[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 #21 from biopython-bugzilla at maubp.freeserve.co.uk  2008-04-08 11:04 EST -------
Regarding comment 20, you're right to say the one record/many records issue is
cloudy.  Lets stick with using Bio.Entrez.read() then.

Regarding returning objects or dictionaries, my feeling was that attributes and
doc strings could be used to help explain how to interpret the results. 
However, if as you say the python dictionary is a natural representation of the
XML data, then that should suffice - provided the NCBI have been clear with
their field naming conventions.

If we are all happy with this, then we should update the Bio.Entrez chapter of
the tutorial.  I would remove some of the longer cut-n-paste sections of XML
output, as it doesn't look very good in the PDF output.

Getting back to the NCBI taxon issue in BioSQL, did Hilmar's reply on the
BioSQL mailing list clarify the use of the left/right fields?
http://lists.open-bio.org/pipermail/biosql-l/2008-April/001233.html


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