Ontological Resources for the Translational Researcher

1. Olivier Bodenreider Lister Hill National Centerfor Biomedical CommunicationsBethesda, Maryland - USA Navigating the Translational ResearcherThrough A Complex of Animal and Biological Resources NIH, March 6, 2006 Ontological Resourcesfor the Translational Researcher

2. Overview • Information integration • Through terminology integration • Animals in ontological resources • Other (ontological) resources • Some issues

3. Information integration

4. Subdomains of interest Clinical repositories Geneticknowledge bases Other subdomains Biomedical literature Model organisms Genome annotations Anatomy

5. Subdomains of interest Clinical repositories bench bedside Geneticknowledge bases Other subdomains Biomedical literature Model organisms Genome annotations Anatomy

6. Integrating subdomains Clinical repositories Geneticknowledge bases Other subdomains Biomedical literature Model organisms Genome annotations Anatomy

7. Integrating subdomains Clinical repositories Geneticknowledge bases Other subdomains SNOMED OMIM … Biomedical literature MeSH NCBI Taxonomy GO Model organisms UWDA Genome annotations Anatomy

8. Clinical repositories Geneticknowledge bases Other subdomains SNOMED OMIM … Biomedical literature MeSH NCBI Taxonomy GO Model organisms UWDA Genome annotations Anatomy Integrating subdomains ontology

9. Clinical repositories Geneticknowledge bases Other subdomains SNOMED OMIM … Biomedical literature MeSH NCBI Taxonomy GO Model organisms UWDA Genome annotations Anatomy Integrating terminologies UMLS UMLS

10. Terminological resources Collections of terms(e.g., controlled vocabularies) Useful for indexing and annotation MeSH, GO Ontological resources Collections of kinds of entities (substances, qualities, processes) relations among them Useful for reasoning UMLS Semantic Network, SNOMED CT Terminology vs. ontology Ontological gradient

11. Animals in ontological resources

13. Animals in the biomedical literature • Check tags in MEDLINE citations • General: Animals, Comparative Study, Humans,In Vitro, Pregnancy • Specific animals • Others: Age groups, Gender, Chronologic tags

14. Example from MEDLINE

15. Animals in MeSH

16. … Mice in MeSH

17. Mice in UMLS

18. Mice in UMLS

19. Other (ontological) resources

20. Open Biological Ontologies (OBO) • Extended family of the Gene Ontology (GO) • Collaborative development • http://obo.sourceforge.net/ • National Center for Biomedical Ontology • http://bioontology.org/

23. Some issues

24. Ontology vs. formalism • Ontology languages • OWL • Protégé • Markup languages(format/syntax for exchanging data) • CellML • MAGE-ML

25. Ontology and granularity • The information represented in most ontologies may not be fine-grained enough for some biological applications • Strain • … • Ontologies: represent classes of entitiesvs.Biological experiments: refer to instances

26. Examples from PATO Phenotype ontologies • Emerging ontologies • Fine-grained • Attributes • Relative Age • Carbohydrate Concentration • Values • Round • Tactile Hyperresponsive • Multiple organisms

27. Information integration through ontology Clinical repositories Geneticknowledge bases Other subdomains ontology Biomedical literature Model organisms Genome annotations Anatomy

28. MedicalOntologyResearch Contact: Web: olivier@nlm.nih.gov mor.nlm.nih.gov Olivier Bodenreider Lister Hill National Centerfor Biomedical CommunicationsBethesda, Maryland - USA