Chemistry with meaning

Online shopping and music downloads are full of meaning, apparently. But, they don’t mean meaning like some deep philosopical property, they mean semantics – the meta data that is hidden from shoppers and downloaders but that makes the whole consumer experience work on the web. Now, my old friends Henry Rzepa and Omer Casher, of Imperial College London, hope to adapt the semantics of other sectors of the internet to provide a richer browsing and downloading experience for chemists.

They suggest that publishers of electronic scientific journals – whether learned societies or commercial publishers – should latch on to the semantic web sooner, rather than later so that the information revolution that is underway in scientific publishing can be complete.

The Semantic Web will foster information exchange by putting documents with computer-processable meaning (semantics) on the Internet so that software agents can help in the dissemination of information. Chemistry is well stacked with latent information that is lost if meta data – such as spectra, physical properties, searchable chemical structures, is abandoned, as occurs when a research paper is published electronically as a two-dimensional PDF file, for instance.

Writing in the journal Chemical Information and Modeling, the researchers describe SemanticEye, a semantic web application that adapts the digital music model to chemical-related electronic journal articles. It allows journal articles to contain embedded document object identifiers (DOIs) and other material. Those clues enable software to find relationships between new articles and those already published, and collect all the relevant documents for the user’s benefit.

Ironically, their paper is available as one of those simple PDF things, but at least the html version has CrossRef links.