[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 06:38:42 CDT 2008


Sorry to be rather blunt Tony, but most sites 
dealing with prokaryote names usually fall faul 
of the same problems. The strange thing is that 
prokaryote names, like the names of viruses are 
governed by Codes of Nomenclature that actually 
operate a formal system or registration and for 
the recent names  the publication listing all new 
"registrations" is in the Internet. My 
information is that all relevant publications 
back to 1980 (beyond actually) will be available 
in about the next 6 months. In such a system the 
names have usually been verified for Code 
compliance at the time of original registration. 
Going through parts of the SN200 site I was left 
wondering where some of the names were coming 
from and I certainly picked up some rather strange contradictions.
Brian




At 02:07 13.06.08, Tony.Rees at csiro.au wrote:
>Dear Bill,
>
>I appreciate your taking the time to look around 
>the site in your particular area of expertise, 
>and am sorry about the number of errors you 
>encountered so quickly. I actually believe that 
>the Prokaryotes is most likely one of (!) the 
>weaker areas of the site. Those species names 
>(in the main) come from the 2006 Catalogue of 
>Life (which was the most current version when I 
>started this project), and all are identified 
>with their source and/or unique identifier used 
>in the source wherever possible, to give an 
>audit trail, and also to point out where the 
>required error correction needs (actually: 
>needed) to take place (as Rod page points out, 
>re-synchronising the lists is then a separate issue).
>
>The majority of the genus names (across the 
>board) and their family assignments come in the 
>first instance from Sheila Brands' SN2000 
>compilation (now the Taxonomicon). She kindly 
>gave me access to her list of "unverified" names 
>as well as "verified"; since the vast majority 
>of the "unverified" ones are in fact good, I 
>took the decision to include them in IRMNG, 
>however with an "unverified" tag so that they 
>can be hidden or ignored if needed. If there are 
>spelling, authorship, or classification errors 
>that it is possible to detect and correct 
>systematically (no pun intended), then I (or 
>possibly someone) will try to do so over time.
>
>As I said in a previous post, basically I am 
>trying to create a tool for which one can supply 
>an input genus, or genus+species, and wherever 
>possible the tool will say if the taxon is 
>marine or nonmarine (or both), and extant or 
>fossil (or both); also supply some indicative 
>higher taxonomy (although this is not the main 
>purpose of the list). The higher tax. that is in 
>there is an aid to the data management, and also 
>to allow hierarchical (i.e. efficient) 
>generation of the habitat and extant/fossil 
>flags, by vertical propagation (example: all 
>trilobites are fossil, all Anthozoa are marine, 
>most insects are nonmarine, etc. etc.). So at 
>some stage I will be happy to merge what I have 
>at genus+species level with a "better" higher 
>taxonomy, if anyone can supply it, but meanwhile 
>the lack of such does not critically impact on 
>the functionality of the list. Also I have paid 
>least attention to the prokaryotes (with the 
>exception of Cyanobacteria), viruses, and fungi 
>at this time, apologies for that.
>
>I would like to point out that I am choosing to 
>alert folk to the existence of my "list" at an 
>early stage (perhaps too early), before many of 
>the more obvious problems / inconsistencies 
>/legacy issues have been worked through. This is 
>a bit like releasing software at the "alpha" 
>stage (in-house testing, normally a bit 
>embarrassing to show to anyone else) as opposed 
>to the "beta" stage (limited external exposure, 
>to a select client group, in order to detect and 
>rectify the residual bugs), let alone the final 
>"production" stage (where most things should 
>work, unless you are Microsoft :)  ), obviously 
>I will weigh the benefits and drawbacks of such 
>early release according to the comments I receive...
>
>My hope is also to prompt some discussion of the 
>"big picture" issues, such as when can we expect 
>a "complete" Catalogue of Life that can actually 
>be used as such (or, what needs to change to 
>make this happen), the same with a master higher 
>classification of all life (extant and fossil), 
>as well of the practical database issues of how 
>best to physically manage all the required types 
>of content, expose it for searching, cope with 
>misspellings, etc., plus the particular issues 
>surrounding the potential merging of different 
>regional, thematic, or other lists. While these 
>are one or maybe several steps removed from the 
>ground-level tasks of describing and naming 
>taxa, they are important in their own way and 
>there are still many challenges in this domain 
>to be solved, and I think that the persons on 
>this list are in a key position to brainstorm some ways forward.
>
>Regards - 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 11:53 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...
>
>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
>Inhoffenstra├če 7B
>38124 Braunschweig
>Germany
>Tel. ++49 531-2616-224
>Fax  ++49 531-2616-418
>http://www.dsmz.de
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>Local court: Braunschweig HRB 2570
>Chairman of the management board: MR Dr. Axel Kollatschny
>
>DSMZ - A member of the Leibniz Association (WGL)
>
>
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>
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Dr.B.J.Tindall
DSMZ-Deutsche Sammlung von Mikro-
organismen und Zellkulturen GmbH
Inhoffenstra├če 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)





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