[BioSQL-l] Authority in biodatabase table

[Richard Holland]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

BioJava leaves authority blank at the moment.

cheers,
Richard

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
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.2.2 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFHS9fY4C5LeMEKA/QRAnPBAJ48/fwxyJ0rBnIJNZnTpZexXAs6iQCgnuTq
D4MzSndO+Osf/lzSVqQOArQ=
=rOVk
-----END PGP SIGNATURE-----