[BioSQL-l] null title and CRC

[David Scott]

ok, then - in the case of genbank: i'm going to try to treat missing 
titles as null - store them in the object as null - and provide them to 
the hibernate o/r mapping as null - presumably they will go into the 
table as null.

best-

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 :
> ===========================================================
>
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