[ANN] XEMBL - EMBL/Genbank/DDBJ Nucleotide Sequences as XML

Jean-Jack M. Riethoven pow at ebi.ac.uk
Mon Nov 12 05:04:06 EST 2001

XEMBL - EMBL/Genbank/DDBJ Nucleotide Sequences as XML

What is the XEMBL Project?

XEMBL is all about bringing EMBL Nucleotide Sequence data to our users in 
a variety of formats. The publically available EMBL/GenBank/DDBJ data is 
kept at the EBI in an Oracle database, from which flatfiles are created at 
every release for the purpose of distribution.
As you might be aware of, flat-files have severe limitations, and we have 
been asked various times if we are going to distribute the EMBL data in 
different formats as well, XML being the one most prominently mentioned.
In short, the XEMBL project will bring to the user several alternative 
formats of EMBL data.

Which formats do you support?

At the moment, we have BSML (an XML standard from Labbook) and AGAVE (an 
XML standard from DoubleTwist) as our first formats. BSML comes nearest to 
matching the exact information that is contained in EMBL database entries, 
AGAVE is more centred on (genomic) annotations.
Later, we will make available more formats for your use, e.g. GAME, BIOML, 

How do I use these formats?

There are several ways you can make use of these formats. You can write 
your own parsers for the resulting XML files and couple this with database 
import or analysis programs, or you can use available viewers or programs 
that support these formats. 
For the formats we have now (BSML & AGAVE), both Labbook and DoubleTwist 
respectively have free genomic viewers that you can download at their site 
(see below). We imagine other viewers will be available in the near future 
as well.
Important to mention here is that the BioPerl project is writing modules 
that can read and write BSML and AGAVE formats, opening up a whole range 
of usuable applications.

How can I use XEMBL?

XEMBL is running as a normal CGI script AND as a WebService (using SOAP) 
at the main EBI web servers. To reach XEMBL via your browser use the below 
url (which retrieves the Osamy-B gene in rice)


If you want to use it as a real WebService (via SOAP) you can find both 
Perl and Java examples at the XEMBL home page.

Where can I read more?

A comprehensive web page with everything to get you started can be found 
at http://www.ebi.ac.uk/xembl/ 

With kind regards,

drs. Jean-Jack M. Riethoven

EMBL Outstation - Hinxton           pow at ebi.ac.uk     ICQ#: 3433929
European Bioinformatics Institute   Phone: (+44) 1223 494635      
Wellcome Trust Genome Campus        Fax  : (+44) 1223 494468
Hinxton, Cambridge CB10 1SD         URL  : http://industry.ebi.ac.uk/

Need to find bioinformatics or molecular biology web sites or resources? 
Use BioWurld at http://www.ebi.ac.uk/biowurld

More information about the Embl-db mailing list

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