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Query Chem is a new search engine for chemistry. It will accept text search terms, a search string in the SMILES chemical nomenclature, or a drawing of a chemical structure (like Chmoogle). From the description by its developer, Justin Klekota:
Query Chem lets you combine chemical structure and text searches by finding the names of structures similar to your query structure and combining them with user-specified search terms which are all then sent to Google. Query Chem's search results are prioritized by their relevance to your chemical structure and your optional search terms combined. Query Chem has many of the features of Scifinder Scholar since it also links to Google Scholar (with the added bonus that it's free). Its greatest strength is that it's not limited to a single database, but instead it captures the structure-property relationships embedded in the text of journals, commercial web sites, public databases, and any other HTML document indexed by Google.
The OA Journal of Postgraduate Medicine has reached the milestone of 100,000 downloads in a single month. It had 112,218 in November. From the announcement:
These downloads are from the journal's primary website, apart from this website, the full text of the journal is also available from [the] Bioline International, OAI-complaint repository at the University of Toronto and from a number of secondary aggregating agencies such as Thomson Gale, EBSCO Publishing and ProQuest. Thus, the actual downloads per month are much higher. Open access sources, DOAJ, PubMed and Wikipedia were amongst the top five referrers (except search engines) for the journal's website. Over 270 institutions utilize the LinkOut facilities from PubMed to access the journal.
Scott Jaschik, Radical Change for Tenure, Inside Higher Ed, December 30, 2005. Excerpt:
Three years ago, all members of the Modern Language Association received a letter from Stephen Greenblatt, then the group’s president, warning of a crisis facing language and literature departments. Junior faculty members were unable to publish the books that they needed to win tenure and cuts in library and university press budgets left open the possibility that higher education “stands to lose, or at least severely to damage, a generation of young scholars.” He called for academic departments to rethink the way they considered publication as a tenure requirement, and his letter set off considerable debate. Thursday night, a special panel of the MLA [Modern Language Association] offered the first glimpse at its plan to overhaul tenure — and in many ways the plans go well beyond the reforms Greenblatt proposed. As he suggested, the panel wants departments — including those at top research universities — to explicitly change their expectations such that there are “multiple pathways” to demonstrating research excellence, ending the expectation of publishing a monograph. But the panel does not appear likely to stop there. It plans to propose that departments negotiate “memorandums of understanding” with new hires about what factors will go into their tenure reviews. It wants departments to end a bias that favors print over online publications....The panel, which has been meeting privately, surveying departments, and interviewing administrators about their receptivity to changes, has still not released a final report and probably will not do so for months. There may be changes along the way. But panel members last night indicated that key recommendations had been agreed upon, and that they were ready to start sharing them....Donald E. Hall, who holds the Jackson Chair in English at West Virginia University, was the panel member who focused on alternatives to the monograph as a tenure requirement. Hall said that in the committee’s discussions with provosts and deans, one concern was whether administrators would permit such a change. Hall said that the uniform reaction was that “the fetishization of the monograph” was a product of departments and that if they made a case for change, administrators would not object....A candidate’s chances for tenure “should never depend on the vagaries of the scholarly publishing market,” Hall said. Sean Latham, associate professor of English and director of the Modernist Journals Project at the University of Tulsa, said that departments need to recognize that scholarship — good, bad and everything in between — is being produced online and needs to be evaluated without any media-based bias.
Comment. There are two OA connections here. First, skyrocketing journal prices in the sciences have caused most research libraries to cut into their book budgets, which has greatly reduced the demand for monographs, which has greatly reduced the number of new book manuscripts accepted by university presses. If spreading OA can help libraries rebuild their book budgets, then humanities departments will be freer to return to the monograph standard for tenure. Second, the old bias in favor of print publication was a major disincentive to publish in OA journals, and one not justified by any considerations of quality or impact. Deemphasizing monographs and print publications for tenure are both long-overdue recognitions of reality. Kudos to the MLA.
Tom Wilson, Citations to papers in Information Research, Information Research Weblog, December 29, 2005. Excerpt:
Citations to papers in Vol.7 No.1 of Information Research: Eleven papers published, with 40 citations according to Google Scholar (Ave. 3.6). Three papers had no citations....The list of journals suggest that the availability of papers in an open access e-journal not only increases the probability of citation as Steve Lawrence has shown, but perhaps also widens the range of journals that papers are likely to be cited in. A number of the journals listed could not be described as information science or information management journals by any stretch of the imagination. I haven’t done an analysis of the locations of the non-journal documents, but they range widely internationally from New Zealand and Brazil to Switzerland and the USA, and I suspect that the geographic span of citing sources is wider than one might expect with closed access journals. This looks like an interesting project for a student paper - anyone like to take it on?
Dean Giustini, Google Medicine and open access (OA): teamplayers in knowledge-based healthcare, December 29, 2005. Excerpt:
In a December 2005 editorial appearing in the British Medical Journal (BMJ) “How Google is changing medicine”, I introduced the idea of a central web portal to access the best medical information worldwide. Centralizing medical information currently scattered across the Internet would make it easily searchable....However, other than thinking that Google Medicine would ultimately cost a truckload of money to create (and yet produce huge dividends at the same time), I wrote the BMJ editorial with no further concrete or specific suggestions in mind. So when a number of physicians e-mailed me from around the world excited by the idea of Google Medicine, I started to think: what would Google Medicine contain? What issues might it attempt to address? How would it need to improve on what Google already does? Here are some further thoughts about Google Medicine as I envision it....From the outset, let me say that I have no interest in Google Inc, financial or otherwise, and no interest in seeing it gain more market share. I am only interested in access....[N]umerous studies show a linkage between access to information and good patient care but few have shown how search tools like Google have a positive impact on patient care. Note to self: apply to PhD programs in library science for a sabbatical on this subject....Google has benefited from the National Library of Medicine by allowing it to crawl PubMed. The irony is that some librarians have asked if Google will eventually replace PubMed, the lynchpin of medical searching....Google’s computer power and open access to the medical literature is a potential winning combination. At the very least, institutional repositories must facilitate archiving and indexing by major search tools. The bulk of research created in open access journals may not make it into MEDLINE and EMBASE or second-tier tools such as the International Pharmaceutical Abstracts. So, Google will need to index this material and ensure content from almost 600 institutions (see OAIster in the United States) is easily searchable....An historic opportunity exists for the open access movement and search engines to work together to achieve true open access. As many librarians will tell you, academia’s reliance on traditional publishing models has created a crisis for us, with crippling subscription costs being the result. We need to wrest control back for our users and establish more open models of scholarly publishing. But we also need to think about how this content is accessed and whether it will be findable....[Peter Suber said] "the more knowledge matters, the more open access to that knowledge matters." I say this is the quote of the year.
Canadian libraries join race to digitize books, CBC, December 29, 2005. An unsigned news story. (Thanks to LIS News.) Excerpt:
A major effort to digitize millions of books and other documents at libraries is beginning across Canada. Canadian research libraries have formed a digitization alliance called Alouette Canada to get their books online. The process involves scanning the millions of books available in Canadian libraries so they can be read by internet users. Parts of the virtual library should be available beginning next year — and it'll be free to use. Tim Mark, executive director of the Canadian Association of Research Libraries, says Alouette is taking on a large project that will extend over several years. "The initial estimate is three to four million titles so the scope is huge," he says. "I think it's fair to say that librarians and research libraries in particular have seen the vision and the possibility and the potential for universal access to all knowledge." University of Toronto chief librarian Carol Moore will head a group of 27 major Canadian academic research libraries that have joined the Alouette Canada project....Alouette will step up the digitizing process. Even rare documents will be available. Among them are fragile works from the 16th century, Banting and Best's papers about their discovery of insulin and, from Memorial University, important documents related to the history of Newfoundland. The Canadian group is working with a big international effort to digitize books, the Open Content Alliance, based in San Francisco. Canada's libraries will be co-operating with international libraries, such as the U.S. Library of Congress and the British Library, which already have large digitized collections....Publishers and authors groups fear that books still under copyright protection will be put online. In Canada, the focus is on works in the public domain, so the copyright controversy is not an issue.
Congoo is a forthcoming search engine that will give registered users free online access to selected toll-access publications. Users will download a 200 KB browser plug-in, register with Congoo, run searches, and find some fee-based content in the hit list. When they click on an item from a willing publisher, Congoo will pass the user's registration info on to the publisher, and the publisher will give the user free access to full text, at least temporarily. Users get free online access to texts that aren't ordinarily free, and one-time registration for all publishers that eventually participate. But what's in it for publishers? Some of their content is more visible to users (the amount, the pieces, and apparently the duration always under publisher control) and they get the contact info for users interested enough to click through. Congoo should launch in January. For more details see the Congoo page for publishers or Anthony Gonsalves' story in yesterday's InformationWeek
Comment. It's not OA, but it's an interesting new model. I like the theory that greater visibility and impact benefit publishers, not just authors, and might lead them to remove access barriers. I like the way Congoo creates an incentive for publishers to convert enhanced visibility and impact into revenue without returning to access barriers. How many publishers will like it? How many users will be attracted to a search engine that requires downloading a plug-in and can only offer a continually varying random shot at access? Will users find themselves spammed with publisher solicitations to subscribe? We'll find out. I suspect Congoo will face a chicken-and-egg problem: Publishers may wait until it's clear that many users are using it, and users may wait until it's clear that many publishers are participating.
Marilynn Marchione, Drug firms make more study results public, Associated Press, December 28, 2005. Excerpt:
Drug companies are making public more information about medical studies they are conducting, but some still withhold key details, a new analysis of a federal registry finds. Merck & Co., stung by allegations that it hid information on Vioxx's dangers, gets somewhat better marks in the new analysis than it did in an earlier one. However, Pfizer Inc., GlaxoSmithKline PLC and Novartis are lagging, according to the report in Thursday's New England Journal of Medicine. In May, the journal's editor-in-chief accused Merck, Pfizer and Glaxo of making a mockery of efforts to increase the transparency of such experiments, called clinical trials. The new report shows some progress, said its chief author, Dr. Deborah Zarin of the National Library of Medicine, which runs the registry. "We're getting a lot of trials being registered," including many that American drug companies are doing in foreign countries, she said. The registry was created in 2000 as part of an overhaul of Food and Drug Administration monitoring. It requires certain types of studies to be listed, such as late-stage experiments involving life-threatening illnesses like cancer. But it didn't get wide participation from industry or many voluntary listings until September 2004, when editors of leading medical journals said they would no longer publish results of any studies that were not first listed in a public registry....In an editorial, journal editor-in-chief Dr. Jeffrey Drazen and Dr. Alastair J.J. Wood, a Vanderbilt University drug expert who has served on many FDA advisory panels, call for complete compliance with the registry, saying it "makes moral sense." "When patients put themselves at risk to participate in clinical trials, they do so with the tacit understanding that their risk is part of the public record, not merely the secret record of the sponsor," they wrote. They also urged scientists and patients to refuse to participate unless studies are fully registered.
The US Office of Management and Budget (OMB) has released guidelines on how government agencies should make their information accessible online for the public. Senator Joe Lieberman, author of the E-Government Act of 2002, doubts that the new guidelines live up to the statutory requirements and will ask the OMB to explain. I don't plan to cover this issue thoroughly, but I can recommend Jason Miller's story in the December 23 issue of Government Computer News. Excerpt:
Patrice McDermott, deputy director for government relations for the American Library Association, called the policy “disturbing.” “Essentially, what OMB appears to be saying is, for information you want to make publicly accessible, if you put it on your Web site or post it electronically, you have fulfilled all requirements of law,” McDermott said. “That is not true. That is not the spirit or intent of the law.” She added that intent of law was to give the public the ability to know about and gain access to all information the government creates.
Earlier this month the Government Services Administration (GSA) released the comments from government and industry experts, showing that a majority thought the benefit of adding metadata tags to online government information was not worth the cost.
Heather Morrison, Open Access Textbooks, Imaginary Journal of Poetic Economics, December 27, 2005. Excerpt:
There are many curious ironies about the open access movement, and indeed the shift from print to electronic in general. Not least of these is that while advocacy efforts focus on the peer-reviewed research article, progress towards open access is happening in areas where no advocacy efforts are directed at all, to my knowledge. One such area is open access textbooks. This came to my attention one day when searching for online math textbooks. I was not expecting to find free texts at all, on the assumption that textbooks were an area where the commercial sector would obviously prevail - after all, who would write an entire textbook without expectation of financial compensation? Imagine my surprise, then, to find the extensive list of Textbooks, Lecture Notes and Tutorials in Mathematics by Alexandre Stefanov. All resources are free, and are divided into topics such as general mathematics, number theory, algebra, algebraic geometry, topolisis, analysis, geometry, mathematical physics, probability theory, formatting documents (TEX, LATEX, etc.). Alexandre links to a number of other substantial lists, including the list of Online mathematics textbooks, including over 40 textbooks as of October 2005, maintained by George Cain, School of Mathematics, Georgia Institute of Technology.....The more I think about it, the more open textbooks make sense, particularly in mathematics. Printed textbooks are expensive - one cannot ask students to purchase more than one mathematics textbook. Yet it seems obvious that the student is much better off having access to the dozens of free textbooks that are already available. If a student is having difficulty understanding a concept explained one way, does it not make sense to provide an alternative explanation?
(PS: There's a growing number of OA textbook sites, but as far as I know just one searchable portal that tries to be comprehensive: Jason Turgeon's Textbook Revolution. Check it out.)
Gavin Rabinowitz, India Builds Database to Stop Theft of Lore, Associated Press, December 23, 2005. (Thanks to Subbiah Arunachalam.) Excerpt:
For thousands of years Indian villagers have used an extract from seeds of the neem tree as an insecticide. So when a U.S. company patented a process for producing the substance in 1994, India reacted with outrage. After spending millions of dollars in legal fees to successfully overturn the patent, India's government now is creating a 30-million-page [open-access] database of traditional knowledge to fend off entrepreneurs trying to patent the country's ancient lore....The database, called the Traditional Knowledge Data Library, will make information available to patent offices around the world to ensure that traditional remedies are not presented as new discoveries....The government also has successfully challenged patents on the use of the spice turmeric to heal wounds and rashes and a patent on a rice strain derived from India's famed Basmati rice. But that is a tiny fraction of the problem. A 2003 study by...[India's National Institute of Science Communication and Information Resources or NISCAIR] estimated some 7,000 patents worldwide are based on Indian indigenous knowledge, far too many for India to challenge in expensive legal fights....Currently it is difficult for overseas patent office researchers to prove purported innovations are really based on old lore because, while the information is widely published in India, it is often in ancient languages like Sanskrit or modern regional languages like Tamil. "We decided we have to break the language and access barrier," [V.K.] Gupta [Chairman of NISCAIR] said....More than 10 million pages already have been loaded into the system and 20 million more will be available by the end of 2006, Gupta said....The issue is not just a matter of national pride. It also has financial implications. A pharmaceutical company, for instance, could develop a medicine from a treatment long-used by an indigenous group and reap big profits while also charging those very people to use it. So India and its allies want to ensure that profits arising from traditional knowledge are shared with local people. "Developing countries as a whole are saying that there should be benefit sharing," said Dua, the Commerce Ministry official.
Renu Vinod, Open access to information, New Delhi Business Standard, December 27, 2005. Excerpt:
India has finally passed an information legislation, and much to the government’s credit, it has kept its promise of making the newly formulated Right to Information (RTI) Act participatory, progressive and meaningful. Now, however, is the time to move as efficiently and effectively as possible from a duty to furnish information regime to a duty to publish one....The RTI portal of the National Informatics Centre...could be the starting point for the move towards a participatory and proactive flow of information. According to the officials at the National Informatics Centre, the RTI portal has been set up to create a central repository of information for citizens to access information through a user-friendly search engine. An efficient and easy-to-use proactive disclosure system would provide many benefits to both government officials as well as the public. Instead of the work being wholly shouldered by the government, as it currently is, even private individuals can participate. This would not only reduce the burden on the government, there also won’t be repetitive information requests. In countries like the US, the government has already placed a lot of information in the public domain. This information relates to what people need to know on a daily basis. The idea is that people should have to put minimum effort to access what is their right, and no government should shy away from its duty to fulfil that right.
Huanming Yang is one of the co-winners of this year's Prize in Biology from the Third World Academy of Sciences. From today's press release:
China was the only developing country to play a role in the sequencing of the human genome, which was published in 2001. As director of the Beijing Genomics Institute since 1999, Huanming Yang was a key player in this effort. Since then, Yang's group in China has published the complete genome sequence of Indica rice and the silkmoth, and steady progress is being made on the genomes of other commercially important species, including the chicken, pig and soybean. Yang and his team also made international headlines when they announced that they had sequenced the genome of the SARS virus in just a few days. Information derived from the sequence led to the development of diagnostic kits for the virus that greatly facilitated the control of the disease throughout China. Currently, Yang and other scientists at the Beijing Institute of Genomics are working on another project linked with the human genome as part of the International HapMap Consortium. The aim is to compare the genomes of three different races of human beings and to identify all the single base substitutions in blocks of DNA (or haplotypes) between them. Scientists believe that these variations are at the root of such ailments as heart disease and asthma, the incidence of which varies between races. Yang has also promoted science for developing countries in developing countries, and promotes the ethical use of genomic data and open access publishing for all the information generated at the Beijing Institute of Genomics.
Grants Will Give Developing World Access to Scientific Research, a press release from Yale University, December 22, 2005. Excerpt:
Two grants totaling $500,000 will support Yale University participation in an international consortium to make prestigious scientific journals in the environment sciences available online to the developing world at little or no cost. The William and Flora Hewlett Foundation and the John D. and Catherine T. MacArthur Foundation gave $250,000 to Yale to help establish Online Access to Research in the Environment (OARE). A digital internet library for developing countries, OARE, will provide access to peer-reviewed scientific literature of leading international publishing houses. Organizations eligible to use OARE include approximately 1,000 public, nonprofit institutions in more than 100 underdeveloped nations in Africa, Asia, Latin America, the Caribbean and Eastern Europe. Literature in environmental chemistry, economics, law and policy, and other environmental subjects such as botany, conservation biology, ecology and zoology will be available through a portal presented in world languages, including Arabic, English, French, Portuguese and Spanish. Yale’s OARE activities will be directed by Oswald Schmitz, professor of population and community ecology and associate dean of academic affairs for the School of Forestry & Environmental Studies, and Ann Okerson, associate university librarian for collections and international programs....Published in the United States and Europe under copyright and with annual subscription fees averaging $1,000, the prestigious journals in which a majority of scientific research is published are too costly for purchase in most developing nations. OARE will enable countries to build their own higher education programs in the environmental sciences, educate their own leaders, conduct their own research, publish their own scientific findings and disseminate information to policy makers and the public. Next year in the first phase of the project’s implementation, OARE will be offered to users in 70 developing nations with a per capita gross national product (GNP) of $1,000 or less. In the project’s second phase, approximately 45 more countries with GNP per capita between $1,000 and $3,000 will be enrolled. Yale will develop OARE in cooperation with the United Nations Environment Programme, the World Health Organization, the Food and Agriculture Organization, Cornell University and leading scientific publishers around the world. Yale will create software for OARE’s secure internet portal, organize and update its database of scientific literature, recruit publishers to the consortium, and develop partnerships between the consortium and American and European institutions to expand internet connectivity and offer training. Paul-Bendiks Walberg, a recent graduate of the Yale School of Management and Yale School of Forestry & Environmental Studies, and Kimberly Parker, head of the university library’s electronic collections, conceived the OARE project. The project is inspired by the Health InterNetwork Access to Research Initiative, a World Heath Organization program in which Yale has played a leading role and that has strengthened public health services in developing countries by providing access to research in the medical sciences.
UNESCO supports training for building digital libraries in Africa, UNESCO News, December 20, 2005. A brief report on the Greenstone workshop at the University of Cape Town, South Africa, November 30 - 1 December 2005. Excerpt:
The meeting that was co-organized by UNESCO, the Coalition of South African Library Consortia (COSALC) and Sivulile, a South African open access initiative, brought together 30 participants from Ethiopia, Lesotho, Namibia, New Zealand, Swaziland, Sudan and host country South Africa. This workshop was the third in a series of activities organized by COSALC and Sivulile (“we are open” in isiXhosa) aimed at raising awareness on open access models for information exchange, and ICT capacity building of information professionals in Africa institutions. These efforts are aimed at supporting the creation of digital libraries and providing archivists, librarians in Africa with skills to utilize electronic information tools and resources in their work and enhance access to online resources.
(PS: I can't find a web site for the workshop itself.)
Unique digital library opening on December 28, Deccan Herald, December 26, 2005. An unsigned news story. Excerpt:
The soon to be inaugurated state-of-the-art digital library at Bangalore Medical College (BMC) is unique in scale and concept. A gift by the alumni of the college to mark its golden jubilee celebrations, users of the library can have access to full text articles from leading international and national journals, multimedia presentations by leading doctors and can also access materials in other libraries like the Rajiv Gandhi University of Health Sciences and Nimhans. The information is catalogued using open sources database Dspace. BMC Alumni Association claims the facility is the “best and biggest” in any medical college in the country. Association President Dr H C Satya and Vice-President K M Srinivasa Gowda told reporters that the entire library was wi-fi-enabled.
Klaus Graf has posted his comments for the EU's i2010 consultation on digitization. Excerpt:
Christian Wagner, Breaking the Knowledge Acquisition Bottleneck Through Conversational Knowledge Management, Information Resoures Management Journal, January/March 2006. (Thanks to John Daly.)
Abstract: Much of today's organizational knowledge still exists outside of formal information repositories and often only in people's heads. While organizations are eager to capture this knowledge, existing acquisition methods are not up to the task. Neither traditional artificial intelligence based approaches nor more recent, less-structured knowledge management techniques have overcome the knowledge acquisition challenges. This article investigates knowledge acquisition bottlenecks and proposes the use of collaborative, conversational knowledge management to remove them. The article demonstrates the opportunity for more effective knowledge acquisition through the application of the principles of Bazaar style, open-source development. The article introduces wikis as software that enables this type of knowledge acquisition. It empirically analyzes the Wikipedia to produce evidence for the feasibility and effectiveness of the proposed approach.
Yin Ping, Open access, China Daily, December 26, 2005. Excerpt:
Is the system of intellectual property (IP) that we had in place at the end of the 20th century the most appropriate one for the 21st century? That is the question John Howkins raised at a forum on creative industries and IPR protection during Shanghai International Creative Industry Week which ended on December 6. Howkins brands the question "the elephant in the room,"something very big and important but so embarrassing that everyone pretends it isn't there. A leading British expert in the creative industries, Howkins has 30 years experience in the film and TV industries, and is well versed in the need for effective IP laws. It is universally accepted that IP laws provide a way to register ownership and protect property. But, as Howkins points out, IP laws have another purpose, one he believes is widely underestimated. "They should also enable people to have access to what has been created," Howkins says. These two purposes appear contradictory. According to Howkins, major industrial companies, led by US, European and Japanese entertainment, publishing, design, pharmaceutical and engineering industries, all put heavy emphasis on the first purpose. Western governments, which are keen to make their national economies competitive and to protect jobs, also believe IP assets must be protected as much as possible and at all costs, Howkins says. "To them, the more IP, the better." But Howkins prefers another approach, which puts access above protection. To him, access to existing ideas, knowledge and data is the starting point of all new ideas. "New ideas are two old ideas meeting together," he says. "The creative industry is the reuse of ideas." Historically, Europe, the United States and Japan industrialized when their patent and copyright laws were weak and enforcement was patchy, he says. Likewise, many developing countries would benefit from similarly weak IP as they look to industrialize. Major steps forward continue to be made by those who choose not to seek IP protection, for example, free and open source software, the World Wide Web, the Global Positioning System and the map of the human genome. "My argument is that IP certainly offers incentives and rewards but may do so at the cost of slowing down and inhibiting future work," Howkins says.