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

Roderic Page r.page at bio.gla.ac.uk
Fri Jun 13 07:38:45 CDT 2008


Dear Brian,


On 13 Jun 2008, at 13:00, B.J.Tindall wrote:

> Rod
>
> 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.
>

Sure, but this is not what I meant (sorry for not being clearer).  
Contacting people by email and asking for access to data simply  
doesn't scale. There are simple ways to make this work. NamesForLife  
could have a RSS feed with new and/or changed names that others could  
harvest and make use of.

In the same way, would you expect to email each journal publisher each  
week to find out the latest articles in each journal? No, you'd expect  
them to provide you with a list, ideally in a form (e.g., RSS) that  
you can consume in whatever way suits you.

>
>> 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.

Touché! However, the copyright notice on TreeView doesn't place limits  
on people using it, and it's descendant, TreeView X is released under  
the GPL -- eventually I saw the light ;-)

The copyright statements on the bacteriological web sites are pretty  
restrictive. From http://www.bacterio.cict.fr/copyright.html:
1) The person using List of Prokaryotic names with Standing in  
Nomenclature may browse, search, retrieve, view, or store copies of  
files provided that the files are used only for their personal, non- 
commercial use.

2) No material on this Internet site may be copied, downloaded,  
disseminated or published without the prior written permission of the  
author (J.P. Euzéby).

3) The person using List of Prokaryotic names with Standing in  
Nomenclature may not: (i) distribute a copy (electronic or otherwise)  
of any file; (ii) alter any file; or (iii) charge for a copy  
(electronic or otherwise) of any file.

Now, in one sense anybody who goes to the trouble of making something  
can decide how it is distributed. But, the conditions above seem  
expressly designed to thwart use, beyond browsing web pages. This  
attitude only inhibits progress.

Likewise, Taxonomic Outline states "This work may not be transferred  
or copied in whole or in part without the express written permission  
of Michigan State University except for brief exerpts in connection  
with reviews and scholarly analyses."

I somewhat doubt that harvesting names and links to literature is  
permitted by this statement.

These lists would be much more useful if released, either in the  
public domain, or under a Creative Commons license that permitted use  
(say, with attribution, but without commercial exploitation).

The point here is that the taxonomic community is not helping itself  
when it slaps copyright on lists.

>
>
>> 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.
>

Re iSpecies, there are clearly things I could do to make it more  
useful, including separating results for homonyms such as Jonesia  
(which is indeed a bacterium, a plant, and an ostracod), although this  
requires that the source themselves provide enough information to  
permit me to work out which "Jonesia" they are referring to. Note that  
this is a different question from whether the information is reliable,  
as such.

Regards

Rod



> 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
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>> >
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>> >
>> >
>> > _______________________________________________
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>> > 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
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>
> 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)
>
>

---------------------------------------------------------
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





---------------------------------------------------------
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









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