Path: utzoo!utgpu!watserv1!watmath!att!emory!swrinde!cs.utexas.edu!usc!apple!bionet!UH.EDU!Davison
From: Davison@UH.EDU (Dan Davison)
Newsgroups: bionet.molbio.genbank
Subject: Re: Suggestion for keywords in genbank
Message-ID: <9102010509.AA07940@menudo.uh.edu>
Date: 1 Feb 91 05:09:27 GMT
References: <9102010448.AA15467@genbank.bio.net>
Sender: daemon@genbank.bio.net
Lines: 43


> 	Twice in the last couple of days, the same thing has happened to
> me.  J. Random biologist walks into my office and wants to find an entry in
> genbank.  I try hard to extract some useful keywords.  In this case, I got
> from said JRB the name of a gene, FemA.  Unfortunately, FEMA isn't a
> keyword that the entry is indexed under, but "FEMA PROTEIN" is [...]
> I'd be interested to hear comments from other people about what
> is the best way to generate good keyword/keyphrase indicies for genbank.


Geez, I thought it was only me.  This happens a lot; one of the most
brain-damaged things about GenBank in its flat-file incarnation is
that the "keywords" are essentially a joke.  J. Random Faculty Member
or J. Random Gradual Student asks for this kind of thing once a week
or so.  And people always want such thing from the e-mail server (UH,
not GenBank's, presumably they want it from GB too).  I have just
about finished an awk script to let people do lookups by keyword, but
it uses GB's-provided keyword index.  The solution is to do a baby
IRX; index all the words in the headers.  (If the Gene-Server grant is
funded I think I'll do this, thanks for the idea, Roy).


The thing to do is to somehow get the flat file format "keyword" line
improved.  Since there is YAGCC in the winds (Yet Another GenBank
Contract Change) I won't hold my breath, but it sure would be nice if
the GenBank curator project would have the curators attach
"significant" (to others in the field) keywords.  Paul?



> but after my flame last week about personalized reformatting of
> files on the distribution tapes, I'd probably just end up getting
> into a shouting match with myself :-)

I know how you feel...see my .sig...

dan

-- 
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77054-5500/davison@uh.edu/DAVISON@UHOU
Disclaimer: As always, I speak only for myself, and, usually, only to
myself.