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

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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
• UniversityMedical Center
• Freiburg, Germany

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Ontological Layers
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Ontological Layers
OBO (GO, SO, ChEBI, )
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Ontological Layers

• Transcription
• DNA-dependent transcription
• antisense RNA transcription
• mRNA transcription
• rRNA transcription
• tRNA transcription
• (from Gene Ontology)

OBO (GO, SO, ChEBI, )
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Ontological Layers
DOLCE
BFO
GFO
OBO (GO, SO, ChEBI, )
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Ontological Layers

• Entity
• Continuant
• Dependent Continuant
• Realizable Entity
• Function
• Role
• Independent Continuant
• Object
• Object Aggregate
• Occurrent
• (from BFO)

DOLCE
BFO
GFO
OBO (GO, SO, ChEBI, )
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Ontological Layers
DOLCE
BFO
GFO
OBO (GO, SO, ChEBI, )
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Ontological Layers
DOLCE
BFO
GFO
OBO (GO, SO, ChEBI, )
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Ontological Layers
DOLCE
BFO
GFO
OBO (GO, SO, ChEBI, )
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Ontological Layers
DOLCE

• Organism
• Body Part
• Cell
• Cell Component
• Tissue
• Protein
• Nucleic Acid
• DNA
• RNA
• Biological Function
• Biological Process
• Taxon

BFO
GFO
OBO (GO, SO, ChEBI, )
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Ontological Layers
DOLCE
BFO
Simple Bio Upper Ontology
GFO
GFO-Bio
GENIA
OBO (GO, SO, ChEBI, )
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Ontological Layers
DOLCE
BFO
Simple Bio Upper Ontology
GFO
GFO-Bio
BioTop
GENIA
OBO (GO, SO, ChEBI, )
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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

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Classes and Relations
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Full Definitions

• Classes defined by necessary and sufficient
  conditions
• Rationales
• Precise understanding of meaning
• Empowering the classifier for automated
  validation processes

Necessary conditions of class Nucleotide
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BioTop Metrics
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Ontology Integration
BioTop
OBO Ontologies
Upper Level
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
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Ontological Layers
DOLCE
BFO
GFO
BioTop
OBO (GO, SO, ChEBI, )
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Ontological Layers
DOLCE
Upper Ontology / Top Ontology
BFO
GFO
Domain Upper Ontology / Top Domain Ontology
BioTop
Domain Ontology
OBO (GO, SO, ChEBI, )
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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 sitehttp//purl.org/biotop

BioTop
BioTop
BioChemTop
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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