Difference between revisions of "FMA (Protege) links to Slicer"

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|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
 
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]
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|[[Image:SmallOntologyBrowser.png|thumb|320px|SPN Ontology visualization in Query Atlas.]]
  
 
|}
 
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===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
* Stanford: Michael Hall.
+
* Isomics: Steve Pieper
  
  
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<h1>Objective</h1>
 
<h1>Objective</h1>
  
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.  
+
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.  
  
  
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<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 protege ontologies. We will use this capability to develop a ontology browser for FMA.  
+
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.  
<foo>.
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 +
 
  
Our plan for the project week is to first try out <bar>,...
 
 
</div>
 
</div>
  
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<h1>Progress</h1>
 
<h1>Progress</h1>
 +
During the Na-Mic week
 +
# Normalized concepts of Freesurfer, BIRNLEX,Neuro-Names and FMA.
 +
# Finalized the design of reasonig system that will work the functional ontology.
 +
# Stared working on integrating FMA explorer to QueryAtlas.
  
1. Integration of FMA browser with Atlas.
 
2. Integration of Query engine to Ion-Florin et al's physiological  ontology of brain.
 
  
 +
</div>
 +
 +
 +
<div style="width: 40%; float: left;">
 +
 +
<h1>Future work</h1>
 +
 +
# Integrate FMA explorer to Query Altas
 +
# Complete the design of ontology reasoner for the Motor cortex's functional ontology.
  
 
</div>
 
</div>
 +
  
 
<br style="clear: both;" />
 
<br style="clear: both;" />
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===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.

Latest revision as of 14:49, 27 June 2008

Home < FMA (Protege) links to Slicer
Exploration of Foundational Model of Anatomy's representation of brain
SPN Ontology visualization in Query Atlas.




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

During the Na-Mic week

  1. Normalized concepts of Freesurfer, BIRNLEX,Neuro-Names and FMA.
  2. Finalized the design of reasonig system that will work the functional ontology.
  3. Stared working on integrating FMA explorer to QueryAtlas.



Future work

  1. Integrate FMA explorer to Query Altas
  2. Complete the design of ontology reasoner for the Motor cortex's functional ontology.



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.