The updates section tracks the latest developments in ongoing debates in scientific publishing. Follow the links on the right to access news, downloads and links by subject areas. Within each topic, updates are grouped by month.
Technology and Scientific Communication
For review articles and discussion see Research Tools
*04/03/07: Yet more developments on the social networking front! Nature has launched its Nature Network site, which already features some interesting looking forum, including one on 'e-science'. For more discussion of the aims for the site and its soon-to-be launched London division see our recent interview with Timo Hannay and Nature's press release. Second Life announced in its blog that it would be releasing a new update called 'my second life'. According to the developers, 'These tools could include everything from organizing group memberships to editing your profile to browsing recommended in-world locations, all done via our site. It is our hope that these tools will provide you much greater flexibility and control over your Second Life experience. Our goal is to allow better integration of Second Life with the 2d Web and ultimately extend out to mobile devices and more'. Finally, a new business networking site at www.meetjobpros.com.
*04/03/07: Since our article on mashups, including those using Google Earth to display data, nterest in the use of online mapping tools such as Google Maps and Common Census for scientific projects continues to grow. An article in this month's First Monday, Many, many maps: empowerment and online participatory mapping by David Tulloch notes the diversity of uses. The examples he cites range from allowing indigenous people in the Amazon rainforest to monitor and prevent illegal logging, to a Second Life collaboration to design landing lights for an airport. Tulloch concludes that 'as an increased number of local citizens use these tools to look at patterns of growth, crime, commercial development and open space, the data and applications will result in a new form of democratization'. Nature also disucussed the phenomenon of participatory mapping in an issue of 16 February 2006 they noted the use of 'virtual globes' to predict epidemics of cholera, track migration patterns of walruses. Enthousiasts for the application of geogrphical information systems (GIS) also view the transfer of such data to virtual globes as a democratising process. As both features note, the power of the applications to present visually striking results must be matched by appropriate training for those involved in large scale participatory mapping projects to prevent the distortion of research results.
*31/01/07: The British Medical Journal has recently voted sanitation the most important medical milestone since 1840, the year the BMJ was first published. Readers were given 10 days to vote on a shortlist of 15 milestones, and sanitation topped the poll, followed closely by the discovery of antibiotics and the development of anaesthesia. A total of 11 341 people voted on the shortlist, which was chosen by a panel of experts from a list nominated by readers. The work of the 19th century lawyer Edwin Chadwick, who pioneered the introduction of piped water to people's homes and sewers rinsed by water, attracted 15.8% of the votes, while antibiotics took 15%, and anaesthesia took 14%. The next two most popular were the introduction of vaccines, with 12%, and the discovery of the structure of DNA (9%).
*31/01/07: Put simply, the new service Twitter enables the wide broadcast of anything one can fit into a text message. A text message sent to Twitter is subsequently broadcast to all of one’s ‘Twitter friends’. It is sort of microblogging - blogging a sentence or two. To express a wide range of thoughts and experiences while on the go, type it into your phone or Blackberry and, instantly, your friends are enlightened. Twitter also serves as an archive of your messages, a chronology of all of these occurrences that can be shared and linked.
*12/01/07: Jimmy Wales, founder of Wikipedia, has recently announced that he plans to take on Google with a new project called Wikiasari, which is expected to launch this quarter. Wales, a former options trader, says his new search engine will be better than Google’s because it relies on human judgment rather than algorithms to choose relevant websites. “Essentially, if you consider one of the basic tasks of a search engine, it is to make a decision: ‘This page is good, this page sucks’,” Mr. Wales was quoted by the Times as saying. “Computers are notoriously bad at making such judgments.”
Wikiasari will order query results using a Google-like page rank system, ranking Web sites according to how often they are linked to or accessed. But users will also be able to reorder the results they get using an additional edit function. The new order will be saved by Wikiasari and combined with the rankings of other users. Therefore there is a good chance that in early days of Wikisari, or in niche subject areas, the results will be virtually no different than the Goolge ranking system. Several articles have been published discussing this topic, including a piece in Forbes magazine, and the aforementioned interview with Wales in the Times. To get involved with Mr. Wales and the Wikiasari search engine, visit the Wikia website.
*2/12/06: Quickywiki, a new tool from Wikipedia that condenses long articles, is now available. On the front page you can run a simple keyword search and if you like add focus words to help you narrow down your query (You can also leave that blank and QuickyWiki will suggest focus words for you.) At the end of the abbreviated article are links to related links, Web links, and news links.
*16/11/06: Elsevier has expanded their health science team with an in-house expert on medical informatics. In a continuing effort to meet the evolving requirements of clinicians in today’s healthcare environment, Elsevier has hired Dr. Jonathan Teich as chief medical informatics officer. Teich will be responsible for directing the development of the vision, strategy, and broad product design to translate Elsevier’s content base and publication resources into products that provide a sophisticated level of support to clinical practice and healthcare delivery.
In the Elsevier press release, Brian Nair, chief executive officer of Elsevier’s Health Sciences, commented on the new post: "Today clinicians are charged with the complicated task of delivering state-of-the-art health care in a cost-effective manner," The addition of Jonathan Teich to Elsevier’s already outstanding health science team will add a new level of expertise as we develop innovative solutions to address the most critical needs of the healthcare community."
A practicing physician, Jonathan Teich brings with him a wealth of experience in the scientific and technical fields. Teich is an assistant professor of medicine at Harvard, and a board-certified attending physician in emergency medicine at Brigham and Women's Hospital (BWH), where he has practiced since 1983. He is a recognized pioneer in merging technology with the logistics of health science, in domains including health information infrastructure, e-prescribing, and clinical decision support. He was the primary designer of many of BWH's award-winning clinical information applications, including the computerized physician order entry system, ambulatory record, clinical decision support systems, emergency medicine systems, and the Handbook electronic information library. A peer-reviewed 1998 study showed that BWH's order entry system has reduced significant adverse drug events by 55%.
*15/11/06: According to the Slashdot weblog, Assistant Professor Marin Soljacic and colleagues at MIT have outlined a system that could deliver power wirelessly to battery operated devices. Slashdot explains that their solution entails installing special 'non-radiative' antennae with identical resonant frequencies on both the power transmitter and the receiving device. Any energy not diverted into a gadget or appliance is simply reabsorbed. The system currently under development is designed to operate at distances of 3 to 5 meters, but the researchers claim that it could be adapted to factory-scale applications. BBC News offers further information on this scientific breakthrough.
*15/11/06: Faculty of 1000 Biology, the award-winning literature awareness service for the life sciences, launched its Pharmacology and Drug Discovery Faculty on 30 October. The world's top pharmacologists will highlight and evaluate the most important research articles in their field.
Faculty head Floyd Bloom is a past Editor-in-Chief of Science and Professor Emeritus at The Scripps Research Institute in La Jolla, California. He acknowledged the benefit of the new Pharmacology and Drug Discovery Faculty, "No one can keep up with the literature, so having colleagues point out the recent important advances in unfamiliar areas is enormously useful."
The leaders in the field associated with the Faculty of 100 Biology have helped recruit over 200 experts to act as new Section Heads and Faculty Members. A full list of the researchers involved in this new faculty is available on the Faculty of 1000 Biology website. The new faculty includes 14 sections: Antimicrobial agents, Cancer therapeutics, Cardiovascular & respiratory pharmacology, Drug discovery & design, Endocrine & metabolic pharmacology, Gastrointestinal & renal pharmacology, Genito-urinary & reproductive pharmacology, Immunopharmacology & hematologic pharmacology, Molecular pharmacology, Musculoskeletal & dermatologic pharmacology, Neuropharmacology & psychopharmacology, Pharmacogenomics, Pharmacokinetics & drug delivery and Toxicology.
*10/11/06: The BMJ has acknowledged Google, the world's most popular internet search engine, as an increasingly important tool in difficult clinical diagnoses. In a paper from the Department of Respiratory and Sleep Medicine, at the Princess Alexandra Hospital, in Brisbane, Australia, 26 diagnostic case studies were selected from the 2005 New England Journal of Medicine. Doctors were blind to the actual diagnosis as published. The percentage of correct diagnoses reached via Google search was then determined. Google searches revealed the correct diagnosis in 15 (58%, 95% confidence interval 38% to 77%) cases. *10/11/06: On 8 Nov, Stewart Brower, a University of Buffalo library coordinator, launched the Pubdrug wiki. As announced on his blog , Steweart has become frusterated with the exorbitant costs associated with obtaining drug resources. He hopes to create an copyright and royalty free database targeting health practitioners, researchers, informaticians, and the general public. As described on Stewart's clog, current short-term goals include development of a robust template for drug monographs, creation of policies and procedures to guide site development without interfering with the viral nature of wiki-building, and recruiting lots of people to assist in building this resource.
*30/10/06: Second Life, the virtual world launched in 2003 has attracted millions of participants and famously has a GDP larger than that of some actual nations. There have been recent moves to chanel the vitality of Second Life towards real world issues. Nature has recently launched its own virtual presence as the Second Nature island, currently hosting an updated version of their M4 (Magical Molecular Model Maker), which builds in-world models of chemical structures by querying the NIH's PubChem database. A recent example is the visualisation of weather data, a collaboration between the US National Oceanic and Atmospheric Administration (NOAA) and Aimee Weber's Studio and described on the blog Second Life Insider. METAR data is received from NOAA by scripted reporting stations dispersed across a map of the US and decoded and rendered into models of the current weather in each area. Thus far the system may only represent what Brady Forrest termed the 'poor man's 3D geoviewer', but along with a host of other real world uses of Second Life, ranging from virtual conferences to fundraising, it demonstrates the potential of data visualisation in a collaborative environment.*04/10/06: Netvibes and Pageflakes, Ajax desktop competitors (see our article Writing on the Web for more details) have both announced upgrades to their services. Netvibes' 'Cinnamon' upgrade allows the user's 'digital life' to encompass more targeted searches of blogs, film and feeds and tag, Flickr and video modules, and more integrated access to MySpace and Digg. The new release will have improved language settings, with community translations and local support, leading to the development of a netvibes page for each country. A final interesting addition is 'box.net' which gives the user 1 mg free storage space. Pageflakes move to 2.0 status will involve giving the user more control over sharing the content they 'publish' on their page with other users. See Techcrunch for a more in-depth review. Meanwhile Google has lifted some of its 'gadget' services from its online desktop to offer the code to web developers to enhance their own sites. The 'moon phase' gadget to the right of this page is an example, and there are a range of specialised gadgets such as an earthquake watch as well as headlines. For more information read Google's press release or the review by Research Buzz. Finally, Nokia has introduced a selection of mobile widgets (WidSets) designed for use with Java MIDP 2.0 phones (reviewed in O'Reilly Radar).
*03/10/06: Following First Author's recent article on data mining, some interesting new techniques are emerging. A Connotea (First Author review) user Robert Muetzelfeldt is pioneering the use of Simile to use the bookmarking service to store xml data. Simile is a visual modelling environment for life sciences that translates diagrams and mathematical equations depicting the relationships between elements of a visual model into machine-readable code (see also the discussion of Simile in Scientific Computing). Ben Lund discusses this and other ways of using Connotea as a database in Nascent.
Meanwhile, new debates over the ethics of data mining have been sparked off by the New York Times, which demonstrated that it was possible to determine the identity of an individual based on search data released by AOL on a site briefly made available for academic research. Google has responded by releasing a video presentation on how to preserve privacy in data mining.
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*28/09/06: Dissect Medicine, a service based on a similar concept to that of the popular technology news ranking site Digg, was launched this spring by Nature in association with Macmillan Medical Communications (MMC), a medical communications agency set up in June this year. Dissect Medicine is a collaborative medical news website, which indexes and ranks international medical news, blogs, press releases, medical research and other items based on the votes of participants. Users need to be logged in and can then post news items, which are tagged with keywords that function in a similar way to the tags used in Connotea and are linked to other relevant keywords. You can request an RSS feed of results under the various topic headings and start discussion of the various topics using the comments function. Postings are also grouped into catagories such as 'diseases and conditions', 'food and nutrition', 'public health and policy', and the amusing 'offbeat medical news'. As noted by David Rothman the service has some similarities with BioWizard but focuses more on news, the only moderation being the ranking by user votes, while Biowizard only accepts postings of material that has already been included in PubMed. The two sites could perhaps learn some lessons from one another: for example, despite its catagory system, DissectMedicine lacks a search function, while Biowizard, somewhat suprisingly, fails to incorporate RSS feeds unlike DissectMedicine (although not all those I tried worked). Both services seem to have attracted some loyal users over a range of topics and DissectMedicine plans to expand further using MMC to set up parallel services in other languages.
*22/09/06: Interest in mapping spaces and pinning data to geographical locations continues to grow. Flickr fans have been quick to geotag their pictures to a Yahoo-based world map. The Google Blog has a good discussion of this with tips on how to export photos to Google Earth or to Google's answer to Flickr, PicasaWeb and the 'Google Maps Mania' blog has a list of tools that can be used to associate photos with Google Maps locations. For bloggers who want to anchor their words to a geographical point, Geopress is new technology that enables users of the new technology WordPress to add spatial locations to their posts. Wikimapia combines mashups and the wiki format to use text and graphics to 'describe the world'. There are multiple scientific uses of these technologies: one of the first groups to experiment is the Marine Geoscience Data System project, who have employed it to create high resolution maps of the ocean floor, sediment cores, and tectonic plates. They offer the open source Java application GeoMapApp that can be used for data exploration and visualisation, including creating custom maps to display selected data drawn from a range of relevant data sets. NASA's Scientific Visualization Studio (SVS) has created a series of educational animations of environmental change. Tom Gaskell writing at Java.net, explains how to use these with mapping software EarthFlicks. As New Scientist reports, projecting blueprints onto online maps can also aid planners to forecast the environmental impacts of future developments.
*21/08/06: Doctors.net.uk have launched a wiki-based online medical reference source, Medipaedia. Like Wikipedia, the site will be available for addition of information, but only by the medical community. Registration to doctors.net.uk precludes access to the site, for both viewing and updating.
*4/08/06: HarperCollins Publishers has announced that they will let readers see excerpts of its authors’ books on its own Web site as well as those of the authors themselves. Today the company will introduce a program called “Browse Inside” on its website, providing readers access to the first three pages of most chapters in 135 titles by 10 authors, including well-known writers like Michael Crichton and Paulo Coelho. This is a natural extension of HarperCollins announcement last year that it would be digitizing all its books. So far it says it has digitized 10,000 of its existing titles, with continuing plans to digitize the remaining 15,000 books on its so-called backlist. All of its forthcoming books will be available digitally as well.
*1/08/06: The new website Aggademia is now up and running. Nature has compiled selected features that have been posted on the 50 top science blogs, according to its recent rankings. Readers can browse through the postings and vote whether articles should be moved 'up' or 'down'. A popularity list is also compiled. Further, the site features discussion groups in which readers can voice their opinions on a wide range of scientific topics. Currently the site is a prototype version to gauge the community's interest and explore features; over the next few months more sophisticated features may be made available.
*25/07/06: A non-profit, donation-based project in open source journalism has just been launched by Jay Rosen, NewAssignment.net. The site uses open source methods to develop good assignments and help bring them to completion; it employs professional journalists to being a story, persevere with its completion, and set high standards so the work remains of quality. There are accountability and reputation systems built in that should make the system reliable. The hope is that individuals will donate to works they can see are going to be successful because the open source methods allow for insight into an endproduct. According to Rosen, 'In this sense it’s not like donating to your local NPR station, because your local NPR station says, “thank you very much, our professionals will take it from here.” And they do that very well. New Assignment says: here’s the story so far. We’ve collected a lot of good information. Add your knowledge and make it better. Add money and make it happen. Work with us if you know things we don’t.' For more information, visit the site.*21/07/06: Yesterday, Bill and Melinda Gates announced that the Gates foundation would donate $287 million to a international, collaborative effort to develop a vaccine for AIDS. 16 groups around the globe were beneficiaries; all research groups received funds on the condition that they would work in a collaborative effort in which data, protocol, and results sharing will be mandatory. This sort of agreement is unprecendented in science, in which the normal protocol is to withhold data until appropriate journal articles or patents have been published. The Gates Foundation hopes to expedite the process of AIDS vaccine development by eliminating these inefficiencies.
*1/07/06: It is now possible to display your Connotea bookmarks in the form of a 'touchgroup'. This feature has been available on PubMed's alternative interface, HubMed, for some time and provides a visual representation of related articles. The new tool utilises a Java applet developed by HubLog and allows the user to display their saved citations connected by shared tags.
*28/06/06: A conference was held today at Imperial College London on the subject of 'data webs'. Participants emphasised that as increasing numbers of scientists were depositing work in distributed databases, the need for effective mechanisms for querying and harvesting metadata from those databases. Suggested solutions included SPARQL, OAI-PMH and central ping servers/metadata registries. More information on data webs is available from the website of Robert Grossman, the creator of the open source 'DataSpace', a web services based infrastructure for exploring, analyzing, and mining remote and distributed data. A more recently initiated data web project was also represented at the meeting. BioImageWeb aims to brings together scientists, developers, librarians, publishers and others with the aim of easing the process of finding scientific images online.
*13/06/06: After a period of lively discussion on Nature's science and technology blog, Nascent and elsewhere (see First Author's article on text mining) some changes have been made to Nature's OTMI tool. These include extra information about the article, such as the digital object identifiers (DOI's) of articles that are referenced and information about figure titles and captions. More information is also available about the sections of articles from which passages of text are drawn. Nature have also augmented their system of 'word vectors' by adding other options for text scrambling, in a bid to encourage other publishers to join the project (more information from Nascent).
*31/05/06: Several interesting results are emerging from the WWW2006 conference that took place last week in Edinburgh, the papers from which have now been released. One of the most interesting discusses the concept of the 'semantic wiki', a project that is now being trialled in the Onto World wiki. The project, discussed in a paper Semantic Wikipedia by Max Völkel, Markus Krötzsch, Denny Vrandecic, Heiko Haller, Rudi Studer, presented at the conference, focuses on the use of 'typed links' and 'attributes' as well as extending the current uses of categories. Typed links are designed to provide information about the type of link that is being created, so that, for example, the article 'London' would be linked to 'England' with the link 'is capital of', with the capitals of other countries being connected in a similar way. It would then be possible for user inline queries posing questions such as 'what is the capital of England?' and retrieve the article on London in response. Aggregated queries intended to retrieve, for example, all capital cities in Europe would then also be possible. A further way of attaching semantic data is to use numerical data such as numbers, coordinates and dates as 'attributes' that identify such data without creating pages so that, for example, a query 'what is the population of London?' would retrieve the response 741,328 within an article without the need for there to be a, largely redundant, article for that value. The project will of course require the creation of a large number of typed links and attributes to be effective: currently inline queries bring up some unexpected results (e.g. 'caffeine' on a search for all articles in the catgeory 'animals'!). This may be aided by the use of templates and the text required to enter semantic categories is fairly simple and therefore unlikely to discourage wiki enthousiasts. There is also potential for the semantic wiki to be further integrated into desktop applications such as KDE and amaroK. The semantic wiki is a logical meeting of two of the new web technologies and should to produce some interesting results - one to watch (and, of course, add to).
*31/05/06: Another experimental software being previewed at the Edinburgh conference was mspace, which was used to provide information relating to the conference schedule. mspace is described by its developers as a mashup of iTunes and Google that has applications outside music. In essence, it enables the user to view several subsets of information within a single window, search for related information and bookmark pieces of information that are of particular interest.
*30/05/06: In a Nature interview, Nigel Shadbolt, who chaired the panel 'The Next Wave of the Web' at the www2006 conference in Edinburgh last week. Asked about the future of the Internet he stressed in particular the rising important of Internet access from mobile devices as well as the importance of the semantic web and machine readable databases. The presentations from the panel on mobile devices are now available and explore some of the possibilities raised in First Author's recent article on mobile devices for connecting social networking to physical location. Julian Bleecker's 'What's your social doing in my mobile?' discusses some emerging projects, including his own, PDPal, which allows users to create maps of associations connected with physical location. Projects such as Dodgeball that inform participants of their friends' physical locations and finally an Intel-Berkeley collaboration, Jabberwocky, an interesting, if somewhat unsettling project designed to allow PDA users to map their interactions with their 'familiar strangers'.
*30/05/06: An new take on social software comes from Illumio an instant messenging service that runs on a network of computers, designed for a workplace environment by Tacit Software. The service rates its users on their expertise on a particular subject, entered as a keyword search by another user, based on the files on their computer, including files and emails. To resolve the security issues that are bound to arise from such a suggestion, Illumio's blog explains that the software is installed separately on each user's computer so that the actions of submitting the request is performed by the software on the computer of the person submitting the request, the search is performed on the recipient's computer and the results are not automatically transmitted back but submitted to the owner of the recipient computer, who can then make the decision about how to respond. Tacit supply similar products to communities, but are planning to release Illumio as a free Internet download to individuals (sign up to participate in testing). Although the quantity of information relating to a subject stored on a computer is not necessarily a good guide to the quality of the owners' knowedge about the subject, it does give some indication that they may have useful documents to exchange, and the screen shots available so far imply that there could be a learning process involved, as a user is enabled to report a bad recommendation. Presumably the system could also learn which users are likely to respond to requests for information. Illumio's focus on documents or emails stored on individuals' computers also excludes information stored by users on the web, which may become an issue in future (see Writing on the Web (2.0)?) and perhaps could therefore be most useful alongside tools for self-identification such as the RDF identification systems pioneered by the 'Geek Code' and more recently adopted by FOAF. With some refinements, therefore, and provided that users could be convinced of the security of the system Illumio could be a useful addition to plans to develop social networking services for academic purposes.
*26/05/06: An interesting project was proposed on the Java.net community page. The Neurona Project proposes the use of distributed computing to create a network that functions like the human brain by combining various sensory clues detected by the computers, or 'neurons', that make up the network. Like previous discussions of sensor web technology, proposed uses include medicial monitoring and security. The project is illustrated by this diagram.
*16/05/06: Google Notebook has now been released. The notebook requires you to download it as a browser plugin on your first visit, but will then remember details by cookies rather than login. Thereafter it is possible to 'note' pages by right-clicking anywhere on the screen and clicking the 'note this' option. The URL is then retained with any notes that the user adds and can be viewed and edited in the notebook, accessible through a popup window that appears when you add a note. Like most similar services, Google Notebook allows the user to choose whether they want their bookmarks and notes to remain private or be available for other users to view. However, as a rather scathing Techcrunch review notes, Google Notebook does not make use of the tagging systems around which most online bookmarking systems are centred. This is perhaps likely to make the new service more popular with those who are less familiar with the 'Web 2.0' breed of applications and prefer the simplicity that has been Google's trademark. However, the Techcrunch review also makes the good point that, suprisingly, the new service does not seem to be integrated into other labs services such as Google Bookmarks, or indeed Google Desktop.
*16/05/06: HubMed has added a Greasemonkey script that allows users to have the HubMed options displayed in the google results page when any PubMed article is retrieved (announcement in HubLog).
*11/05/06: Google made a series of new announcements in a press release yesterday. A series of new options are now available to allow users to further personalise their searches. Google Co-op allows users to subscribe to a choice of 'subscribed links', offered by organisations or individuals with expertise in the area and arranged within catagories such as news, lifestyle and health. The choice of subcribed links is small so far, but will undoubtedly grow fast. The health section is particularly well developed, with major contributors including NIH and Harvard's medical school. The Google Desktop service (an Ajax desktop, discussed in First Author's recent article Writing on the Web (2.0)?) has also added new features, including 'gadgets', mini-applications similar to those offered by Windows Live. Interacting with these two services will be Google Notebook, a service due to be released next week that combines bookmarking with the ability to leave 'notes' relevant to the content of the links that are being bookmarked. The service will integrate the concept of 'social bookmarking', enabling the user to share their links and note with selected other users. Finally, Google Trends allows the users to map how popular a product or concept is in a particular place by creating a graph showing the frequency of searches on specified terms over time with bars below showing the regions and countries from which searches using that term were run most frequently.
* 10/05/06: After much speculation from search engine watchers and commentators, Google's new "Google Health" service is due to be launched soon, perhaps today. A trial version is available at http://64.233.167.99/. The new service narrows down searches on medical terms or conditions to those providing medical information about the condition. Although these intial results do not seem to differ much from those provided by running a standard Google search, the results can then be narrowed down to options such as treatment options, symptoms, new, research papers, alternative medicine or 'medical establishment'. Google has attracted criticism in the past after patients have been alramed by discovering misleading information or rare side-effects related to their conditions, so this new service promises to deliver more targeted information for patients and physicians.
*Nature has released the API (application programing interface) of their social bookmarking service, Connotea. The API allows developers to integrate Connotea into other web applications by sending html requests for certain tasks, currently including creating and editing posts to Connotea as well as retrieving entries with specified atgs. The API is available as a wiki on the Connotea community pages. It will be interesting to see what types of new services (or 'Mashups') will emerge from this release, NGP's first public service for web developers.
*Both Google Scholar and HubMed have introduced new limiting features allowing the searcher to retrieve only 'recent articles' by limiting the date range using Google scholar's built-in date range function or Lucene's range syntax. in the case of HubMed.
*In last week's Nature, the journal announced the launch of its text mining tool, the Open Text Mining Interface (OMNI), first presented at a recent Life Sciences and IT Conference in Boston and given a trial run on Nature's recent issue on Computing in Science. The model proposes a solution to the problem of indexing the full text of diverse publishers' output, to allow more comprehensive searching, or 'text mining', to be conducted. Although the full text would be available to machines, subscriber-pays publishers would be able to maintain their traditional access barriers. This is achieved through encryption: using 'word vectors'; the number of words in the article is recorded, while their order to not. To allow more 'semantic' searching, the file also contains 'snippets'; sentences presented out of context. Bibliographic data is also recorded. Nature hope to use this aspect of confidentiality to persuade other publishers to join them in the initiative: as they point out, the project will only be successful if carried out as a collorative venture.
The technology behind OMNI is an Atom Entry document with various XML namespace extensions to allow the inclusion of extra information. The project is still very much in its early stages, discussion of issues such as whether RDF could be a more useful tool and whether the encryption will inhibit traditional modes of searching such as proximity searches are ongoing in Nature's blog, Nascent, as well as O'Reilly's Radar and HubMed's HubLog.
*A new academic search engine enters Beta this month. Windows Live's academic search delievers results from open and access-restricted academic journals, currently focusing mainly on compter and material science . There are some interesting options for presenting the results, including BibTex and Endnote styles and the search results can be integrated as an RSS feed into a personalised online desktop function similar to those offered by Google Desktop and Netvibes. There are also searches specifically for feeds, news, or images. As Dean Guistani points out, the limitation of the search to publisher's material may exclude some interesting material: on the other hand, it should ensure the quality of what is retrieved. A more serious flaw, however, might lie in its lack of compatibility with PubMed: unlike Google Scholar, it attempts to bypass the popular NIH tool by loading records directly from publishers in an attempt to avoid duplication.
*A new database for bioinformaticians, the Protein Circular Dichroism DataBank (PCDDB) aims "to provide a resource for the structural biology and bioinformatics communities, by creating open access and archiving facilities for circular dichroism spectra". The project is currently in the early stages of development: an outline is published in this month's Chirality.
*A simple tool to integrate news feeds into your website or blog, FeedoStyle has now entered Beta phase. The tool allows you to customise the format in which feeds appear. It is also compatible with online desktops like Google Desktops, Pageflakes, and Netvibes. As an example, we've integrated into this page some relevant feeds: from Nascent, Nature's blog on web technology and scientific communication; Netwatch, Science's Netwatch, looking at the latest online tools related to science; Research Buzz, commentary on the latest web tools; and Open and Shut, Richard Poydner's blog on open access. As a review in Techcrunch points out, some additional features such as the ability to integrate several feeds at once could be useful, however, there are some advances in keeping feeds separate for future modifications and the appearance of the feeds can be customised further using CSS.
*Nature has added a new 'Community Page' to its social bookmarking service, Connotea (First Author* review). The page is wiki-based so that users can write and edit articles about Connotea, and refer to their own collections of bookmarks. An RSS feed of the changes users have made to their collections is also available. So far most contributors are Nature staff, but the service might eventually serve as a useful guide to the different collections stored on Connotea.
*The recently launched Omics Gateway from Nature provides a portal for life scientists working with large data sets. Including the abstracts of Nature Publishing Group papers from 2001 onwards, the portal uses an intial simple list of subject areas, such as Systems Biology, Cancer Genomics and Proteomics or a visual, 'Tree of Life' representation of organisms. Clicking through to an item on either of these lists gives sub-groupings of subject areas related to the organism or vice versa. The most recently items are displayed first with the option to browse earlier publications by year of publication or subject area.
*Google Scholar announced this month that it is now possible to search publications in Chinese and Portuguese, as a result of collaboration with the Chinese journal database, VIP Information and a Brazilian equivalent, SciELO. Other lanaguages are hoped to follow, meaning that papers in these languages will be included in Google scholar's rating system.
*A tag-based search engine, Keotag, which recently entered its beta phase, scans the various sites that make use of tagging, including Technorati, De.licio.us, Google blog search, and Feedster. The results are all displayed within Keotag's site and it is possible to receive an RSS feed of a specific query. The range of sites covered means that the results retrieved by the search cover a good range. From a science point of view, the site seems more useful for keeping up-to-date with current debates than for serious research: for example a search on 'peer review' produces a range of relevant recent articles, at least from some of the featured sites, while searches for medical or technical terms found irrelevant sites or produced no results.
*Del.icio.us has launched a new bookmark loader that can automatically transfer firefox bookmarks into Del.icio.us. Generic tags can be added during the transfer and later to each individual bookmark.
*Yahoo has bought the social bookmarking tool Del.icio.us. The original site will continue to run and Yahoo! will incorporate more linking tools into its own bookmarking service, MyWeb. For more information about social bookmarking see the First Author* review of Connotea, Nature's service for academic bookmarking.
*Nature's editorial for the first December issue is devoted to the issues of the new web technologies, wiki, blogging, and open access databases s and evaluates their significance for science. This piece, and the news features that follow, urge scientists to rethink their approach to publihsing their work and taking part in the exchange of ideas: Let data speak to data. Nature 438, 531 (1 December 2005) | doi:10.1038/438531a URL: www.nature.com/nature/journal/v438/n7068/full/438531a.html
For more information on blogging and scientific communication see the First Author* article 'Will Science Blast into the Blogsphere?'
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*The Royal Society is initiating research into the question of how developments in technology affect scientific communication. The focus is on health care and on communicating remotely with, as well as treating, patients using mobile phone technology and image recognition tools (more details). A separate study by the Royal Society investigates the issue of factors affecting communication by scientists from the point of view of researchers, funders, and institutions. The study is based in the UK and the findings will be published next year (more details)
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Impact Factors and the alternatives
First Author* guide
*22/05/06 HubMed is due to introduce a new 'stats' button in HubMed search results that provides an improved graph of occurrences of query terms in MEDLINE abstracts over time, plus an analysis of the most frequent authors of papers matching the query terms, providing an innovative way of tracking top authors in a given field in an up-to-date manner. An example of this type of analysis for molecular biology is provided by the Gene Oncology service GoPubMed. (More from HubMed.)
*17/05/06 A recent paper by Philipp Mayr, Constructing experimental indicators for Open Access documents notes the lack of indictors to show the access and download rates of documents stored in open access repositories. Although the web impact factor (WIF) has been in existence for several years (see our overview of impact factors) and many open access journals, such as those published by BioMed Central do have impact factors, this system does not take into account access or citations received by papers deposited in open access repositories, whether directly or after publication in a journal. The paper proposes a simple system of monitoring downloads according to methods of access. The proposed system certainly provides a workable system of monitoring downloads, but, as the author conceeds, will need to be supplemented by measurements of citations and linking data. A combination of such systems will need to become standard practise in order for such statistics to provide a real indicator of the status of scientific papers in open access repositories, but such a system would be invaluable in encouraging authors to archive their papers, as it would demonstrate that this is a way of increasing impact.
*Another alternative to the IFI's Impact Factor was suggested this month : Johan Bollen of the Research Library of Los Almos National Laboratory, New Mexico based their system on Google's PageRank (PR) algorithm. The PR system of evaluation focuses on the prestige of links that a webpage receives. Applied to peer reviewed journals, this means evaluating not only the number of citations a paper recevies, but the number of citations received by the papers who cite it. The proposal put forward by these researchers is that this method of assessment is combined with the IFI Impact Factor to give a 'Y'-factor, which redresses certain traditional imbalances such as the weight given by the Impact Factor to review articles, giving more weight to journals regarded as publishing high-quality original research. (Abstract published on Arxiv).*Scopus has introduced a new tool for citation analysis, allowing searches to be conducted on named individuals and subject areas and to examine research trends over specific time periods. An Elsevier project manager responsible for the new tool commented that it had been developed in response to the demands of user to 'move away from pre-defined metrics, and analyze what's going on at the level of the individual author or article' (Elsevier press release).
*The new service Faculty of 1000 Medicine (see Peer Review section) as introduced an alternative rating system based on their core membership of 2,500 specialists. Selected papers are rated according to content by giving a score of 3, meaning 'recommended', 6 for 'must read' or 9 for 'exceptional'. The total F1000 Factor' of the paper is then calculated by the formula: 1000M Factor = Mean of Highest Two Scores + (Sum of All Scores/30). Despite its restricted nature, this system provides another example of how systems for assessing the impact of scientific papers are gradually becoming detached from the status of the journal to become more concerned with the content of individual papers. Another interesting feature is the semantic categories which reviewers can attach to the papers: they can select tags to attach to a paper describing the study design, methods, and population, as well as indicating their reaction to the study by selecting tags to describe it as 'controversial', 'interesting hypothesis' or issuing a 'refutation'. This feature makes use of some of the concepts behind the semantic web technologies and the reliant on expert opinion rather automated ranking is an interesting feature that seems to be becoming more popular in new methods of classifying research.
*The ‘H-index’ – One of the most controversial uses of journal impact factors is their use in evaluating the status of scientists according to where they have published. A new proposed new method of ranking individual scientists, intended to be of use in selecting members of prestigious bodies such as the British Royal Society or the American Physical Society, has recently sparked interest among decision makers. The ‘h-index’, proposed by physicist Jorge Hirsch, of the University of San Diego awards researchers a score based on both the number of papers they produce and their impact. The score is based on the highest number of papers that a scientist has written that have had at least that number of citations, so that a h-index of 20 would signal publication of twenty papers with at least twenty citations each. Like the ISI impact factor, the scores would differ according to discipline, with top biologists achieving scores up to three times higher than physicists, for example. The research has also been criticised by some who favour non-quantitative methods of judging scientific performance such as expert panels, but most have greeted it as a welcome counter-balance to judgments based solely on journal impact factors. Hirsch has placed his work on the preprint server Arvix.
Hirsch, J.E. (2005). An index to quantify an individual's scientific research output. URL: http://arxiv.org/abs/physics/0508025 (accessed 3/10/2005).
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*Citation analysis: A recent article published in DiLib magazine (Bauer and Bakkalbasi 2005) evaluations Elsevier's citation analysis software, Scopus, and that of Google Scholar, comparing them with the ISI web of science impact factor. Scopus, which was released at the end of 2004, indexes more journals than Web of Science, and has greater coverage of open access and international journals, but lacks ISI's depth of coverage in years of scientific journals. Google, also introduced last year, offers a citation analysis function that inlcude material such as preprints/ postprints from ArXiv and RePec, conference proceedings, technical reports, books, and dissertations as well as major journals. The authors argue that if impact factors are to continue to be used for the assessment of grant proposals and tenure applications, the use of several different citation analysis tools in combination could yield a more balanced assessment of the relative impact of a piece of research. They found that newer and more unconventionally disseminated work received higher citations in Google Scholar, but warned that its refusal to disclose which material it is indexing presents a severe limitation and therefore recommend that it is used to supplement rather than replace resources such as Scopus of the ISI web of science. Less variation was found between the Elsevier and ISI tools, although the web of science found more citations for older articles.
Bauer, K and Bakkalbasi, N (2005). An Examination of Citation Counts in a New Scholarly Communication Environment. D-Lib Magazine, 11;9. URL: http://www.dlib.org/dlib/september05/bauer/09bauer.html (accessed 3/10/2005).
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Download First Author* guide
Nature has ended the ongoing open peer review trial that commenced on 1 June, and written up the results. For Nature subscribers, there's also an editorial. The Nascent blog has provided the following paragraphs as a good summary of the trial:
In the trial, the papers selected for traditional peer review were, in a parallel option offered to authors, hosted for public comment. In the event, 5% of authors took up this option. Although most authors found at least some value in the comments they received, they were small in number, and editors did not think they contributed significantly to their decisions.
This was not a controlled experiment, so in no sense does it disprove the hypothesis that open peer review could one day become accepted practice. But this experience, along with informal discussions with researchers, suggests that most of them are too busy, and lack sufficient career incentive, to venture onto a venue such as Nature's website and post public, critical assessments of their peers' work.
The limiting factor in the peer review trial was certainly not public interest, or willingness of the author’s to participate. Rather it was the number and value of comments posted by scientists in the field. The Nature results summary provides an excellent breakdown of the number of comments, and the usefulness of the comments from the editors’ points of view. Timo Hannay of Nascent has speculated about the reason for the disappointing results from the peer review trial. He believes that three options are possible: (1) Open peer review doesn't work, (2) The particular approach used by Nature does not work, or (3) Scientists are not prepared for a profound shift in traditional peer review.
Hannay is of the opinion that (3) is mostly to blame, an opinion that First Author* is in agreement with. He made the point that contrary to many generalizations, scientists are trailblazers in the realm of the internet. In fact, scientists and clinicians as a whole (with the exception of computer scientists of course) are very conservative when it comes to making the most of information technology. First Author* has yet to meet a young scientist or doctor who operates a blog, has a presence in any virtual world, or uses any social networking software at its full capability. Therefore it goes without saying that the majority of established scientists, of the caliber that could really contribute to a forum of open peer review, are most likely reticent to spend valuable time engaging in a virtual debate.
Hannay believes that scientists will eventually catch up with the multitudes of information technology available, and feels that it is a role of Nature to facilitate that. To that end, the Nature editorial concludes on a more positive note:
Another form of peer review emerges after publication, when work is replicated — or not. If this kind of discussion is to make it into the open, rather than be confined to gossip at conferences, it requires a forum where peers are able to comment on individual papers, with minimal editorial intervention. Would commenting on Nature papers be more widely adopted by researchers after they have been formally published than before? We intend to introduce this function next year, and find out.
*Nature's peer review trial is now complete, after running for three months. Some interesting paper published during the summer, were divided into the topic headings, 'systems', 'quality and value', 'ethics', 'technical solutions' and 'perspectives. Among the commissioned articles were a discussion of peer review of interdisciplinary scientific papers, which raises the issue of possible discrimination against the most innovative papers due to the difficulty in finding referees qualified to assess the impact of the paper in both subject areas and urges greater discriminatin between fact and opinion on the part of reviewers as well as cooperation between referees from different backgrounds. Other interesting suggestions included a suggestion for group peer review, ongoing open peer commentary and a combination of open and closed systems. Discussion on the peer review commenting forum was sparked over whether online systems improves review processes by increasing transparency and accuracy or actually slow them down by shifting more administrative responsibility to reviewers and in response to a piece by the Director of Sense About Science entitled 'I don't know what to believe', on the role of peer review in presenting scientific findings to the general public, which drew the comment that it is impossible to subject philosophical propositions to quality control 'in the same way as a washing machine'. Despite the interesting and lively debate that has sprung from the experiment, Nature as yet remain silent on their own conclusions.*28/06/06: Biowizard has launched a new tool for sorting through PubMed retrievals. PubMed Wizard enables users to retrospectively post open peer reviews regarding the thousands of articles already searchable via PubMed. PubMed Wizard searches will return information in an almost identical format to that standard to PubMed; however there will also be options of posting feedback, rankings, and searching past discussions of an article. To read more, visit Biowizard.
*16/06/06: The trial of open peer review, and the corresponding debate, that Nature has recently launched is now up and running. Five papers, in diverse areas of scientific interest, have been posted for publication; comments in accordance with open peer review have yet to be posted. The debate has generated a larger volume of input from researchers internationally. All who have been involved in this debate applaud Nature's innovation in peer review; the efforts of the journal to update an aging system, appear to be much appreciated. However the merits of the open peer review system seem to be a more controversial topic. On one hand, open peer review is perceived by some to bring a fresh air of egalitarianism and fairness to peer review. Reviewers from a broad background may provide valuable input to a scientific study. However, other researchers are concerned that confidentiality of a submitted work is compromised by allowing the public to see it prior to acceptance by a journal. Further, perhaps by vastly broadening the definition of the word "peer" from a select panel of researchers in the particular field of an article to the wider community, peer review may no longer be suited to select articles for publication in certain journals. First Author* continues to be very interested in this topic--for further discussion check back in the weeks to come. Investigate open peer review and the debate for yourself!
*07/06/06: Nature has recently announced that it will begin a trial of an alternative method of peer review. In this alternative, papers submitted for confidential peer review at Nature will also have the option of simultaneously undergoing an open peer review. The manuscript will be posted on the Nature website, and aspiring critics will have the opportunity to post feedback. To complement this trial, Nature will also host a forum for debate regarding the merits and pitfalls of conventional peer review (more details from Nature).
*31/05/06: A study published in BioMed Central Medicine compared the quality of peer reviewers choosen by editors with those suggested by authors found that the two sets of reviewers produced reports of comparable quality, but that those suggested by the authors were more likely to recommend that papers be accepted, perhaps due to closer relationships with authors and therefore concluded that journals that use author suggested reviewers should balance the decision of whether to accept or reject the paper with editorial imput.
*A proposal to extend the peer review system to monitor patent applications is currently under consideration by the US patent office. The proposal is to use an online community such as Slashdot to rate applications. There are some clear problems with this approach, such as the lack of representiveness or reliability of online polls, and presumably with the confidentiality of the inventions or intellectual property not yet protected by patents (suprisingly this aspect does not yet seem to attracted official concern). However, in combination with a system of selecting experts whose credentials and trustworthiness could be verified, this has the potential to provide an interesting supplement to the traditional system of patent applications and perhaps in other areas of science where the peer review system is in use (more details from Nature).
*In the wake of the scandals of the faked results of Woo Suk Hwang, and most recently, the admission of Norweigan scientist Jon Sudbo that he had invented the data of 900 test subjects, the peer review system will again come under fire from some quarters for its failure to detect such fabrications. As the editor of Lancet commented in a Nature interview this month, unless the public and policy-makers understand the strengths and limitations of the peer review system, misunderstandings are bound to continue regarding what it should be able to detect and what it is unlikely to examine. Richard Horton was explaining the decision of his journal, along with the British Medical Journal and Annals of Internal Medicine to participate in a survey of the peer review system instigated by researchers at the University of California, San Francisco documenting the process of 1,000 papers through the peer review system. The results of the study so far are positive, showing that, although peer reviewers often disagree with one another, the system does ensure the quality of the methodology of the papers it screens. The study also found that, although authors of manuscripts that report null results are less likely to submit them to journals, a significant problem in medicine, there was no evidence of bias towards manuscripts that did not report statistically significant results.*Biomed Central's lastest open access journal, Biology Direct, has initiated an innovtive system of open peer review, in which authors are responsible for selecting peer reviewers, and the referee reports are published alongside the articles. The aim is to increase the openness of peer review and to allow readers a greater insight into the value and drawbacks of a particular work (more details).
*BioMed Central's new service , Faculty of 1000 Medicine provides another example of the idea of ongoing peer review : medical research papers are reviewed by a network of around 2,500 top researchers and clinicans, who are asked to review at least two papers each month, rating those they found most interesting or useful. These comments are posted in a format similar to a blog alongside the paper and the papers can be searched on the basis of who they have been recommended by or by their 'F1000 factor' (see Impact Factors section) . Unlike many of the other services BioMed Central is associated with, Faculty of 100 Medicine is a subscription-based service.
*A recently released draft study, to be published in full in May 2006, has suggested the use of social network analysis to map relationships between scientists to prevent conflicts of interest when selecting peer reviewers. Although some may welcome this as a way of challenging the biases thought to be involved in the peer review system, others might be more concerned about the invasion of privacy involved in enquiring into personal relationships. It could be argued that a simpler way to ensure impartiality in peer review would be double-blinding during the review process.
Aleman-Meza et al. (2005) Semantic Analytics on Social Networks: Experiences in Addressing the Problem of Conflict of Interest Detection. [Draft copy available at http://ebiquity.umbc.edu/_file_directory _/papers/237.pdf, accessed 23/01/06]
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Open Access and ownership of scientific information
*20/02/07: More than 500 delegates from nearly 50 countries attended a major European Commission conference last week in Brussels to discuss the future of scientific publishing in the European Research Area.
The EU Commissioner for Science and Research received a petition, as described on First Author* and elsewhere, which was signed by more than 20,000 individuals and nearly 750 organisations, indicating the level of public support for the principle of open access.
In his blog, Peter Suber noted that the conclusion of the EC was that research should be accessible to all, after an optional period of time. The EC agreed to include the cost of publishing in open access journals in research grants. Further, the EC committed millions of euros to building and maintaining an accessible open access infrastructure.
On his blog Open Access Archivangelism, Stevan Harnad also has published his thoughts following the EC Meeting. His overall impression was that the EU Commissioners, Directors-General and Directors (or rather those of their delegates who were in attendance) were favorable to OA, and that concrete developments such as funding can be expected as a result of the conference and the petition. It is Harnad's opinion that researcher and industrial support for OA and OA Self-Archiving Mandates will now be very vigorously consolidated.
*07/02/07: From 17 Jan 2007, a petition has been published urging the European Commission (EC) to adopt, in full, the findings of the European Commission published the Study on the Economic and Technical Evolution of the Scientific Publication Markets of Europe. The Study resulted from a detailed analysis of the current scholarly journal publication market, together with extensive consultation with those that are extensively involved in the scholarly communication process. The Study noted that 'dissemination and access to research results is a pillar in the development of the European Research Area' and it made a number of balanced and reasonable recommendations to improve the visibility and usefulness of European research outputs.
In particular, the petition focuses on one conclusion of the study report: RECOMMENDATION A1. GUARANTEE PUBLIC ACCESS TO PUBLICLY-FUNDED RESEARCH RESULTS SHORTLY AFTER PUBLICATION
Research funding agencies have a central role in determining researchers' publishing practices. Following the lead of the NIH and other institutions, they should promote and support the archiving of publications in open repositories, after a (possibly domain-specific) time period to be discussed with publishers. This archiving could become a condition for funding.
The petition has certainly generated public enthusiasm. First Author recently became the 17738th signatory since the petition was published on 17 Jan. The Open Access Archivangelism blog has published a very thorough article on the petition’s supporters and progress since publication Visit here to read the petition and sign for yourself! It can also be reached via the BMC’s own website.
*26/01/07: Most biomedical research in the United Kingdom will be made freely available online in a database that went live this month and which is supported by nine of the UK's biggest research sponsors. UK PubMed Central (UKPMC) mirrors the US PubMed Central database, a free online archive of life science research administered by the US National Institutes of Health. Many of the groups behind the UK initiative, which has been led by the Wellcome Trust, now require that the results of research they support are made available to the site once they are accepted for publication by a peer reviewed journal. The UKPMC service will ensure that articles resulting from research paid for by any member of the funding consortium will be freely available to everybody, fully searchable and extensively linked to other online resources.
The British Library will run the service, promote it to researchers, as well as offering support for those who want to include their research papers in UKPMC. The University of Manchester hosts the service and will support the process of engaging with higher-education users. EBI, which is part of the European Molecular Biology Laboratory (EMBL), will contribute its biomedical domain knowledge and state-of-the-art text-mining tools to integrate the research literature with the underlying bioinformatics databases.
The UKPMC funding group consists of: Arthritis Research Campaign, The Biotechnology and Biological Sciences Research Council, The British Heart Foundation, Cancer Research UK, The Association of Medical Research Charities, The Chief Scientist Office of the Scottish Executive Health Department, the Department of Health, The Joint Information Systems Committee, the Medical Research Council and the Wellcome Trust.
*12/01/07: The BMC’s journal Biology Direct has been accepted by Thomson Scientific (ISI) for inclusion in the Science Citation Index and is on track to receive an Impact Factor in 2008. Biology Direct considers original research articles, hypotheses and reviews in selected subject areas, and will eventually cover the full spectrum of biology. Subject areas already launched include Genomics, Bioinformatics and Systems Biology, and Immunology. Also, interestingly, Biology Direct aims to assess submissions via a novel open system of peer review. This will include making the author responsible for obtaining reviewers' reports, via the journal's Editorial Board; making the peer review process open rather than anonymous; and publishing the reviewers' reports along with the articles, thus increasing both the responsibility and the reward of the referees and eliminating sources of abuse in the refereeing process.
*19/12/06: The Nature Publishing Group and the European Molecular Biology Organization (EMBO) have announced that from January 2007, the EMBO Journal and EMBO reports will have an open access option available for authors. Upon publication, authors will have the option of paying a publication fee that ensures their article will be freely accessible by the public. Subliscription fees to the journals will remian unaltered.
*11/12/06: Oxford Journals, a division of Oxford University Press has announced a new agreement with the National Library of Medicine (NLM) that will allow all content published as open access under its Oxford Open model to be available from PubMed Central. The agreement is designed for authors publishing with Oxford Journals to meet the requirements of their funding bodies, including the National Institutes of Health (NIH), who request all NIH-funded content to be deposited into PubMed Central within 12 months of online publication. The new agreement means that all content published under Oxford Open will be immediately deposited into PubMed Central by Oxford Journals directly. Oxford Journals has published almost 2000 open access articles in 2006 through its Oxford Open models, including optional open access for 49 journals, and full open access with Nucleic Acids Research. *11/12/06: Scientists from Brazil, China, Ethiopia, India and South Africa have set guidelines for developing countries to freely access publicly funded research.
The guidelines were agreed at a workshop in Bangalore, India in the beginning of November in which international participants, including scientists and policymakers, discussed ways to promote open access.
As described in the First Author piece entitled, scientists in the developing world have long complained about access to the work of scientists in North America and Europe published in paid journals, as well as dissemination of their own work.
While participants agreed on the policy, there was lively debate on how to make governments adopt it, according to website SciDev.Net. The workshop policy urges governments to require all publicly funded research published in peer-reviewed journals be deposited in an institutional digital database as soon as publication is accepted. This should be a condition for research funding for any papers partly or fully funded by the government. The workshop revealed that Bioline, an online publisher for developing countries, saw a huge increase in requests for scholarly papers when it became open access. This shows "how much information was unused, unknown, un-accessed before open access", according to SciDev.Net. *Here is yet more evidence, from the same website as the previous posting, that supports the efficacy of self-archiving among individual authors. Researcher Michael Kurtz has discovered that articles relating to astrophysics that were self-archived by their authors in Arxiv were downloaded and cited twice as much as those that were not. He traced this enhanced citation impact to two factors: early access and quality bias advantage. Early access stems from the fact that the self-archived preprint was accessible earlier than the publisher's version. Quality bias refers to a selective tendency for more important articles to be self-archived by their authors, as inferred from the fact that the proportion of self-archived articles turns out to be higher among the more highly cited articles. Kurtz’s findings are mirrored in the realm of condensed-matter physics. Henk Moed has confirmed that the impact advantage occurs early (within 1-3 years of publication). After article-age is adjusted to reflect the date of deposit rather than the date of publication, the enhanced impact of self-archived articles is again interpretable as quality bias, with articles by more highly cited authors (based only on their non-archived articles) tending to be self-archived more. *06/11/06: Chris Armbruster, a contributor to the website Open Access Archivangelism , has suggested that the way forward regarding open access publication starts with individual authors. Encouraging authors to self-archive published articles in an open access format offers an immediate solution to the problem of widespread access to novel science. Armbruster goes on to suggest that more formalized measures, such as open access mandates and open access to increasing numbers of peer-reviewed journals, could follow suit from this individual action.
*30/10/06: Chemistry Central is one of BioMed Central's new open source services, alongside the soon-to-be launched PhysMath. The site is already featuring some interesting articles discussing how the concept of open access can be extended to be included in the research and writing processes. An article recently published in BMC bioinformatics introduces UniFrac, an open source web tool that allows several phylogenetic tests for differences among microbial communities to be easily applied and interpreted. Another recent feature, 'Open Source Research, the Power of Us' originally published in the Australian Journal of Chemistry, discusses the
application of
open source collaboration to the solution of specific biochemical problems. The paper
illustrates its point by posing a challenge to collaborate in order to develop a cheaper method for the catalytic enantioselective synthesis of Praziquantel, a drug used to treat the severe tropical disease, Schistosomiasis, the synthesis of which is currently prohibitively costly.
The authors explain that: 'The open source collaboration works in both armchair and wet-laboratory modes. Contributors (academics, industrialists, students, or the public) may contribute intellectually by posting possible routes to Praziquantel, by suggesting suitable reactions for the asymmetric step, or by sharing their experiences on chemical steps suggested. Those with access to a chemistry laboratory can actually attempt reactions of interest and post results, either as part of spare-time activities or as more formal student projects. Rigorous and accurate (rather than anecdotal) reporting here reduces the effort required in self-policing. Contributors with access to relevant materials (such as intermediates or catalysts) may physically share these with others willing to spend time on the problem. Open source communities thus expand the borders of what is already commonplace within chemistry schools.' The project is one of several undertaken by The
Synaptic Leap
a forum that aims to develop collaborative research communities and is currently also tackling malaria and tuberculosis. *This month has seen a large number of public institutions, including several of Britain's Research Councils, adopt self archiving mandates, which require authors whose work they fund to archive their work in freely available form a certain period (ofetn six months) after publication. Open Access Evangelism and Open Access News have full details of the particular policies of each institution. (top) *18/09/06: Following more research showing that most academics are unlikely to self-archive their papers unless required to do so, mostly from a lack of time rather than commitment, pressure is now increasing on institutions to require authors to immediately self-archive their work. Under an initiative known as the Immediate-Deposit/Optional Access (ID/OA) model, members of an institution would be required to deposit their work in an institutional repository as soon as it was published, but given the option to dely access for a certain period of time in order to comply with embargoes imposed by publishers. Users requesting items that were unavailable at the time would be given an option to have a link to the paper emailed to them as soon as the embargo was lifted (after a maximum of six months). Meanwhile, support for the Federal Research Public Access bill continues to grow among academics. The SPARC coalition is running a petition to endorse the bill. *29/08/06: Open Access Central, and the included repository Chemistry Central, have recently been launched by the organization that runs the OA publisher Biomed Central. Future open access initiatives such as PhysMath Central will also be included within Open Access Central.
BioMed Central Publisher, Matthew Cockerill, says: "The rapid growth of open access publishing in biomedicine has attracted the attention of researchers and funders in other disciplines. It has become clear that open access journals are equally necessary in fields such as chemistry and physics. With the launch of Open Access Central, we are making the open access journal publishing system available to groups of researchers in other fields who wish to start open access journals."
Chemistry Central will publish peer-reviewed research in chemistry and makes it immediately available online with no access charges or subscriptions. Chemistry Central will soon be launching further chemistry journals, including Chemistry Central Journal, a major new open access title covering all areas of chemistry.
PhysMath Central (www.physmathcentral.com) is planned for launch at a future date, and will feature peer-reviewed research in all areas of mathematics and physics.
*21/08/06: The National Environmental Research Council (NERC) has committed itself to the principles recently articulated in the RCUK statement in regard to open access to scientific research.
From 1 October 2006 NERC will require that, for new funding awards, an electronic copy of any published peer-reviewed paper, supported in whole or in part by NERC-funding, is deposited at the earliest opportunity in an e-print repository. NERC also encourages award-holders to deposit published peer-reviewed papers arising from awards made before October 2006.
NERC will establish an e-print repository to improve access to the outputs of its research centres. NERC staff will be expected to deposit copies of any published peer-reviewed papers, supported in whole or in part by NERC-funding, in the NERC repository. NERC award holders who do not have access to an appropriate repository through their host institution will be able to deposit in the NERC repository.
*21/08/06: Elsevier announced the signing of a three-year agreement for the provision of vital scientific and medical information to the Jordanian Consortium. The agreement provides all Jordanian undergraduates, graduates, researchers, faculty and staff within the consortium with access to ScienceDirect collection of 2,000 journals from 2002 onwards. The agreement includes high impact factor journals such as The Lancet and Cell.
The Jordanian consortium is composed of: The University of Jordan, Yarmouk University, Mu'tah University, Jordan University of Science & Technology, Hashemite University, Al-Al Beit University, Al- Balqa'a Applied University, Al- Hussein Bin Talal University. The agreement not only provides the Jordanian research community with complete access to full-text articles on ScienceDirect, but also includes library access to physical copies of journals.
*21/08/06: Biomed Central has announced the Open Access launch of its publication Acta Veterinaria Scandinavica, the official journal of the Veterinary Associations of the Nordic Countries. It was founded in 1959 as a traditional print journal. In May 2006, Acta Veterinaria Scandinavica took the novel step of becoming 'open access', making its content, describing all aspects of veterinary research and medicine of domestic and wild animals, freely available online.
*14/08/06: A study will be published in the September 2006 edition of Health Information and Libraries Journal describing the impact of the author pays model of OA on the literature that actually gets published. The author pays system shifts cost of journal upkeep from subscribers to authors. The article, from Surabhi S. Liyanage and C. Raina MacIntyre, investigated the impact of author page charges on the nature and type of published research, and the association of industry funding with types of published research. The study found that authors from developing countries were significantly less likely to be published in author pays journals. Also clinical trials published in any journal were likely to be funded by industry, and this sort of research was significantly less likely to focus on diseases that are important in the developing world. Clearly, this study indicates a potential for publication bias must be considered when planning for open access models. For more details regarding statistics and the methods employed in this study, view the abstract at Peter Suber's OA News blog.
*14/08/06: 25 University Provosts from American institutions such as Harvard, Dartmouth and Michigan State, have signed a letter endorsing the Federal Research Public Access Act of 2006 (FRPAA). The FRPAA is a bill that will be discussed in the US Senate requiring that all research funding bodies with budgets of more than $100 million should develop policy to ensure that resultant science is freely available to the public. The letter cites the billions of dollars of scientific research that takes place at the universities represented, and asserts, "The broad dissemination of the results of scholarly inquiry and discourseis essential for higher education to fulfill its long-standing commitment to the advancement and conveyance of knowledge." Certainly if the FRPAA is made a US law the impact on OA publishing would be enormous, bolstering the status of OA journals such as the BMC and increasing the importance of OA repositories for the archiving of post-prints. Currently US institutions such as the NIH mandate that funded research is made open access, along with British funding bodies such as the RCUK and the Wellcome Trust. To view the original letter, visit the BMC home page.
*02/08/06: The Nature Publishing Group (NPG) has announced that as of January 2007, all archived material from its research and society journals, published before January 2003, will be available free of charge. The license-only archived period will remian at a four-year time lag. NPG hopes that this move will encourage more widespread usage of its content. For more information, read the press release from Nature.
*25/07/06: Recently, there has been significant progress in the development of Open Access (OA) self-archiving mandates. Two major OA registers, the Registry of OA Repository Material Archiving Policies (ROARMAP) and the Registry of Open Access Repositories (ROAR) now have 497 institutionally-mandated repositories registered, list 29 institutional or funder policies, 6 institutional mandates, and 4 funder mandates. Some funders include the RCUK funding bodies and the the Wellcome Trust in the UK, in the USA, Case Western Reserve University and the NIH, in Australia the University of Queensland, in India the National Institute of Technology, and in Europe the CERN *19/07/06: Yesterday, Elsevier announced that 6 of their nuclear physics based journals would delve into the realm of openly accessible publication. In the Sponsored Articles initiative, authors of articles that have already been accepted for publication will have the option of paying a fee to ensure that the article will be available to the public via ScienceDirect. Elseveir is adament that their conception of Sponsored Articles is not a form of open access publishing (OA), but a different model to give the public access to science. They claim that OA refers to several distinct publishing strategies, including the author-pays model, which they do not condone. The director of strategy at Elsevier has stated that they are "explicitly opposed to the author-pays journal model because if you are an author and you submit an article and I’m editor, who knows I’ll get paid if I accept your article.”
Sketpics claim that this Elsevier initiative is merely a response to the recent announcement that the particle physics centre CERN has adopted open access. However, even rival company Springer has acknowledged that the fact that Elsevier has joined the debate regarding various models of accessible science is a good thing. Fro more information, see the Information World Review site.
*06/07/06: In an important advance to the open access movement, the UK Research Councils have mandated that all funded research be publicly archived within 6 months of publication. The Medical Research Council (MRC), Economic and Social Research Council (ESRC) and the Biotechnology and Biological Sciences Research Council (BBSRC) have all issued individual statements to outline the specifics of their new policy. The MRC, for example, will require that all research that they fund be deposited as a full-text article in PubMed Central within 6 months of publication. While the change in policy does not, in all cases, offer highly specific guidelines for open access publication of funded research, this advance certainly marks a milestone for the Open Access movement. The UK research councils join both the Wellcome trust and the National Institutes of Health in the United States, which also mandate public access to research that they fund. To read more about the potential impact to the OA movement, visit BioMed Central.
*05/07/06: Nature has recently published an article describing the financial situation of the Public Library of Science (PLoS), a leading open access publisher. Though PLoS Biology has received an impact factor that is quite encouraging for a new journal, PLoS continues to struggle financially. Nature has reported that the publisher's revenue, from advertising and author publication fees, covers only 35% of total operating costs. Further, PLoS has experienced a significant loss in assets since its establishment founded on large philanthropic gifts. PLoS has remained optimistic about the situation, however, pointing out that the majority of their journals have only recently been launched. The publisher is optimistic that once these new revenue sources are established and a pending rise to author publication fees takes effect, they will begin to break even financially. Nature's article adds an interesting element to the debate regarding the feasibility of running an open access publishing company. Read the article directly from Nature or read a detailed summary on Nature correspondant Declan Butler's personal blog. June 2006 *01/06/06: The campaign for open access to clinical trial data attracted the support of drug company GlaxoSmithKline, which announced in a press release that it would deposit summaries of more than 2,600 clinical trials conducted in 50 countries to study 52 GSK prescription medicines and vaccines in its open access Clinical Trial Register. The company called on academic institutions and government sponsors to make similar moves towards making information on clinical trials freely available and a Lancet editorial pointed out that it was crucial for journals to change their policies regarding publishing data that has been deposited online in order to encourage authors to share such data. This follows on from calls by the International Committee of Medical Journal Editors and the WHO to make clincial trial data freely available and the launch of two new open access journals devoted to the issue: BioMed Central's Trials and PLoS's Clinical Trials. *01/06/06: This week Nature's Declan Butler posted a call for open access to data on the avian flu pandemic on his blog. He points out that national governments are failing to share information on virus samples and data swiftly enough and that international health organisations such as the WHO are hampered by diplomatic and bureaucratic constraints. He called for an initiative similar to that of the Human Genome Project in which all data would be deposited in GenBank rather than locked into private networks such as the closed databases of the WHO. Following up on his blog Open Access News, Peter Suber suggested the application of a similar agreement to the Bermuda Agreement to the issue. The question of sharing data on avian flu has previously been discussed in the April edition of the SPARC newsletter and Nature's editorial 'Dreams of Flu Data'. May 2006 *25/05/06: Some more interesting resources discussing open access emerged this week. Richard Poynder's interview with the BioMed Central founder Vitek Tracz provides a history of the development of the open access movement as well as of BioMed Central itself, including his involvement in the development of NIH's PubMed Central. A summary of current developments in open access in the US and, to a lesser extent, the UK and Canada, was given by Deanna B. Marcum. Her keynote address at the 148th Membership Meeting of the ARL (Ottawa, May 17-19, 2006) was entitled International Dimensions of Digital Science and Scholarship and looks specifically at the challenges for libraries in a world
'where everyone is a publisher'. Two further papers focus on specific projects: Dean Krafft's webcast, part of the Educause webinar series, discusses the development of the National Science Digital Library (NSDL), an open access digital library of science, technology, engineering, and mathematics resources built up since 2000. Finally, a paper by Simon Coles and coworkers entitled An E-Science Environment for Service Crystallography-from Submission to Dissemination discussess the new small molecule crystallography service from sample receipt to results dissemination developed by the U.K. National Crystallography Service (NCS). *17/05/06: An interesting chapter of Neil Jacob's forthcoming book Open Access
Key strategic, technical and economic aspects by Clifford Lynch entitled Open Computation: Beyond Human-Reader-Centric Views of Scholarly Literatures discusses proposals for making the text of scholarly journals readable by machines while remaining protected by authentication barriers to human access. An example of this is the OTMI recently proposed by Nature. Other solutions were proposed at the Integration of Services - Integration of Standards Conference covered in this month's Dlib Magazine. *The Mellon foundation has issued a call for nominations for two awards valued $25,000 and $100,000 for not-for-profit organisations that have been involved in developing open source technology. The awards are intended to 'recognize not-for-profit organizations that have demonstrated exceptional leadership in the collaborative development of open-source software through the contribution of substantial, self-funded organizational resources to the open-source project for which they are nominated'. *17/05/06: Two pieces of work emerged this week that raise some important questions about the success of the open access movement in improving participation in scientific research in developing countries. An interview with Professor Subbiah Arunachalam by Richard Poydner looks at the question of open access in India. Pointing out that India is one of several developing countries whose per capita GNP is below $1,000 and yet who are denied free access to the HINARI and AGORA journals, Professor Arunachalam accuses major publishers of paying only lip service to the concept of free access for developing countries and of attempting to stiffle services like PubChem. The interview also discusses the issue of the 'digital divide' and initatives such as the $100 computer. Another report which raises some questions about the success of the open access movement comes from Alan Story, Colin Darch, and Debora Halbert (eds.), The Copy/South Dossier, The Copy South Research Group, May 2006. While the open access has the advantage of free content, the authors warn that author charges are likely to present a new barrier to authors in the South publishing their work, while small publishing houses in developing countries could also be harmed by the open access model. *Following the NIH's recent statement that all publications resulting from research it funds in should be freely and publicly available online by six months after publication, the US Senate is currently considering a bill, the Federal Research Public Access Act of 2006, that would require all federal agencies with a annual budget of more than $1 billion to do the same. The bill would represent a huge step forward, as the voluntary nature of previous commitments has allowed scope for compromise with unwilling publishers: a requirement covering all major research institutes would, however, make open access publishing a standard process and place less responsibility, and risk, on the shoulders of authors who wish to allow open access to their research. For discussion of the criticism of the bill coming from publishers see Ted Agres. Publishers, societies oppose 'public access' bill. The Scientist *A podcast of the Open Science session hosted by the Creative Commons' science team is available here. The Science Commons has also added new material to its Neurocommons and Material Transfer projects. April 2006 *A new survey by The Journal of the Royal Society of Medicine reported that low levels of awareness about open access persisted among the majority of scientists, with many considering that open access journals were of lower impact and lacked mechanisms for quality control. *An EC report focusing on the market for journal publishing in Europe was published this month. Highlighting the power wielded by publishers who control access to essential research, it emphasizes the potential for alternatives to existing scientific journals. Open access journals are suggested as valuable alternative means of disseminating research, as are searchable repositories and self-publishing initiatives. BioMed Central has welcomed the report and issued some comments. *The National Institutes of Health (NIH) this month reaffirmed its commitment to Open Access, reiterating its call for all NIH-funded research to be made available on PubMed within six months of publication. The advisory working group to NIH on the issue and journals including the New England Journal of Medicine called for the proposal to be strengthened by making the requirement to post work on PubMed mandatory (more). Publishers including Elsevier have entered into negociations with NIH since the original statement was released last May, however, the issue of which version of the paper will be published, as well as the question of the length of the embargo remain contentious (more). March 2006 *ChemSpy launched a new tool this month: ChemRef is a free Internet add-in allowing the user to search chemistry-related open access resources. The results are not very extensive so far, but are from reputable journals. *PubMed's latest refinements to its search will give a boost to the visibility of open access research: it is now possible to narrow down your search of the NIH database to include only those articles of which the full text is freely available online (for more details see New Publications). *A study published by Nature comparing the accuracy of articles published in the authoritative Encyclopaedia Britannia and the open access, editable Wikipedia has caused controversy. The study found a large number of scientific errors in both works: the number of factual errors, omissions or misleading statements was 162 and 123 in Wikipedia and Britannica, respectively. The article was picked up on in the news, the gap between the error rates of the two publications being downplayed in many cases. Encyclopaedia Britannia issued a statement accusing Nature of misrepresentation and poor evaluative standards and even of including articles not published by the encyclopaedia, concluding that Nature's findings were 'completely without merit'. Nature issued a response explaining their methodology in detail, pointing out that the encyclopaedia had refused an earlier offer to address the study findings, and refusing to retract their article. February 2006 *The Science Creative Commons announced this month that the World's largest database of proteins, Uniprot.org, is now licensed under a creative commons attribute license, meaning that any part of the database can be copied and reused as long as the source is acknowledged (more information). *A recently-published study by the Deutsche Forscchungsgemeinschaft (DFG) on open access in Germany has revealed strong support among the scientific community for the movement (read the report). *Nobel Laureate Richard Roberts, the editor of the open access journal Nucleic Acids gives his view on the Royal Society's open access policy in an interview with Richard Poynder.
The Royal Society issued what was widely viewed as an negative counter to the Research Council UK's statement on Open Access issued last autumn. The statement claimed that OA could 'disastrous for the research community', and warned against introducing 'policies that force researchers to adopt new models that are untried and untested' without fully investigating 'the likely costs and benefits to all'. *SPARC has launched a new survey of open access institutions' seminars, conferences and other educational events and programs. Browse or submit your events to the portal at https://db.arl.org/oap/ *The Research Councils UK (RCUK), an umbrella bodies representing the eight UK Research Councils, has published its draft policy on access to research outputs. The policy would promote open access by
making it a condition of grant that researchers deposit copies of their
journal articles and conference proceedings (subject to copyright
restrictions) in suitable open repositories at the earliest
opportunity. The Research Councils will also make funds available to
pay for open access publication charges. *Professor Steven Harnard, one of the most outspoken critics of current methods of scientific publishing and a strong advocate of Open Access, has published new claims that restricting publicly-funded research to journals that only a few libraries can afford to subscribe to is holding back the dissemination of research. Backing the recent statement by the Research Councils UK, that the results of publicly-funded research should be made available on the institution website (see news), he calculates that if all published work was self-archived, the research impact would be the equivalent of a further yearly investment of £1.5 bn in UK science. Harnad, S. (2005) Maximising the Return on UK's Public Investment in Research. University of Southhampton. URL: http://eprints.ecs.soton.ac.uk/11220/ (accessed 3/10/05). (top) *BioMed Central has issued an open letter to the UK Science Minister, Lord Sainsbury, in response to his testimony, given to the House of Commons’ Science and Technology Committee on 19 October. The letter is in response to the suggestion made during the testimony that, although there should be a ‘level playing field’ between the different models of publishing, Open Access was in decline due to the financial implications involved. The open access publishers countered this suggestion by pointing out that their own subscriptions had grown ahead of the sector during 2005 and that many traditional publishers, including Blackwell Publishing, Springer and Oxford University Press were now experimenting with their own open access archives. The level of knowledge about open access among authors has also continued to grow during 2005, with 29% having published in an open access journal. The implication that the cost of open access publishing is higher than that of traditional models was also countered by pointing to research by the Wellcome Council that open access is less costly to the scientific community. BioMed Central called on the government to take forward the proposal of the Research Councils UK requiring authors to archive their work in an open access format and not to submit to pressure from traditional publishers to water down the statement. (top) (top)
*With effect from Monday 12 September 2005 the International Standard Randomized Controlled Trials Number (ISRCTN) Register and numbering protocol, together with the current registrations and records, has been transferred to a not-for-profit organisation. This change in ownership of the ISRCTN scheme means that the ISRCTN Register now complies with the requirements set out by the International Committee of Medical Journal Editors.
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