Transcript slides - MGED Open Source Projects

Welcome to mini-symposium on
ontologies for biological sample
description
EMBL-EBI
Wellcome Trust Genome Campus
Deceber 5, 2001
Gene Expression Database
Genes
Samples
Gene
annotations
Sample
annotations
Gene expression
data matrix
Gene annotation
• Let gene sequence databases – EMBL,
Swissprot, EnsEMBL and other
consortiums, such as Gene Ontology do it
for us – we can’t do it any better than they
can
Sample (biomaterial) annotations
• Species – NCBI taxonomy
• Organism part (anatomy) – species specific
– Cell cultures and lines
• Development (mostly species specific)
• Disease (e.g., cancer classification)
• Treatment
– Chemical compounds
– Other (e.g., heat shock, calory restriction)
– The result effect of the treatment
• Genetic variation
• …
Agenda today
• Ontologies in bioinformatics and tools for
building them
• MGED working group on ontologies
• Particular examples of ontolgies
• Gene Ontologies
• Our attempts at the EBI
Hidden agenda for the EBI
• How we are going to describe samples in
the ArrayExpress database?
How to describe biomaterial in
gene expression databases
• Short term – 1- 2 year
• Medium term – 3 – 5 years
• Long term – the ultimate goal in an ideal
world
Short term proposal
• Building up controlled vocabularies: (qualifier, value,
source) triplets
• How to curate this? E.g., how to disapprove synonyms?
• Building organism or problem specific hierarchical
vocabularies (which organisms and which problems?)
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Yeasts (S.Cerevisiae, S.Pombe)
Drosophila
Mouse
Human
Plants
…?
Toxicology
Cancer
…?
Medium term questions
• How to use biomaterial ontologies (BO) for
annotations in a public repository for microarray
data (ArrayExpress)? Annotation by “approved”
GOBO terms?
• Important difference between genes and
biomaterial – biomaterial should be not just
annotated but fully described by BO
• How to coordinate the relevant ontology
development efforts? Is GOBO the answer?
• GOBO or BMO term annotation tool?
• Should we try to initiate a major biomaterial
ontology project? Who could fund it?
Ultimate goals
• ???????????????????????????????????????
Next step
• Should we (Helen, Midori, Suzanna, John,
Liz?) organise a larger conference on bioontologies next year?