title: Granularity issues in the alignment of upper ontologies.
abstract: OBJECTIVE
  The application of upper ontologies has been repeatedly advocated for to support the interoperability between different domain ontologies for facilitating the shared use of data within and across disciplines. BioTop is an upper domain ontology that aims at aligning more specialized biomolecular and biomedical ontologies. The integration of BioTop and the upper ontology Basic Formal Ontology (BFO) is the objective of this study.
  
  
  METHODS
  BFO was manually integrated into BioTop, observing both its free text and formal definitions. BioTop classes were attached to BFO classes as children and BFO classes were reused in the formal definitions of BioTop classes. A description logics reasoner was used to check the logical consistency of this integration. The domain adequacy was checked manually by domain experts.
  
  
  RESULTS
  Logical inconsistencies were found by the reasoner when applying the BFO classes for fiat and aggregated objects in some of the BioTop class definitions. We discovered that the definition of those particular classes in BFO was dependent on the notion of physical connectedness. Hence we suggest ignoring a BFO subbranch in order not to hinder cross-granularity integration.
  
  
  CONCLUSIONS
  Without introducing a more sophisticated theory of granularity, the described problems cannot be properly dealt with. Whereas we argue that an upper ontology should be granularity-independent, we illustrate how granularity-dependent domain ontologies can still be embedded into the framework of BioTop in combination with BFO.
authors.affiliation: Universitätsklinikum, Institut für Medizinische Biometrie und Medizinische Informatik, Stefan-Meier-Strasse 26, 79104 Freiburg, Germany. stschulz@uni-freiburg.de
authors.forename: Stefan
authors.initials: S
authors.lastname: Schulz
authors.forename: Martin
authors.initials: M
authors.lastname: Boeker
authors.forename: Holger
authors.initials: H
authors.lastname: Stenzhorn
authors.forename: Jörg
authors.initials: J
authors.lastname: Niggemann
mesh_terms: D003198:Computer Simulation; D005858:Germany; D006751:Hospital Information Systems / Q000458:organization & administration*; D006801:Humans; D016015:Logistic Models; D008962:Models, Theoretical; D009626:Terminology as Topic