XMLPipeDB is an open source suite of Java-based tools for automatically building relational databases from an XML schema (XSD) with minimal manual processing of the data. While its applicability is intended to be 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 has a modular architecture with three components that may be used separately or together. XSD-to-DB reads an XSD (XML Schema Definition) and automatically generates an SQL schema, Java classes, and Hibernate mappings. XMLPipeDB Utilities provides functionality for configuring the database, importing data, and performing queries. GenMAPP Builder is based on the XMLPipeDB Utilities and exports GenMAPP-compatible Gene Databases based on data from UniProt and Gene Ontology (GO).
- Complete list of documentation available.
- Documentation available from this Wiki:
- Using Microsoft Excel to Compare ID Lists
- Complete list of XMLPipeDB-related publications, presentations, and abstracts.
- Abstracts about XMLPipeDB for group-editing on this Wiki.
- xmlpipedb-developer mailing list archive
- LMU Biological Databases Course Materials
Gene Database Testing Reports for Released Gene Databases
- Gene Database Testing Report E. coli K12 20090529
- Gene Database Testing Report H. pylori 20101130
- Gene Database Testing Report M. smegmatis 20110128
- Gene Database Testing Report M. tuberculosis 20110303
- Gene Database Testing Report P. aerugenosa 20100212
- Gene Database Testing Report P. falciparum 20090604
- Gene Database Testing Report S. typhimurium 20110301
- Gene Database Testing Report S. aureus MRSA252 20100218
- Gene Database Testing Report V. cholerae 20101022
Current Project Members
Former Project Members
- General Task List
- Species Task Lists
- List of XML sources to try with XSD-to-DB
- Back to XMLPipeDB Wiki Main Page
- Task List
- Gene Database Testing Template
- List of all XMLPipeDB Wiki pages