Stefan Schulz Medical Informatics Research Group University Medical Center Freiburg, Germany
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BioTop: A Domain Top Level Ontology for the Life Sciences Dagstuhl Seminar 08131 - Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives Stefan Schulz Medical Informatics Research Group University Medical Center Freiburg, Germany
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BioTop : A Domain Top Level Ontology for the Life Sciences Dagstuhl Seminar 08131 - Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives. Stefan Schulz Medical Informatics Research Group University Medical Center Freiburg, Germany. Ontological Layers. Upper - PowerPoint PPT Presentation
Transcript of Stefan Schulz Medical Informatics Research Group University Medical Center Freiburg, Germany
BioTop: A Domain Top Level Ontology for the Life Sciences
Dagstuhl Seminar 08131 - Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives
Stefan Schulz
Medical Informatics
Research Group
UniversityMedical Center
Freiburg, Germany
Upper
Ontology /
Top Ontology
Domain Ontology
Ontological Layers
Upper
Ontology /
Top Ontology
Domain Ontology
OBO (GO, SO, ChEBI, …)
Ontological Layers
Upper
Ontology /
Top Ontology
Domain Ontology
OBO (GO, SO, ChEBI, …)
• Transcription • DNA-dependent transcription
• antisense RNA transcription• mRNA transcription• rRNA transcription• tRNA transcription • …(from Gene Ontology)
Ontological Layers
Upper
Ontology /
Top Ontology
Domain Ontology
OBO (GO, SO, ChEBI, …)
DOLCE
BFO
Ontological Layers
GFO
Upper
Ontology /
Top Ontology
Domain Ontology
OBO (GO, SO, ChEBI, …)
DOLCE
BFO
Ontological Layers•Entity• Continuant• Dependent Continuant• Realizable Entity• Function• Role• Independent Continuant • Object• Object Aggregate• Occurrent (from BFO)
GFO
Upper
Ontology /
Top Ontology
Domain Ontology
OBO (GO, SO, ChEBI, …)
DOLCE
BFO
Ontological Layers
GFO
Domain Upper
Ontology /
Top Domain Ontology
Upper
Ontology /
Top Ontology
Domain Ontology
OBO (GO, SO, ChEBI, …)
DOLCE
BFO
Ontological Layers
GFO
Upper
Ontology /
Top Ontology
Domain Upper
Ontology /
Top Domain Ontology
Domain Ontology
OBO (GO, SO, ChEBI, …)
DOLCE
BFO
Ontological Layers
GFO
Upper
Ontology /
Top Ontology
Domain Upper
Ontology /
Top Domain Ontology
Domain Ontology
OBO (GO, SO, ChEBI, …)
DOLCE
BFO
• Organism• Body Part• Cell• Cell Component• Tissue• Protein• Nucleic Acid• DNA• RNA• Biological Function• Biological Process• Taxon
Ontological Layers
GFO
Upper
Ontology /
Top Ontology
Domain Upper
Ontology /
Top Domain Ontology
Domain Ontology
OBO (GO, SO, ChEBI, …)
Simple Bio Upper Ontology
GFO-Bio
DOLCE
BFO
GENIA
Ontological Layers
GFO
Upper
Ontology /
Top Ontology
Domain Upper
Ontology /
Top Domain Ontology
Domain Ontology
OBO (GO, SO, ChEBI, …)
Simple Bio Upper Ontology
GFO-Bio
GENIA
DOLCE
BFO
BioTop
Ontological Layers
GFO
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
Classes and Relations
• Classes defined by necessary and sufficient conditions• Rationales
- Precise understanding of meaning- Empowering the classifier for automated validation
processes
Necessary conditions of class ‘Nucleotide’
Nucleotide
Ribose
BasePhosphate
Full Definitions
BioTop: Metrics
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
BioTop OBO Ontologies
Ontology Integration
Upper Level
Ontology
↔BFO
(DOLCE)
OBO RO
↔
↔
Upper
Ontology /
Top Ontology
Domain Upper
Ontology /
Top Domain Ontology
Domain Ontology
OBO (GO, SO, ChEBI, …)
DOLCE
BFO
BioTop
Ontological Layers
GFO
Upper
Ontology /
Top Ontology
Domain Ontology
OBO (GO, SO, ChEBI, …)
DOLCE
BFO
Ontological Layers
GFO Domain Upper
Ontology /
Top Domain Ontology BioTop
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 BioTopBioChem
Top
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
