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

Outline ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

How GenMAPP Works http://www.GenMAPP.org ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Maintaining and Updating GenMAPP Gene Databases has been a Bottleneck for Development ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

XSD-to-DB is based on Hyperjaxb2 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

UniProtDB and GODB Required Only Nominal Post-processing ,[object Object],[object Object]

XMLPipeDB Utilities are Reusable ,[object Object],[object Object]

GenMAPP Builder then produces…

GenMAPP Gene Databases ,[object Object],[object Object],[object Object],[object Object]

Workflow for Interdisciplinary Undergraduate Student Projects ,[object Object],[object Object]

How robust is our system to changes in XML formats? ,[object Object],[object Object]

How robust is our system to changes in XML formats? ,[object Object],[object Object],[object Object],[object Object]

How Well Do Bioinformatics XML Formats Perform with XMLPipeDB? Multiple dependent XSDs or DTDs could not be processed SBML MathML CellML Multiple other NCBI DTDs Error: property with the same name is generated from more than one schema component MiniML (NCBI GEO) GPML (GenMAPP) BioMart PDBML HUP-ML (proteomics data) PubChem RNAML Syntax error with naming or datatypes; would require post-processing EMBL Nucleotide EMBL CDS mzML (Mass spec data) AGML (2D gel data) dbSNP (NCBI) N/A KEML (KEGG) ,[object Object],UniProt XML GO OBO-XML Export Gene Database with GenMAPP Builder Successful build of XMLPipeDB Utilities with ant and import of XML data into PostgreSQL Successful creation of PostgresQL database with automatically generated schema.sql XSD-to-DB Data Source

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

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