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!
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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
