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

2. Ontological Layers
Upper
Ontology /
Top Ontology
Domain Ontology

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

4. OBO (GO, SO, ChEBI, …) Ontological Layers Upper Ontology /
Top Ontology
Transcription
DNA-dependent transcription
antisense RNA transcription
mRNA transcription
rRNA transcription
tRNA transcription …
(from Gene Ontology)
The synthesis of either RNA on a template of DNA or DNA on a template of RNA. 
Domain Ontology
OBO (GO, SO, ChEBI, …)

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

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

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

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

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

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

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

12. BioTop OBO (GO, SO, ChEBI, …) Ontological Layers DOLCE BFO GFO
Upper
Ontology /
Top Ontology
BFO
Simple Bio Upper Ontology
GFO
Domain Upper
Ontology /
Top Domain Ontology
GFO-Bio
BioTop
GENIA
Domain Ontology
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
Classes defined by necessary and sufficient conditions
Rationales
Precise understanding of meaning
Empowering the classifier for automated validation processes
Nucleotide
Ribose
Base
Phosphate
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. BioTop OBO (GO, SO, ChEBI, …) Ontological Layers DOLCE BFO GFO Upper
Ontology /
Top Ontology
BFO
GFO
Domain Upper
Ontology /
Top Domain Ontology
BioTop
Domain Ontology
OBO (GO, SO, ChEBI, …)

19. BioTop OBO (GO, SO, ChEBI, …) Ontological Layers DOLCE BFO GFO 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:
BioTop
BioTop
BioChem Top

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