[BioSQL-l] entrez gene into biosql

[Hilmar Lapp]

Bioperl has an EntrezGene SeqIO parser, so load_seqdatabase.pl should 
be able to load it.

What I still haven't gotten to, however, is to validate that the 
resulting data structure is compatible with the one created by the 
SeqIO::locuslink parser.

I.e., the mappings ought to be very similar, in spirit where the 
annotation didn't exist in LL, and literally where the annotation was 
also present in the LL format.

The validation I was referring foremost pertains to the SeqIO parser, 
as without further customary processing that will pretty much determine 
the resulting structure in BioSQL.

As a start, you can load the old LL download into BioSQL and see where 
things go. (Pretty straightforward - most of the tags end up as 
annotation.)

	-hilmar

On Dec 13, 2005, at 9:29 PM, mark.schreiber at novartis.com wrote:

> Hello -
>
> Has any one ever tried to squeeze Entrez gene records into BioSQL? Was 
> it
> successful? What mappings did you use?
>
> Thanks,
>
> - Mark
>
> Mark Schreiber
> Research Investigator (Bioinformatics)
>
> Novartis Institute for Tropical Diseases (NITD)
> 10 Biopolis Road
> #05-01 Chromos
> Singapore 138670
> www.nitd.novartis.com
>
> phone +65 6722 2973
> fax  +65 6722 2910
>
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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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