Bio-ontologies in bioinformatics: Growing up challenges
Upcoming SlideShare
Loading in...5
×
 

Like this? Share it with your network

Share

Bio-ontologies in bioinformatics: Growing up challenges

on

  • 1,003 views

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.

Statistics

Views

Total Views
1,003
Views on SlideShare
682
Embed Views
321

Actions

Likes
0
Downloads
3
Comments
0

5 Embeds 321

http://www.bioontology.ch 268
http://bioontology.ch 46
http://glencore-tomcat-ch.orientedhosting.com 3
http://213.173.161.40 2
http://www.linkedin.com 2

Accessibility

Categories

Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

CC Attribution License

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment
  • More relations (axioms), more complex hierarchies

Bio-ontologies in bioinformatics: Growing up challenges Presentation Transcript

  • 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