link betw phenotype and genotype

link betw phenotype and genotype - BMC Bioinformatics...

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BMC Bioinformatics Research Phenotypic and genotypic data integration and exploration through a web-service architecture Angelo Nuzzo 1 ,A lber toR iva 2 andR iccardoBe l lazz i* 1 Address: 1 Department of Computer Engineering and Systems Science, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy and 2 Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA E-mail: Angelo Nuzzo - angelo.nuzzo@unipv.it; Alberto Riva - ariva@ufl.edu; Riccardo Bellazzi* - riccardo.bellazzi@unipv.it *Corresponding author from Bioinformatics Methods for Biomedical Complex Systems Applications (NETTAB2008) Varenna, Italy 19 21 May 2008 Published: 15 October 2009 BMC Bioinformatics 2009, 10 (Suppl 12):S5 doi: 10.1186/1471-2105-10-S12-S5 This article is available from: http://www.biomedcentral.com/1471-2105/10/S12/S5 © 2009 Nuzzo et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Linking genotypic and phenotypic information is one of the greatest challenges of current genetics research. The definition of an Information Technology infrastructure to support this kind of studies, and in particular studies aimed at the analysis of complex traits, which require the definition of multifaceted phenotypes and the integration genotypic information to discover the most prevalent diseases, is a paradigmatic goal of Biomedical Informatics. This paper describes the use of Information Technology methods and tools to develop a system for the management, inspection and integration of phenotypic and genotypic data. Results: We present the design and architecture of the Phenotype Miner, a software system able to flexibly manage phenotypic information, and its extended functionalities to retrieve genotype information from external repositories and to relate it to phenotypic data. For this purpose we developed a module to allow customized data upload by the user and a SOAP-based communications layer to retrieve data from existing biomedical knowledge management tools. In this paper we also demonstrate the system functionality by an example application of the system in which we analyze two related genomic datasets. Conclusion: In this paper we show how a comprehensive, integrated and automated workbench for genotype and phenotype integration can facilitate and improve the hypothesis generation process underlying modern genetic studies. Background One of the most challenging goals of current biomedical research is to link the genotypic and phenotypic information generated by high-throughput experimental
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link betw phenotype and genotype - BMC Bioinformatics...

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