InChI on Crossref

XMP in RSC PDFs

Crossref — Tue, 03 Aug 2010 00:00:00 +0000

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. Alternatively you can extract the InChIKeys with a regular expression.
Ontology terms: we’re using HTTP URIs again and pointing to either Open Biomedical Ontology URIs (biology, biomedicine; slashy) or RSC ontology terms (chemistry; hashy). Often the OBO URIs resolve to a specific web page, but for the moment the RSC URIs just point to a large OWL file. Slashy URIs are quite a bit more involved so we’ll have to see what the demand is like.

There’s only about 4K to play with, so it’s only ever going to be a best-of. More detailed article metadata has to go in either a sidecar file, as Tony has pointed out before, or ideally on the article landing page. The example files are here and I’ve posted something with a different slant on the RSC technical blog.

Crossref Labs

Geoffrey Bilder — Tue, 13 Oct 2009 00:00:00 +0000

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. To that end, we have created a Crossref Labs site. Here you can find links to various tools and services that either make it easier to use Crossref services (e.g. Blog/Ubiquity plugins and OpenSearch Description files) or that serve to illustrate a concept that has been of interest to our members (InChI lookup, TOI-DOIs). Oh, yeah- and when we update these experiments, you should be able to find the updates on their respective pages. Sorry about that Noel… Finally, I will quote from the Crossref Labs home page:

“Most of the experiments linked to here are running on R&D equipment in a non-production environment. They may disappear without warning and/or perform erratically. If one of them isn’t working for some reason, come back later and try again.” Have fun.

Standard InChI Defined

Tony Hammond — Sat, 17 Jan 2009 00:00:00 +0000

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 1.02beta)”.

On a practical level this means that the 27-character length InChIKeys (a hashed form of the InChI), with the following generic form

AAAAAAAAAAAAAA-BBBBBBBBFV-P

can now be readily and reliably generated and will start to be used in search indexing and linking applications.

InChIKey

Tony Hammond — Tue, 02 Oct 2007 00:00:00 +0000

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. Compare a regular InChI identifier:

InChI=1/C49H70N14O11/c1-26(2)39(61-42(67)33(12-8-18-55 -49(52)53)57-41(66)32(50)23-38(51)65)45(70)58-34(20-29-1 4-16-31(64)17-15-29)43(68)62-40(27(3)4)46(71)59-35(22-30 -24-54-25-56-30)47(72)63-19-9-13-37(63)44(69)60-36(48(7 3)74)21-28-10-6-5-7-11-28/h5-7,10-11,14-17,24-27,32-3 7,39-40,64H,8-9,12-13,18-23,50H2,1-4H3,(H2,51,65)(H,54,56 )(H,57,66)(H,58,70)(H,59,71)(H,60,69)(H,61,67)(H,62,68)(H,73,74) (H4,52,53,55)/f/h56-62,73H,51-53H2

with its InChIKey counterpart:

InChIKey=JYPVVOOBQVVUQV-UHFFFAOYAR

That’s some saving.

RSC’s Project Prospect v1.1

rkidd — Thu, 31 May 2007 00:00:00 +0000

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…

So the RDF code for the OBO terms and InChIs looks like this:

<tt><br /> <rdf:li><br /> <content:item rdf:about="info:inchi/InChI=1/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,15H,7,10,14H2,1-5H3/b9-6-,12-11+,16-8+,17-13+"/><br /> </rdf:li><br /> <rdf:li><content:item rdf:about="http://purl.org/obo/owl/CL#CL:0000210"/><br /> </rdf:li><br /> </tt>

We now have over five hundred 2007 articles enhanced, so we’ve brought the majority back into controlled access. There are always examples from each journal freely available.

At Last! URIs for InChI

Tony Hammond — Mon, 19 Feb 2007 00:00:00 +0000

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

info:inchi/InChI=1/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H

The info URI scheme exists to support legacy namespaces get a leg up onto the Web. Registered namespaces include PubMed identifiers, DOIs, handles, ADS bibcodes, etc. Increasingly we’ll be expecting to see identifiers (both new and old) represented in a common form - URI.

RSC launches semantic enrichment of journal articles

rkidd — Thu, 01 Feb 2007 00:00:00 +0000

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. All this stuff is currently available from an enhanced HTML view, with the additional information and links to related articles accessed via highlights in the article and popups.

The mark-up tools have been developed together with UK academics based at the Unilever Centre of Molecular Informatics and the Computing Laboratory at Cambridge University.

At launch we have about 100 articles from our 2007 publications, with the enhanced views currently free-to-air. Feel free to take a look.