Data mining and data
annotation in genomics and
proteomics
Bonnie Webber
School of Informatics
University of Edinburgh
Informatics (5*A)
• Language Technology
• Learning from Data
• Database Systems / XML Technology
Highlight: Theory and practice of
annotation in scientific databases
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•
•
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How to characterise annotations?
How to describe their attachment to data?
How to pass annotations through queries?
How to make programs “annotation
conscious”?
• (Buneman, Koch, Bickmore, …)
Example
Serves fine French Cuisine
in elegant setting. Jackets
required.
Extensive wine list!
NYRestaurants (Source Table)
Restaurant
Peacock Alley
Bull & Bear
Pacifica
Soho Kitchen & Bar
Cost
Type
Zip
$$$
$$$
French 10022
Seafood 10022
$
$
Chinese 10013
American 10022
Yummy chicken curry!!
All Restaurants (View 1)
Restaurant
Peacock Alley
Bull & Bear
Pacifica
Soho Kitchen & Bar
Cost
Cheap Restaurants (View 2)
Type
$$$
$$$
French
Seafood
$
$
Chinese
American
Restaurant
Pacifica
Soho Kitchen & Bar
Cost
$
$
Type
Chinese
American
Highlight: large-scale sequence
annotation
• To use phylogenomic methods to propagate
gene and sequence annotation through large
families of “neglected” organisms
• This extends the use of available functional
annotation from well-annotated organisms to
“neglected” ones
• (Blaxter, Parkinson, Williams)
Highlight: Probabilistic Modelling of
Biological Systems and Sequences
• Use conditional random fields to model the
promoter region of genes, to capture “long
distance” dependencies (Osborne, Ghazal)
• Use genetic algorithms to explore a vast
space of gene network topologies, to find
ones consistent with expression data
(Armstrong, Levine)
• Induce dynamic Bayesian models that can
express non-linear temporal relations in gene
networks (Armstrong, Barber)
Behavioural and genetic responses to gravity:
Flies in Space
J. Douglas Armstrong
havioural Assay
9
8
7
6
5
4
3
2
1
Problem context: behavioural and
genetic responses to gravity
• In flies, expression levels of 208 genes
change in response to changes in gravity.
• About 70 mutant strains respond abnormally
to gravity.
• The goal is to induce the relevant gene
networks and understand how gravity affects
them.
• It is inappropriate to assume these networks
have a strictly linear response.
Fly walking
up tube
Flip tube
Ellipsoid body
inactivated
Highlight: Statistical Methods for
Haplotype Reconstruction
in Livestock Genetics
Michael T. Schouten
Dr. Chris Williams
Department of Informatics
University of Edinburgh
Professor Chris Haley
Department of Genetics
The Roslin Institute
Marker-Trait Association
SNP
Haplotypes
…ACGCTTGAA…
CA
…ACGCTTGTA…
CT
…ACGGTTGAA…
GA
…ACGGTTGTA…
GT
Marker Sequencing
TCG ACGGCA
+
G T
TCGGCGTCA
+
A
TCG G
G
CG T CA
Develop a Bayesian Model to Reconstruct Haplotypes for
a Breeding System that
•Has Limited Pedigree Information
•Does Not Conform to Hardy-Weinberg Assumptions
Future
• Our MSc program in bioinformatics is
growing.
• Successful MSc students are feeding into our
PhD program.
• PhD students in bioinformatics are being
funded under EPSRC quota studentships and
targetted bioinformatics studentships from
BBSRC and (we hope) the MRC.
• We hope to attract new staff and students to
bioinformatics and retain those we have.