XMLPipeDB
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Title: XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources Author: Kam Dalquist
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XMLPipeDB
- 1. A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources BOSC Vienna, Austria July 20, 2007 Kam D. Dahlquist Department of Biology Jeffrey Nicholas John David N. Dionisio Department of Electrical Engineering & Computer Science http://xmlpipedb.cs.lmu.edu Loyola Marymount University
- 7. MAPPFinder Determines Which GO Terms Are Overrepresented in a GenMAPP Expression Dataset
- 10. GenMAPP Gene Database Schema for Escherichia coli K12
- 11. Data Sources Required for a “Minimal” GenMAPP Gene Database UniProt • UniProt complete proteome sets for many species are made available as XML downloads by the Integr8 resource Gene Ontology • OBO XML format UniProt to GO associations • GOA downloads also available at Integr8
- 12. XMLPipeDB Use Case Diagram
- 13. XMLPipeDB Use Case Diagram
- 14. Produces: Java source code SQL DDL file Hibernate mappings Apache Ant build.xml
- 15. XMLPipeDB Use Case Diagram
- 17. XMLPipeDB Use Case Diagram
- 19. XMLPipeDB Use Case Diagram
- 20. GenMAPP Builder Interacts with PostgreSQL in Three Ways
- 21. GenMAPP Builder Uses the XMLPipeDB Utilities Library to Configure the PostgreSQL Database … and import XML
- 23. The User Chooses Which Gene ID Systems and Relations to Export to the Gene Database
- 25. The Next Challenge was to Create a Gene Database for the Plant, Arabidopsis thaliana
- 28. XSD-to-DB Adam Carasso Jeffrey Nicholas Scott Spicer XMLPipeDBUtils David Hoffman Babak Naffas Jeffrey Nicholas Ryan Nakamoto UniProtDB Joe Boyle Joey Barrett GODB Scott Spicer Roberto Ruiz GenMAPP Builder Joey Barrett Jeffrey Nicholas Scott Spicer Special Thanks GenMAPP.org Development Group Caskey L. Dickson, Wesley T. Citti NSF CCLI Program (http://recourse.cs.lmu.edu) http://xmlpipedb.cs.lmu.edu LMU Bioinformatics Group Kam D. Dahlquist http://myweb.lmu.edu/kdahqui [email_address] John David N. Dionisio http://myweb.lmu.edu/dondi [email_address]
Editor's Notes
- Both relatively new to LMU Dondi’s background in medical informatics, data visualization, person-computer interactions During my postdoc I had served as project manager for GenMAPP, want to extend features of GenMAPP, especially for other species I am not a software developer (last time I took a computer science class was AP Pascal in high school), but I’ve had a lot of experience interacting with developers I’m proud of GenMAPP, especially that it is user-friendly for biologists, and is relatively bug free (result of my extensive testing) However, I never would have been standing up in this community to talk about it because although we believed strongly that GenMAPP should be free-of-charge, we were slow to make the source code available (it is now available on SourceForge) It has only been my collaboration with Dondi that I have been educated as to what Open Source software development truly means (Cathedral and Bazaar) This is the perfect forum for talking about our work because, while I am using the fruits of XMLPipeDB for GenMAPP as first imagined, we designed this project to have components that are resusable for other purposes and that the bioinformatics developer community is our target audience