Aligning the Foundational Model of Anatomy and the Gene Ontology using Protégé

The Foundational Model of Anatomy (FMA) is a large (70,000 terms) ontology covering macro- and micro-level anatomical components of human anatomy. The Gene Ontology (GO) is a controlled vocabulary of genetic terms that can be applied to multiple organisms. An additional valuable element to GO is their database of gene products, or annotations, which are associated with several of the terms in the ontology. The FMA and GO overlap in the domain of subcellular components, and we proposed a merging of information, utilizing the structure of the FMA the GO annotations displayed as a new slot widget in Protégé. The following steps were undertaken:

  • Extract the portion Of the FMA containing subcellular components

    This made the ontology much more manageable in size (1,100 terms)

  • Map relationships between the FMA and GO

    The foundation of this merging of ontologies is a set of mappings, linking one or more FMA terms to one or more GO terms. As an initial proof of concept, these mappings were performed by hand, and resulted in 148 relationships between the two ontologies (as of January, 2004).

  • Develop a slot widget to display GO annotations in the FMA extract

    After these relationships were stored in a MySQL database, a Protégé slot widget was developed to display related GO annotations as a user browsed through an the FMA extract:

    Selecting an annotation from the list brings up the Annotation detail:


    Last updated December, 2004 by Adam Silberfein