[Biojava-l] taxanomical API

Alan Robinson alan@ebi.ac.uk
Wed, 6 Feb 2002 09:11:01 +0000 (GMT Standard Time)

Hello everybody,

> Subject: RE: [Biojava-l] taxanomical API
> Date: Tue, 5 Feb 2002 08:40:56 +1300
> From: "Schreiber, Mark" <mark.schreiber@agresearch.co.nz>
> To: "Matthew Pocock" <matthew_pocock@yahoo.co.uk>,
>  Hi -
>  I had some prior experiences with the NCBI taxonomy database. If the
> EMBL one is pretty much the same then it would strongly get my vote
>  Mark Schreiber

The EBI uses the NCBI taxonomy database for its taxons. The data in the
databases is identical.

With regard to the API: <http://www.Species2000.org/> was looking at CORBA
technology to define interfaces for its taxonomic data (no idea of its
current status though):

  "The Quiet Revolution: Biodiversity Informatics and the Internet."
   Frank A. Bisby 
   Science 2000 September 29; 289: 2309-2312"

Also, the EBI has been making its copy of the NCBI taxonomy server
available through a CORBA server for the last 5 years(!):


The interface is defined in the IDL and is very simple (though we do
include a method to return a translation table for an organism):

  Taxonomy API:	http://corba.ebi.ac.uk/idl/taxonomy.txt

Errors, exceptions, etc. are defined in a common types module that is
used by a number of EBI CORBA servers:

  Types:	http://corba.ebi.ac.uk/idl/types.txt

Documentation about the interfaces:


The IOR:


Regardless of people's views on CORBA technology as a transport protocol,
I do hope some of the ideas & concepts about *data modelling* in these
respective IDL's are examined. As a BioJava API for taxonomy data emerges,
I'll look to getting a compliant CORBA/SOAP server running and/or facade

Best wishes,

Alan J. Robinson, D.Phil.             Tel:+44-(0)1223 494444
European Bioinformatics Institute     Fax:+44-(0)1223 494468
EMBL Outstation - Hinxton             Email:  alan@ebi.ac.uk
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD, UK                http://industry.ebi.ac.uk/~alan/