[bionet.molbio.genbank] feature table parsers - what's it all mean?

davison@MENUDO.UH.EDU (Dan Davison) (10/04/90)

> 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.

toms@fcs260c2.ncifcrf.gov (Tom Schneider) (10/04/90)

In article <9010031956.AA08670@largo.ig.com> davison@MENUDO.UH.EDU (Dan Davison) writes:
>A complete definition is available from the GenBank staff at Los

Ok, I've asked them for the latest version of a complete definition.

>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.

A full definition does not break software, it encourages good software.  Not
breaking software is a "great" reason for never making changes.

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

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