Producing MAGEML from SMD

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Producing MAGE-ML from SMD

• Gavin Sherlock
• Stanford University
• sherlock_at_genome.stanford.edu

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How to approach the problem?

• Understand MAGE-OM and MIAME
• Expand database to be MIAME compliant
• Map relational schema to MAGE-OM
• Write code to produce MAGE-ML from data in the
  database

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Understanding MAGE-OM

• Split up the problem among people
• Post questions to the mailing list
• Read the RFP all the way through!!!
• Report back to your group frequently
• Hold your own mini-jamborees
• Participate in and interact with the MAGE
  community

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Expand Database to be MIAME compliant

• We specifically had to add tables to deal with
  Experimental Factors.
• We had most of the other requirements for MIAME,
  though they were not necessarily fully fleshed
  out.

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Mapping Schema to MAGE-OM

• Decide what MAGE classes you have data for
• Create a spreadsheet to plan the mapping
• Separate by MAGE Package and Class
• Start filling in the attributes
• this was time consuming!

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Write the code

• Where do you start?

• Use MAGE-stk

• Use MAGE-stk

• Use MAGE-stk

• We use the Perl implementation of MAGE-stk,
  which requires the XMLXerces perl xml parser to
  be installed.

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Writing code, continued

• Deal with identifiers
• We wrote a utility class, that would generate
  identifiers for us in a consistent fashion, in
  the LSID format.
• ALWAYS use this utility for id creation

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Writing code (cont.)

• Jason Stewart advised us to create a utility
  package that exported a number of static objects.
• This proved invaluable for creating consistent
  MAGE-ml from program to program

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Writing code (cont)

• We then wrote a number of mapping classes, that
  dealt with mapping various data within SMD to the
  MAGE-OM, e.g. DbuserToMAGE, ExptDesignToMAGE,
  ProtocolToMAGE
• This allows you to then write much simpler clients

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Yet more code

• We chose to export data files separately from the
  MAGE-ML file holding holding the experimental
  annotation.
• It was not obvious from the MAGE-stk API how to
  do this.
• writer-gtexternal_data(1)
• writer-gtcube_holds_path(1)

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Resources

• SMD documents detailing the process of mapping
  SMD to MAGE-OM, and the mappings themselves
  http//www.mged.org/Workgroups/MAGE/mage.html
• SMD code - coming soon (honest)