[Bioperl-l] Could not load GO terms to BioSQL

Hilmar Lapp hlapp at gmx.net
Sun Jan 4 17:26:15 EST 2004

On Sunday, January 4, 2004, at 01:09  PM, Holland, Richard wrote:

> Simple fix is to adjust the size of the accession column in dbxref. I
> have doubled it to 64 characters. Could someone verify this is sensible
> and see if the schema could be updated to match?

I encountered the same problem a while ago and applied the exact same 
fix, although I wasn't extremely happy with this solution, as it is 
caused by GO references in a way hijacking dbxref and not necessary for 
any other reason.

The real fix requires substantial code changes though across the 
bioperl and bioperl-db board, as the object model has the real flaws 
here. Juguangs fixes to Bio::Ontology::Term may have actually brought 
us closer to that goal.

The reason why the fix isn't in cvs is that we maintain a local version 
of the biosql-schema repository for our Symgene project. This has 
caused synchronization issues a number of times and generally annoys 
me; I'll remedy this situation as soon as biosql is released the first 
time. Another aspect that's driving me to really make this happen now.

Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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