TDWG/GBIF GUID-1 Workshop Report

Tue Feb 21 09:08:34 CST 2006

Dear David,
Well I agree that there are differences between intent and execution. My
intent is to draw people's attention to the unique nature of the prokaryote
system and also to point out that what works in zoology and botany can well
have a disastrous effect for the "bacteriologists".

While I understand the need for complete lists of names, bacteriology (and
virology) are unique in having a system of registration/indexing. This not
only has an affect on new names, but also on older names which have been
"abandoned". Thus we have
a) names which are "abandoned" and which have no meaning in the post 1980
taxonomy (e.g. "Nitrobacter punctata" on the ITIS-UBIO list)
b) names which are "abandoned", but have a link to a names which are in
use: i.e. "Bacillus pestis", "Pestisella pestis", "Pasteurella pestis",
"Bacterium pestis", all of which unambiguously point to Yersinia pestis,
the only name recognised by the Bacteriological Code in a post 1980
nomenclature and taxonomy
c) the complete list of names "adopted" under the system of
registration/indexing, with a new starting date of 1.1.1980 (note that we
DO take older literature into account with respect to dates and authors) -
this was the "Approved Lists of Bacterial Names"
d) those names which have been registered/indexed post 1.1.1980 - the index
now being updated once a month. De facto Jean Euzéby's list is the most
accurate list of names registered/indexed under the Bacteriological Code
(points c) and d), but with also reference to most of the names under b))
e) about 5% of all names are not registered/indexed because the authors
don't know that they should do so - this is because neither taxonomy,
nomenclature or the Bacteriological Code is taught properly to students

In the process of "abandoning" older names lists were also drawn up of as
many names as possible - these list are available in printed form with
reference to original publications etc. These lists comprise about 30,000
names.

So where is my problem? Easy, if you are going to list ALL names then you
have to comment on whether these names are:
a) of historical value, but have no modern meaning
b) have historical value, but MUST be linked to a "post 1980" name
c) are "adopted" under the Bacteriological Code

These citeria are VERY important at the nomenclatural level. If you haven't
sorted out that level then you can't build up a sensible (post 1980)
taxonomy. Having pioneered registration/indexing and also created lists of
"protected names" the last thing we want to see is the uncritical listing
of all names.

Add to that the additional problems of:
a) validly published (botany/bacteriology) = available name (zoology)
b) correct name ((botany/bacteriology) = valid name (zoology)

and lists in which the term "valid name" is applied to bacteriological
names (does one mean correct or validly published?), then the system gets
very confusing. 

While I do appreciate the need to bring order into botanical and zoological
names, one cannot apply the same criteria to bacteriology where we did most
of the work (which botany and zoology still needs to do) in the period
1960-1980 - our system has been sorted out and names evaluated in a
nomenclatural context - if they are all to go on the Internet, then please,
please, in consulation with experts who can save us (the bacteriologists
and the scientific community) a lot of heart-ache and needless confusion.

As you said David intent and execution are two different things and it is
important to get things right.
With thanks for your reply and the chance to perhaps spell out in a little
more detail where the problems are.
Brian

At 10:06 17.02.06 -0500, David Remsen wrote:
>Let me see if I can salvage a few things from this thread regarding  
>uBio.   First, I think the original complimentary part was regarding  
>our separation of conceptual elements, which I think is sound.   The  
>criticisms, which to some extent I agree with, concern execution, not  
>intent.   We would gladly dispose of the referenced list if we are  
>able to represent a more up-to-date prokaryote classification within  
>our SOAP service.   I'd like nothing more than access to this via  
>some federated updating mechanism.  In the meantime, I will update  
>the header information to reference the DSMZ and clarify that the  
>hierarchy is really a non-authoritative list.
>
>Pre-1980 prokaryote names will exist within our names index,  
>NameBank, because these names continue to annotate content.    
>NameBank is an index of recorded names, not current or correct  
>names.    We have indexed all the names that appear in Medline which  
>references literature back into the 1940s and may continue to roll  
>back even earlier.   This index includes all names, the good, the bad  
>and the ugly.   The fundamental value of these names is that they  
>annotate content that someone may be interested in accessing and  
>therefore, we need to know about them. Name-related access  
>impediments are well known and significant.   Addressing them is  
>complicated by conceptual properties (string, nomenclatural,  
>taxonomic) and requires a combination of taxonomic and informatics  
>perspectives.  It requires an interconnected layering of these  
>perspectives so that access to current authoritative views can be  
>enabled starting at "ground" level, with for example, a Medline  
>citation.  Names without nomenclatural standing stay at the index  
>level and are not a component of the ICSP (nomenclatural) which  
>represents those part of the index that are.   Those that are may be  
>components of different taxonomic concepts.
>
>That's a bit about our intent.  Execution can sometimes be rusty but  
>it improves.    Pointing out our flaws invites solutions and that's  
>what the process is about.
>
>David Remsen
>
>On Feb 17, 2006, at 3:12 AM, B.J.Tindall wrote:
>
>> Nice website. Took a look at the prokaryote section (listed as  
>> Bacteria).
>> Nice mixture of Jean Euzéby's website:
>>
>> http://www.bacterio.cict.fr
>>
>> to the genus level, fairly up-to-date with the "validly published  
>> names"
>> (i.e. registered/indexed and not be be mixed up with zoological valid
>> names) and with a very nice list from ITIS - again all very nice and
>> correct if you are reyling on an outdated set of names and taxonomic
>> concepts which I think probably date from 1957 (with a few modern  
>> names
>> thrown in for good measure). I often hear that our system is confusing
>> because of the different lists of names which are out there - to  
>> which I
>> can only reply if the lists of names are put up without consulting  
>> with the
>> sole registering/indexing authority, the International Committee on
>> Systematics of Prokaryotes (ICSP) then you can't blame us for the  
>> confusion
>> which others cause. I have written to some of those responsible,  
>> even sat
>> around a table with them. The errors persist - for which the ICSP  
>> is not
>> responsible. Is it too much to ask the experts?
>>
>> Brian J. Tindall
>> Chair of the ICSP Judicial Commission
>> Member of the Editorial Board of the Bacteriological Code
>>
>>
>>
>> At 15:05 16.02.06 -0600, Ginzbarg, Steve wrote:
>>> Thanks for replies received off line. David Patterson (reply below)
>>> called my attention to uBio, http://www.ubio.org/. The  
>>> presentation on
>>> dealing with taxon names is excellent. I think the separation of
>>> objective synonyms, e.g. nomenclatural synonyms from subjective
>>> synonyms, e.g. heterotypic synonyms is very important.
>>>
>>> With regard to Alec McClay's question about referencing FNA taxon ID
>>> numbers in other databases, Peter Stevens at MO Bot writes
>>>
>>> I checked down the hall, and these are apparently internal numbers.
>>>
>

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