O'Really?

There is an interesting review [1] (and special issue) in the Biochemical Journal today, published by Portland Press Ltd. It provides (quote) “a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment”. Here is a quick outline of the publishing projects the review describes and discusses:

• Blogs for biomedical science
• Biomedical Ontologies – OBO etc
• Project Prospect and the Royal Society of Chemistry
• The Chemspider Journal of Chemistry
• The FEBS Letters experiment
• PubMedCentral and BioLit [2]
• Public Library of Science (PLoS) Neglected Tropical Diseases (NTD) [3]
• The Elsevier Grand Challenge [4]
• Liquid Publications
• The PDF debate: Is PDF a hamburger? Or can we build more useful applications on top of it?
• The Semantic Biochemical Journal project with Utopia Documents [5]

The review asks what advances these projects have made  and what obstacles to progress still exist. It’s an entertaining tour, dotted with enlightening observations on what is broken in scientific publishing and some of the solutions involving various kinds of semantics.

One conclusion made is that many of the experiments described above are expensive and difficult, but that the costs of not improving scientific publishing with various kinds of semantic markup is high, or as the authors put it:

“If the cost of semantic publishing seems high, then we also need to ask, what is the price of not doing it? From the results of the experiments we have seen to date, there is clearly a need to move forward and still a great deal of scope to innovate. If we fail to move forward in a collaborative way, if we fail to engage the key players, the price will be high. We will continue to bury scientific knowledge, as we routinely do now, in static, unconnected journal articles; to sequester fragments of that knowledge in disparate databases that are largely inaccessible from journal pages; to further waste countless hours of scientists’ time either repeating experiments they didn’t know had been performed before, or worse, trying to verify facts they didn’t know had been shown to be false. In short, we will continue to fail to get the most from our literature, we will continue to fail to know what we know, and will continue to do science a considerable disservice.”

It’s well worth reading the review, and downloading the Utopia software to experience all of the interactive features demonstrated in this special issue, especially the animated molecular viewers and sequence alignments.

Enjoy… the Utopia team would be interested to know what people think, see commentary on friendfeed,  the digital curation blog and youtube video below for more information.

References

1. Attwood, T., Kell, D., McDermott, P., Marsh, J., Pettifer, S., & Thorne, D. (2009). Calling International Rescue: knowledge lost in literature and data landslide! Biochemical Journal, 424 (3), 317-333 DOI: 10.1042/BJ20091474
2. Fink, J., Kushch, S., Williams, P., & Bourne, P. (2008). BioLit: integrating biological literature with databases Nucleic Acids Research, 36 (Web Server) DOI: 10.1093/nar/gkn317
3. Shotton, D., Portwin, K., Klyne, G., & Miles, A. (2009). Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article PLoS Computational Biology, 5 (4) DOI: 10.1371/journal.pcbi.1000361
4. Pafilis, E., O’Donoghue, S., Jensen, L., Horn, H., Kuhn, M., Brown, N., & Schneider, R. (2009). Reflect: augmented browsing for the life scientist Nature Biotechnology, 27 (6), 508-510 DOI: 10.1038/nbt0609-508
5. Pettifer, S., Thorne, D., McDermott, P., Marsh, J., Villéger, A., Kell, D., & Attwood, T. (2009). Visualising biological data: a semantic approach to tool and database integration BMC Bioinformatics, 10 (Suppl 6) DOI: 10.1186/1471-2105-10-S6-S19