[Bioperl-l] bioperl-db: exporting data

Hilmar Lapp hlapp at gmx.net
Wed Jul 6 03:47:21 EDT 2005

The way you're describing doesn't sound too far off. The rank is an 
ordering index as well as a component of the unique key constraint, 
i.e.,  you can't have two seqfeature qualifier values for the same 
feature and tag name unless the rank is different.

Have you convinced yourself that you con log in to the database and 
retrieve those additions by hand (using SQL)?

Can you reduce this to a test case where you load a single sequence 
record, then issue SQL to add your custom annotation, and then retrieve 
the record again. Email me the entry you loaded, the SQL statements you 
issued, and the entry you got out.


On Jul 5, 2005, at 8:01 AM, Johan Viklund wrote:

> Hi
> I'm trying to add COG annotations from Entrez Gene to sequences (from
> refseq in genbank format) I have in a biosql database (on mysql). The
> problem is I can't get them out again with the bioentry2flat.pl script
> (the bioentries appears without what i've added).
> I don't use bioperl for this (i've got ~40000 COG annotations (linked
> to GeneIDs)). Instead I add it to the seqfeature_qualifer_value table
> similar to the way GeneID:s are represented (as far as i've figured),
> with term_id corresponding to db_xref, the same seqfeature_id as the
> GeneID had and rank i've tried a few different variations but none
> seem to work (the first free that's larger than GeneID and 1).
> How should I add this annotation to the database so it gets exported
> when I use bioperl?
> I've also got another question: What is rank for?
> -- 
> Johan Viklund
> E-mail: <johan.viklund.0705 at student.uu.se>
>         <johan.viklund at gmail.com>
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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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