[Biopython-dev] [Bug 2475] New: 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

           Summary: BioSQL.Loader should reuse existing taxon entries in
                    lineage
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: BioSQL
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


Based on a report on the mailing list by Eric Gibert,
http://lists.open-bio.org/pipermail/biopython/2008-March/004137.html
http://lists.open-bio.org/pipermail/biopython/2008-March/004147.html

The _get_taxon_id() function will add new entries to the taxon and taxon_name
tables when a species isn't already defined.  It will also generate entries for
the lineage (for which we don't know the NCBI taxon names).  At this point it
*should* be re-using any existing entries for elements of the lineage.

Note - this is complicated due to the re-use of the same latin names in
different classes.  It might be easier/safer just not to write the lineage at
all?


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