Readers of this blog will know that I'm sceptical about the current value of linked data and RDF in biodiversity informatics. But I came across an interesting paper on RDF and biocuration that suggests a good "use case" for RDF in constructing and curating taxonomic databases.The paper is "Catching inconsistencies with the semantic web: a biocuration case study" (PDF here) by Jerven Bolleman and Sebastien Gehant.

Update : Mark wrote up a blog post on the RDF that the ChEMBL team itself. Yesterday, the paper “The ChEMBL database as linked open data” (doi:10.1186/1758-2946-5-23) by Andra Waagmeester (@andrawaag), Ola Spjuth (@ola_spjuth), Peter Ansell (@p_ansell), Antony Williams (@chemconnector), Valery Tkachenko, Janna Hastings, Bin Chen (@binchenindiana), David J Wild (@davidjohnwild), and me appeared in the OA JChemInf journal.

Update: this work is now described in this paper.

Readers of my blog know I have been using the Citation Typing Ontology, CiTO (doi:10.1186/2041-1480-1-S1-S6). I allows me to see how the CDK is cited and used. CiteULike is currently adding more CiTO more functionality, which they started doing almost one and a half years ago.

Quick final comment on the TDWG Challenge - what is RDF good for?. As I noted in the previous post, Olivier Rovellotti (@orovellotti) and Javier de la Torre (@jatorre) have produced some nice visualisations of the frog data set:Nice as these are, I can't help feeling that they actually help make my point about the current state of RDF in biodiversity informatics.

OK, a bit of hyperbole in the morning. One of the goals of RDF is to create the Semantic Web, an interwoven network of data seamlessly linked by shared identifiers and shared vocabularies. Everyone uses the same identifiers for the same things, and when they describe these things they use the same terms. Simples.Of course, the reality is somewhat different.

Update 2021-02 : this post is still the second-most read post in my blog. Welcome! Some updates: Ammar Ammar in our BiGCaT group has set up a new SPARQL endpoint. Please use and tweet. blog, or otherwise let others now how you use the ChEMBL RDF. Since this post I have blogged a lot more about ChEMBL. Update : this work is now written down in this paper.

I noted earlier this week that [d]uring the week [in Oxford ], someone (name and address is know at the editorial office) commented on the fact that my blog posts are somewhat difficult to follow;

Being in an unusually constructive mood, I've spent the last couple of days playing with the TreeBASE II API, in an effort to find out how hard it would be to replace TreeBASE's frankly ghastly interface.After some hair pulling and bad language I've got something to work. It's very crude, but gives a glimpse at what can be done.

One of the potentially powerful features of TreeBASE II is availability of a RDF version of a study. This means that, in principle, one could take the RDF for a TreeBASE study, combine it with RDF from other sources, and generate a richer view of a particular study.