FMA (Protege) links to Slicer - Revision history

Aviswanath: /* Key Investigators */

2008-06-27T14:49:22Z

Key Investigators

Aviswanath: /* Key Investigators */

2008-06-27T14:14:43Z

Key Investigators

Millerjv: /* Key Investigators */

2008-06-20T20:38:03Z

Key Investigators

Millerjv: /* Key Investigators */

2008-06-20T20:37:26Z

Key Investigators

Millerjv at 20:36, 20 June 2008

2008-06-20T20:36:30Z

Vissu 330 at 20:11, 20 June 2008

2008-06-20T20:11:56Z

Vissu 330: /* Key Investigators */

2008-06-20T20:10:39Z

Key Investigators

Vissu 330: /* Key Investigators */

2008-06-20T20:09:57Z

Key Investigators

Vissu 330: /* Key Investigators */

2008-06-20T20:09:46Z

Key Investigators

Vissu 330: /* Key Investigators */

2008-06-20T20:08:34Z

Key Investigators

@@ Line 52: / Line 52: @@
 <h1>Future work</h1>
-During the Na-Mic week
 # Integrate FMA explorer to Query Altas
 # Complete the design of ontology reasoner for the Motor cortex's functional ontology.

@@ Line 40: / Line 40: @@
 <h1>Progress</h1>
-Our plan for the project week is to work on
+During the Na-Mic week
-# Integration of FMA browser with QueryAtlas.
+# Normalized concepts of Freesurfer, BIRNLEX,Neuro-Names and FMA.
-# Assesment of appropriate prefuse data-structures to hold FMA ontology data.
+# Finalized the design of reasonig system that will work the functional ontology.
-# Integration of Query engine to Talos et al's functional ontology of brain.
+# Stared working on integrating FMA explorer to QueryAtlas.
 </div>
 <br style="clear: both;" />

@@ Line 43: / Line 43: @@
 # Integration of FMA browser with QueryAtlas.
 # Assesment of appropriate prefuse data-structures to hold FMA ontology data.
-# Integration of Query engine to Ion-Florin et al's functional ontology of brain.
+# Integration of Query engine to Talos et al's functional ontology of brain.

@@ Line 41: / Line 41: @@
 <h1>Progress</h1>
 Our plan for the project week is to work on
-. Integration of FMA browser with QueryAtlas.
+# Integration of FMA browser with QueryAtlas.
-. Assesment of appropriate prefuse data-structures to hold FMA ontology data.
+# Assesment of appropriate prefuse data-structures to hold FMA ontology data.
-. Integration of Query engine to Ion-Florin et al's functional ontology of brain.
+# Integration of Query engine to Ion-Florin et al's functional ontology of brain.

@@ Line 12: / Line 12: @@
 ===Key Investigators===
 * GE: Viswanath Avasarala, Jim Miller
-* Harvard: Ion-Florin Talos
+* Harvard: Ion-Florin Talos, Michael Halle, Wendy Plesniak
-* Stanford: Michael Hall.
+* Isomics: Steve Pieper
@@ Line 22: / Line 22: @@
 <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.
@@ Line 31: / Line 31: @@
 <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.
+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: @@
 . Integration of FMA browser with QueryAtlas.
 . Assesment of appropriate prefuse data-structures to hold FMA ontology data.
-. Integration of Query engine to Ion-Florin et al's physiological  ontology of brain.
+. Integration of Query engine to Ion-Florin et al's functional ontology of brain.
@@ Line 54: / Line 54: @@
 ===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.
+* 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.

@@ Line 1: / Line 1: @@
 {|
 |[[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 32: / Line 32: @@
 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.
- <foo>.
 Our plan for the project week is to first try out <bar>,...