[BioSQL-l] bioentry.name and bioentry.identifier only 40 characters?

[Hilmar Lapp]

Interesting. I see your logic and I guess you have a point.

I've almost exclusively been loading all kinds of genbank,  
{swiss,uni}prot, unigene etc files, which don't suffer from this  
problem, as the name then is either identical to the accession, or is  
a short gene symbol, and the identifier is the GI#, or empty.

I myself wouldn't load FASTA files w/o any processing/parsing the  
identifier token, but maybe that's not a reasonable expectation to put  
on everyone else?

	-hilmar

On Sep 26, 2008, at 9:56 AM, Peter wrote:

> Hi All,
>
> In BioSQL v1.0.1, fields bioentry.accession and dbxref.accession were
> increased from 40 to  128 characters.  See
> http://lists.open-bio.org/pipermail/biosql-l/2008-August/001311.html
>
> However, bioentry.name and bioentry.identifier are still only 40
> characters - which seems a bit short, given that BioPerl's
> load_seqdatabase.pl seems to put the full contents of a FASTA
> identifier (up to the first space) in both bioentry.name and
> bioentry.identifier fields.  I've just been dealing with Biopython and
> loading FASTA files into BioSQL (Bug 2425) and a similar concern
> applies here.
>
> Has anyone had any real world problems with the bioentry.name and
> bioentry.identifier fields being too small?
>
> Peter
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> BioSQL-l at lists.open-bio.org
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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