K2/Kleisli and GUS: Experiments in integrated access to genomic data sources

The integration of heterogeneous data sources and software systems is a major issue in the biomed ical community and several approaches have been explored: linking databases, "on-thefly" integration through views, and integration through warehousing. In this paper we report on our experiences with two systems that were developed at the University of Pennsylvania: an integration system called K2, which has primarily been used to provide views over multiple external data sources and software systems; and a data warehouse called GUS which downloads, cleans, integrates and annotates data from multiple external data sources. Although the view and warehouse approaches each have their advantages, there is no clear "winner". Therefore, users must consider how the data is to be used, what the performance guarantees must be, and how much programmer time and expertise is available to choose the best strategy for a particular application. Comments Postprint version. Published in IBM Systems Journal, Volume 40, Issue 2, March 2001, pages 512-531. Publisher URL: http://search.ebscohost.com/login.aspx?direct=true&db=aph&AN=4628447&site=ehostlive Author(s) Susan B. Davidson, Jonathan Crabtree, Brian P. Brunk, Jonathan Schug, Val Tannen, Chris Overton, and Christian J. Stoeckert This journal article is available at ScholarlyCommons: http://repository.upenn.edu/db_research/23 K2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources Susan B. Davidson, Jonathan Crabtree, Brian Brunk, Jonathan Schug, Val Tannen, Chris Overton and Chris Stoeckert Center for Bioinformatics Dept. of Computer and Information Science University of Pennsylvania Philadelphia, PA 19104 fsusan,crabtree,brunkb,jschug,[email protected], [email protected] To appear in the IBM Systems Journal.