[BioSQL-l] Genbank loading time

[Chris Fields]

On Jan 28, 2009, at 11:17 AM, Peter wrote:

> On 1/28/09, Chris Fields <cjfields at illinois.edu> wrote:
>>
>> My bad, I'm thinking of the taxonomy loader (need more coffee).  I'm
>> wondering, though, whether it would be feasible to have a direct  
>> loader for
>> the most common database formats (GenBank/EMBL/Swiss), something
>> similar to the taxonomy loader that doesn't rely on any specific  
>> Bio* package.
>>
>
> You could re-invent the wheel, and write yet another
> GenBank/EMBL/Swiss parser in standalone perl for use within
> load_seqdatabase.pl but I really don't see any point to this.  Reusing
> the BioPerl parser seems most sensible, especially given that
> bioperl-db is an extension to bioperl in the first place - and the
> BioPerl parsers already exist and are well tested.
>
> Peter

My point is, instead of first mapping record data to a specific object/ 
class then mapping the object data to the database, bypass the object  
completely and generically map relevant data directly in the database  
according to the BioSQL schema.

If anything this may force some consistency between the various Bio*  
languages.

chris