Generic Genetic Studies Database

Project Motivation and Description

Continuing advances in genotyping technology are fundamentally changing the way researchers investigate disease. These new technologies are allowing researchers to assay genetic variation at hundreds of thousands of markers across the entire genome simultaneously. Unfortunately, this progress in genotype data generation has not been matched with an increase in the sophistication and capabilities of data management tools. The trend toward highly collaborative projects and the number of subjects, markers, and phenotypes being investigated in each project simply overwhelms the traditional way of managing data with flat files.

The Generic Genetic Studies Database (GGSD) is an open-source data management software package for large scale genetic studies. GGSD is a web-integrated, relational database driven system that stores and appropriately links: (1) pedigree/individual information; (2) genotype data for both SNPs and microsatellites; (3) phenotype data for both quantitative and qualitative traits; and (4) disease definitions and individuals' status for those diseases. GGSD allows researchers to store and manage several projects all through a single interface, and manages the users of the system to track the project(s) each user has access to and their type of access (e.g. upload/delete/update or search/download). GGSD is an extremely flexible system. For example, it allows batch entry of data via file uploads, manual entry and editing of data through web forms, entity-centric web forms for complex querying of any table in the database, pedigree drawing, Hardy-Weinberg equilibrium determination for markers, and sends emails to registered users when data is added/edited/deleted. In addition the data can be downloaded in the preMakeped file format or the users can generate input files for 28 different analysis programs through the system's integration with the Mega2 software.

The GGSD system was designed around the LAMP and LAPP stack paradigm of constructing dynamic, interactive web-based applications. The entire system was designed and programmed using JavaScript, Perl, PHP, and ANSI SQL. Utilizing this open-source software design framework makes GGSD extremely versatile, portable, and economical.

Project Status

GGSD is now available for download. Please click the 'Download Application' link on the left tool bar to get the application. Thank you for your interest. If you have any questions or problems please contact the Lead Developer.