Paul Flicek talks with
ScienceWatch.com and answers a few questions about
this month's Fast Breaking Paper in the field of Biology
Article Title: Ensembl 2008
P, et al.
Journal: NUCL ACID RES
Year: Sp. Iss. SI JAN 2008
* European Bioinformat Inst, Wellcome Trust Genome Campus,
Cambridge CB10 1SD, England.
* European Bioinformat Inst, Cambridge CB10 1SD,
* Wellcome Trust Sanger Inst, Cambridge CB10 1SD,
(addresses have been truncated)
Why do you think your paper is highly
Our paper describes one of the fundamental bioinformatics resources on
which many other researchers build analysis and bioinformatics tools. One
resource within the project that many people find integral to their work is
the collection of Ensembl gene annotations. These genes sets are created
across all of the genomes we support (approximately 45 chordates) and
ensure a high standard for all downstream analysis.
Ensembl also provides an open infrastructure for genome information. We
encourage all researchers to write custom applications that reuse Ensembl
code and directly access the Ensembl data. By providing an open-source code
base, we are integral to the bioinformatics analysis pipelines of many
groups around the world and a number of custom applications based on our
code and our results are listed on our web site.
Does it describe a new discovery, methodology, or
synthesis of knowledge?
We are integrating multiple and diverse data sources into consistent and
sensible results. As more biological data is created, integration analysis
leading to comprehensive genome annotation is required to make sense of the
various sources and create knowledge that can be used in other ways.
The Ensembl human gene set is an example which now sensibly integrates
information from protein sequences, cDNAs, manual annotation, CAGE, and
ditag sequences and sequence-based expression data. Going forward, we have
created a first, "best guess" computational annotation of genome regulatory
regions by integrating data from multiple sources.
Would you summarize the significance of your paper in
The role of computers, databases, and bioinformatics in the field of
biology has risen dramatically over the last two decades. We are one of the
reference databases for genomics and we create and maintain annotation on
the collection of sequenced mammalian and chordate genomes. Our results are
used by many other researchers in many ways to support their work in many
fields of modern biology, including human and model organism genetics,
comparative genomics, and bioinformatics.
How did you become involved in this research, and were
there any problems along the way?
The Ensembl project was started approximately nine years ago and has grown
steadily since its beginnings. I joined the project in 2005 and I am now
joint head of the effort. Our project is spread over two institutes,
several dozen scientists, and hundreds of thousands of lines of computer
We are continually developing our methods and expanding the scope of our
project to address the challenges of more and larger data sets supporting
genome annotations. Our largest challenges and greatest problems are
currently associated with using next generation sequencing data sets. To
put things in perspective, the Ensembl project started before the human
genome was finished and at a time when the total amount of DNA sequence in
GenBank was less than the amount now produced daily by major genome
Where do you see your research leading in the
In the future, a major goal for a genome annotation resource such as
Ensembl will be to understand and annotate human variation and connect the
variation with phenotype. We are associated with the 1000 Genomes
project and the data produced in this project will
be a major step toward a more complete catalog of human variation. This
type of variation data and some of the other resources that we and
others are creating will likely be used in many future studies with
Do you foresee any social or political implications for your
Our project already includes the genome sequences of James Watson and
(see also). In the very near future, we will include
additional individual genome sequences from the 1000 Genomes project and
other sources. These first cases are just the beginning of the era of
personal and individual genome sequences, which has already captured the
public imagination as evidence by the response to companies such as
"23andme" and "decodeme."
As more people are able to access their own genetic information, some
(possibly many) of them, will come to Ensembl to investigate the data
resources and results that we have produced as they seek to understand
their own genome. The social and political impacts of personal genomics
will be incredibly large. How this impact will affect or guide our research
remains to be seen, but it will surely play some role.
Paul Flicek, D.Sc.
Team Leader, Vertebrate Genomics
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Honorary Faculty Member
Wellcome Trust Sanger Institute
Keywords: ensembl gene annotations, ensembl human gene set,
ensembl code, ensembl data, open infrastructure for genome information,
reference database for genomics, bioinformatics resource, genome
annotations, sequenced mammalian and chordate genomes.