Prokaryotic Taxonomic Identifiers in Databases

[Peter Floriani]

Has there been a "standard" formulation of
taxonomic/phylogenetic names for the prokaryotes?
(and, for that matter, the eukaryotes?)

I am working on software to assist the biology
department at RPI, specifically making use of the
RDP (Nucleic Acids Research, 20 Supplement, 2199-2200)
and the Belgian "Compilation of small ribosomal
subunit RNA sequences" (Nucleic Acids Research,
20 Supplement, 2075-2081).

What names (if any) are the "accepted" identifiers
for prokaryotic taxonomic levels?  The following are 
those used either in the current RDP (1) or 
in the Belgian database (2):


  2 Alpha group
1   AlphaPurple
1   Archaea
1 2 Bacteria
  2 Bacteroides
  2 Beta group
1   BetaPurple
  2 Chlamydiae
  2 Chloroflexus group
1   Crenarchaeota
  2 Cyanobacteria
  2 Cytophaga
1   DeinococcusGroup
  2 Delta group
1   DeltaPurple
1   Euryarchaeota
  2 Eukaryote uncertain affiliation
  2 Firmicuta
1   Flavobacteria
  2 Flavobact.
  2 Flavobacterium Group
1   Fusobacteria
  2 Gamma group
1   GammaPurple
1   GramPositive
1   GreenNonsulphur
  2 Green non sulfur bacteria & rel.
1   GreenSulphur
  2 Green sulfur bacteria
1   Halobacteria
1   HighG+CGramPositive
  2 High G+C
1   JohnsonGroup1
1   Lactobacillus/Bacillus
1   LowG+CGramPositive
  2 Low G+C
1   Methanobacteriales
1   Methanococcales
1   Methanomicrobiales
1   Methanosarcinales
1   Mycoplasmasandrelatives
  2 New line of descent
  2 Photosynthetic org.
1   Plancromyces
  2 Planctomyces & rel.
  2 Proteobacteria
  2 Radioresistant micrococci & rel.
  2 Related to low G+C firmicuta
  2 Species with gram-negative walls
1   Spirochetes
  2 Spirochetes and rel.
  2 Thermomicrobium group
  2 Thermophiles group
  2 Thermophilic eubacteria
1 2 Thermotogales
  2 Uncertain affiliation

I would like to know if there is a reference or
other publication which would clarify the nomenclature,
or set forth the "accepted" names for these categories.

Also, is there an accepted form for genus/species/strain
denotation?  The typical form is:

    Mygenus myspecies str. xxx

Does the biological standards organization handle 
formal (i.e. software-related) names such as these?

Thanks.


Peter J. Floriani
florianp at cs.rpi.edu
Dept. of Computer Science
Rensselaer Polytechnic Institute