Alignment of biomedical ontologies using life science literature

  • Authors:

  • He Tan;Vaida Jakonienė;Patrick Lambrix;Johan Aberg;Nahid Shahmehri

  • Affiliations:

  • Department of Computer and Information Science, Linköpings universitet, Linköping, Sweden;Department of Computer and Information Science, Linköpings universitet, Linköping, Sweden;Department of Computer and Information Science, Linköpings universitet, Linköping, Sweden;Department of Computer and Information Science, Linköpings universitet, Linköping, Sweden;Department of Computer and Information Science, Linköpings universitet, Linköping, Sweden

  • Venue:
  • KDLL'06 Proceedings of the 2006 international conference on Knowledge Discovery in Life Science Literature
  • Year:
  • 2006

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Abstract

In recent years many biomedical ontologies have been developed and many of these ontologies contain overlapping information. To be able to use multiple ontologies they have to be aligned. In this paper we propose strategies for aligning ontologies based on life science literature. We propose a basic algorithm as well as extensions that take the structure of the ontologies into account. We evaluate the strategies and compare them with strategies implemented in the alignment system SAMBO. We also evaluate the combination of the proposed strategies and the SAMBO strategies.