[Bioperl-l] Bio::Species/Bio::Taxonomy changes

[Chris Fields]

> > Maybe the file parser could have its own organelle() method
> > and leave all taxonomic classes without such a method. Or it could
> > stay
> > as is, I don't know.
> 
> Like I said above, at the end of the day there needs to be a way to
> qualify a sequence by the genome it is part of.

Agreed.  I think Sendu's right in one regard, it doesn't seem to have
anything to do with the taxonomy itself.  See below...

There should be a way of containing this somehow, maybe using a
Bio::Annotation::SimpleValue object or having a get/set somehow.

> > Do different organelles in the same species get unique taxonomy ids?
> 
> I would have to confirm, but I believe so. As I said, from a genome/
> sequence-centric viewpoint, the organelle and nuclear genomes are two
> different things.

Looks like the organelle sequence data uses the organism TaxID.  I couldn't
find organelle-specific taxon information using the TaxBrowser for
mitochondrion, chloroplast, or plastid.  

     source          1..426
                     /organism="Reticulitermes tibialis"
                     /organelle="mitochondrion"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:186107"
                     /haplotype="T9"

TaxID refers to the organism ("Reticulitermes tibialis"), not the
mitochondrion.  

     source          1..814
                     /organism="Porterinema fluviatile"
                     /organelle="plastid:chloroplast"
                     /mol_type="genomic DNA"
                     /strain="SAG 124.79"
                     /db_xref="taxon:246123"
                     /country="Germany"

TaxID refers to the organism ("Porterinema fluviatile"), not the
chloroplast.

Chris