Consumer access to clinical drug trial data

Shari Roan, Did the study work? Consumers can find out, Los Angeles Times, September 26, 2008.  (Thanks to ResourceShelf.)  Excerpt:

Many of the most promising new medical treatments are just beyond the grasp of consumers simply because they don’t know about them. But that’s about to change. Beginning tomorrow, the nation’s database for clinical trials,, will begin adding the results of trials of drugs, medical devices and biologic products (such as vaccines) conducted in the United States. was launched in 2000 to provide people with easy access to information about clinical trials. But until now, consumers who went to the website could find only details about the trial’s launch, such as the study’s design and who is eligible to enroll. Under the new rule, researchers sponsoring the trial must go back and post their results (except for very early-stage experiments, which are called Phase 1 trials) online within one year of the study’s conclusion or within 30 days of approval of a product by the Food and Drug Administration. The database will carry results of trials that were underway as of Sept. 27, 2007. However, researchers of previously completed trials have been encouraged to post their results, too.

The rule is a result of a law passed last year to demand more transparency in clinical trials. Consumer health advocates hope the requirement will make it harder for study sponsors to hide unexpected or harmful reactions to drugs or devices….


  • ClinicalTrials.COM is new, but ClinicalTrials.GOV is not.  When Roan said that the .com version was launched in 2000, she must have meant the .gov version.  Despite the plan to launch the .com version on September 27, it’s still not open.
  • For more background on the new federal law requiring OA for clinical drug trial data, see our past posts on the FDA Amendments Act (FDAAA).

Update (9/29/08).  Also see this September 26 announcement from the NLM, which describes an expansion of but doesn’t mention  The expansion will provide OA to results, or trial data themselves, not just to information about the trials.

Are Elsevier prices going down yet?

According to correspondence from an Elsevier correspondent to Rosie Redfield, Elsevier is charging authors a rather substantial amount ($3,000 per article), because they do not plan to charge subscribers for author-sponsored content.


Has any librarian heard the other side – subscription fees going down because of author-sponsored content?

Authors: if you’re going to pay for open access, make sure you are getting open access! There is a lot more to OA than just free access from one website. Here is the definition of OA, from the Budapest Open Access Initiative:

By “open access” to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.

“Hassles” from Elsevier on sponsored OA

Rosie Redfield has posted (1, 2, 3) about her experiences providing OA to her article accepted for publication in an Elsevier journal.

  • First she notes that Elsevier’s publication agreement requires her to hand over her copyright to the journal, permitting her to self-archive the final manuscript but not the journal-quality PDF.
  • Then she notes that for $3,000, her article can be available OA from the journal’s Web site, but this still requires a transfer of copyright and does not permit the use of Creative Commons licenses.
  • Finally, she shares her correspondence with an Elsevier customer service representative, going back and forth on how she can pay the $3,000 fee, since her funding agency (the Canadian Institutes of Health Research) doesn’t have a specific agreement with Elsevier on paying hybrid OA fees.

Updates to Open Shakespeare

Jonathan Gray, What can you do with Open Shakespeare?, Open Knowledge Foundation Weblog, September 26, 2008.

We’ve recently updated Open Shakespeare. The project was started a while back as an open knowledge ‘exemplar project’ – i.e. as a simple ‘hello world’ type open knowledge package (for more on this see the FAQ).

It aims to:

  1. Provide the complete works of Shakespeare, along with textual apparatus (introduction, notes) and tools (concordance, search etc) all in an open form.
  2. Deliver this material as a knowledge package that allows for easy deployment, redistribution and reuse.

Recent changes include:

Blog notes on OA in chemistry

Jan Kuras, Chemistry Central host OA session at EuCheMS Congress, Chemistry Central Blog, September 26, 2008.

Chemistry Central hosted an engaging open session – An Introduction to Open Access Publishing in Chemistry – at the recent EuCheMS Chemistry Congress in Torino, Italy [(September 16-20, 2008)].

Jan Kuras, Associate Publisher at Chemistry Central, provided an overview of the strategy and business model of OA publishing and positioned it within the publishing landscape, highlighting the beneficiaries throughout the research community.

Dr Livia Simon Sarkadi, from the Budapest University of Technology and Economics, then examined the benefits (as well as some disadvantages) of OA publishing to the chemistry community and shared some initiatives that could be implemented to progress OA in chemistry. These included: soliciting articles from leading chemists in areas of high topicality to raise the profile of an OA journal; engaging with young chemists for whom OA publications will be part of their careers; and seeking support for OA publishing from national societies and divisions. …

Open Access Service Charges: Hydrology and Earth Systems Science

The open access journal Hydrology and Earth Systems Science uses an approach they call service charges which may be of interest to publishers looking for ways to transition to open access.

Service charges vary by the number of pages (not unlike the traditional page charges), but also by the format the author uses to submit articles. In other words, an author can keep the fee down by submitting in Latex rather than Word, and/or by submitting according to the technical specifications for either Latex or Word. A 10-page article submitted in Latex according to the technical specification is €450 + 19% VAT, $657 US before taxes, $800 US total with taxes. Not bad!

Authors can choose to pay for copyediting, or take responsibility for this themselves.

The service charges approach seems to have some merits. At the very least, it is helpful, in my opinion, to think about publishing as a service.

This post belongs to the series Resources & Tips for Publishers.

More on OA to U.S. presidential debate videos

Lawrence Lessig, Free Debates: Round Two, Lessig Blog, September 25, 2008.

As reported on the LA Times blog, during the primaries, a bunch of us (both Democrats and Republicans) called on the parties to demand that the networks adopt “open” or “free debate” principles, to assure that the debates would be available to everyone to use or reuse as they choose.

We’re back. In the extended entry below is another letter, signed by another bipartisan mix, calling on McCain and Obama to commit to “open debate principles.” You can get a PDF of the letter here. …

Specifically, we ask you to embrace these two “open debate” principles for the 2008 debates:

  1. The presidential debates are for the benefit of the public. Therefore, the right to speak about the debates ought to be “owned” by the public, not controlled by the media.

    During the primaries, a large
    coalition asked
    that media companies release rights to presidential debate
    video to ensure that key moments can be legally blogged about, shared on YouTube, or otherwise shared without fear of legal repercussion.

    CNN, ABC, and NBC agreed to release video rights. But one media company threatened legal action against Senator McCain for using a debate clip to spread a message. Such control over political speech is inconsistent with our democracy.

    We therefore call upon both candidates to commit to a principle that whenever you debate publicly, the raw footage of that debate will be dedicated to the public domain. Those in charge of the video feed should be directed to make it free for anyone to use. …

See also our post on the earlier call for OA to the primary debates.

French journal drops its embargo on the OA edition

André Gunthert, Etudes photographiques revient en ligne avec ses images, Études photographiques, September 17, 2008Read it in French or Google’s English.  (Thanks to Peter Hirtle.)

An editorial announcing the relaunch of the journal’s online edition, which will now appear simultaneously with the print edition.  Gunthert concludes that embargoes (or moving walls) harm readers and that online and print editions serve different users in different ways. 

OAD list of videos about OA

The Open Access Directory (OAD) just opened a list of Videos about OA for community editing and enlargement.

Like the list of Educational materials about OA launched last week, this one is timed to support Open Access Day (October 14, 2008) and capture the many new resources now under development for it.

The first version of the list is short, just enough to justify a launch.  If you know of videos about OA (not just videos which happen to be OA), please take a moment to add them.  OAD contributors must register, but registration is free and easy.

Integrating seven OA databases of carbohydrate sequences

R. Ranzinger and three co-authors, GlycomeDB – integration of openaccess carbohydrate structure databases, BMC Bioinformatics, September 19, 2008.  From the abstract:

Background: Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases.

Results: We have implemented procedures which download the structures contained in the seven major databases, e.g., the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100,000 datasets were imported, resulting in more than 33,000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators.

Conclusions: GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource.

Comment.  GlycomeDB illustrates a scenario that should become more and more common:  first make resources OA, and then make related resources consistent and interoperable.  OA resources are not only useful because users (human and machine) can access their contents, but because third parties can build on them to offer users (human and machine) the benefits of their combined strengths and synergies.

Obstacles to OA in Sweden

Mathias Klang, Open access barriers: An action research, in Chrisanthi Avgerou, Matthew L. Smith, and Peter Van den Besselaar (eds.), Social Dimensions Of Information And Communication Technology Policy: Proceedings of the Eighth International Conference on Human Choice and Computers (HCC8), Pretoria, South Africa, September 25-26, 2008, Springer, 2008.  Only this abstract is free online, at least so far

ICT has provided the infrastructure to enable easy access to scientific information. Despite this, libraries are suffering from the rising of journal subscriptions. Additionally, the structure of scholarly publications is creating a wasteful situation where publicly funded research is being paid for several times over. University libraries are struggling to deal with these new realities at the same time as they provide a level of service with acceptable access to publications. The work of librarians is being heavily affected by the influence of copyright and licensing which together are creating barriers to open access. The work in this chapter draws from an action research in progress undertaken by Lund’s University in order to explore the barriers to open access to scientific research output in Sweden.

Open data from Scalablast

Darren Curtis, Elena Peterson and Christopher Oehmen, A Secure Web Application Providing Public Access To High-Performance Data Intensive Scientific Resources – Scalablast Web Application, a presentation at WEBIST 2008 (Madeira, Portugal, May 4-7, 2008).  Scroll about 1/8 down the file.  I’ve only been able to find this abstract:

This work presents the ScalaBLAST Web Application (SWA), a web based application implemented using the PHP script language, MySQL DBMS, and Apache web server under a GNU/Linux platform. SWA is an application built as part of the Data Intensive Computer for Complex Biological Systems (DICCBS) project at the Pacific Northwest National Laboratory (PNNL). SWA delivers accelerated throughput of bioinformatics analysis via high-performance computing through a convenient, easy-to-use web interface. This approach greatly enhances emerging fields of study in biology such as ontology-based homology, and multiple whole genome comparisons which, in the absence of a tool like SWA, require a heroic effort to overcome the computational bottleneck associated with genome analysis. The current version of SWA includes a user account management system, a web based user interface, and a backend process that generates the files necessary for the Internet scientific community to submit a ScalaBLAST parallel processing job on a dedicated cluster.