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.

Instructions for Use of this Template

1. Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/Project-Name
2. Copy the entire text of this page into the page created above
3. Link the created page into the list of projects for the project event
4. Delete this section from the created page
5. Send an email to tkapur at bwh.harvard.edu if you are stuck

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 based on Protege's frame based representation.

Approach, Plan

Our plan is to integrate capabilities to browse foundational model of anatomy (FMA)'s ontology with the QueryAtlas ontology browser. <foo>.

Our plan for the project week is to first try out <bar>,...

Progress

Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the DTI Software Infrastructure project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

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.