[Biopython-dev] [Bug 2405] BioSQL gives UserWarning: ... not recognised as database type: temporarily accepting key

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sat Nov 24 09:22:39 UTC 2007


------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2007-11-24 04:22 EST -------
Based on talking to a couple of the BioPerl guys, they don't do any mapping of
the db_xref at all.  I see two options:

(a) Continue with the historical mapping in Biopython, and simply remove the

(b) Remove the mapping, just store the raw NCBI supplied db_xref terminology.

(c) Remove the mapping, except when reading data from the database in order to
retain backwards compatibility with data written using older versions of
Biopython [may not be required; until I fixed it recently the db_xref wasn't
even loaded for SeqFeatures]

I favour option (b) because its simpler and more compatible with the other Bio*

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