[Taxacom] validation of taxon names

Tony.Rees at csiro.au Tony.Rees at csiro.au
Fri Feb 17 19:19:11 CST 2012


Further to my message below, and at the risk of minor self promotion, he/one could also use my global genera compilation (not 100% complete but not too bad) to discover that Stilbospora is a fungus in the first place...

http://www.marine.csiro.au/mirrorsearch/ir_search.go?searchtxt=Stilbospora&hlevel=genus

Or for example if it is misspelled (e.g. Stibospora for Stilbospora):

http://www.marine.csiro.au/mirrorsearch/ir_search.go?searchtxt=Stibospora&hlevel=genus

Hopefully this is a useful product as a first step towards, or a component of, a global TNRS (taxonomic name resolution service) as previously mentioned.

Regards - Tony

________________________________________
From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Tony.Rees at csiro.au [Tony.Rees at csiro.au]
Sent: Saturday, 18 February 2012 9:32 AM
To: stephen_thorpe at yahoo.co.nz; armand.turpel.mnhn at gmail.com; taxacom at mailman.nhm.ku.edu
Subject: [ExternalEmail] Re: [Taxacom] validation of taxon names

Dear all,

Of course I agree with Stephen and Chris that the work needs to be done, funded, and by relevant specialists. However where that work has been done, the issue is then how to access it. For example Armand asked:

> Stilbospora angustata Pers. 1801 > Is it a synonym and if yes of what?

The answer is here (providing you accept MycoBank's opinion):

http://www.mycobank.org/MycoTaxo.aspx?Link=T&Rec=194690

Species: Stilbospora angustata Pers. 1801

MycoBank's opinion:
this name is a synonym of Truncatella angustata (Pers.) S. Hughes 1958 (MB307155)
...
Obligate synonym(s):
Truncatella angustata (Pers.) S. Hughes 1958 [LEG; MB307155]
Pestalotia angustata (Pers.) Arx 1981 [LEG; MB115996]
Sporidesmium angustatum (Pers.) Corda 1829 [LEG; MB229553]
...
Taxonomic synonym(s):
Pestalotia affinis Sacc. & Voglino 1885 [LEG; MB201735]
Phragmotrichum lignicola Corda 1838 [LEG; MB178084]
Alternaria lignicola (Corda) Fr. 1849 [LEG; MB507274]
Pestalotia lignicola Cooke 1871 [LEG; MB208762]
Seiridium lignicola (Corda) Sacc. 1884 [LEG; MB182142]
Pestalotia truncata var. lignicola (Cooke) Grove 1937 [LEG; MB255200]
Pestalotia truncata Lév. 1846 [LEG; MB357321]
Truncatella truncata (Lév.) Steyaert 1949 [LEG; MB291629]

So the question is really, has someone you can trust placed such opinions online, and if so where, and how can these be addressed in any integrated manner.

Of course there are associated questions - which sources do you trust the most, which have been updated most recently and on what evidence, what do do when equally trusted sources give diverging opinions, and so on, but where the "work" has been done it hopefully does not have to be repeated from scratch for every enquiry. In essence we are using the nomenclators and taxonomic specialists as our proxy to the original literature, and for their expertise in wighing and assessing the available evidence and coming to appropriate conclusions (at least for today).

If Armand would care to give a few more cases one could presumably look for patterns and see which resources are the most appropriate to answer his questions. He could even then construct an automated distributed search (similar to the ING portal described earlier) which would query a chosen set of resources and see what they hold. For example if I know something is an extant fish I would try Eschmeyer's Catalog, for an alga AlgaeBase, for a fly Systema Dipterororum (except that just now you can't), and so on...

Cheers - Tony
________________________________________
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: Saturday, 18 February 2012 8:10 AM
To: Armand Turpel; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] validation of taxon names

to answer these sorts of questions requires a *vast* amount of work, checking names against the original primary literature, work that is increasingly difficult to get funded ...



________________________________
 From: Armand Turpel <armand.turpel.mnhn at gmail.com>
To: taxacom at mailman.nhm.ku.edu
Sent: Friday, 17 February 2012 10:25 PM
Subject: Re: [Taxacom] validation of taxon names

I'm not a taxonomist or a biologist but a simple computer scientist  who
have to fight nightmares when taxonomy hits his door.

There are different levels of validation of taxons in our database or
species observation files we receive. Here a few examples:


Crouan{?} ex Nyl. > ????

SULZER > Sulzer

Schmitt > Schmit, Schmith, Schmidt, Schmitd, Schmid : we need the right
Schmi*

Muller > Müller, Mueller: Some one couldn't find ü on his keyboard

1903 > 1907, 1902 or no year

(Schrank, 1789) > Schrank, 1789

Bombasta testosterosa (Schwarzeneggerii, 1971) > Family of Bodyaceae or
Brainaceae or, hey, what's this?

Stilbospora angustata Pers. 1801 > Is it a synonym and if yes of what?

Onthophagus somalicus > Is it a homonym?


Then there are lsids, genetics and quantic effects ...., next week as
promised!

Nevertheless I enjoy this discussion which, in my opinion, is really
necessary.

a+
arm

On 17/02/2012 00:10, Richard Zander wrote:
> It seems to be best that informatics deals best with as objective,
> factual information, minimizing the gray area.
>
> Regarding "subjective," however, taxonomists wrestle mightily with
> decisions every day, trying to make reasonable and fact-based name
> changes of benefit to all users of taxonomy. They use discursive logic
> based on examination of dozens or hundreds of specimens in the context
> of evolutionary theory, and this is not particularly subjective to me.
>
> Yes, deciding which name is "correct" ("valid" for botanists) is a
> problem for those not familiar with the subject matter. Using the latest
> name is a good rule of thumb, although I've argued against the newest
> molecular phylogenetic names interminably in the past.
>
> One might make an analogy with scientific theorization in other fields.
> Which theory is right, photon or wave? Is the world round or flat? Is
> the red shift a property of an expanding universe or a function of
> decreasing energy associated with intervening gravity wells? Is the
> value of pi different if you have a large enough circle, like one around
> the whole universe? Is the black maple a species or only a variety of
> the sugar maple?
>
> Note that the above are, however some are strange, scientific questions.
> Scientific intuition helps solve them. Each question in valid/correct
> names needs a FermiLab of scientists to do the molecular, growth,
> ethology, allozyme, biogeography, cytology, population, and etc. studies
> needed to get a definitive answer.
>
> This is why it is easy to say decisions are subjective when they are
> merely poorly funded. If every informatics person spent half his/her
> time in biosystematics work, these problems would be less "subjective."
>
>
>
> * * * * * * * * * * * *
> Richard H. Zander
> Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA
> Web sites: http://www.mobot.org/plantscience/resbot/ and
> http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> Modern Evolutionary Systematics Web site:
> http://www.mobot.org/plantscience/resbot/21EvSy.htm
>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Chuck Miller
> Sent: Thursday, February 16, 2012 1:58 PM
> To: Roderic Page; taxacom
> Subject: Re: [Taxacom] validation of taxon names
>
> Dear Rod,
>
> I would propose to extend your phrase to "person(s) x in publication y
> asserted that two names are synonyms or lexical variants of each other"
> The assertion of related names occurs in a publication by that/those
> person(s).  Publication y's assertion should just be an objective fact
> and immutable.
>
> But, the sticky wicket comes when point 6 is posed: "Which of all the
> related names is the best one to use to refer to the organism right
> now"?   The issue of best is invariably subjective.
>
> Chuck
>
> here
>
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