20 Apr 2007

Introduction of the issue

For the past couple months, we have been trying to adopt MAGE as our standard, and make our existing BIRN Micro-array database to be MAGE compliant. Since BioWarehouse has the API and database framework that supports MAGE, we have decided to migrate our existing database to BioWarehouse.

Primary goal: Create MouseBIRN or BIRN group instance of MAGE by itemizing those packages in MAGE that are applicable to most MouseBIRN or BIRN group, and mapping our existing data model to MAGE-OM.

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Background

So far, we have our initial MouseBIRN MAGE instance created based on MPTP data. This is a very preliminary form, and still open for suggestion. After our meeting with Stanley Nelson’s group, we found that they are also revolutionizing their existing MAGE instance, and we may not share similar data structures. However, they provide valuable input, and based on those and our research, here are some issues hopefully we can get it ironed out ASAP so that we can move forward.

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Tasks

1. Standardize some of the entries format across Mouse BIRN or BIRN test beds like
   • the identifier prefix
   • database reference code
   • ontology entries
   • acceptable data file format
   • log entries information
2. Compare and differentiate the information between MAGE and XCEDE.
3. Compare and differentiate the information between MAGE and BioWarehouse framework.
   • We may need to write our own MAGE loader to cover those packages that are not supported by the existing MAGE loader created by BioWarehouse.
4. Compare and differentiate the information between BioWarehouse framework, CHADO Model, and Gemma database.

Link to the MAGE Entries Working page

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References or links of interest

Affymetrix and EPI sites do provide very detailed explanation and examples of their usage of MAGE.

• The MAGE Good Practice section at EBI
• MAGE at the The MGED Site
  • The Excel spreadsheet for mapping the MAGE-OM to data within Stanford Microarray database
  • Model views:
    • Graphic display of MAGE OM
    • an HTML view
• BioWarehouse
  • BioWarehouse BMC Bioinformatics article - March 2006
  • the BioWarehouse MAGE Loader page
• The Generic Model Organism Database consortium
  • CHADO data schema
  • See specifically the Expression module.
• Adopting Gemma database from UBiC(UBC Bioinformatics Center)
  • HTML Version of the model

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Developer work based on our “official” first draft of BIRN MAGE

• Create XSLT to transform BIRN Microarray data or GeneNetwork data to MAGE format.
• Import the MAGE files to BioWarehouse.
• Create webservices to export the data from BioWarehouse to MAGE or other XML format that the client application supports.
• Create XSLT to transforma MAGE to XCEDE and vice versa.

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Minutes and Plans

• MAGE_04_25_07.doc: 04/25/07: minutes from first MAGE meeting, overview and plan

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