Monday, March 31, 2008

Parataxonomy vs. taxonomy

I just read Krell's (2004) interesting article about Parataxonomy, a organism sorting method based on the identification of so called recognizable taxonomic units (RTU) instead of 'real' species.

Simplification of taxonomy is also very common in paleontology (-related) investigations.


Yes I confess I also submitted studies without clarifying my taxonomic concepts, to repent I enclose a jpg of what I formerly regarded as Neogloboquadrina pachyderma Ehrenberg 1861
As far as I remember from my former life as as 'foram picker', the proper use of taxonomy is quite uncommon in e.g. paleoclimte studies. A large amount of data based on organism counts with very unclear taxonomic basis therefore already exists (which was a motivation for TaxonRank).

After reading Krell I wondered how good actually taxonomic documentation in the current literature of my former discipline today is. Therefore, I decided to perform a quick test on the 2007 Volumes of Marine Micropaleontology. I scanned 40 articles (surely not enough, but I just wanted to have a quick impression) and the result confirmed more or less my bad expectations.

Only 2 articles included a complete systematics section where the species concepts have been described including synonymy lists. At least 15 Articles provided a species list in the appendix, 6 of these lists included references to the original reference of the treated taxon. 1 article used DNA analysis.
However, the majority of articles (22) used species names but did not include any taxonomic documentation. And this was a bit surprising to me. Three of these articles included electronical supplements with species lists - unavailable for readers of the printed version. Nine of these articles at least included one or more references as taxonomic key.

But still, more than 25% of all scanned publications used species names but did not document their taxonomic concepts at all! So there surely is a lack of proper methodological documentation.

Reference:

Krell(2004): Parataxonomy vs. taxonomy in biodiversity studies-pitfalls and applicability of 'morphospecies' sorting. Biodiversity and Conservation Vol. 13, p.795-812.

Friday, March 28, 2008

Introducing Agenames

We are proud to announce a first 'alpha' release of 'Agenames' , a new Stratigraphy.Net project we started last year.

Agenames is very much inspired by the geonames initiative which collects and publishes geographical names and their coordinates. In analogy, Agenames aims to collect stratigraphic terms in relation to their chronostratigraphic position (relative age).
So if you need to find out what e.g. the 'Ammergauer Schichten' or the 'Black Donald Pluton' means Agenames might help..

But Agenames will offer more! We have started some first experiments with Ageparser a text parsing tool which uses the Agenames index and is able to scan documents for stratigraphic terms, thus identify the stratigraphic context of a publication.
We will use Ageparser for stratigraphic indexing of geoscientific documents with the ultimate goal of a 4D (space and time) search engine ... sometimes...

To learn more visit the Agenames homepage at http://agenames.stratigraphy.net or visit the EGU 2008 in Vienna where Jens will give a talk on Agenames at Wednesday, 16 April 2008.

Thursday, March 27, 2008

The end of the sandbox

Originally, we have provided TaxonConcept's sandbox as a testing area for persons interested in the functionalities of TaxonConcept. The sandbox was a complete mirror of TaxonConcept, it was intended to be the site where people could just play around with the tool without obligations and risks after a short online registraton.
We have offered free access to the sandbox for several months, but we found that despite comparably many people have registered, none of them did really use it. After more than one year, there was only a hand full of testing entries. After comparing this little impact with the efforts required to maintain the sandbox we decided to close the sandbox.
I now wonder why that many people registered to the sandbox and apparently have decided not to use it. OK, TaxonConcept is not an easy tool, but we have now two students working with it and it took just one or two days to train them.
Probably people who registered simply did expect something completely differend to receive after clicking on the 'register me!' link, maybe something like a newsletter?