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The skeleton is subdivided into two major divisions—the axial skeleton and the appendicular skeleton. The axial skeleton forms the vertical, central axis of the body. It includes all of the bones of the head, neck, chest, and back. It protects the brain, spinal cord, heart, and lungs. It also serves as the attachment site for muscles that move the head, neck, and back and for muscles that act across the shoulder and hip joints to move their corresponding limbs.
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Knowledge of anatomy is essential to understand human biology and medicine. Anatomists and health care professionals use standard terminology to describe the human body with more precision and no ambiguity. Anatomical terms have mostly Greek and Latin-derived roots. Because these languages are rarely used in conversation, the meaning of words remains the same. Each term is made up of a root in between the prefixes and suffixes. The root of a term often refers to an organ, tissue, or condition,...
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From frames to OWL2: Converting the Foundational Model of Anatomy.

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The Foundational Model of Anatomy (FMA) was converted from Frames to OWL, resolving over 73% of unsatisfiable classes. This standardized OWL version facilitates its use in bioinformatics and semantic web development.

Keywords:
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Area of Science:

  • Bioinformatics
  • Ontology Engineering
  • Semantic Web Technologies

Background:

  • The Foundational Model of Anatomy (FMA) is a key human anatomy ontology.
  • FMA was originally developed in Protégé Frames, an outdated modeling language.
  • A modern OWL version is needed for current bioinformatics and semantic web applications.

Purpose of the Study:

  • Develop a generalizable tool to convert FMA from Frames to OWL.
  • Convert and clean up the FMA ontology into a standardized OWL format.
  • Ensure the converted FMA classifies under an EL reasoner for improved usability.

Main Methods:

  • Developed a Java-based conversion tool using Protégé and OWL-APIs.
  • Configured the conversion process using XML files in consultation with FMA authors.
  • Utilized Protégé's Explain feature to identify and rectify classification errors under ELK reasoner.

Main Results:

  • Successfully converted FMA to OWL, retaining most of the original information.
  • Eliminated unsatisfiable classes; prior to cleanup, 73% of >100,000 classes were unsatisfiable.
  • The converted FMA is the only complete OWL version classifying under an EL reasoner.

Conclusions:

  • The standardized FMA in OWL should be the sole official release, supplanting older versions.
  • This OWL version will significantly aid informatics research and global knowledge base development.
  • Anatomically structured information frameworks will accelerate with the adoption of FMA in OWL.