[BioSQL-l] null title and CRC

[Richard Holland]

Sounds good.

cheers,
Richard

On Fri, 2006-07-14 at 14:31 -0400, Hilmar Lapp wrote:
> In the table you store the value of the attribute, not a default that
> substitutes for it in some calculation. I.e., either null or an empty
> string, depending on what the value is. (in Oracle an empty string is
> treated as null.)
> 
> 
> -hilmar
> On Jul 14, 2006, at 1:48 PM, David Scott wrote:
> 
> > we are currently using "<undef>" in the crc calculation for the case
> > where the title is empty (or null) - i can extend that for authors
> > and location - what should we be storing the the table: "<undef>",
> > empty, or null?
> > 
> > thanks-
> > david
> > 
> > p.s. fog for sale:
> > http://www.sfgate.com/liveviews/
> > 
> > 
> > Hilmar Lapp wrote: 
> > > The CRC for references uses the authors, title, and location  
> > > attributes in Bioperl-db, and empty (or null) strings default to the  
> > > string "".
> > > 
> > > If title is empty and authors and location do not distinguish two  
> > > references, then why do you want to have two rows for those  
> > > references? Basically, there are identical for all intents and  
> > > purposes, or are they not?
> > > 
> > > 	-hilmar
> > > 
> > > On Jul 9, 2006, at 11:03 PM, mark.schreiber at novartis.com wrote:
> > > 
> > >   
> > > > Hi -
> > > > 
> > > > We are having a problem in biojava parsing some genbank records that
> > > > contain references with no title. These cannot have a CRC value  
> > > > which is
> > > > required in BioSQL. If we make the title an empty string then we  
> > > > quickly
> > > > get non-unique CRC numbers.
> > > > 
> > > > What does BioPerl do in these cases?
> > > > 
> > > > - Mark
> > > > 
> > > > Mark Schreiber
> > > > Research Investigator (Bioinformatics)
> > > > 
> > > > Novartis Institute for Tropical Diseases (NITD)
> > > > 10 Biopolis Road
> > > > #05-01 Chromos
> > > > Singapore 138670
> > > > www.nitd.novartis.com
> > > > 
> > > > phone +65 6722 2973
> > > > fax  +65 6722 2910
> > > > 
> > > > _______________________________________________
> > > > BioSQL-l mailing list
> > > > BioSQL-l at lists.open-bio.org
> > > > http://lists.open-bio.org/mailman/listinfo/biosql-l
> > > > 
> > > >     
> > >   
> > 
> 
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
> 
> 
> 
> 
> 
> 
> 
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416