[Taxacom] CoL and ZooBank

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Thu Jul 8 17:50:23 CDT 2010


Bob,

Although I am the last person to be defending the acronyms, I shall play devil's 
advocate slightly just for a moment. There is a sense that comes out of what you 
write that the acronyms don't do anything useful for you ,so they are bad. I 
agree that they can be rightly criticised for a bit of "misleading advertising", 
i.e.

>"a comprehensive catalogue of all known species of organisms on Earth" (CoL) and 
>"a uniform and validated index to the world's known species" (Species2000)?

But basically I think the main point of the acronyms is just to provide certain 
beauracrats/managers with "the best available" citation opportunities. So, for 
example, a biosecurity 'crat can cite CoL as "the best available" info on the 
species currently placed in a genus, etc., and move on, without worrying too 
much about whether it is actually true or not. In other words, it functions as a 
rubber stamping excercise for 'crats. It provides them with a standard protocol 
to blindly follow, just like any good 'crat should!

If this is the primary purpose of the acronyms, then it is hard to see how they 
could fail to fulfil their purpose, and as you are not their intended user, it 
is a bit pointless complaining that they don't provide you with anything useful 
...

Still, potential data providers might like to ask themselves why they would want 
to hand over all their data to an acronym for free!

Stephen




________________________________
From: Bob Mesibov <mesibov at southcom.com.au>
To: TAXACOM <taxacom at mailman.nhm.ku.edu>
Sent: Thu, 8 July, 2010 8:33:42 PM
Subject: Re: [Taxacom] CoL and ZooBank

The closer I look at the acronym situation in zoology, the more wonderful it 
gets.

I've found recent-species pages on EoL with the annotation "Name not in Species 
2000 & ITIS Catalogue of Life: Annual Checklist 2009". These were contributed by 
the journal ZooKeys, which means the names are in ZooBank, too.

I've also found that for at least one annoyingly out of date CoL name, the 
'Latest Taxonomic Scrutiny' was 6 years before the source database was actually 
accepted as a CoL contributor, back in 2008. It's good that CoL tells us this, 
but where does that leave the user who wants what CoL says it hopes to offer, 
namely "a comprehensive catalogue of all known species of organisms on Earth" 
(CoL) and "a uniform and validated index to the world's known species" 
(Species2000)?

Alastair Culham writes "Perhaps CoL need to set up an adoption process for 
orphaned databases to ensure they don't go unloved for ever :-)" Yes, and a 
promotion process for groups without databases. Both voluntary, of course.

Another answer for the user is to flee to ION, the Index to Organism Names 
(http://www.organismnames.com/), a free Thomson Reuters web service with links 
to ZooBank. Every name I've so far missed in CoL and EoL I've found in ION 
(think 'Zoological Record'). ION has one-species pages, too, but the situation 
ain't ideal. Recent taxonomic publications using the name are listed, but to see 
the reference citation you need to be a Zoological Record subscriber.

Then there are ION's external links, e.g. to EoL and GBIF. Sometimes the ION 
species page has a link-graphic to GBIF specimen data. You click the link and 
get taken to GBIF's data-use agreement, and after reading this densely written 
document you click Accept and find that no, actually GBIF doesn't have any data 
for this name. At other times the *same* ION page reports "GBIF Distribution Map 
and Specimen Data - No GBIF distribution map available for this name".

Let me be clear about this: I am not complaining about particular, nit-picking 
data validity issues. I am pointing out that there are systemic failures in the 
acronym universe to share nomenclatural data, to ensure that these data are 
complete and up to date, and to offer pointers to users who need/want to further 
check the data.

What to do? Well, I'm sure the acronymists mean well and are working hard on 
such problems, and no doubt some of these issues could be handed to a working 
group at yet another bioinformatics conference somewhere. But down here in 
Userland, here's my recommendation:

(1) Go straight to a bottom-up, online classification for the group in question, 
well-referenced, and produced and maintained by a specialist or specialists. If 
none exists, go to (2).
(2) Browse through ION, CoL, EoL and Wikispecies. Note any differences and try 
to work out how they arose. If this fails or leads you in circles, go to (3).
(3) Go to a library with a subscription to Zoological Record. Check out some 
primary sources and take digital notes.

(2) sounds like comparison shopping. It takes time, and isn't that what 
'cybertaxonomy' is supposed to save us?
-- 
Dr Robert Mesibov
Honorary Research Associate
Queen Victoria Museum and Art Gallery, and
School of Zoology, University of Tasmania
Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
03 64371195; 61 3 64371195
Webpage: http://www.qvmag.tas.gov.au/?articleID=570

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