FMA (Protege) links to Slicer

Exploration of Foundational Model of Anatomy's representation of brain

Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.

Key Investigators

• GE: Viswanath Avasarala, Jim Miller
• Harvard: Ion-Florin Talos
• Stanford: Michael Hall.

Objective

We are building algorithms to browse protege's frame based ontologies. This capability will allow us to integrate some very extensive anatomy ontologies like the Foundational Model of Anatomy into slicer3. Also, we plan to develop reasoning algorithms to work with physiological ontologies of brain based on Protege's frame based representation.

Approach, Plan

Based on the idea's presented in the paper, "OQAFMA Querying Agent for the Foundational Model of Anatomy", we will build a query-engine that allows a software program to navigate through protege ontologies. We will use this capability to develop a ontology browser for FMA.

Progress

Our plan for the project week is to work on 1. Integration of FMA browser with QueryAtlas. 2. Assesment of appropriate prefuse data-structures to hold FMA ontology data. 3. Integration of Query engine to Ion-Florin et al's physiological ontology of brain.

References

• Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.
• C. Rosse and J.L.V. Mejino, A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed Inform. 36:478-500, 2003.
• P. Mork, J.F. Brinkley, and C. Rosse, OQAFMA querying agent for the Foundational Model of Anatomy: providing flexible and efficient access to a large semantic network. J. Biomed Inform. 36:501-517, 2003.
• Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.