From: ostell@object.nlm.nih.gov (Jim Ostell)
Newsgroups: bionet.molbio.genbank
Subject: GenBank Divisions
Date: 22 Dec 92 15:07:10 GMT
Organization: National Library of Medicine
X-Newsreader: Tin 1.1 PL4


  Recently the issue of GenBank divisions has been raised in this forum.  
One must remember that the current system of GenBank divisions is really 
based on the pragmatic issue of where most of the sequence data comes 
from and what is a "convenient" sized file.  I don't think anyone would 
argue that "primate" and "rodent" and "other mammal" are the kinds of 
divisions a taxonomist might think relevant.  Further, it is very common 
that a researcher is really interested in "human" not primate, so one 
typically finds oneself doing sub processing of a division anyway.

   It is NCBI's intent to gradually move to a position where what files 
the data is divided into is irrelevant, and can change as appropriate to 
the amount of data from any particular systematic group.  We would 
prefer to provide indexes that reflect a particular tree.  The index 
would give you the taxonomic division and index by file number and 
offset within file for the first entry, and file number and offset for 
the last entry.  Entries would then be sorted within the file by 
taxonomic group in a hierarchical scheme.  Thus "rodent" and "primate" 
are sorted within "mammal" and "human" and "African green monkey" are 
sorted within primate and so on.  With this scheme you could actually 
pull entries at whatever level of taxonomic hierarchy you wanted.

   We planned to base our initial sort on classical taxonomy.  Thus the 
disappearance of the organelle division.  I would note that within the 
ASN.1 for Bioseq is a type called GIBB-mod.  This has attributes that 
tell you if the sequence is from "mitochondria", "chloroplast", etc.  
Thus, it would be a simple filter to pull all organelles of any type 
from any division.  Our plan to have minimal impact was to make any
expected changes to the division structure now (split out EST, absorb
ORG).  Then the hierarchical indexes could be build as transparent
additionsf, while still keeping the files split in the old divisions.
Once the indexes were being reliably added, we thought we could phase
out specific divisions reflected in the files themselves.  This way there
would be lots of notice that divisions were going away and lots of overlap
to move to an indexing scheme.  It is our intent to give advance notice
of changes to the distribution format.  We just made an error in writing
the release notes about the ORG divisionl.  While we are human, so we
err, we will certainly do our best not let an oversight like that happen
again.

   While we must pick a particular taxonomy for sorting the data, and 
only one at a time can be selected, we recognize that there are many 
equally valid taxonomies.  We would expect to provide at least two as 
indexes; the classical taxonomy and a taxonomy based on molecular 
comparison (which would, of course, move the organelles into their own 
section).  Scott Federhen at NCBI has built a tool for comparing tree 
structured data, and we have begun an effort to integrate and 
rationalize the taxonomies from GenBank, EMBL, PIR, and SWISSPROT.  We 
are adding taxonomy/nomenclatures from experts, such as the recently 
available Viral Nomenclature.  Mitch Sogin has volunteered expert 
advice and he is convening a group of both classical and molecular 
taxonomists to attempt to select a best pair of trees for us to start 
with, and for on-going advice in the morass of organism nomenclature and 
taxonomy.

    We have no hope of ever coming up with a "definitive" taxonomy, but 
I think we can come up with an acceptable taxonomy(s) with a rational 
foundation, a regular maintenance cycle, and a public presentation, 
first by building on the work by other database groups, then by advice
by a panel of experts on an ongoing basis.  As usual, anyone who is
willing to do constructive work is encouraged to participate in this
process.

    Jim Ostell
    NCBI