[Bioperl-l] Some problems about Bioperl-sql database structure

[Hilmar Lapp]

SeqFeatureI::display_name() is stored and retrieved in the current 
biosql/bioperl-db combination. Note though that no SeqIO parser sets or 
uses this attribute, so unless you populate it yourself it will be 
undef.

The location_qualifier_value table is intended solely (even though you 
could use it for more purposes of course) for fuzzy location 
information. The current bioperl-db doesn't preserve fuzzy locations - 
it treats them as simple locations (with the coordinate policy 
determining what this means). This needs to be fixed at some point, but 
it's not a high priority on many people's agenda ...

Keywords are stored as bioentry_qualifier_value rows.

	-hilmar

On Tuesday, May 13, 2003, at 05:49  AM, Nicolas Rueff wrote:

> While using bioperl-db/scripts/load_seqdatabase.pl script to fill a
> (mysql) database based on biosql-schema/sql/biosqldb-mysql.sql 
> structure
> whith some data from SwissProt, I saw that human-readable informations
> about seqfeatures (seqfeature.display_name) and locations
> (location_qualifier_value.value) was ignored. Is there any way to fill
> those fields ?
>
> Moreover, the "keywords" table as disappear from the database. I think
> it could be useful to put it in again.
>
>
> -- 
> Nicolas Rueff <rueff at mediagen.fr>
>
> Mediagen SAS
> Institut Pasteur de Lille
> 1, rue du Professeur Calmette
> Bâtiment Guérin, 3eme étage, BP 245
> 59019 LILLE Cedex
> Tel +33 3 20 87 72 76
> Fax +33 3 20 87 72 82
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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