MAGE-TAB - The ArrayExpress Production Experience

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MAGE-TAB - The ArrayExpress Production
Experience
Helen Parkinson, PhD
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Content

• All change at ArrayExpress
• Data acquisition
• Validation
• Extension
• Downloads
• Long Term Future
• Tutorial submitting in MAGETAB format

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(No Transcript)
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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 formatsefficient
  curation
• 1600 Experiments processed (1600/3700)
• All curated
• Subset of ArrayExpress MAGETAB data will be
  re-curated at migration

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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

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Extensibility

• Solexa data
• Proteomics
• Metabolomics

• Array Genotype data (Gen2Phen)
• Association study data (Gen2Phen, Engage)
• Locus specific SNP data
• Clinical Data
• ..

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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-gtMAGETAB)
• 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

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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-gtMAGETAB)
• Data import, meta analysis

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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 doesnt vary in an experiment

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Acknowledgments

• Anna Farne
• Ele Holloway
• James Malone
• Margus Lukk ArrayExpress 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

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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/