Difference between revisions of "FMA (Protege) links to Slicer"
From NAMIC Wiki
| Line 12: | Line 12: | ||
===Key Investigators=== | ===Key Investigators=== | ||
* GE: Viswanath Avasarala, Jim Miller | * GE: Viswanath Avasarala, Jim Miller | ||
| − | * Harvard: Ion-Florin Talos | + | * Harvard: Ion-Florin Talos, Michael Halle, Wendy Plesniak |
| − | * | + | * Isomics: Steve Pieper |
| Line 22: | Line 22: | ||
<h1>Objective</h1> | <h1>Objective</h1> | ||
| − | We are building algorithms to browse | + | 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 functional ontologies of brain based on Protege's frame based representation. |
| Line 31: | Line 31: | ||
<h1>Approach, Plan</h1> | <h1>Approach, Plan</h1> | ||
Based on the idea's presented in the paper, "OQAFMA Querying Agent for the Foundational Model of Anatomy", we will build | 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 | + | a query-engine that allows a software program to navigate through Protege ontologies. We will use this capability to develop an ontology browser for FMA. |
| Line 43: | Line 43: | ||
1. Integration of FMA browser with QueryAtlas. | 1. Integration of FMA browser with QueryAtlas. | ||
2. Assesment of appropriate prefuse data-structures to hold FMA ontology data. | 2. Assesment of appropriate prefuse data-structures to hold FMA ontology data. | ||
| − | 3. Integration of Query engine to Ion-Florin et al's | + | 3. Integration of Query engine to Ion-Florin et al's functional ontology of brain. |
| Line 54: | Line 54: | ||
===References=== | ===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. | * 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. | + | * 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. | + | * 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. | * 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. | ||
Revision as of 20:36, 20 June 2008
Home < FMA (Protege) links to Slicer
Key Investigators
- GE: Viswanath Avasarala, Jim Miller
- Harvard: Ion-Florin Talos, Michael Halle, Wendy Plesniak
- Isomics: Steve Pieper
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 functional 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 an 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 functional 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.
