[BioSQL-l] alternative taxonomic hierarchies in BioSQL?

[Peter]

On Thu, Dec 4, 2008 at 4:28 PM, Bánk Beszteri <Bank.Beszteri at awi.de> wrote:
>
> Dear BioSQLers,
>
> do I understand right that the current BioSQL schema allows for a single
> taxonomy per database only?

Not quite.  If you ignore that fact that the taxon table's external
taxonomy ID is explicitly labelled as the ncbi_taxon_id, you could
store any taxonomy in the taxon and taxon_name tables.  You could even
have multiple independent taxonomies in these tables.

However, each bioentry can only point to one taxon entry (and thus
belongs to only one taxonomy), which is a big limitation.

It would be useful to have a bioentry point to multiple taxon entries
(and thus multiple taxonomies, e.g. NCBI and ITIS), which might
require some sort of link table between the taxon and bioentry tables.
 This would also solve the issue of how to support chimeric sequences
which has been noted on
http://www.biosql.org/wiki/Enhancement_Requests

> When looking into the tables taxon and taxon_name, it looks like neither
> taxa nor their neighborhood relationships can belong to different taxonomies.
> Is this correct, or am I missing something?

True - but why would you want to interlink taxon entries like that?

> If this is so: are there any plans to add such a feature in the future? I
> think (besides that I could use it) it could probably be useful for others
> as well (to have the possibility to e.g. have an ITIS taxonomy or just a
> user?s own private taxonomy parallel to NCBI taxonomy in a single BioSQL
> DB). I didn?t find anything about this on the BioSQL pages, please direct me
> to the right place if I missed it!

I think the issue has been raised before on the mailing list, and IIRC
it was agreed that there was room for improvement.  Maybe this is
something for BioSQL v1.1.x?

Peter