[Bioperl-l] postgres 8.3 - load_seqdatabase.pl / swissprot

[Erik]

On Sun, March 23, 2008 02:40, Hilmar Lapp wrote:
> But maybe load_seqdatabase.pl or even BioSQL or BioPerl
> aren't suitable for your use-case?

well, that may turn out to be the case, but I'm not quite
deterred yet.

I am in a situation like many others, I think: microarray,
mass spec, and chipseq (Solexa) data all need
annotation,and while it is easy to retrieve some useful
records from public data sources (entrez, ensembl &
biomart, etc.), it is not so easy to have such high
atomicity in the locally stored annotation data that
fine-grained filtering and sorting on a sql level becomes
possible.  I hope the bioperl parsers, together with the
biosql schema, will give SQL access to all or most data
bits.

And I understand GBrowse can run on top of BioSQL/Pg too,
albeit somewhat preliminary; this is another usage I will
need.

btw, should not all those references to postgres 7.3 be
upgraded to something newer, like 8.2.7 (maybe not yet 8.3
heh) ?  7.3 is not supported anymore by the pg project.

Sprot loaded in 20 hours. Only 170 were rejected - not too
bad.

Thanks,

Erik Rijkers