[BioSQL-l] Getting gene name, function etc. from biosql

[Michael Muratet]

On Aug 23, 2010, at 2:08 PM, Nick Loman wrote:

> Hi Michael
>
> You need a join on seqfeature_qualifier_value to get this detail.  
> This table stores feature qualifiers as key/value pairs, with the  
> corresponding key name ('name', 'product', etc.) belonging to the  
> relation 'term', so you'll need to join on that too.

Hi Nick

Yes, that does the trick. I knew it would be something simple ;-)

Thanks

Mike

>
> HTH
>
> Cheers
>
> Nick
>
>
> Michael Muratet wrote:
>> Greetings
>>
>> I am working on assembling gene CDS sequences on a medium scale,  
>> e.g.,  for all S. aureus strains, and I'm trying to find a way to  
>> get gene  names from biosql entries I created from Genbank files  
>> with  load_seqdatabase.pl. I'm using a query like this:
>>
>> SELECT
>>     c.seqfeature_id, b.strand, SUBSTR(a.seq, b.start_pos,  
>> b.end_pos- b.start_pos+1) as seq
>> FROM
>>     biosequence a
>>     JOIN
>>     seqfeature c
>>     ON (a.bioentry_id=c.bioentry_id)
>>     JOIN
>>     location b
>>     ON (b.seqfeature_id=c.seqfeature_id)
>> WHERE
>>     c.type_term_id=12
>>     AND
>>     c.bioentry_id=221
>>
>> This seems to work OK to get the sequence with the provision that  
>> one  needs to reverse complement the sequence if the strand is minus.
>>
>> But I don't see anything in the schema that will allow me to  
>> identify  the gene name or product from the seqfeature_id.
>>
>> Is gene name or product in the schema somewhere and I've missed it?
>>
>> Thanks
>>
>> Mike
>>
>>
>> Michael Muratet, Ph.D.
>> Senior Scientist
>> HudsonAlpha Institute for Biotechnology
>> mmuratet at hudsonalpha.org
>> (256) 327-0473 (p)
>> (256) 327-0966 (f)
>>
>> Room 4005
>> 601 Genome Way
>> Huntsville, Alabama 35806
>>
>>
>>
>>
>>
>> _______________________________________________
>> BioSQL-l mailing list
>> BioSQL-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>>
>

Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806