names & numbers

B. J. Tindall bti at DSMZ.DE
Tue Oct 16 09:01:49 CDT 2001

Adding to what Richard Pyle and Doug Yanega wrote:
It's not that easy even at the species and genus level if you have
taxonomies which are subject to current dynamic change. This is
particularly true when there is re-structuring of taxonomies with competing
alternatives. We have this situation in bacteriology at present where the
species A.b is placed in genus C. by X et al. 2000 and in genus D. by Y et
al. 2000. Both names are "CURRRENT" and according to a particular (current)
taxonomic opinion both are "CORRECT". The situation may be resolved in 10
years, but that does not help databases now! Bacteriology does have a
system of registering names which means we have complete listed of all new
names or new combinations. However, the other problem which is arising is
that when taxonomic opinion changes and there is no change in the names or
combinations, these are not "officially recorded". The object of these
"central registering systems" is not to be restrictive, but to have a
central reference point where you can find all the names which may be used
under the Bacterological Code. The things which seem to be slipping through
the net are the circumscriptions, and this is causing problems in certain
areas. Most databases seem to have been built up on the assumption that
each species has only one name which is in use at present, this is
certainly not true for all species. Extend this to higher taxa and you have
problems. TAXACOM users will know how much this also applies to botany and

At 09:59 15.10.2001 -0700, Doug Yanega wrote:
>Richard Pyle wrote:
>>To do it right, you only need two separate entities:  NAMES, and ASSERTIONS
>>(=circumscriptions).  Everything you enter into the database is OBJECTIVE -
>>no opinions by the data gatherers required.  If ITIS or some other agency
>>wants to select one particular taxonomy, then they need only designate one
>>assertion record for each name record to serve as the "current" or "correct"
>>circumscription of that name. From a data concept perspective, it's pretty
>>straightforward.  The real work is in trudging through all those
>>publications to capture all those taxonomic assertions in electronic form.
>>Incidentally, you need not restrict it to just "published" references.  Any
>>identification of a Museum specimen can serve as an assertion, just as any
>>unpublished pers. comm. from an expert.
>I don't think this claim applies to higher classification, however:
>most people have databases designed in a strict "parent:child"
>hierarchy. If taxon X belongs to subfamily Y of family Z in one
>classification, and to tribe A of subfamily B of family C in another,
>you have VERY different parent:child links all leading down to the
>same terminal taxon. If anything, this sort of variant supra-generic
>classification is probably *more* common (in terms of numbers of
>species involved) than disagreement about species and genus placement.
>Maybe others here will see a simple workaround to accommodate it, but
>I don't - it's an extremely complex thing to do. I think it
>necessitates a disassociation of the terminal taxa and the
>alternative hierarchies within the data (in other words, taxa are
>stored *without* being classified, and the phylogenies are stored as
>separate data sets, so you only get the computer to spit out a
>classification for a taxon after you choose which phylogeny you wish
>to view), OR, you stick with the default, reliance on a single
>classification. Right now, *all* the major on-line databases,
>including ITIS, choose the latter option; a single, invariant higher
>classification. You can't have a child link to two different parents,
>so ITIS will presumably *never* be able to designate alternative
>classifications above the terminal taxa - unless they radically
>change their data structure.
>Doug Yanega        Dept. of Entomology         Entomology Research Museum
>Univ. of California - Riverside, Riverside, CA 92521
>phone: (909) 787-4315 (standard disclaimer: opinions are mine, not UCR's)
>   "There are some enterprises in which a careful disorderliness
>         is the true method" - Herman Melville, Moby Dick, Chap. 82

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