Thursday, May 06, 2010

Linnaeus meets the Internet: PLoS + Botany = #fail

C2914D0E-13E9-4CA6-BE0A-7A8645BC6A72.jpgTo much fanfare (e.g., Nature News, "Linnaeus meets the Internet" doi:10.1038/news.2010.221), on May 5th PLoS ONE published Sandy Knapp's "Four New Vining Species of Solanum (Dulcamaroid Clade) from Montane Habitats in Tropical America" doi:10.1371/journal.pone.0010502. To quote the Nature News piece:
The paper represents the culmination of a campaign to institute the electronic publication of scientific names, a case Knapp and others have made in journals including Nature[doi:10.1038/446261a]. Allowing electronic publication should make accessing information easier for scientists worldwide — especially those in developing countries who may not have access to fully stocked libraries. This, in turn, will aid conservation efforts, Knapp says.

Given the profile of this paper, "...the first time new plant names have been published in a purely electronic journal and still complied with ICBN rules", you'd think the participants would ensure the electronic aspects of the publication worked. Sadly, this is not the case.

The four names in question have apparently been deposited in IPNI with the following LSID's:

  • Solanum aspersum:

  • Solanum luculentum:

  • Solanum sanchez-vegae:

  • Solanum sousae:

Today is May 6th. None of these names are returned by a search of IPNI, for example returns this:


Resolving the LSID returns this:

<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF xmlns:xsi=""
<tn:TaxonName rdf:about="">
<tcom:versionedAs rdf:resource=""/>

Hmmm, so apparently this record has been "deleted"?

The paper also states that:
The IPNI LSIDs (Life Science Identifiers) can be resolved and the associated information viewed through any standard web browser by appending the LSID contained in this publication to the prefix

This sentence mirrors similar ones in other PLoS ONE papers saying we can resolve ZooBank LSIDs by appending the LSID to (e.g., see doi:10.1371/journal.pone.0001787).

Thing is, URLs such as return a 404 from Kew (any IPNI LSID I've tried does this).

Update As per Alan Paton's comment below, the prefix now works.

So, to recap:

  1. The names aren't in IPNI

  2. The LSIDs state the record has been deleted

  3. The LSID's can't be resolved by the means stated in the paper

Now, I don't know what happened (perhaps IPNI wanted to hold off until the paper actually appeared before releasing the names), but the paper is out, the buzz in Nature is out, and IPNI doesn't have the resolver in place, yet alone the names.

Given the milestone this paper represents, and the fuss over the publication of the name Darwinius, you'd expect the bioinformatics side of it to be, you know, actually working. In these circumstances, how on Earth do we make the case that the LSID and name databasing side of taxonomic publication is useful?