Re: [Gusdev-gusdev] LoadNRDB - Versioning

[Deborah F. P. <pi...@pc...>]

Hi,

I'll try to answer your questions.

The plugin is designed to load from fasta files downloaded directly from 
NCBI. We download the full db file and the plugin updates our database 
including deleting obsolete entries when the --delete option is used. 
Therefore, I think it would do well with update/change files but in this 
case the --delete option would NOT be used.

The plugin loads entries into dots.NRDBEntry and dots.ExternalNASequence, 
in each case inserting if new, updating existing data, and deleting but 
only if that option is used. The NRDB data would change with each update, 
although existing ids should be more or less stable. I think that would 
mean that analyses should be rerun after updates but there should be only 
incremental differences. Specific queries can be done to test whether an 
analysis is "stale".

You may have had a problem because a complicated command line is required 
as well as a fairly large set of 
sres.externaldatabaserelease.external_database_release_id's. Below is an 
example command line:

(ga GUS::Common::Plugin::LoadNRDB --temp_login "$temp_login" --sourceDB
$sourceDB --temp_password "$temp_password" --dbi_str "$dbi_str"
$restart --gitax $gitax --nrdb $nrdb --extDbRelId $nrdbReleaseId
--maketemp --plugin --delete > nrdb.out) >& nrdb.err &


$nrdbReleaseId = 4194
$nrdb = /files/cbil/data/thirdpart/nrdb/2004-01-07/nr
$gitax = /files/cbil/data/thirdpart/taxonomy/2004-01-07/gi_taxid_prot.dmp
$restart = for restarting the interrupted plugin(use with plugin
             option), use number from last set number in log

$dbi_str =       fill these in with what you want
$temp_password = I kept these because I have to grant
$temp_login =    permissions and truncate the table but they should be
                  eliminated at some point

$sourceDB =
hum:
6501:gb,6502:emb,6503:dbj,6504:pir,6505:prf,6506:sp,6507:pdb,6508:pat,6509:bbs,6510:gnl,168:ref,6633:lcl,6511:genpept,7333:tpe,8035:tpd


You will need to supply your own external_database_release_id's. The 
gi_taxid_prot.dmp is another file downloaded from NCBI 
(ftp://ftp.ncbi.nih.gov/pub/taxonomy).

Another requirement is that the taxonomy tables (sres.taxon, 
sres.taxonname, and sres.geneticcode) must be filled with NCBI taxonomy 
data. (ftp://ftp.ncbi.nih.gov/pub/taxonomy). That can be done using the 
LoadTaxonomy.pm plugin.

If you need a sample command line for LoadTaxonomy.pm, let me know.

                                                            Debbie





On Mon, 12 Jul 2004, Pablo Nascimento Mendes wrote:

> Hello all,
> we have some questions on loading a new release of NR into a live
> database. Maybe some of you have already addressed these issues. We
> would appreciate any help.
>
> 1) How does GenBank release new versions of the NR database?
> 	- Whole DB downloads?
> 	- Updates/changes only?
>
> 2) Has anybody used the LoadNRDB GUS plug-in successfully with a FASTA
> version of the NR DB obtained directly from NCBI?
> We have the version 1.22 of LoadNRDB GUS plug-in and we're having
> difficulty using it to load the NR database. It crashes when it finds,
> for instance, a header like this:
>> gi|25506335|pir||B90058 conserve (...)
> So, do we need to fix all the supposedly incorrect headers?
>
> 3) How are sequences updated in GUS? Is the whole DB version loaded each
> time? Or only sequences whose accession/ids have changed?
>
> 4) How are analyses that were run from a previous db release version
> affected? What about analyses performed on sequences that didn't change?
>
> 5) How can we determine what analyses stored in GUS are "stale" when a
> new version of NRDB is released?
>
> Thanks in advance
> --
> -----------------------------
> Pablo N. Mendes
> Research Scholar
> Kissinger Lab
> Department of Genetics
> University of Georgia
> C210 Life Sciences Bldg.
> Athens, Georgia 30602
> Phone:706 542-1447
> E-mail: pa...@ug...
>
>
>
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