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Producing MAGEML from SMD

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Split up the problem among people. Post questions to the mailing list ... Create a spreadsheet to plan the mapping. Separate by MAGE Package and Class ... – PowerPoint PPT presentation

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Title: Producing MAGEML from SMD


1
Producing MAGE-ML from SMD
  • Gavin Sherlock
  • Stanford University
  • sherlock_at_genome.stanford.edu

2
(No Transcript)
3
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

4
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

5
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.

6
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!

7
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.

8
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

9
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

10
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

11
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)

12
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)
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