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Kanterakis bosc2010 molgenis

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  • The envisioned system should include suitable user interfaces for researchers, programmatic interfaces for analysis protocols and data federation, and should be easily extended to accommodate diverging local needs. None of the available (open source) systems seemed to provide this and meanwhile GEN2PHEN [2] started ‘database-in-a-box’ projects including a microarray system based on the MAGE-TAB file format [3] and the MOLGENIS [4,5] biosoftware platform. BBMRI-NL chose to sponsor this project with the following results:
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    • 1. Towards a federated microarray gene expression repository using MOLGENIS and MAGE-TAB
      AlexandrosKanterakis, Tomasz Adamusiak, JuhaMuilu, Helen Parkinson, DespoinaAntonakaki, Morris A. Swertz
    • 2. About BBMRI-NL
      Biobank research infrastructure
      Exploit the wealth of information in microarray and GWAS
      Data currently fragmented between individual biobanks (>6500) samples
    • 3. Objectives (1/2)
      Establish: web-based national repository for microarray gene expression data
      Populate: with well-annotated microarray experiments
      Share: the software as ‘microarray database in-a-box’ such that all BBMRI biobanks can reuse it locally
      Requirements
      Interfaces
      Programmatic Interfaces
      Extendable
      Data federation
      User Interface
      Analysis Protocols
      Diverging local needs
    • 4. Objectives (2/2)
      Combine gene expression data from multi-platform microarray experiments with GWAS studies in order to create novel eQTL datasets for complex diseases
      +

    • 5. MAGE-TAB (1/2)
      MAGE-TAB: simple, human readable, tab-delimited.
      Comprised by 4 parts:
      Investigation Description Format (IDF). General information, contact details, bibliographic references,...
      Array Design Format (ADF). What sequence is located at each position on an array and what the annotation of this sequence is.
      Raw and processed data files. ASCII or binary files.
      2006
    • 6. MAGE-TAB (2/2)
      Sample and Data Relationship Format (SDRF). Relationships between samples, arrays, extracts, hybridizations and other objects used in the investigation.
    • 7. MAGE-TAB Object Model
      From MAGE-TAB specifications we created a data model* in XML format..
      .. and parsers for MAGE-TAB files.
      http://www.mged.org/mage-tab/MAGE-TABv1.0.pdf
      http://magetab-om.sourceforge.net/magetab_idf.xml
      *data model is the set of definitions of classes, elements and properties of the data
    • 8. Visualization of MAGE-TAB OM
      SDRF
      ADF
      data
      IDF
    • 9. MOLGENIS MAGE-TAB
      From MAGE-TAB Object Model we created a web environment for managing Microarray Experiments:
      850 lines of maintainable code
      60K lines of automatic generated code
    • 10. MOLGENIS MAGE-TAB
    • 11. Testing..
      For testing and validation purposes we populated the database with data from ArrayExpress:
      • 7665 experiments from Gene Expression Omnibus, curated by ArrayExpress
      • 12. 3940 non-GEO experiments from ArrayExpress
      • 13. 320.000 samples, 550 species, 2.400 human conditions
    • Discussion
      Features:
      APIs: R, Java
      Web services: SOAP, REST
      Semantic Interfaces: RDF, SPARQL
      MAGE-TAB parsers, validators and visualization
      Future work:
      • Populate with local data
      • 14. Plug-in analysis tools
      • 15. Data and tool sharing among local installs
      • 16. Privacy sensitive biobanking community
    • Thank you
      Acknowledgements:
      Morris Swertz
      Joeri van derVelde
      LudeFranke
      Danny Arends
      Email: alexandros.kanterakis@gmail.com
      Posters: