Stefan Schulz Medical Informatics Research Group University Medical Center Freiburg, Germany

1. BioTop: A Domain Top Level Ontology for the Life SciencesDagstuhl Seminar 08131 - Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives Stefan Schulz Medical Informatics Research Group UniversityMedical Center Freiburg, Germany

2. Ontological Layers Upper Ontology / Top Ontology Domain Ontology

3. Ontological Layers Upper Ontology / Top Ontology Domain Ontology OBO (GO, SO, ChEBI, …)

4. Ontological Layers Upper Ontology / Top Ontology Domain Ontology • Transcription • DNA-dependent transcription • antisense RNA transcription • mRNA transcription • rRNA transcription • tRNA transcription • … • (from Gene Ontology) OBO (GO, SO, ChEBI, …)

5. Ontological Layers Upper Ontology / Top Ontology Domain Ontology DOLCE BFO GFO OBO (GO, SO, ChEBI, …)

6. Ontological Layers Upper Ontology / Top Ontology Domain Ontology • Entity • Continuant • Dependent Continuant • Realizable Entity • Function • Role • Independent Continuant • Object • Object Aggregate • Occurrent • (from BFO) DOLCE BFO GFO OBO (GO, SO, ChEBI, …)

7. Ontological Layers Upper Ontology / Top Ontology Domain Ontology DOLCE BFO GFO OBO (GO, SO, ChEBI, …)

8. Ontological Layers Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology DOLCE BFO GFO OBO (GO, SO, ChEBI, …)

9. Ontological Layers Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology DOLCE BFO GFO OBO (GO, SO, ChEBI, …)

10. Ontological Layers Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology DOLCE • Organism • Body Part • Cell • Cell Component • Tissue • Protein • Nucleic Acid • DNA • RNA • Biological Function • Biological Process • Taxon BFO GFO OBO (GO, SO, ChEBI, …)

11. Ontological Layers Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology DOLCE BFO Simple Bio Upper Ontology GFO GFO-Bio GENIA OBO (GO, SO, ChEBI, …)

12. Ontological Layers Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology DOLCE BFO Simple Bio Upper Ontology GFO GFO-Bio BioTop GENIA OBO (GO, SO, ChEBI, …)

13. BioTop Principles • Formal Ontology, using logics for domain representation • Fill the gap between domain-independent upper-level ontologies and specific biomedical domain ontologies • Taxonomy of most general entity types for the Life Sciences • Textual and formal definitions • Use Semantic Web standards: OWL-DL, Pellet, Protégé • Link to Ontology standards: OBO relation ontology

14. Classes and Relations

15. Full Definitions Nucleotide Base Phosphate Ribose • Classes defined by necessary and sufficient conditions • Rationales • Precise understanding of meaning • Empowering the classifier for automated validation processes Necessary conditions of class ‘Nucleotide’

16. BioTop: Metrics

17. Ontology Integration Upper Level BioTop OBO Ontologies Biological Process↔Biological ProcessGene Ontology Protein Function ↔ Molecular FunctionGene Ontology Cell Component ↔ Cellular ComponentGene Ontology Cell ↔ CellCell Ontology and CellFMA Atom ↔ AtomsChEBI Organic Compound↔ Organic Molecular EntitiesChEBI Structured Biological Entity ↔ Anatomical StructureFMA Tissue ↔ TissueFMA DNA, RNA ↔ DNASequence Ontology, RNASequence Protein ↔ ProteinSequence Ontology ↔ BFO (DOLCE) OBO RO ↔ ↔ Ontology

18. Ontological Layers Upper Ontology / Top Ontology Domain Upper Ontology / Top Domain Ontology Domain Ontology DOLCE BFO GFO BioTop OBO (GO, SO, ChEBI, …)

19. Ontological Layers DOLCE Upper Ontology / Top Ontology BFO GFO Domain Upper Ontology / Top Domain Ontology BioTop Domain Ontology OBO (GO, SO, ChEBI, …)

20. Current State • BioTop: work in progress ! • Modularization: • Making it as neutral as possible wrt upper level assumptions: compatible with both BFO and DOLCE • Carving out specialized biochemistry classes • BioTop site:http://purl.org/biotop BioTop BioTop BioChemTop

21. BioTop related publications • Stefan Schulz, Martin Boeker,Holger Stenzhorn. The Ontology of Biological Taxa. Accepted for ISMB 2008 • Stefan Schulz, Martin Boeker, Holger Stenzhorn. How Granularity Issues Concern Biomedical Ontology Integration. Accepted for Medical Informatics Europe (MIE 2008) • Udo Hahn, Elena Beisswanger, Holger Stenzhorn, Stefan Schulz. BIOTOP: An Upper Domain Ontology for Life Sciences. A Description of its Current Structure, Contents, and Interfaces to OBO Ontologies. Forthcoming in: Applied Ontologies, 2008 • Holger Stenzhorn, Stefan Schulz, Elena Beisswanger. Towards a Top-Domain Ontology for Linking Biomedical Ontologies. 12th World Congress on Health (Medical) Informatics (Medinfo 2007), Brisbane, Australia, August 2007 • Stefan Schulz, Elena Beisswanger, Udo Hahn, Joachim Wermter, Holger Stenzhorn, Anand Kumar. From GENIA to BioTop - Towards a top-level Ontology for Biology. International Conference on Formal Ontology in Information Systems (FOIS 2006), Baltimore, USA, November 2006 • Stefan Schulz, Elena Beisswanger, Joachim Wermter, Udo Hahn. Towards an Upper Level Ontology for Molecular Biology. American Medical Informatics Association Annual Conference (AMIA 2006), Washington, November 2006