From frames to OWL2: Converting the Foundational Model of Anatomy

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• FMA was originally developed in Protégé Frames, an outdated modeling language.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.