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DESPRAD-Meeting 02/09/2003

DESPRAD-Meeting 02/09/2003. Steffen Schulze-Kremer (until 7/2003) Bernd Drescher (since 8/2003) Robert Wagner. RzpdExpress. Public database for gene expression data Based on MAGE-OM Simple query and analysis interface Available as of 11/2003. Data Import.

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DESPRAD-Meeting 02/09/2003

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  1. DESPRAD-Meeting02/09/2003 Steffen Schulze-Kremer (until 7/2003) Bernd Drescher (since 8/2003) Robert Wagner

  2. RzpdExpress • Public database for gene expression data • Based on MAGE-OM • Simple query and analysis interface • Available as of 11/2003

  3. Data Import • Import from primary database of RZPD • Export to MAGE-ML • Affymetrix Data • CDF and sequences available in MAGE-ML • GDAC Exporter converts EXP, CEL and CHP into MAGE-ML • Buggy • MIAMExpress

  4. Web Interface • Query for experiments by certain criteria (name, type, species, ...) • Display of hybridizations, samples, arrays, reporters • Simple statistical analysis • Histogram • Scatterplot tool • Normalized ratios • T-test

  5. Content • 19 experiments, 103 bio assays • 79 arrays of 42 array designs • 64 bio sources • 370 protocols

  6. Implementation • Oracle • Tomcat • Java, Perl • Generated APIs from Oracle data dictionary • Object-relational mapping • Database interface • R, Bioconductor • Lose coupling to Java Interface

  7. Problems • Data aquisition • Data not MIAME compatible • Operating system restrictions • Performance

  8. Next Steps • Automated analysis pipeline • Further cooperations with new partners • User training • Integration into RZPD system (clone ordering) • Use GO annotations for analysis

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