Open Access: Taking Full Advantage of the Content

This Journal and the Public Library of Science (PLoS) at large are standard bearers of the full potential offered through open access publication, but what of you, the reader? For most of you, open access may imply free access to read the journals, but nothing more. There is a far greater potential, but, up to now, little to point to that highlights its tangible benefits. 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 (http://www.pubmedcentral.nih.gov/). 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). 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. In these two examples, it means free to read, but with variation in what is implied by copyright. For PNAS, authors have full rights for print use and readers can freely use figures and tables (with attribution); and for Bioinformatics, a Creative Commons license applies, but only for non-commercial use. This issue was recently addressed in more detail in a PLoS Biology Editorial [1]. 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. When publishers make XML versions available, most conform to the National Library of Medicine (NLM) Document Type Definition (DTD) (http://dtd.nlm.nih.gov). In addition, several markup languages have been developed, such as CellML (http://www.cellml. org) and MathML (http://www.w3.org/ Math), which can be used in addition to the NLM DTD to further describe the semantic content of a paper. Semantically aware markup is further elaborated in a systematic fashion in the construction of the semantic Web [2], where the XML tags are related to each other in explicit ontologies. The analogy between an XML file of content offered by a publisher and XML content provided by a database provider should not be missed. As a community, we have been at the forefront of using the latter; will we be at the forefront of using the former? While the DTD and markup languages provide for extensions to meet the needs of each discipline, publishers and researchers have made little use of them to date. 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. Simply put, a mashup is an integration of Web content from multiple sources to provide a new and more powerful service beyond what can be achieved by any of the individual sources of information it comprises. This type of integration is facilitated if the semantic content from each information source can be identified and thus allow meaningful integration to take place. Specifically in relation to publishing, the mashup manifests the blurring of the distinction between databases and journals, which will continue in future [3,4]. We already have a significant corpus from a variety of publishers sitting in PubMed Central that is ripe for mashup and other uses. Certainly, the growth rate of the archive hoped for by the NIH has not been met at this time [5], but new laws in the US and elsewhere are changing this situation. Something significant can be done with what we have—so where are the killer apps? 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. Firstly, BioLit (http:// biolit.ucsd.edu) attempts to bridge the database and journal worlds [6]. Databases are rich in semantics, which are most often manifest in the form of a database schema with associated referential integrity to strictly impose access to those semantics. On the other hand, journal text, as we have