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Dahlquist_XMLPipedB_BOSC2009
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Dahlquist_XMLPipedB_BOSC2009
- A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources BOSC Stockholm, Sweden June 27, 2009 Kam D. Dahlquist Alexandrea Alphonso Chad Villaflores Department of Biology John David N. Dionisio Derek Smith Department of Electrical Engineering & Computer Science http://xmlpipedb.cs.lmu.edu Loyola Marymount University
- XMLPipeDB Use Case Diagram
- GenMAPP Builder then produces…
- Acknowledgments http://xmlpipedb.cs.lmu.edu Initial Development Joey Barrett Joe Boyle Adam Carasso David Hoffman Babak Naffas Ryan Nakamoto Jeffrey Nicholas Roberto Ruiz Scott Spicer Current Development Alexandrea Alphonso Derek Smith Chad Villaflores … and the rest of the undergraduates from the Fall 2008 Biological Databases class Kam D. Dahlquist [email_address] John David N. Dionisio [email_address] http://sourceforge.net/projects/xmlpipedb
Editor's Notes
- The UniProt and GO XML schemas have each changed twice during GenMAPP Builder development In all instances, updating GenMAPP Builder to use the new schemas consisted of these fairly mechanical steps: 1. Re-run XSD-to-DB on the updated schema 2. Re-run name-clash adjustment utilities on the new file set 3. Redefine the SQL tables into the relational database 4. Replace the Java libraries in GenMAPP Builder None of these steps involved manual recoding of UniProt or GO code The changes only affected GenMAPP Builder code if the schema changes affected tables or fields whose data are exported to the GenMAPP Gene Database Underscores, slashes, periods not uniformly carried over into same UniProt XML fields
- The UniProt and GO XML schemas have each changed twice during GenMAPP Builder development In all instances, updating GenMAPP Builder to use the new schemas consisted of these fairly mechanical steps: 1. Re-run XSD-to-DB on the updated schema 2. Re-run name-clash adjustment utilities on the new file set 3. Redefine the SQL tables into the relational database 4. Replace the Java libraries in GenMAPP Builder None of these steps involved manual recoding of UniProt or GO code The changes only affected GenMAPP Builder code if the schema changes affected tables or fields whose data are exported to the GenMAPP Gene Database Underscores, slashes, periods not uniformly carried over into same UniProt XML fields
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