1. EBI is an Outstation of the European Molecular Biology Laboratory. MAGE-TAB - The ArrayExpress Production Experience Helen Parkinson, PhD

2. www.ebi.ac.uk/arrayexpress Content All change at ArrayExpress Data acquisition Validation Extension Downloads Long Term Future Tutorial – submitting in MAGETAB format

3. www.ebi.ac.uk/arrayexpress MAGEML AE M.EXPRESS MAGETABULATOR Tracking M.EXPRESS MAGETABULATOR AE 2 MAGETAB MIGRATION MAGETAB

4. www.ebi.ac.uk/arrayexpress Data acquisition MAGETAB data acquisition is integrated with existing tab2mage submissions MAGETAB export is being added to the MIAMExpress system All MAGE-ML submissions will be converted to MAGETAB We will unify data acquisition on MAGETAB We decided to do most curation/validation/ontology matching at the end for MAGETAB submissions MAGETAB makes curator edit and user update much easier Human readable tab delimited formats=efficient curation 1600 Experiments processed (1600/3700) All curated Subset of ArrayExpress MAGETAB data will be re-curated at migration

5. www.ebi.ac.uk/arrayexpress Automated processing and validation Sections MAGETAB Column Headers MAGTAB Column Orders MAGETAB Content – length, terms External data files – released monthly vs. ArrayExpress content MIAME score DW candidates

6. www.ebi.ac.uk/arrayexpress Extensibility Solexa data Proteomics Metabolomics Array Genotype data (Gen2Phen) Association study data (Gen2Phen, Engage) Locus specific SNP data Clinical Data …..

7. www.ebi.ac.uk/arrayexpress Downloads All ArrayExpress data will be available in MAGETAB format now (exported direct from AE) ~90% is currently available and passes checks (issues with MAGE-OM->MAGETAB) More ontology term sources will be added incrementally – NCI thesaurus/OBI/ArrayExpress Factor Ontology Beta MAGETAB ArrayExpress Bioconductor Module (Huber, Kauffman) All MAGETAB generation code is available All validation code is available

8. www.ebi.ac.uk/arrayexpress Ontologies Working to develop OBI to replace MGED ontology Generating a sample/factor ontology for ArrayExpress based on data content Developed in Protégé/OWL format Will be served from OLS Also mapping to external ontologies for samples e.g NCI thesaurus Text mining to annotate external data using dictionaries based on NCI thesaurus and some custom ones (GEOimporter, tab2mage->MAGETAB) Data import, meta analysis

9. www.ebi.ac.uk/arrayexpress Future: ArrayExpress and Community ArrayExpress Submission in MAGETAB ADF format All ArrayExpress ADF in MAGETAB format Alpha ArrayExpress-MAGETAB BioConductor MAGETAB importer AE2 AE2 data migration More people post their MAGETAB examples and we agree on a gold std validated set for typical cases Community lists of MAGETAB supportive tools where people can register their interests and describe their applications (like GO tools) Addressing HLA MAGETAB model, firm up the spec Decide what factors really are, and whether the MAGE case is still valid – controlled vs uncontrolled variables instead? Issues with global variables - inter experiment comparison of compounds needs to know dose even if dose doesn’t vary in an experiment

10. www.ebi.ac.uk/arrayexpress Acknowledgments Anna Farne Ele Holloway James Malone Margus LukkArrayExpress Production Team Helen Parkinson Tim Rayner Faisal Rezwan Eleanor Williams Mengyao Zhao Holly Zheng Mohammad Shojatalab ArrayExpress Development Team Funding EC - FELICS, EMERALD, Gen2Phen, MUGEN NIH - MAGE grant

11. www.ebi.ac.uk/arrayexpress Tutorial Creation of MAGETAB templates Completion of a pre-made template Curation Scoring and validation templates Viewing Data in ArrayExpress Backend of the template generation/tracking system www.ebi.ac.uk/~parkinso/MAGETAB_tutorial/