Abstract
This paper describes the application of an information technology infrastructure aimed at supporting translational bioinformatics studies which need the joint management of phenotypic and genotypic data. The system provides an integrated and easy to use software environment, based on data warehouse and data mining tools, to discover the most frequent complex phenotypes and search their penetrance and heritability by mapping them on the population pedigree. We first use a logical formalization to define phenotypes of interest in order to retrieve individuals having that phenotype from the electronic medical record. We then use an open-source Web-based data warehouse application for analyzing phenotypic data and presenting the results in a multidimensional format. Relationships between the selected individuals are automatically visualized by integrating in the system an ad-hoc developed pedigree visualization tool. Finally, the application of the system to support a genetic study of an isolated population, the Val Borbera project, is presented.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Lander, E.S., Schork, N.: Genetic dissection of complex traits. Science 265(5181), 2037–2048 (1994)
Botstein, D., Risch, N.: Discovering genotypes underlying human phenotypes: past successes for Mendelian disease, future approaches for complex disease. Nature Genetics 33, 228–237 (2003)
Sala, C., Bione, S., Crocco, L., Gatti, M., Poggiali, E., Bellazzi, R., Buetti, I., Rognoni, C., Camaschella, C., Toniolo, D.: The Val Borbera Project: epidemiological and genealogical analysis of an isolated population in Northern Italy. European Society of Human Genetics (submitted, 2006)
Kinball, R., Ross, M.: The Data Warehouse Toolkit, 2nd edn. Wiley and Sons, Inc., Chichester (2002)
Wyderka, K.: Data Warehouse Technique for Outcomes Management. Health Management Technology 20(10), 16–17 (1999)
Hyde, J.: Mondrian OLAP project, Pentaho Analysis Service http://mondrian.pentaho.org/
Spofford, G., Harinath, S., Webb, C., Huang, D.H., Civardi., F.: MDX Solutions, 2nd edn. Wiley Publishing Inc., Chichester (2006)
Agarwala, R., Biesecker, L.G., Hopkins, K.A., Francomano, C.A., Schaffer, A.A.: SchafferSoftware for Constructing and Verifying Pedigrees Within Large Genealogies and an Application to the Old Order Amish of Lancaster County. Genome Research 8, 211–221 (1998)
Dudbridge, F., Carver, T., Williams, G.W.: Pelican: pedigree editor for linkage computer analysis. Bioinformatics 20(14), 2327–2328 (2004)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Nuzzo, A., Segagni, D., Milani, G., Sala, C., Larizza, C. (2007). An Integrated IT System for Phenotypic and Genotypic Data Mining and Management. In: Bellazzi, R., Abu-Hanna, A., Hunter, J. (eds) Artificial Intelligence in Medicine. AIME 2007. Lecture Notes in Computer Science(), vol 4594. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73599-1_23
Download citation
DOI: https://doi.org/10.1007/978-3-540-73599-1_23
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-73598-4
Online ISBN: 978-3-540-73599-1
eBook Packages: Computer ScienceComputer Science (R0)