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

[Barry Moore]

I've tweaked some of those varchars in the past on local  
installations, but I can't remember off the top of my head if I did  
that for name - probably not.  I would to agree with the emerging  
view though - I don't know that I would need longer names right now,  
but it hardly makes sense to have an accession length of 128 and a  
name length of 40 since the name may well be or include the accession.

B

Barry Moore
Senior Research Specialist
Eccles Institute of Human Genetics
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




On Sep 26, 2008, at 8:46 AM, Peter wrote:

> On Fri, Sep 26, 2008 at 3:24 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
>>
>> 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.
>
> In my case its also been mostly GenBank files, where long names are
> not an issue.
>
>> 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?
>
> I think is not unreasonable to want to import FASTA files directly  
> (but this
> is not something I've actually done other than for testing).  For  
> example,
> I might want to import NCBI FASTA files directly, but these  
> probably have
> names under 40 letters.  Another example would be sequencing or  
> assembly
> output, but I don't have a feel for what kind of length names are  
> used here.
>
> I was half expecting someone on the list to say "Oh yes - we had to  
> increase
> the field size when we were importing XYZ".
>
> Peter
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