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ArrayExpress: Helen Parkinson
ArrayExpress: Helen Parkinson
ArrayExpress: Helen Parkinson
ArrayExpress: Helen Parkinson
ArrayExpress: Helen Parkinson
ArrayExpress: Helen Parkinson
ArrayExpress: Helen Parkinson
ArrayExpress: Helen Parkinson
ArrayExpress: Helen Parkinson
ArrayExpress: Helen Parkinson
ArrayExpress: Helen Parkinson
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ArrayExpress: Helen Parkinson

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  • 1. MAGE-TAB - The ArrayExpress Production Experience Helen Parkinson, PhD
  • 2. Content <ul><li>All change at ArrayExpress </li></ul><ul><li>Data acquisition </li></ul><ul><li>Validation </li></ul><ul><li>Extension </li></ul><ul><li>Downloads </li></ul><ul><li>Long Term Future </li></ul><ul><li>Tutorial – submitting in MAGETAB format </li></ul>
  • 3. MAGEML MAGEML MAGEML MAGEML AE M.EXPRESS MAGETABULATOR Tracking M.EXPRESS MAGETABULATOR AE2 MAGETAB MIGRATION MAGETAB MAGETAB
  • 4. Data acquisition <ul><li>MAGETAB data acquisition is integrated with existing tab2mage submissions </li></ul><ul><li>MAGETAB export is being added to the MIAMExpress system </li></ul><ul><li>All MAGE-ML submissions will be converted to MAGETAB </li></ul><ul><li>We will unify data acquisition on MAGETAB </li></ul><ul><li>We decided to do most curation/validation/ontology matching at the end for MAGETAB submissions </li></ul><ul><li>MAGETAB makes curator edit and user update much easier </li></ul><ul><li>Human readable tab delimited formats=efficient curation </li></ul><ul><ul><li>1600 Experiments processed (1600/3700) </li></ul></ul><ul><ul><li>All curated </li></ul></ul><ul><ul><li>Subset of ArrayExpress MAGETAB data will be re-curated at migration </li></ul></ul>
  • 5. Automated processing and validation <ul><ul><li>Sections </li></ul></ul><ul><ul><li>MAGETAB Column Headers </li></ul></ul><ul><ul><li>MAGTAB Column Orders </li></ul></ul><ul><ul><li>MAGETAB Content – length, terms </li></ul></ul><ul><ul><li>External data files – released monthly </li></ul></ul><ul><ul><li>vs. ArrayExpress content </li></ul></ul><ul><ul><li>MIAME score </li></ul></ul><ul><ul><li>DW candidates </li></ul></ul>
  • 6. Extensibility <ul><li>Solexa data </li></ul><ul><li>Proteomics </li></ul><ul><li>Metabolomics </li></ul><ul><li>Array Genotype data (Gen2Phen) </li></ul><ul><li>Association study data (Gen2Phen, Engage) </li></ul><ul><li>Locus specific SNP data </li></ul><ul><li>Clinical Data </li></ul><ul><li>… .. </li></ul>
  • 7. Downloads <ul><li>All ArrayExpress data will be available in MAGETAB format now (exported direct from AE) </li></ul><ul><li>~90% is currently available and passes checks (issues with MAGE-OM->MAGETAB) </li></ul><ul><li>More ontology term sources will be added incrementally – NCI thesaurus/OBI/ArrayExpress Factor Ontology </li></ul><ul><li>Beta MAGETAB ArrayExpress Bioconductor Module (Huber, Kauffman) </li></ul><ul><li>All MAGETAB generation code is available </li></ul><ul><li>All validation code is available </li></ul>
  • 8. Ontologies <ul><li>Working to develop OBI to replace MGED ontology </li></ul><ul><li>Generating a sample/factor ontology for ArrayExpress based on data content </li></ul><ul><li>Developed in Protégé/OWL format </li></ul><ul><li>Will be served from OLS </li></ul><ul><li>Also mapping to external ontologies for samples e.g NCI thesaurus </li></ul><ul><li>Text mining to annotate external data using dictionaries based on NCI thesaurus and some custom ones (GEOimporter, tab2mage->MAGETAB) </li></ul><ul><ul><li>Data import, meta analysis </li></ul></ul>
  • 9. Future: ArrayExpress and Community <ul><li>ArrayExpress Submission in MAGETAB ADF format </li></ul><ul><li>All ArrayExpress ADF in MAGETAB format </li></ul><ul><li>Alpha ArrayExpress-MAGETAB BioConductor MAGETAB importer </li></ul><ul><li>AE2 </li></ul><ul><li>AE2 data migration </li></ul><ul><li>More people post their MAGETAB examples and we agree on a gold std validated set for typical cases </li></ul><ul><li>Community lists of MAGETAB supportive tools where people can register their interests and describe their applications (like GO tools) </li></ul><ul><li>Addressing HLA </li></ul><ul><li>MAGETAB model, firm up the spec </li></ul><ul><li>Decide what factors really are, and whether the MAGE case is still valid – controlled vs uncontrolled variables instead? </li></ul><ul><li>Issues with global variables - inter experiment comparison of compounds needs to know dose even if dose doesn’t vary in an experiment </li></ul>
  • 10. Acknowledgments <ul><li>Anna Farne </li></ul><ul><li>Ele Holloway </li></ul><ul><li>James Malone </li></ul><ul><li>Margus Lukk ArrayExpress Production Team </li></ul><ul><li>Helen Parkinson </li></ul><ul><li>Tim Rayner </li></ul><ul><li>Faisal Rezwan </li></ul><ul><li>Eleanor Williams </li></ul><ul><li>Mengyao Zhao </li></ul><ul><li>Holly Zheng </li></ul><ul><li>Mohammad Shojatalab ArrayExpress Development Team </li></ul><ul><li>Funding </li></ul><ul><ul><li>EC - FELICS, EMERALD, Gen2Phen, MUGEN </li></ul></ul><ul><ul><li>NIH - MAGE grant </li></ul></ul>
  • 11. Tutorial <ul><li>Creation of MAGETAB templates </li></ul><ul><li>Completion of a pre-made template </li></ul><ul><li>Curation </li></ul><ul><ul><li>Scoring and validation templates </li></ul></ul><ul><li>Viewing Data in ArrayExpress </li></ul><ul><li>Backend of the template generation/tracking system </li></ul><ul><li>www.ebi.ac.uk/~parkinso/MAGETAB_tutorial/ </li></ul>

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