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Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
Bio-ontologies in bioinformatics: Growing up challenges
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Bio-ontologies in bioinformatics: Growing up challenges

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Bio-ontologies are growing up, and their use is becoming widespread in many areas of computational science. The new maturity is bringing new challenges, however, in particular visualization of complex …

Bio-ontologies are growing up, and their use is becoming widespread in many areas of computational science. The new maturity is bringing new challenges, however, in particular visualization of complex ontologies; moving from OBO to OWL; using multiple ontologies in conjunction; training appropriate for biologists and community building.

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  • More relations (axioms), more complex hierarchies
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    • 1. Robinson-Rechavi 2-day Group Meeting Lausanne, June 4-5 2012Ontologies in Bioinformatics: Growing-up challenges Janna Hastings1,2,3 1 Cheminformatics and Metabolism, European Bioinformatics Institute 2 Swiss Center for Affective Sciences, University of Geneva 3 Swiss Institute of Bioinformatics
    • 2. STANDARDS: RESEARCH ANALYSIS: REPRODUCABILITY, ENRICHMENT, BIOCURATION, SEMANTIC SIMILARITY, DATA INTEGRATION, … EXCHANGE, SEMANTIC WEB … DATABASE MANAGEMENT: BROWSING, VISUALIZATION, CLASSIFICATION, AUTOMATED REASONING, …Applications of ontologies in bioinformatics
    • 3. Growing-up challenges for ontologies in bioinformatics1. Visualization2. Moving from OBO to OWL – tools, software3. Moving from single ontologies to multiple ontologies (using cross-products)4. Training aimed at biologists and bioinformaticians5. Community building
    • 4. Selected ontology-related publications (JH @EBI)• Janna Hastings et al., Structure-based classification and ontology in chemistry. Journal of Cheminformatics. 2012 Apr 5; 4:8.• Barry Hardy, [...] Janna Hastings et al. Toxicology ontology perspectives. ALTEX 2012, 29 (2), 139.• Janna Hastings et al. The Chemical Information Ontology: provenance and disambiguation for chemical data on the biological semantic web. PLoS ONE, 6(10).• Melanie Courtot, *…+ Janna Hastings et al. Controlled vocabularies and semantics in Systems Biology. Molecular Systems Biology, 7:543.• Janna Hastings et al., Modularization requirements in bio-ontologies: A case study of ChEBI. Frontiers in Artificial Intelligence and Applications Volume 230, p. 63--70.• Kirill Degtyarenko, *…+ Janna Hastings et al., ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344-D350.
    • 5. ChEBI: Chemicals of Biological Interest
    • 6. 1. Ontology visualizationThere is a need to hide irrelevant information and concisely display relevant information
    • 7. ChEBI has introduced a new heuristic forhiding redundant paths in the visualiation
    • 8. See also http://ols.wordvis.com/
    • 9. 2. Moving from OBO to OWL OBO-Edit is the most commonly used bio-ontology editor, but it is no longer actively being developed
    • 10. Protégé is the tool that will replace OBO-Edit, but it urgently needsinvestment in usability improvements for use by biologists and curators
    • 11. APIs for programmaticaly working with OWL ontologies• OWLTools (Java) … wrapper for, and much easier to use than, the OWL API (Java)• OntoCat (R)• POSH (Prolog, Unix shell)• InfixOWL (Python)
    • 12. Normalization of ontologies + automated reasoning for hierarchies FBbtNon-Normalized: Normalized:Only is-a, maybe part-of relations More relationshipsAll relevant relations are not asserted, only More inferred classificationsthose found salient by the human annotators Easier to maintain but harder to navigate
    • 13. 3. Working with multiple ontologies• Cross-products, e.g. chemicals in GO (for terms such as ‘carbohydrate metabolism’)• No online visualization tools yet are able to display cross-products across ontologies• Most databases don’t support annotation with composite terms, necessitating pre- composition
    • 14. 4. Training
    • 15. 5. Community building• ICBO conference• ISMB Bio-ontologies SIG Not well attended by biologists/curators? • Bio-curation conference Not well attended by ontologists? • OBO Foundry COMPUTER SCIENCE Not very active lately? BIOLOGY • OntoSIBOntology @Pub nights Blog: www.bioontology.ch
    • 16. Thank you, AcknowledgementsChristoph Steinbeck Barry SmithColin Batchelor Kevin MulliganMarcus Ennis Werner CeustersVenkatesh Muthukrishnan Nicolas le Novere David Osumi-SutherlandJane LomaxChris MungallBBSRC FNS (SNF)EU-OPENSCREEN EMBL

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