Overview 16 Databases investigated 4 Systems MIAME Compliant –ArrayExpress, SMD, LAD and GeneX 2.x 2 Systems Support MAGE-ML import and export –ArrayExpress and GeneX 2.x Many systems undergoing overhaul for MIAME compliance and MAGE support

Array Express –Pros MIAME 1.1, MAGE-ML import/export Accepted public repository –Cons Upload is limited to MAGE-ML or forms. No user friendly way to submit large experiments. –Info Schema is very normalized could benefit from optimizations

SMD/LAD Stanford MicroArray Database –Pros MIAME 1.1 compliant Mature system with large number of experiments –Cons Perl, C implementation. No MAGE-ML import/export yet. –Info LAD is SMD ported to Red Hat Linux and PostgreSQL.

GeneX –Pros MIAME 1.1 compliant, MAGE-ML import/export Uses MAGE-stk –Cons Perl implementation Undergoing major revision 2.x to get more MAGE compliant schema –Info Three separate efforts GeneX VA, GeneX Lite, GeneX 2.x

Recommendation Contact ArrayExpress, SMD and GeneX teams to obtain more information and discuss possible collaboration