1. The Penn Experience with MAGE-TAB John Brestelli Elisabetta Manduchi Junmin Liu Jonathan Schug Chris Stoeckert NCI MAGE Workshop Jan 24, 2008

2. http://www.cbil.upenn.edu/RAD/

3. Support diabetes research

4. Support research on protozoan parasites

6. Example MAGE-TAB spreadsheet

9. Do MAGE-TAB templates have to follow MAGE-TAB specifications? Of course, but the biologists filling them out don’t need to know that!

11. Handling MAGE docs in unified way processors validators translator O/R layer GUS DB mage doc Mage doc in other formats graph common objects ontology matrix

12. MR_Ti overview Reader Processor Validator Translator Study->submit Reporter Tester VO’ VO VO GusObj MagemlReader MageTabReader SoftReader BaseProcessor ProcessModule MergeTreatmentSerials NamingBioSamples NamingScans BaseValidator ValidationRule ProtocolHasMageType StudyDesignHasMageType AssayHasFactorValues make ServiceFactroy GUS Commit MR_Tilogger SqlReporter SqlTester Config.xml read-in use use use use use use MR_TiException VoToGusTranslator VoToMageTab VoToDot

13. MAGE-TAB Tools and Process Initial contact with investigator/ Review publication Provide appropriate MAGE-TAB template Get filled in template Download SOFT files from GEO/ Review publication If Affymetrix, use ArrayExpress converter tool to generate MAGE-Tab; if cDNA array, in-house script to generate template . Review tab files and fill in protocols, experimental factors, ontology terms as needed. Validate, load, and check graph MAGE-ML files From ArrayExpress Convert to MAGE-Tab using mage2tab Convert to MAGE-Tab using template2tab