ayout 1 - EMBL Grenoble

EMBL Research at a Glance 2009
The External Services Team
Previous and current research
The External Services team is in charge of the development, management and maintenance of
web and FTP resources at EMBL-EBI. These are in high demand as more and newer types of data
are archived and distributed from the EBI’s databases. The group’s responsibilities include:
Rodrigo Lopez
Vet. Med Degree 198, Oslo
Vet. Hoyskole and NASAS
Cand. Scient.
Molecular Toxicology and
Informatics 1987, University
of Oslo.
Team leader at EMBL-EBI
since 2001.
• maintaining the main EBI web portal as well as several Wellcome Trust, BBSRC and
EU-funded projects websites (amongst others), including: 1000 Genomes Project, 2can,
BioCatalogue, BioSapiens, European Genotype Archive (EGA), ELIXIR, EMBRACE,
ENFIN, FELICS, IMPACT, INSDC, MIBBI and SYMBIOmatics;
• monitoring and supporting use of EBI services, such as the global search and retrieval
services that include the EB-eye search engine and SRS (SRS especially for the European
Nucleotide Archive – ENA), and core sequence search and analysis services such as
BLAST, FASTA, InterProScan, as well as several mainstream multiple sequence alignment
(MSA) services such as ClustalW2, MAFFT, T-Coffee, etc. Today all these services
have SOAP/REST web services interfaces, which allows programmatic and systematic
use;
Future projects and goals
• user support for EBI developers as well as general users. In this context, various members
of the team have been heavily involved in training and conference activities and
participation at local and international workshops.
The adoption of web services and XML technologies, which started during 2002, translates to better and more robust services today. Users
now have systematic access to our analytical tools. Our web services present a uniform API for a wide variety of bioinformatic applications
that count more than 250 individual algorithms. Access to these represents slightly over 900,000 compute jobs per month.
In the context of facilitating querying by our users, the group is involved in the development of browsable catalogues that will enable users to
find web services, tools and databases. These projects are run in collaboration with members of the EMBRACE project (the EMBRACE service
registry) and the staff at the University of Manchester (BioCatalogue). The projects are financed by the EU and the BBSRC respectively.
The aims of these catalogues are to produce a much-needed ‘yellow pages’ for life sciences resources and their outcome will be linked with
mainstream search engines such as EB-eye and Google.
Work in relation to sequence patents is continuing as part of the team’s collaboration with the EPO. The latest developments in this context
include non-redundant sets of data, level 1 and level 2 equivalencies, and additional patent sequence databases from both Korea and China.
This work leads to a much clearer understanding of when and where a patent was first filed, but importantly, what is actually covered by a
patent or by its application. This work is of particular importance to patent examiners currently using EBI services, which include the EPO
(based in The Hague, Netherlands and Munich, Germany), Spain, UK, USPTO, KIPO and JPO.
Selected references
Chica, C. et al. (2008). A tree-based conservation scoring method for
short linear motifs in multiple alignments of protein sequences. BMC
Bioinformatics, 9, Article 229
Cochrane, G. et al. (2008). Priorities for nucleotide trace, sequence
and annotation data capture at the Ensembl Trace Archive and the
EMBL Nucleotide Sequence Database. Nucleic Acids Res., 36, D5-
D12
Robinson, J. et al. (2008). The IMGT/HLA database. Nucleic Acids
Res., 37, D1013-D1017
Larkin, M.A. et al. (2007). Clustal W and Clustal X version 2.0.
Bioinformatics, 23, 297-298
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