Biomedical ontologies: what part-of is and isn't

  • Authors:

  • Stefan Schulz;Anand Kumar;Thomas Bittner

  • Affiliations:

  • Department of Medical Informatics, University Hospital, Freiburg, Germany;Institute for Formal Ontology and Medical Information Science (IFOMIS), University of Saarbrücken, Germany;Department of Philosophy, Department of Geography, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo

  • Venue:
  • Journal of Biomedical Informatics - Special issue: Biomedical ontologies
  • Year:
  • 2006

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Abstract

Mereological relations such as part-of and its inverse has-part are fundamental to the description of the structure of living organisms. Whereas classical mereology focuses on individual entities, mereological relations in biomedical ontologies are generally asserted between classes of individuals. In general, this practice leaves some basic issues unanswered: type constraints of mereological relations, e.g., concerning artifacts and biological entities, the relation between parthood and time, inferred parts and wholes as well as a delimitation of parthood against spatial inclusion. Furthermore, mereological relations can be asserted not only between physical objects but also between biological processes and medical procedures. We analyze these ambiguities and make suggestions for a standardization of mereological relations in biomedical ontologies.