Eric A. Wernert
ABSTRACT
We describe the design and implementation of PViN (Pedigree Visualization and Navigation), a scalable and flexible software system that enables the visualization, analysis, and printing of hierarchical relations typically stored in relational databases. Although the concept of visualizing and printing pedigree databases is not new, we have developed a novel implementation based on modern approaches for several important reasons: (1) Our university's center of hereditary diseases has accumulated very large amounts of hereditary information from various populations for ongoing research projects, and has difficulty managing and effectively printing the associated pedigree trees with legacy FORTRAN software; (2) The size of some of these databases (over 40,000 entries covering seven generations) is too large for existing commercial pedigree software to handle; and (3) Our researchers and support staff need more effective ways to perform visual analysis tasks, such as the comparison of multiple pedigrees and the cross-referencing of individuals that appear in multiple families (through re-marriage.) The PViN system addresses these fundamental problems while also providing a number of additional features and functions, including: context-free drawing routines that enable rendering onto screen and printer contexts interchangeably; a generic framework that allows the system to interface with multiple databases and database servers; a multiple view user interface that provides side-by-side comparisons and "focus+context" rendering; and advanced node searching and cross-referencing capabilities.
- Fischer, C., Schweigert, S., Spreckelsen, C, and Vogel, F. (1996) Programs, databases, and expert systems for human geneticists - a survey. In Human Genetics. 97 (2) Springer-Verlag Heidelberg, 129--137.Google Scholar
- Pedigree Reviews -- Pedigree Drawing Programs / Software Reviews. University of Kansas Medical Center, http://www.kumc.edu/gec/prof/pedrev.htmlGoogle Scholar
- Meaney, F. J. (1987) Databases for genetic services - current usages and future directions. In Journal of Medical Systems 11:227--232. Google ScholarDigital Library
- Beidlemen K, Gersting J (1985) Plotting human pedigrees. In Journal of Medical Systems 9:87--108Google Scholar
- Cyrillic Software, http://www.cyrillicsoftware.com/Google Scholar
- Lineage -- Pedigree visualization and analysis software. Animal Science Department, Cornell University, http://www.ansci.cornell.edu/lineage/index.htmlGoogle Scholar
- CancerGene - Breast Cancer Risk Evaluation System. University of Texas Southwestern Medical Center at Dallas, http://www3.utsouthwestern.edu/cancergene/ cancergene.htmGoogle Scholar
- Pedigraph. Department of Animal Science, University of Minnesota, http://animalgene.umn.edu/pedigraph.htmlGoogle Scholar
- PED 4.2 -- Pedigree Drawing Software. MedGen Software, http://www.medgen.de/ped/index.htmGoogle Scholar
- Information Visualization Resources, http://www.infovis.org/Google Scholar
- Lamping, J. Rao, R., and Pirolli, P. (1995) A Focus+Content Technique Based on Hyperbolic Geometry for Viewing Large Hierarchies. In Proc. CHI '95, 401--408. Google ScholarDigital Library
- Graham, M. and Kennedy, J. (2001) Combining linking & focusing techniques for a multiple hierarchy visualisation. In 5th Int'l Conf. on Information Visualisation - IV2001, University of London, IEEE Computer Society Press, 425--432. Google ScholarDigital Library
- Munzner, T., Guimbretiere, F. Tasiran, S., Zhang, L., and Zhou, Y. (2003) TreeJuxtaposer: Scalable Tree Comparison using Focus+Context with Guaranteed Visibility. In SIGGRAPH 2003, published as ACM Transactions on Graphics 22(3), pages 453---462. Google ScholarDigital Library
- Geiger, K. Inside ODBC (Microsoft Programming Series), Microsoft Printing, Aug. 1995. Google ScholarDigital Library
- Sanders, R. E. ODBC 3.5 Developer's Guide, McGraw Hill publishing, Sept. 1998. Google ScholarDigital Library
- Fisher, M., Ellis, J., and Bruce, J. JDBC API Tutorial and Reference, Third Edition, Addison-Wesley Professional, June 2003. Google ScholarDigital Library
- Woo, M. et. al. OpenGL programming Guide, 3rd Edition, Version 1.2, Addison-Wesley Developers Press, 1997.Google Scholar
- Warnock, J. PostScript Language Reference, 3rd Edition, Addison-Wesley Press, 1996. (Adobe Postscript Red Book).Google Scholar
- Geuzaine, C. GL2PS: An OpenGL to PostScript printing library, Version 1.2.1, 13 July 2004. http://www.geuz.org/gl2ps/Google Scholar
- IBM 221 Monitor, http://www-l.ibm.com/businesscenter/cpe/download8/19460/G2216585.pdfGoogle Scholar
- Humphreys, G. Houston, Ml, Ng, R., Frank, R., Ahern, S., Kirchner, P., Klosowski, J. Chromium: A Stream-Processing Framework for Interactive Rendering on Clusters. In Proceedings of SIGGRAPH 2002, pp. 129--140, 2002. Google ScholarDigital Library
Index Terms
- PViN: a scalable and flexible system for visualizing pedigree databases
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