TDWG/GBIF GUID-1 Workshop Report

[David Remsen]

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.
>>