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Tuesday, January 04, 2005
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.' Posted by Peter Suber at 1:54 PM.

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.' Posted by Peter Suber at 1:45 PM.

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.' Posted by Peter Suber at 11:43 AM.
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.' Posted by Peter Suber at 11:32 AM.
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. Posted by Peter Suber at 11:20 AM.

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." ' Posted by Peter Suber at 9:23 AM.

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.) Posted by Peter Suber at 8:45 AM.

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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.) Posted by Peter Suber at 11:15 PM.
Many roads to OA
Dick Kaser and Marydee Ojala, Open Access Forum: Many Roads toOpen Access, Information Today, January 3, 2005. Not even an abstract is free online, at least so far. (Thanks to Charles W. Bailey, Jr.) Posted by Peter Suber at 3:32 PM.
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."' Posted by Peter Suber at 2:55 PM.
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.' Posted by Peter Suber at 1:58 PM.
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."' Posted by Peter Suber at 1:21 PM.
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.' Posted by Peter Suber at 11:06 AM.
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.'