NAMIC Wiki - User contributions [en]

FMA (Protege) links to Slicer

2008-06-27T14:49:22Z

Aviswanath: /* Key Investigators */

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|SPN Ontology visualization in Query Atlas.]]

|}

__NOTOC__

===Key Investigators===
* GE: Viswanath Avasarala, Jim Miller
* Harvard: Ion-Florin Talos, Michael Halle, Wendy Plesniak
* Isomics: Steve Pieper

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<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 functional ontologies of brain based on Protege's frame based representation.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<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.

</div>

<div style="width: 40%; float: left;">

<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.

</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;" />

</div>

===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.

FMA (Protege) links to Slicer

2008-06-27T14:14:43Z

Aviswanath: /* Key Investigators */

{|
|[[Image:Fma.JPG|thumb|320px|Exploration of Foundational Model of Anatomy's representation of brain ]]
|[[Image:SmallOntologyBrowser.png|thumb|320px|SPN Ontology visualization in Query Atlas.]]

|}

__NOTOC__

===Key Investigators===
* GE: Viswanath Avasarala, Jim Miller
* Harvard: Ion-Florin Talos, Michael Halle, Wendy Plesniak
* Isomics: Steve Pieper

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<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 functional ontologies of brain based on Protege's frame based representation.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<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.

</div>

<div style="width: 40%; float: left;">

<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.

</div>

<div style="width: 40%; float: left;">

<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.

</div>

<br style="clear: both;" />

</div>

===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.