taxonomy database ?

Heikki Lehvaslaiho heikki at ebi.ac.uk
Tue Nov 17 09:57:50 EST 1998

Peter Rice wrote:
> Heikki Lehvaslaiho <heikki at ebi.ac.uk> writes:
> > Peter Rice wrote:
> >
> > > But how do I download the EBI's views.i ?
> >
> > I suppose you can not. Sorry. A link will be added into SRS web
> > interface in due time.
> >
> > Put this into your views.i and then srssection:
> OK, now I get the view (except I do not see taxonomy as the default view
> for the database).

TAXONOMY_DB: add "defaultView:@Tax_View"

> When I look at the up link (red arrow) it looks fine up to "Eukaryota"
> but then I see 12 other Taxons including "lobe-finned fish and
> tetrapod clade" and "Fungi/Metazoa group" (on my server and the EBI
> server). Strange because "Eukaryota" has a parent-id of 1 which should
> be straight up to "root".

I was afraid you'd eventually ask that.  8-). At the moment we have to
show the entries in the order they apper in the (flat file) database and
the (relational) database does not have an easy handle to sort them
easily and fast other than by rank. The ones that are clustered on the
top of the list below root all have rank: 'no rank'. We really have to
wait for the next SRS & Icarus version to do better.

> The common name(s) do not seem to be indexed. Can they be added?

They are indexed but since there are 10 different fields that contain
other than the accepted scientific name, there are no specific search
fields for all of them. You can search them using AllText field. 


______ _/      _/_____________________________________________________
      _/      _/                      http://www2.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________

More information about the Bio-srs mailing list

Send comments to us at biosci-help [At] net.bio.net