[Taxacom] WTaxa ...: PS

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Sat Jul 30 01:07:51 CDT 2011

well ... Paul ... where to start??

Nomenclators vs. "taxonomic databases": nomenclators are relatively neat and 
tidy, but not very useful or interesting to many users. Taxonomic databases are 
more interesting and useful, but also a lot messier. So, no Paul, I mean to set 
out each name somewhere sensible in a *taxonomic database*, i.e., a database 
which attempts to integrate taxonomic *and* nomenclatural data into a sensible 
whole. This is what I try to do on Wikispecies. I attempt to express a sensible 
"state of taxonomy" for each group. Not easy!

I don't know enough about the Botanical Code to know what you mean about 
combinations, but I think they are more formal entities in botany than in 
zoology, where things are perhaps a tad messier. The point though with the 
Agathinus example is that CoL, EoL, etc. have the same taxon listed both in 
Belidae as Agathinus tridens and in Curculionidae as Curculio tridens, which 
seems quite bad to me ...

Legalov's (2009) publication is problematic in that it adds considerable 
complexity, but without a phylogenetic basis. There isn't, however, a perfectly 
clear dichotomy of sound vs. unsound taxonomy, it is somewhere in between, and 
so it is difficult to know what to do with it. We need to be able to say "this 
is Legalov's (2009) opinion, for what it is worth", but neither CoL or EoL have 
the infrastructure to manage data in such a sophisticated manner, and it is 
difficult also on Wikispecies ...


From: Paul Kirk <p.kirk at cabi.org>
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; Chris Lyal <C.lyal at nhm.ac.uk>; 
"taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
Sent: Sat, 30 July, 2011 5:47:38 PM
Subject: RE: [Taxacom] WTaxa ...: PS

The somewhere sensible where all name should be set out is in Nomenclators - 
that is what they do. One of the 'minor' problems with CoL is that, for very 
good reasons, the aggregation mechanism has not required the component databases 
to build on nomenclators because for animal names there isn't one (yet) and for 
plant names not many use IPNI IDs (including some databases from Kew if I 
understand correctly). I note the post from Chris Lyle used the 'c' word ... 
combination ... which if I understand zoological nomenclature do not exist - but 
in managing names the c's are very useful. I'm unclear why the cited 2009 
publication creates a complication; if it's unsound taxonomy then it's effects 
on nomenclature w.r.t. the taxonomically correct names are ignored - yes?

From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] on 
behalf of Stephen Thorpe [stephen_thorpe at yahoo.co.nz]
Sent: 30 July 2011 05:49
To: Chris Lyal; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] WTaxa ...: PS

I am still working on Oxycoryninae
(http://species.wikimedia.org/wiki/Oxycoryninae), and it gets more and more
complex, and further and further away from what is on CoL, EoL, etc. The main
complication arises from the work of Legalov (2009), who offered a
reclassification which appears to be highly subjective and lacking phylogenetic
basis. Quite how to handle it is hard to know. Bouchard et al. (2011) seem to
have made some somewhat arbitrary acceptance/rejection choices of Legalov's
work, so that isn't entirely satisfactory either. The main thing, though, is to
have all the names set out somewhere sensible, and problems flagged, which I am
working towards on Wikispecies, but quite what the likes of CoL, EoL, etc. can
make of stuff of this complexity, I have no idea! Seems like they must
somehow squeeze square pegs into round holes ...


From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
To: Chris Lyal <C.lyal at nhm.ac.uk>; taxacom at mailman.nhm.ku.edu
Sent: Sat, 30 July, 2011 12:01:49 PM
Subject: Re: [Taxacom] WTaxa ...: PS

PS: you might also wanna check this out for a laugh!

From: Chris Lyal <C.lyal at nhm.ac.uk>
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; taxacom at mailman.nhm.ku.edu
Sent: Sat, 30 July, 2011 1:04:34 AM
Subject: RE: [Taxacom] WTaxa and data harvesting via CoL, EoL, etc.

Apologies for the issues with names in WTaxa.  We are still in the
process of completing the database, so many of the names are not of
valid species.  The first pass in the project was to enter as many names
as possible, from the secondary literature; we received funds from GBIF
to help us with that.  The second pass is to check the original papers
and correct entries, working from oldest to newest, checking
availability and validity as we go, and this is underway.  We also have
had a problem with the database about displaying links between original
and subsequent combinations, which is the issue that Stephen highlights,
and which is fixed in WTaxa but will not transmit through to CoL until
the next data upload.  We are lucky that we have been able to obtain
some funds though partnership with Species 2000 in an EU project, and
later this year we will be able to use some of those funds to improve
the harvesting from WTaxa to Species 2000-CoL.  The fundamental problem
still pertains - a small number of taxonomists who are working to
complete a large task with insufficient time and resources.  However,
without the 'acronyms' we would not have been able to achieve anything
at all.

Aside from natural disappointment that despite the rather intensive
efforts of a number of people to capture data and disseminate them the
data are not yet perfect, we might consider several serious questions.

How we develop opportunities for funding data population on a large
scale.  Given the amount of data currently available on the web and the
relatively low investment there has been in data population (leading
many of us to work in 'spare' time on this activity) how do we press the
arguments to finish the job.  There are global level policy agreements
through the CBD that this work should be done, so what are people's
experiences in successful arguments for funding?

Secondly, should we (as taxonomists) should expose incomplete
information (it was a condition of the first grant that we received for
WTaxa that we do so).  I have been in meetings where users were appalled
that nomenclators were freely available, since they were using them as
if they listed only valid names (actually a similar situation to WTaxa
as it currently is), but I guess we would generally agree that
nomenclators are a useful tool.

Finally, a related point; should we develop a standard means in metadata
of indicating fitness for use of any record or item of data - perhaps
TDWG might consider this.

This is not an invitation to debate (again) the relative merits of
different means of putting information on the web - we've really done
that to death.  Suffice to say that I know very few idle taxonomists (or
people in CoL, GBIF etc, come to that) - we are all trying to populate
systems with data in the ways we see fit.  Nor is it an invitation to
argue (again) that money obtained by initiatives exploring and
catalysing dissemination techniques should have been spent in a
different way - it wouldn't have been, and our project for one has
benefitted - and we're not alone.


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