A Project of the LMU Bioinformatics Group
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XMLPipeDB

A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources

XMLPipeDB is an open source suite of Java-based tools for automatically building relational databases from an XML schema (XSD). XMLPipeDB provides functionality for managing, querying, importing, and exporting information to and from XML data with minimum manual processing of the data. While its applicability is fairly general, the original motivation for XMLPipeDB was to create a solution for the management of biological data from different sources that are used to create Gene Databases for GenMAPP (Gene Map Annotator and Pathway Profiler), software for viewing and analyzing DNA microarray and other genomic and proteomic data on biological pathways.

XMLPipeDB was created by the Bioinformatics Group at Loyola Marymount University, a collaborative research group founded by Dr. Kam D. Dahlquist (Department of Biology) and Dr. John David N. Dionisio (Department of Electrical Engineering and Computer Science). XMLPipeDB development began in Spring 2006 as a group project in a special studies course in Bioinformatics (CMSI 698/BIOL 498) team-taught by Drs. Dahlquist and Dionisio. Development continued in a second special studies course, Open Source Software Development Workshop (CMSI 698/598) and has transitioned into an undergraduate Biological Databases (CMSI 367, BIOL 367, HNRS 398) course taught in Fall 2008, Fall 2009, and Fall 2010. XMLPipeDB also follows the philosophy of Dr. Dionisio’s Recourse project, which seeks to introduce an open source culture into the computer science curriculum.

XMLPipeDB is available under the GNU Lesser General Public License (LGPL).