Open Access News

News from the open access movement

Tuesday, April 01, 2008

Freeing users to take full advantage of research

Philip E. Bourne, J. Lynn Fink, and Mark Gerstein, Open Access: Taking Full Advantage of the Content, PLoS Computational Biology, March 28, 2008.  An editorial.  Excerpt:

...We would argue that, as yet, the full promise of open access has not been realized. There are few persistent applications that collectively use the full on-line corpus, which for the biosciences at least is maintained in PubMed Central. In short, there are no “killer apps.” Since this readership, beyond any other, would seem to have the ability to change this situation at least in the biosciences, we are issuing a call to action.

While, first and foremost, open access implies downloading and reading full papers for free, additional possibilities exist depending on how the open access material is licensed. PLoS and BioMedCentral (BMC), for example, publish under a Creative Commons Attribution License (CCAL).  [PS:  Also known as a CC-BY license.]  Under this license authors retain ownership of the copyright for their article, but they allow anyone (commercial or non-commercial) to download, reuse, reprint, modify, distribute, and/or copy articles, as long as the original authors and source are cited. No permission is required from the authors or the publishers. Note that, while this is what PLoS and BMC mean by open access, it is not what other publishers mean, such as the National Academy of Sciences (NAS) in publishing the Proceedings of the National Academy of Sciences (PNAS) or Oxford University Press (OUP) in publishing the journal Bioinformatics....This issue was recently addressed in more detail in a PLoS Biology Editorial. The key point is that these licenses allow us to go far beyond reading material to manipulating it much like data.

Beyond what the licensing laws say about how we might use open access materials, there is then the format in which these materials are available. Papers published as PDFs do not lend themselves to easy manipulation by computer. HTML is better, but the markup has more to do with presentation on a Web page than the semantic content of the paper, which is where the great opportunities lie. XML versions of the paper offer the most promise....

This is somewhat of a chicken-and-egg situation. When significant markup is available, it will be used; then again, why go to the trouble of adding significant markup if there are no applications demanding it? The best way out would seem to be to do something significant with the markup we have, which may then inspire authors, publishers, and others to see the research and commercial potential of the corpus.

The use of such markup is a hallmark of Web 2.0 and is manifest in the idea of a mashup....

Consider the following applications from our own laboratories. They may not be killer applications, but they begin to illustrate what can be done with this online corpus. The key idea is manipulation of article text as “data” and integration of articles with other bioinformatics information resources....

Certainly open access journals, such as the PLoS journals, have an opportunity to try and develop those killer apps. PLoS is using the TOPAZ application framework for a publication application built on a semantic repository....

These are a few ideas that we have come up with for making use of the wealth of knowledge contained in open access articles. We feel that it is now time for the community represented by this readership to act. What say you? It is important we hear from you on the subject of better use of open access content. At the forthcoming Intelligent Systems in Molecular Biology Conference there will be a session on Scientific Publishing where these views will be discussed, and we also encourage feedback via e-mail, blog, or article comment.

Comment.  Exactly.  We will not unleash the full power and utility of OA research until we go beyond the removal of price barriers to the removal of permission barriers.  The greatest promise of OA is to free up creative people to make creative uses of research.  It was precisely to support these creative uses that the BOAI called for more than the freedom to read research articles without charge, but also permission to "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."

Update. Also see Chris Leonard's comments at the PhysMath Central blog.