[BioSQL-l] null title and CRC

[Angel Pizarro]

Hilmar Lapp wrote:
> I think I need to debug this. If bioperl-db stumbles over this, then 
> it sounds like that's what needs to be fixed.
>
> Can you or somebody else provide with two sample records that 
> exemplify (i.e., replicate) the problem and which I can turn into a 
> test case?
>
Since these where bulk loads, I am not sure which records conflicted, 
but I'll have a poke around and see if I can grab a test set for you.
-angel

>     -hilmar
>
> On Aug 3, 2006, at 2:12 PM, Angel Pizarro wrote:
>
>>  From hilmar:
>>> The CRC for references uses the authors, title, and location
>>> attributes in Bioperl-db, and empty (or null) strings default to the
>>> string "<undef>".
>>>
>>> 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
>>
>> Sorry for not replying to the original thread, but I just joined this 
>> list.
>> This was an issue for me with bioperl loading as well, since I was using
>> the same biosql instance to load two different biodatabases with the
>> same entry. Specifically, I loaded IPI, which has no feature table in
>> the entries, and the genbank equivalents to get the feature tables.
>> Namely the constraint caused an error when the the genbank record was
>> loaded.
>>
>> I think that this is primarily an issue with bioperl, but I raise it
>> here to make the java folks aware of the potential pitfall and maybe ask
>> if whether the CRC should be calculated with the biodatabase in mind?
>> Probably not, since as hilmar states, it's still the same reference.
>>
>> BTW - I solved the issue by dropping the constraint, since I really
>> don't care about references. Not optimal, but certainly easiest thing to
>> do ;)
>>
>> -angel
>>
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>>
>
> --===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>

-- 
Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
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