Stefan Schulz Medical Informatics Research Group

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Presentation transcript:

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

Ontological Layers Upper Ontology / Top Ontology Domain Ontology

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

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, …)

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

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, …)

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

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, …)

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, …)

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, …)

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, …)

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, …)

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

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’

BioTop: Metrics

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

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, …)

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, …)

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 BioChem 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