From frames to OWL2: Converting the Foundational Model of Anatomy.

Journal: Artificial intelligence in medicine
Published Date: Apr 27, 2016

Abstract

OBJECTIVE: The Foundational Model of Anatomy (FMA) [Rosse C, Mejino JLV. A reference ontology for bioinformatics: the Foundational Model of Anatomy. J. Biomed. Inform. 2003;36:478-500] is an ontology that represents canonical anatomy at levels ranging from the entire body to biological macromolecules, and has rapidly become the primary reference ontology for human anatomy, and a template for model organisms. Prior to this work, the FMA was developed in a knowledge modeling language known as Protégé Frames. Frames is an intuitive representational language, but is no longer the industry standard. Recognizing the need for an official version of the FMA in the more modern semantic web language OWL2 (hereafter referred to as OWL), the objective of this work was to create a generalizable Frames-to-OWL conversion tool, to use the tool to convert the FMA to OWL, to "clean up" the converted FMA so that it classifies under an EL reasoner, and then to do all further development in OWL.

Authors

  • Landon T Detwiler
    Biological Structure, University of Washington Structural Informatics Group, 1959 NE Pacific Street, Box 357420, Seattle, Washington 98195, USA. Electronic address: det@uw.edu.
  • Jose L V Mejino
    Biological Structure, University of Washington Structural Informatics Group, 1959 NE Pacific Street, Box 357420, Seattle, Washington 98195, USA.
  • James F Brinkley
    Biological Structure, University of Washington Structural Informatics Group, 1959 NE Pacific Street, Box 357420, Seattle, Washington 98195, USA; Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA; Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington 98195, USA.

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