The BiolAD-DB System
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The BiolAD-DB System An Informatics System for Clinical and Genetic Data David A. Nielsen,1 Marty Leidner,2 Chad Haynes,3 Michael Krauthammer4 and Mary Jeanne Kreek1 1 2 3 4
Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, New York, USA Information Technology Facility, The Rockefeller University, New York, New York, USA Laboratory of Statistical Genetics, The Rockefeller University, New York, New York, USA Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
Abstract
The Biology of Addictive Diseases-Database (BiolAD-DB) system is a research bioinformatics system for archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex clinical information, such as response items in genetic questionnaires. Data access and validation is provided by the BiolAD-DB client application, which features a data validation engine tightly coupled to a graphical user interface. Data integrity is provided by the password-protected BiolAD-DB SQL compliant server and database. BiolAD-DB tools further provide functionalities for generating customized reports and views. The BiolAD-DB system schema, client, and installation instructions are freely available at http://www.rockefeller.edu/biolad-db/.
Background In studies into the genetics of addictive diseases, our laboratory has collected data on >3000 subjects. Data include personal, clinical, and genetic information. Clinical data comprise responses from psychiatric and drug abuse scales (e.g. Structured Clinical Interview for DSM-IV Personality Disorders [SCID], Addiction Severity Index [ASI], Kreek-McHugh-Schluger Kellogg [KMSK]), and family origin questionnaires. In addition, we currently have genotype information on >100 genetic variants in genes of interest to our laboratory. The number of subjects and the genetic data per subject are expected to increase dramatically, as there are estimated to be >11 million common single nucleotide polymorphisms in the human genome.[1] There are several commercial products that archive and analyze genetic data. These include the Progeny family of software solutions (Progeny Software, LLC, South Bend, IN, USA; used primarily for family, i.e. linkage, studies), which comprises data storage tools for archiving genetic, phenotype, and pedigree data,[2] Cyrillic 2 (CyrillicSoftware, Oxfordshire, UK), a package for pedigree analysis,[3] HelixTree® (Golden Helix, Inc., Bozeman, MT, USA), a pharmacogenetic analysis tool aimed at the analysis of genetic, clinical, environmental, and drug safety and efficacy data,[4] and
the Visual Genetics package (Visual Technologies, LLC, Phoenix, AZ, USA), which offers storage, genetic, pedigree, and clinical data analysis tools.[5] There are also several freely available (or free to non-profit institutions) programs. These include the Statistical Analysis for Genetic Epidemiology (S.A.G.E.)
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