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Just a quick heads-up to say that we’ve had a go at incorporating InChIs and ontology terms into our PDFs with XMP. There isn’t a lot of room in an XMP packet so we’ve had to be a bit particular about what we include. InChIs: the bigger the molecule the longer the InChI, so we’ve standardized on the fixed-length InChIKey. This doesn’t mean anything on its own, so we’ve gone the Semantic Web route of including an InChI resolver HTTP URI.

The other day Noel O’Boyle wrote to tell me that he had updated the Ubiquity plug-in that we had developed in order to to make it work with the latest version of Firefox. The problem was, I had *also* updated the Ubiquity plug-in, but I hadn’t really indicated to anybody how they could find updates to the plug-in. /me=embarrassed. So it seemed time to provide a home for some of the prototypes and experiments that we’ve been developing at Crossref.

IUPAC has just released the final version (1.02) of its InChI software, which generates Standard InChIs and Standard InChIKeys. (InChI is the IUPAC International Chemical Identifier.) The Standard InChI “removes options for properties such as tautomerism and stereoconfiguration”, so that a molecule will always generate the same stable identifier - a unique InChI - which facilitates “interoperability/compatibility between large databases/web searching and information exchange”. Note also that any “shortcomings in Standard InChI may be addressed using non-Standard InChI (currently obtainable using InChI version 1.

The InChI (International Chemical Identifier from IUPAC) has been blogged earlier here. RSC have especially taken this on board in their Project Prospect and now routinely syndicate InChI identifiers in their RSS feeds as blogged here. As reported variously last month (see here for one such review) IUPAC have now released a new (1.02beta) version of their software which allows hashed versions (fixed length 25-character) of the InChI, so-called InChIKey’s, to be generated which are much more search engine friendly.

We updated our Project Prospect articles today to release v1.1, with a pile of look & feel improvements to the HTML views and links. The most interesting technical addition is the launch of our enhanced RSS feeds, where we have updated our existing feeds for enhanced articles. These now include ontology terms and primary compounds both visually (as text terms and 2D images) and within the RDF - using the OBO in OWL representation and the info:inchi specification mentioned here by Tony only a few weeks ago.

The enhanced entries will soon become more common as we concentrate our enhancements on our Advance Articles, but the current example below from our Photochemical and Photobiological Sciences feed is lovely. RDF code after the jump - just as beautiful to the parents…

The info registry has now added in the InChI namespace (see registry entry here) which now means that chemical compounds identified by InChIs (IUPAC‘s International Chemical Identifiers) are expressible in URI form and thus amenable to many Web-based description technologies that use URI as the means to identify objects, e.g. XLink, RDF, etc. As an example, the InChI identifier for naphthalene is InChI=1/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H and can now be legitimately expressed in URI form as

The RSC has gone live today with the results of Project Prospect, introducing semantic enrichment of journal articles across all our titles. I’m pretty sure we’re the first primary research publisher to do anything of this scope. We’re identifying chemical compounds and providing synonyms, InChIs (IUPAC’s Chemical Identifier), downloadable CML (Chemical Markup Language), SMILES strings and 2D images for these compounds. In terms of subject area we’re marking up terms from the IUPAC Gold Book, and also Open Biomedical Ontology terms from the Gene, Cell, and Sequence Ontologies.