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Descriptive Article

CAVEman: Standardized anatomical context for biomedical data mapping†

  1. Andrei L. Turinsky1,
  2. Elena Fanea1,
  3. Quang Trinh1,
  4. Stephen Wat2,
  5. Benedikt Hallgrímsson3,
  6. Xiaoli Dong1,
  7. Xueling Shu4,
  8. Julie N. Stromer1,
  9. Jonathan W. Hill5,
  10. Carol Edwards5,
  11. Brenda Grosenick5,
  12. Masumi Yajima6,
  13. Christoph W. Sensen1,*

Article first published online: 4 DEC 2007

DOI: 10.1002/ase.3

Issue

Anatomical Sciences Education

Anatomical Sciences Education

Volume 1, Issue 1, pages 10–18, January 2008

Additional Information

How to Cite

Turinsky, A. L., Fanea, E., Trinh, Q., Wat, S., Hallgrímsson, B., Dong, X., Shu, X., Stromer, J. N., Hill, J. W., Edwards, C., Grosenick, B., Yajima, M. and Sensen, C. W. (2008), CAVEman: Standardized anatomical context for biomedical data mapping. Anat Sci Ed, 1: 10–18. doi: 10.1002/ase.3

Author Information

  1. 1

    Sun Center of Excellence for Visual Genomics, University of Calgary, Calgary, Alberta, Canada

  2. 2

    Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada

  3. 3

    Department of Cell Biology and Anatomy, University of Calgary, Calgary, Alberta, Canada

  4. 4

    Department of Computer Science, University of Calgary, Calgary, Alberta, Canada

  5. 5

    Kasterstener Publications, Inc., Red Deer, Alberta, Canada

  6. 6

    Department of Fine Arts, University of Calgary, Calgary, Alberta, Canada

*University of Calgary, HS 1150, 3330 Hospital Dr. NW, Calgary, Alberta, Canada T2N 4N1

  1. †

    This article is dedicated to the memory of our friend Cynthia Steljes, outstanding musical artist and cofounder of the musical quartet “Quartetto Gelato,” who passed away in December 2006. Cynthia's keen interest in our research and her curiosity made us think outside of the box. Cynthias passing is a permanent loss for all of us and she will be missed.

Publication History

  1. Issue published online: 15 DEC 2007
  2. Article first published online: 4 DEC 2007
  3. Manuscript Accepted: 15 SEP 2007
  4. Manuscript Revised: 25 AUG 2007
  5. Manuscript Received: 5 JUN 2007

Funded by

  • Industrial Research Assistance Program. Grant Number: LS-05-G01
  • Western Economic Diversification Canada. Grant Number: 3338
  • Alberta Innovation and Science. Grant Number: LS-05-G01
  • Genome Canada
  • Alberta Science and Research Authority
  • iCORE/Sun Microsystems Industrial Research Chair Program
  • Alberta Network for Proteomics Innovation
  • Canada Foundation for Innovation

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Keywords:

  • virtual reality;
  • anatomical atlas;
  • ontology;
  • gene expression;
  • Java 3D

Abstract

The authors have created a software system called the CAVEman, for the visual integration and exploration of heterogeneous anatomical and biomedical data. The CAVEman can be applied for both education and research tasks. The main component of the system is a three-dimensional digital atlas of the adult male human anatomy, structured according to the nomenclature of Terminologia Anatomica. The underlying data-indexing mechanism uses standard ontologies to map a range of biomedical data types onto the atlas. The CAVEman system is now used to visualize genetic processes in the context of the human anatomy and to facilitate visual exploration of the data. Through the use of Java™ software, the atlas-based system is portable to virtually any computer environment, including personal computers and workstations. Existing Java tools for biomedical data analysis have been incorporated into the system. The affordability of virtual-reality installations has increased dramatically over the last several years. This creates new opportunities for educational scenarios that model important processes in a patient's body, including gene expression patterns, metabolic activity, the effects of interventions such as drug treatments, and eventually surgical simulations. Anat Sci Ed 1:10–18, 2008. © 2007 American Association of Anatomists.

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