[Taxacom] Towards a consensus higher classification of organisms (was: List of Orders of the world), misspellings, etc...

B.J.Tindall bti at dsmz.de
Fri Jun 13 07:00:48 CDT 2008


Rod

At 19:22 12.06.08, Roderic Page wrote:
>Perhaps part of the problem is updating databases as sources change.
>I'm guessing that names prefixed "CoL2006" are from the 2006 edition
>of the Catalogue of Life. Some of these records have since changed.
>
>Updating would be easier if databases made their data more accessible.
>The NamesForLife project has DOIs for Bacteria and Archaea names, for
>example http://dx.doi.org/10.1601/nm.8233 for Pedobacter heparinus.
>Nice as it is to have stable identifiers, there is no (obvious) way to
>harvest the associated data in this case, hence databases such as
>Tony's will struggle to remain up to date.

I am sure that NamesForLife would be the last 
ones to refuse to help. The e-mail address of 
those to be contacted is on their homepage and 
they would certainly be the last ones to object 
to seeing their technology used further.


>Nor does it help that resources such as The Taxonomic Outline of
>Bacteria and Archaea (http://www.taxonomicoutline.org/) have the
>message "Copyright Michigan State University  39
>Board of Trustees 2001-2007, all rights reserved" plastered on every
>page.

The IJSEM, which is the official journal in which 
the registration of prokaryote names is 
undertaken is copyright of IUMS and every article 
has that copyright notice on the first page. Jean 
Euzéby's website also has a copyright notice on 
every nomenclatural page. To my knowledge the 
names themselves are not copyright, but the form 
of the publication in which they occur. Thus one 
can re-work the lists of names, but not simply 
use the original format in which they were 
published. TreeView also has a copyright notice 
attached and is used by lots of folks.

>It is, perhaps, uncharitable to blast somebody trying to
>aggregate names into a useful resource, when some of the sources of
>names seem intent on making this task much, much harder than it needs
>to be.

I don't think I blasted Tony. I just referred to 
problems in general and when he asked I supplied 
him with concrete examples illustrating some of 
the problems. All I was doing is drawing 
attention to the fact that the proliferation of 
inaccurate lists is becoming problematic. While 
it is easy to exchange information on the 
Internet it is problematic to work out what is 
reliable. A quick search of iSpecies, for example 
for "Jonesia" gives me reference to a prokaryote 
name, pictures of flowers and most references 
listed are to the prokaryote taxon - Jonesia 
Brady, 1866 is also an ostracod, according to 
ION. We all know that curating even a 
nomenclatural data base is expensive and time 
consuming, and this rises exponentially as the 
links to other data sets increases.

Brian


>Regards
>
>Rod
>
>
>
>On 12 Jun 2008, at 14:52, B.J.Tindall wrote:
>
> > Dear Tony,
> > But I do appreciate what you are doing and yes,
> > believe me I do know that there are all sorts of
> > errors out there. I am also not being negative
> > because if you had the expertise to appreciate
> > the mess that was out there you would probably be
> > as critical as I am. Examples:
> > Halobacter:
> > Halobacter Wainoe, Tindall & Ingvorsen, 1999 (0)
> > - as a co-author of the paper I can tell you the
> > organism entered the literature as Halorhabdus
> > The other example:
> > Halobacter (1)
> > Halobacter salinaria (Harrison & Kennedy, 1922)
> > Anderson, 1954 makes reference to only one
> > species of many in that genus that didn't make it
> > on to the bench mark of the Approved Lists of
> > Bacterial Names, so why is only one there?
> >
> > Bacillus pestis (Lehmann & Neumann, 1896) Migula,
> > 1900 Bacillaceae CoL2006/BIO-1918-8570 is an
> > older, no longer used name for Yersinia pestis - not even mentioned
> >
> > the entry:
> > 
> http://www.marine.csiro.au/mirrorsearch/ir_search.go?searchtxt=Pedobacter+heparinus&hlevel=species
> > lists only Cytophaga heparina (Payza & Korn,
> > 1956) Christensen, 1980 , Sphingobacterium
> > heparinum (Payza & Korn, 1956) Takeuchi & Yokota,
> > 1993 Pedobacter heparinus (Payza & Korn 1956)
> > Steyn et al., 1998 while Flavobacterium heparinum
> > Payza & Korn 1956 is not mentioned
> >
> > Flavobacterium yabuuchiae Holmes et al., 1988 -
> > no indication of the fact that is also considered
> > to be a synonym of Sphingobacterium spiritivorum.
> >
> > There is absolutely no way of telling whether the
> > names listed are names recognised by the current
> > Bacteriological Code or simply ballast from the
> > past. We are currently running at about 10,000
> > names in use and 20,000 names we would prefer to forget.
> >
> > Haloincola (2) Halomonadaceae SN2000 unverified -
> > but SN 2000 doesn't include this genus in this
> > family (which it doesn't belong to either).
> >
> > and I only sepnt 15 minutes on the site.
> >
> > I am afraid that your site isn't the only one to
> > be dogged by problems with regards names of
> > prokaryotes, some are significantly worse. The
> > major problem is the the average user wouldn't be
> > able to distinguish the problem information from
> > correct information and this just causes
> > unnecessary confusion. This is particularly
> > worrying if one apprecaites that we know all
> > names that the current Code recognises and also
> > the links between the appropriate synonyms etc.
> >
> > Sorry.
> > Brian
> >
> >
> > At 14:04 12.06.08, Tony.Rees at csiro.au wrote:
> >> Penny, Brian,
> >>
> >> First, I was commending Parker as a worthy
> >> exercise that has not yet been surpassed, but
> >> was overdue for an update - including correcting
> >> any shortcomings of course (and yes, I also
> >> noticed the omission of the springtails).
> >> Second, the implied criticism of "uncritically
> >> just hoovering in anything on the web" is
> >> unfair. What I am actually attempting to do is
> >> to fill gaps in the available Catalogue of Life
> >> compilation from other supposedly
> >> "authoritative" lists (including some not
> >> available anywhere in electronic form, and
> >> others not yet published, courtesy of their
> >> authors), and then address some of the issues of
> >> mis-matching names, and hierarchies to a lesser
> >> degree in due course (the latter a secondary
> >> consideration). My ultimate reason for this is
> >> to have a local list (or construct a web
> >> service) that will attempt to answer, at a
> >> machine readable level and in a consistent
> >> manner, the two questions (a) is this genus /
> >> genus + species combination marine or nonmarine,
> >> and (b) is it extant or fossil (or potentially
> >> both), also correcting errors in sources as I
> >> come across them (and I can assure you that the
> >> supposed "gold standard" Catalogue of Life is by
> >> no means error free). Since the alternative
> >> appears to be to wait for the CoL to be complete
> >> (another xx years??) and even then it will not
> >> contain the habitat information that I seek, and
> >> will also miss all the fossil taxa, I feel that
> >> if there is a requirement for such a list "now",
> >> one has no practical alternative to constructing one's own...
> >>
> >> I guess I was hoping for constructive criticism
> >> rather than negativity. If the latter is a
> >> general response, it is a simple matter to
> >> disable the high level search options once more
> >> and just use the system to suit my own needs and
> >> those of my "immediate" clients (principally,
> >> OBIS and others with similar habitat-specific
> >> requirements). But maybe there are persons on
> >> the list who see *some* wisdom in this approach
> >> - note the "Interim" in the IRMNG title - when
> >> there is something better to use, I will be the first to use it.
> >>
> >> - Tony
> >>
> >> -----Original Message-----
> >> From: taxacom-bounces at mailman.nhm.ku.edu
> >> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of B.J.Tindall
> >> Sent: Thursday, 12 June 2008 7:21 PM
> >> To: taxacom at mailman.nhm.ku.edu
> >> Subject: Re: [Taxacom] Towards a consensus
> >> higher classification of organisms (was: List of
> >> Orders of the world), misspellings, etc...
> >>
> >> ...and I hope that real benchmark lists of
> >> formally registered names, like the system in use
> >> in prokaryote nomenclature won't get swamped by
> >> those sites that uncritically just hoover in anything on the web.....
> >> Brian
> >>
> >>
> >> At 10:06 12.06.08, Penny Greenslade wrote:
> >>> I hope any such list will not follow Parker (ed.)'s "Synopsis and
> >>> Classification of Living Organisms" (publ. 1982) too closely as
> >>> that book
> >>> left out a whole (abundant and widespread)
> >> Class of organisms, the Collembola.
> >>>
> >>> Penelope Greenslade
> >>>
> >>> At 01:14 PM 12/06/2008 +1000, Tony.Rees at csiro.au wrote:
> >>>> Parker
> >>>> (ed.)'s "Synopsis and Classification of Living Organisms" (publ.
> >>>> 1982),
> >>>
> >>> Penelope Greenslade
> >>> Division of Botany and Zoology
> >>> Australian National University
> >>> GPO Box
> >>> Australian Capital Territory 0200
> >>> Australia
> >>> Telephone 61 (0) 2 6125 0774
> >>> Faximile    61 (0)2 6125 5573
> >>>
> >>>
> >>> _______________________________________________
> >>> Taxacom mailing list
> >>> Taxacom at mailman.nhm.ku.edu
> >>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >
> > Dr.B.J.Tindall
> > DSMZ-Deutsche Sammlung von Mikro-
> > organismen und Zellkulturen GmbH
> > Inhoffenstraße 7B
> > 38124 Braunschweig
> > Germany
> > Tel. ++49 531-2616-224
> > Fax  ++49 531-2616-418
> > http://www.dsmz.de
> > Director: Prof. Dr. Erko Stackebrandt
> > Local court: Braunschweig HRB 2570
> > Chairman of the management board: MR Dr. Axel Kollatschny
> >
> > DSMZ - A member of the Leibniz Association (WGL)
> >
> >
> > _______________________________________________
> > Taxacom mailing list
> > Taxacom at mailman.nhm.ku.edu
> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >
>
>---------------------------------------------------------
>Roderic Page
>Professor of Taxonomy
>DEEB, FBLS
>Graham Kerr Building
>University of Glasgow
>Glasgow G12 8QQ, UK
>
>Email: r.page at bio.gla.ac.uk
>Tel: +44 141 330 4778
>Fax: +44 141 330 2792
>AIM: rodpage1962 at aim.com
>Facebook: http://www.facebook.com/profile.php?id=1112517192
>
>http://iphylo.blogspot.com
>http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>
>
>
>
>
>
>_______________________________________________
>Taxacom mailing list
>Taxacom at mailman.nhm.ku.edu
>http://mailman.nhm.ku.edu/mailman/listinfo/taxacom

Dr.B.J.Tindall
DSMZ-Deutsche Sammlung von Mikro-
organismen und Zellkulturen GmbH
Inhoffenstraße 7B
38124 Braunschweig
Germany
Tel. ++49 531-2616-224
Fax  ++49 531-2616-418
http://www.dsmz.de
Director: Prof. Dr. Erko Stackebrandt
Local court: Braunschweig HRB 2570
Chairman of the management board: MR Dr. Axel Kollatschny

DSMZ - A member of the Leibniz Association (WGL)





More information about the Taxacom mailing list