Quick notes to self following on from a conversation about linking taxonomic names to the literature. There are different sorts of citation: Paper cites another paper Paper cites a dataset Dataset cites a paper Citation type (1) is largely a solved problem (although there are issues of the ownership and use of this data, see e.g. Zootaxa has no impact factor.

A challenge in working with large taxonomic classifications is how you display them to the user, especially if the user probably doesn't want all the gory details.

The following is a guest post by Bob Mesibov. Nico Franz and Beckett Sterner created a stir last year with a preprint in bioRxiv about expert validation (or the lack of it) in the "backbone" classifications used by aggregators.

I have a love/hate relationship with the Catalogue of Life (CoL). On the one hand, it's an impressive achievement to have persuaded taxonomists to share names, and to bring those names together in one place. I suspect that Frank Bisby would feel that the social infrastructure he created is his lasting legacy.

In browsing the GBIF classification in BioNames I keep coming across cases of wholesale duplication of taxa.

I know I'm starting to sound like a broken record, but the more I look, the more taxonomic databases seem to be full of garbage. Databases such as the Catalogue of life, which states that it is a "quality-assured checklist" have records that are patently wrong.

One visualisation method I keep coming back too is the treemap.

Two papers estimating the total number of species have recently been published, one in the open access journal PLoS Biology :the second in Systematic Biology (which has an open access option but the authors didn't use it for this article): The first paper has gained a lot of attention, in part because Jonathan Eisen Bacteria &

David ("Paddy") Patterson, Jerry Cooper, Paul Kirk, Rich Pyle, and David Remsen have published an article in TREE entitled "Names are key to the big new biology" (doi:10.1016/j.tree.2010.09.004). The abstract states: Do we need names? Reading this (full disclosure, I was a reviewer) I can't wondering whether the assumption that names are key really needs to be challenged.

Time (just) for a Friday folly. A couple of days ago the latest edition of the Catalogue of Life (CoL) arrived in my mailbox in the form of a DVD and booklet:While in some ways it's wonderful that the Catalogue of Life provides a complete data dump of its contents, this strikes me as a rather old-fashioned way to distribute it. So I began to wonder how this could be done differently, and started to think of CouchDB.