1. Welcome to mini-symposium on ontologies for biological sample description EMBL-EBI Wellcome Trust Genome Campus Deceber 5, 2001

2. Gene Expression Database Samples Genes Sample annotations Gene annotations Gene expression data matrix

3. 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

4. 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 …

5. 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

6. Hidden agenda for the EBI How we are going to describe samples in the ArrayExpress database?

7. 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

8. 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?) –Yeasts (S.Cerevisiae, S.Pombe) –Drosophila –Mouse –Human –Plants –…? –Toxicology –Cancer –…?

9. 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?

10. Ultimate goals ???????????????????????????????????????

11. Next step Should we (Helen, Midori, Suzanna, John, Liz?) organise a larger conference on bio- ontologies next year?