices or go out of business."
A news item, Journal rejects article after objections from marketing department by Owen Dyer in BMJ 2004; 328: 244-b, together with the rapid responses to the item, provide a noteworthy example of case study in publication ethics. One of the responses, Correction and addition, includes a reply from the Associate Publisher & Director of Marketing for the Journal (Dialysis & Transplantation). An excerpt: "Publishers reject countless articles every day, and it is their prerogative to do so. It is, of course, any author's prerogative to submit the article to another publisher". [PS: this case is relevant for any journals, including open access journals, that use advertising as a substantial source of revenue].
On December 31, 2003, the entire editorial board of the Journal of Algorithms resigned in order to protest the high price charged by the publisher (Elsevier). On January 21, 2004, the same board then launched a new journal, Transactions on Algorithms (not yet online), published by the Association for Computing Machinery (ACM). For background, see the letter from Donald Knuth to fellow members of the editorial board of the Journal of Algorithms. Also see my list of other declarations of independence. (Thanks to Carol Hutchins.)
Mark R. Graczynski and Lynn Moses, Open access publishing - Panacea or Trojan Horse?, Medical Science Monitor 10, ED1-3 (Jan. 2004). (Freely downloadable with registration.) The authors editorialize on the open access movement with a considerable degree of skepticism. They argue that open access to information is not necessarily a right or a public good, that the question of public access to taxpayer-supported research does not automatically apply from country to country, and that the public want access to reliable, understandable information, not necessarily the primary, specialized literature. They consider the author payment model an unfair burden upon researchers, and instead recommend lower author charges and minimal per-article access fees in lieu of subscriptions or completely free access.
Open Access: A New Model of Scholarly Publishing, Currents, v.5, no.2 (Winter 2004). The Biomedical and Medical Center Libraries at the University of California San Diego present a summary of open access issues in their newsletter, particularly as these affect the UCSD community; a graphic documents precipitous rise in selected titles held by the biomedical library. The UCSD libraries have also set up an extensive website on open access, including an FAQ, a directory of current initiatives and projects, and a bibliography.
In a press release last month, Bioinformatics Organization (a.k.a. Bioniformatics.org) annouced five nominees for its 2004 Benjamin Franklin Award, honoring "an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the scientific field of bioinformatics." The award will be presented at the organization's "Fourth Annual Meeting ... held in conjunction with the Bio-IT World Conference and Expo, Boston, Massachusetts, March 30 to April 1, 2004." Previous honorees include James Kent in 2003 and Michael Eisen in 2002.
Andrea Foster, Legal Scholars Oppose Bill That Would Prevent Reuse of Information From Databases, Chronicle of Higher Education, February 6, 2004 (accessible only to subscribers). Excerpt: "As a committee of the House of Representatives approved a bill last month that would make it illegal to reuse data from someone else's database without permission, eight professors who teach intellectual-property law urged the committee's chairman to reject the measure, saying that no one should be able to claim ownership of facts."
Judy Luther, Ejournal Hosts: The Next Generation, EContent Magazine, February 3, 2004. An introduction to nine services that will give print journals an online edition. Luther also offers advice on making the transition but never mentions the possibility of open access. (PS: All journals contemplating this move are likely to know something about open access. How many of them will trust transition advice from a company that pretends open access doesn't even exist?)
Mike Martin, Iridescent Software Illuminates Research Data, NewsFactor, January 27, 2004. On Iridiscent, sophisticated text analysis software developed at the University of Texas Southwestern Medical Center to help "scientists easily identify obscure commonalities in research data and directly relate them to their own work, saving money and speeding the process of discovery." Like other intelligent text analysis software, Iridescent applies first and best to the ocean of free data on the public internet. In this case, Iridescent is optimized for reading Medline abstracts. Quoting Harold "Skip" Garner, one of the program's authors: "Many new high-throughput technologies, such as microarrays for gene-expression analysis, generate so much data that it is often hard to interpret. Iridescent can do a much better job because it emulates the scientific thought process. Having assimilated all of Medline [12.7 million records], Iridescent can compile diverse facts to present a list of 'hypotheses' to the user for finding hidden knowledge in the data." For more details, also see the Texas press release. There seems to be no web site for Iridescent itself or the team that developed it, Jonathan Wren and Skip Garner, but the program is available from Etexx Biopharmaceuticals. (Thanks to ITRU.)
(PS: If I may quote myself from October 2002: "As we move further into an era in which serious research is mediated by sophisticated software, commercial publishers will have to put their works into the public internet in order to make them visible to serious researchers. In this sense, the true promise of [open access] is not that scientific and scholarly texts will be free and online for reading, copying, printing, and so on, but that they will be available as free online data for software that acts as the antennae, prosthetic eyeballs, research assistants, and personal librarians of all serious researchers.")
The U.S. Environmental Protection Agency (EPA) Council on Regulatory Environmental Modeling has created a draft of a Knowledge Base of 90 models that are highly used by the agency. The agency enables review of the models, soliciting commentary from "model developers, decision makers and the public." It is anticipated that this release will assist environmental management and decision-making. You can browse a complete list of available models, or search by keyword or select from a subject tree, the "hierarchy of environmental indicators. " (Source: EPA models and data are now available on the web, Chemical and Engineering News, February 2, 2004, p.20; access restricted to subscribers.) (See an earlier posting by Peter Suber about open access to EPA projects and data.)
World's science ministers call for open access to scientific data, CordisNews, February 2, 2004. An unsigned news story on Friday's Declaration on Access to Research Data From Public Funding. Excerpt: "Research ministers representing 34 countries, as well as the European Union, have adopted a declaration on access to research data from public funding aimed at enhancing the quality of science systems worldwide....Ministers recognised that open access to data, information and knowledge 'contributes decisively to the advancement of scientific research and innovation' and 'maximise[s] the value derived from public investments in data collection'."
I just mailed the February issue of the SPARC Open Access Newsletter. In addition to the usual round-up of news and bibliography from the past month, it offers some predictions for open-access developments in 2004 and looks at the reasons why open access is progressing more slowly in the humanities than the natural sciences.