ayout 1 - EMBL Grenoble

EMBL-EBI
Ensembl Genomes
Previous and current research
The activities of the Ensembl Genomes team are focussed on the representation of genome and
genome-related data from non-vertebrate species. A huge influx of data is expected for non-vertebrate
species in the near future, driven by the use of ultra-high throughput sequencing technologies.
The group’s core strategy for handling this data is based on the belief that the demands
of these species can be met through the re-use and extension of the Ensembl genome annotation,
analysis and visualisation platform that has been used successfully for vertebrate genomes since
2000, which will become apparent with the public launch of five new sites (Ensembl Metazoa, Ensembl
Protists, Ensembl Plants, Ensembl Fungi and Ensembl Bacteria) in the first half of 2009. At
the same time, we are making a major effort to deepen our links with sections of the scientific
community working on individual species. Our vision is that Ensembl Genomes will evolve as a
project with two faces; to the wider scientific public, we will provide an integrative portal to
genomes and related data; while simultaneously we will support an infrastructure and flexible
toolkit to empower particular communities to manage genome annotation. Through the use of
common technology, we can make it easier for communities to handle genome scale data, and to integrate their systems with the other key
EBI resources.
Future projects and goals
Paul Kersey
PhD 2005, University of
Edinburgh.
Team leader at EMBL-EBI
since 2008.
2009 will see the launch of the Microme Project, a 13-member European partnership to develop a database and downstream services for
metabolic pathways in bacteria. Based on the successful Reactome software infrastructure, Microme is especially timely as pathway-based inference
is likely to become increasingly important in the annotation and functional interpretation of bacterial genome sequence, with the potential
to suggest biotechnological solutions to problems such as energy and food production, waste decontamination and industrial catalysis.
We will continue to work with the UK and international research communities to establish collaborations to exploit the Ensembl infrastructure
in new domains and bring fresh content to Ensembl Genomes. Currently, new proposals are being prepared for human and plant pathogen
data, while we are seeking to deepen existing relationships with established resources in the areas of protist pathogens (EuPath DB) and plants
(Gramene). The relationship between
hosts, vectors and pathogens
is of particular interest as Ensembl
Genomes (and Ensembl) expand to
include increasing numbers of complete
disease systems, and we will be
looking at ways of linking genotypes
to interaction, phenotype and geographic
data. We will also be working
to develop the interface between
genomic and metagenomic data, an
area of increasing scientific interest
and data production.
Ensembl Genomes. The homepage for
the Escherichia/Shigella class within
the new Ensembl Bacteria site.
Selected references
Field, D. et al. (2008a). The minimum information about a genome
sequence (MIGS) specification. Nat. Biotechnol., 26, 51-57
Megy, K. et al. (2008). Genomic resources for invertebrate vectors of
human pathogens, and the role of VectorBase. Infection, Genetics
and Evolution, in press
Mulder, N.J. et al. (2008). In silico characterization of proteins:
UniProt, InterPro and Integr8. Mol. Biotechnol., 38, 165-177
Topalis, P. et al. (2008). How can ontologies help vector biology?
Trends Parasitol., 2, 29-252
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