Name - Gary T. Atkins
School -Fisk University
Classification - Graduating Senior
Major - Business Administration/Computer Science
Organization - Kappa Alpha Psi Fraternity Inc.
Mentor - Richard C. Ward
ABSTRACT
The objective of this research project is to connect a three-dimensional (3D) model of the human body to ontologies or hierachies of knowledge in the corresponding anatomy.
We are implementing this by connecting a visualization program, based on Visualization Toolkit (VTK), to the Foundational Model of Anatomy developed at the University of Washington. The Visualization ToolKit is an open source, freely available software system for 3D computer graphics, image processing, and visualization.
In the future, the user will be able to position the cursor within the 3D space to query the anotomical ontology. Querying the Foundational Model of Anatomy will return other information, including information such as what organs surround a selected organ.
The anotomical ontology is implemented using Web services that provide connection through the Web to various kinds of information and operations.
Web services are base on some recent fundemental Web concepts including: Extensible Markup Language (XML) and Simple Object Access Protocol (SOAP).
SOAP is a lightweight protocol intended for exchanging structured information in distributed environments. Web services are powerful because they provide greater interoperability and extensibility thanks to the use of XML.
Programs providing simple services can interact with each other in order to deliver sophisticated added-value services. In this research project, web servicesare used to connect the Foundational Model of Anatomy, an otology of anatomy, to a 3D representation of anatomy using a Web service. This work supports the ORNL virtual soldier project.
XML Source
Soap Link
Web Services
Ontologies:
Statement from W3C organization: "An ontology defines the terms used to describe and represent an area of knowledge.
Ontologies are used by people, databases, and applications that need to share domain information (a domain is just a specific subject area or area of knowledge, like medicine, tool manufacturing, real estate, automobile repair,
financial management, etc.). Ontologies include computer-usable definitions of basic concepts in the domain and the relationships among them. They encode knowledge in a domain and also knowledge that spans domains. In this way, they make that knowledge reusable."
Ontologies Website
Visualization Toolkit (VTK)
The Visualization ToolKit (VTK) is free, open source software system for 3D computer graphics, and image processing.
VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python.
My project will be using the Tcl/Tk wrappers for the VTK objects in our development.
VTK was developed by Will Schroeder, Ken Martin, and Bill Lorensen. It is maintained now by Kitware, Inc. Bill Lorensen is one of the Principal Investigators of the Virtual Soldier Project.
VTK
Foundational Model of Anatomy
The Foundational Model (FMA) is an ontology or knowledgebase for bioinformatics concerned with the representation of concepts and relationships necessary for the symbolic modeling of the anatomical structures of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy in a form that is understandable to humans but is also navigable by machine-based systems. The FMA is maintained by the Structural Informatics Group at the University of Washington.
My project will connect 3D anatomy to the information on anatomical structures, such as the structures adjacent to a given structure, from the Foundational Model of Anatomy.
Foundational Model Website
Virtual Soldier Project
The DARPA Virtual Soldier Project will produce complex mathematical models to create anatomical and physiological representations of individual soldiers.
The connection of the 3D anatomical model with other information such as vital signs (physiological information) is referred to as the holographic medical representation (or Holomer). The Holomer is a type of visual electronic medical record that will greatly improve medical diagnosis on and off the battlefield.
My project will support the Virtual Soldier Project by providing for the PC platform a means to connect the 3D anatomy (the Holomer) with anatomical information contained in the Foundational Model of Anatomy via Web services.
Virtual Solder
Tcl/TK (Command or Scripting Language)
Tcl (Tool Command Language), a widely used scripting language, has become a critical component of software development in research and industry. For our project it is useful since it has a simple, programmable syntax and can be used as for standalone applications or embedded in application programs.
Tk is a graphical user interface toolkit that makes it possible to quickly create powerful GUIs. It now ships with all distributions of Tcl.
Tcl and Tk were created and developed by John Ousterhout. Both Tcl and Tk are open source and they are used within VTK.
Tcl & Tk Link