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Welcome to mini-symposium on ontologies for biological sample description

Welcome to mini-symposium on ontologies for biological sample description. EMBL-EBI Wellcome Trust Genome Campus Deceber 5, 2001. Sample annotations. Gene annotations. Gene Expression Database. Samples. Gene expression data matrix. Genes. Gene annotation.

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Welcome to mini-symposium on ontologies for biological sample description

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

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

  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?

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