Path: utzoo!attcan!uunet!bionet!lhc!ncifcrf!fcs260c2!toms
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.molbio.genome-program
Subject: Re: feature table parsers - what's it all mean?
Message-ID: <1894@fcs280s.ncifcrf.gov>
Date: 3 Oct 90 18:26:47 GMT
References: <4725@lure.latrobe.edu.au>
Sender: news@ncifcrf.gov
Organization: NCI Supercomputer Facility, Frederick, MD
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I am happy to see a discussion on parsing GenBank after all these years.

The feature table is only part of the problem.  For example, entries of GenBank
now end with a // (an idea taken from the embl database) so that programs could
distinguish where entries ended.  Before Matt Yarus suggested this to me and I
brought the suggestion it to the GenBank staff, it was difficult to tell where
the entry ended.  Indeed, since there is no definition of GenBank, some
programs give one hacked up entry formats that do not end with a // nor do they
have the same format as is on the GenBank tapes.  The authors of these programs
don't understand that the output of their programs should have a // at the end
simply because there is no standard definition of the format.

SUMMARY: we need a FULL DEFINITION of GenBank, not just the feature tables!!!

Example: we should be able to parse out the topology of an entry (circular or
linear sequence) and the references.  The topic is wider than most people have
discussed so far, and I don't understand why GenBank has resisted creating the
definition for so long.  I made the suggestion that a parsable form with an
associated DOCUMENT and DEFINITION is a requirement for the database AT LEAST 8
YEARS AGO.

How many more years will we have to wait for this?

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov