[BioPython] [BioSQL-l] Authority in biodatabase table

[Hilmar Lapp]

(Sorry for this long-too-late reply. Going through old email that got  
left unread or unresponded.)

Peter - you probably implemented something meanwhile that suits your  
needs. Just FYI, BioPerl leaves this empty too. The general notion  
for authority is that of the LSID authority field, but of course you  
won't be able to parse this out of any input file. The value for  
SwissProt would be uniprot.org, for example. For NCBI, I'm not sure -  
NCBI hasn't ever issued any LSIDs, but presumably it would be  
something like ncbi.nlm.nih.gov.

	-hilmar

On Nov 26, 2007, at 2:10 PM, Peter wrote:

> Thank's for all the replies on the db_xref issue.
>
> Today I'd like to ask if there are any established guidelines for the
> biodatabase table - in particular for how to use the "authority" field
> in the biodatabase table, and if there is any agreed terminology for
> the named "sub databases" defined therein i.e. what should I call them
> in our documentation.
>
> By default, unless the user specifies an authority, we end up with a
> NULL when creating entries in the biodatabase table using Biopython.
> For example:
>
>> from BioSQL import BioSeqDatabase
> server = BioSeqDatabase.open_database(driver="MySQLdb", user="root",
>                      passwd = "", host = "localhost", db="bioseqdb")
> db = server.new_database("orchids", description="Just for testing")
> server.adaptor.commit()
>
> I'd like to give some sensible defaults in any worked examples.  Apart
>> from simple test cases (like above), sensible examples that came to
> mind would be creating a "sub database" to contain:
> (*) an entire GenBank release
> (*) the latest SwissProt release
>
> What would you use in these cases.  In fact, what does your
> biodatabase table contain right now?
>
> Thank you all,
>
> Peter
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> BioSQL-l at lists.open-bio.org
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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