Bio-ontologies in bioinformatics: Growing up challenges

Bio-ontologies in bioinformatics: Growing up challenges

• 1.
  Robinson-Rechavi 2-day GroupMeeting Lausanne, June 4-5 2012 Ontologies 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 bioinformatics 1. Visualization 2. Moving from OBO to OWL – tools, software 3. Moving from single ontologies to multiple ontologies (using cross-products) 4. Training aimed at biologists and bioinformaticians 5. 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.
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  ChEBI: Chemicals ofBiological Interest
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  1. Ontology visualization Thereis a need to hide irrelevant information and concisely display relevant information
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  ChEBI has introduceda new heuristic for hiding redundant paths in the visualiation
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  See also http://ols.wordvis.com/
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  2. Moving fromOBO to OWL OBO-Edit is the most commonly used bio-ontology editor, but it is no longer actively being developed
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  Protégé is thetool that will replace OBO-Edit, but it urgently needs investment in usability improvements for use by biologists and curators
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  APIs for programmaticalyworking 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)
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  Normalization of ontologies + automated reasoning for hierarchies FBbt Non-Normalized: Normalized: Only is-a, maybe part-of relations More relationships All relevant relations are not asserted, only More inferred classifications those found salient by the human annotators Easier to maintain but harder to navigate
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  3. Working withmultiple 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
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  4. Training
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  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 • OntoSIB Ontology @Pub nights Blog: www.bioontology.ch
• 17.
  Thank you, Acknowledgements ChristophSteinbeck Barry Smith Colin Batchelor Kevin Mulligan Marcus Ennis Werner Ceusters Venkatesh Muthukrishnan Nicolas le Novere David Osumi-Sutherland Jane Lomax Chris Mungall BBSRC FNS (SNF) EU-OPENSCREEN EMBL