[Biopython-dev] [Bug 2475] BioSQL.Loader should reuse existing taxon entries in lineage

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2475





------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2008-03-30 07:41 EST -------
I quite like the idea of fetching the new taxon information from the NCBI as
needed to record an accurate lineage.  However, what happens if:

(a) The network is down?  Raise an exception maybe?
(b) The NCBI doesn't have this Taxon ID (i.e. its invalid or so new their
database is out of date)?  Raise an exception?

Eric, could you attach your taxonomy XML code to this bug?  We'd probably want
to start by adding taxonomy XML parsing to Bio.Entrez (which I assume you are
using to fetch the XML data).

What about sequences where we don't have a taxon ID, but we do have a species
name?  (which may happen with a sequence which wasn't read from a GenBank
file).


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