TDWG/GBIF GUID-1 Workshop Report

Fri Feb 17 09:12:22 CST 2006

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correct if you are reyling on an outdated set of names and taxonomic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.
>
>P.
>
>> -----Original Message-----
>> From: David Patterson [mailto:dpatterson at mbl.edu] 
>> Sent: Tuesday, February 14, 2006 1:29 PM
>> To: Ginzbarg, Steve
>> Subject: GUID-things
>> 
>> Steve
>> 
>> The uBio system has about 7,000,000 records in NameBank (of 
>> which only about 80% are publicly visible).  NameBank could 
>> be used now as an interim GUID provider.
>> 
>> We treat each 'string' as being a different record.  So 
>> spelling changes and so on get a different NamebankID.  We 
>> then create reconciliation groups in which we map lexical 
>> variants against each other, map nomenclatural variants, 
>> common names; and in a slightly different way heterotypic synonyms.
>> 
>> The judgements we hold in ClassificationBank and are building 
>> editing tools for this, so that the various 'concepts' can be 
>> mapped out in there. This is designed to allow for multiple 
>> co-existing classifications.  This will offer different views 
>> to be expressed through the same vehicle.
>> 
>> I don't know the environment you mentioned, but we have found 
>> it essential to segregate objective aspects of nomenclature 
>> from the subjective elements.  uBio has focussed its energies 
>> mostly on the objective side, but has prepared itself for 
>> dealing with the subjective elements.
>> 
>> Best wishes
>> 
>> David Patterson
>> On Tue, 14 Feb 2006 12:44:41 -0600
>>   "Ginzbarg, Steve" <sginzbar at BIOLOGY.AS.UA.EDU> wrote:
>> > Having worked with USDA PLANTS and ITIS (Integrated Taxonomic  
>> >Information System) taxonomic authority files which receive most of  
>> >their plant names from the BONAP database, I am keenly aware of the 
>> >need  for globally unique identifiers for published taxonomic names. 
>> >John  Kartesz sends annual updates to PLANTS but his database lacks 
>> >stable  identifiers for taxonomic names. Without these identifiers, 
>> >PLANTS must  rely on the text of the name itself to match 
>> the updates 
>> >to the names  they have previously received from John. This 
>> is not easy 
>> >since the text  of the name may have spelling corrections or 
>> changes in 
>> >authors. Because  John's database is a synonymy stored as a 
>> flat file 
>> >the same name may be  listed more than once as a synonym of 
>> different 
>> >names.
>> >John includes the
>> > nature of the synonymy, e.g. "p.p.", "auct. non", or 
>> "sensu" as part 
>> >of  the authors. This results in two names which are 
>> actually the same  
>> >published name being listed more than once. Some specimens  
>> >determinations of a taxon in our collection databases will 
>> end up being  
>> >recorded as one of the duplicate names and some as the other.
>> > 
>> > I hope the GUID workshops will improve the situation. As Anita's 
>> >message  demostrates, TDWG needs to do a better job of 
>> communicating to  
>> >biological community as a whole the relevance of what
>> >they are doing.   
>> > 
>> > Alec McClay's message of 1/26/2006 asks some very good 
>> questions about  
>> >the appropriate use of taxon identifiers:
>> > 
>> > In listings produced from the Flora of North America online 
>> each taxon  
>> >is given a taxon ID number (e.g., 250060722 Polygonum 
>> austiniae, see  
>> >http://www.efloras.org/browse.aspx?flora_id=1&start_taxon_id=126398).
>> > I can't find any discussion on the site about the purpose or 
>> >appropriate  use of these numbers. It's tempting to use them as a 
>> >shorthand code for  that taxon in other reports, databases, 
>> etc., but 
>> >is that an appropriate  use? Is anyone using them in that way or are 
>> >they purely an internal  reference number in the www.efloras.org 
>> >database? What exactly is the  taxon ID number tied to in 
>> the event of 
>> >revisions, nomenclatural  changes, etc.?
>> > Any advice would be gratefully received.
>> > 
>> > Alec McClay, Ph.D.
>> > 
>> >> -----Original Message-----
>> >> From: Taxacom Discussion List
>> >> [mailto:TAXACOM at LISTSERV.NHM.KU.EDU] On Behalf Of Anita F. Cholewa
>> >> Sent: Tuesday, February 14, 2006 7:59 AM
>> >> To: TAXACOM at LISTSERV.NHM.KU.EDU
>> >> Subject: Re: TDWG/GBIF GUID-1 Workshop Report
>> >> 
>> >> What are TCS, RDF, SEEK, ABCD, etc?
>> >> More importantly how does this workshop help thosse of us at  
>> >>university collections who are trying to database the  information 
>> >>from our specimens with few assistants and almost  no money 
>> to do so?
>> >> 
>> >> AFC
>> >> _________
>> >> 
>> >> Anita F. Cholewa, Ph.D.
>> >> 
>> >> Curator of plants and Herbarium manager
>> >> 
>> >> Bell Museum of Natural History
>> >> 
>> >> University of Minnesota
>> >> 
>> >> 1445 Gortner Ave
>> >> 
>> >> St Paul MN 55108
>> >> 
>> >> 612-625-0215
>> >> 
>> 
>> David J Patterson
>> Bay Paul Center
>> Marine Biological Laboratory
>> Woods Hole
>> Massachusetts 02543
>> USA
>> 
>> 1 508 289 7260
>> 
>> http://www.mbl.edu/microscope
>> http://www.mbl.edu/research/resident/lab_baypaul.html
>> 
>
>-Steve Ginzbarg
> 
>Steve Ginzbarg, Collections Manager
>Herbarium (UNA)
>Department of Biological Sciences
>Box 870345
>The University of Alabama
>Tuscaloosa, AL 35487-0345
>(205) 348-1829, FAX: (205) 348-6460
>sginzbar at biology.as.ua.edu
>http://bama.ua.edu/~bsc/herbarium/
>