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

From NAMIC Wiki
Jump to: navigation, search
 
(13 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 
{|
 
{|
 
|[[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.]]
+
|[[Image:SmallOntologyBrowser.png|thumb|320px|SPN Ontology visualization in Query Atlas.]]
  
 
|}
 
|}
Line 8: Line 8:
 
__NOTOC__
 
__NOTOC__
  
−
===Instructions for Use of this Template===
+
 
−
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/Project-Name
 
−
#Copy the entire text of this page into the page created above
 
−
#Link the created page into the list of projects for the project event
 
−
#Delete this section from the created page
 
−
#Send an email to tkapur at bwh.harvard.edu if you are stuck
 
  
 
===Key Investigators===
 
===Key Investigators===
 
* GE: Viswanath Avasarala, Jim Miller
 
* GE: Viswanath Avasarala, Jim Miller
−
* Utah: Tom Fletcher, Ross Whitaker
+
* Harvard: Ion-Florin Talos, Michael Halle, Wendy Plesniak
 +
* Isomics: Steve Pieper
  
  
Line 25: Line 21:
  
 
<h1>Objective</h1>
 
<h1>Objective</h1>
−
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
+
 
 +
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 33: Line 30:
  
 
<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
 +
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.
 +
  
−
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below.  The main challenge to this approach is <foo>.
 
  
−
Our plan for the project week is to first try out <bar>,...
 
 
</div>
 
</div>
  
Line 42: Line 40:
  
 
<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.
  
−
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 [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|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.
 
  
 
</div>
 
</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>
 +
  
 
<br style="clear: both;" />
 
<br style="clear: both;" />
Line 53: Line 65:
 
===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.
Retrieved from "https://www.na-mic.org/w/index.php?title=FMA_(Protege)_links_to_Slicer&oldid=27776"