Path: utzoo!attcan!uunet!bionet!MENUDO.UH.EDU!davison
From: davison@MENUDO.UH.EDU (Dan Davison)
Newsgroups: bionet.molbio.genome-program
Subject: Re: feature table parsers - what's it all mean?
Message-ID: <9010031956.AA19552@genbank.bio.net>
Date: 3 Oct 90 19:56:41 GMT
References: <9010031936.AA18626@genbank.bio.net>
Sender: daemon@genbank.bio.net
Lines: 47


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

A complete definition is available from the GenBank staff at Los
Alamos.  Last I knew the name of the document was "dnaform.dc3".  It's
what I use to guide my programming (sic) that reads GenBank entries.


> 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. 

GenBank et al. can defend themselves, but such a definition does exist
and all you'd have had to do was ask...I did in 1982, that's how I
found out about it.  It has been updated regularly since.

> 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. 

Another person who wants to break even more existing software.  GB
staff are very conservative about changes.  This drives most of
non-GB'ers nuts (because of course we know what's right ;->) but
they're right to be conservative on such  matters.


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

This (genbank-bb) is the place to discuss changes...I'm sure the GB
folk have their flameproof suits on whenever they go near a keyboard.
Fire away.

dan

--
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77054-5500/davison@uh.edu/DAVISON@UHOU

"Comparing bad weather to rape: 'if it's inevitable, just relax and
enjoy it'"  Clayton Williams, Republican candidate for Governor of
Texas. ...And THIS is the kind of person and attitute most Texans find
acceptable...in 1990...very sad.

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.