Exporting MAGEML from the Stanford Microarray Database Using Perl MAGEstk

1
Exporting MAGE-ML from the Stanford Microarray
Database Using Perl MAGE-stk

• Jeremy Gollub and Tina Boussard
• Department of Genetics
• Stanford University
• smd.stanford.edu

2
Decomposing the problem

• Manageable chunks (Meta packages?)
• Experiment Meta Data
• Array Design Data
• Actual Data
• Mapping
• Relationships were hard-coded
• Close correspondences were easy (Person)
• Bad matches were problematic (FactorValues)
• Data fantasies were unavoidable (Protocols)

3
Problems with Software and Model

• Software/Model Source and targets
• Hybridization, for example
• sourceBioMaterialMeasurements
• physicalBioAssayTarget
• Documentation How to tell the XMLWriter that
  your data files are external
  
  
  
• my w BioMAGEXMLWriter-gtnew
• (fh gt\STDOUT,
• external_data gt1,
• Tells writer data is external
• cube_holds_path gt1)
• Tells writer bioDataCube has the file path
• Usage Referencing other outside files

4
Instantiating and Writing Objects

• Abstract classes
• MAGE-stk should warn
• Independence/ownership
• Not all identifiable objects are independent
• Objects do not get written if their owner is not
  present

5
Instantiating and Writing Objects

• Non-identifiable objects (e.g., Describable)
  cannot live on their own
• ExperimentDesign needs an Experiment object to
  belong to.
• The experiment Object has to be passed to the
  MAGE object, not the ExperimentDesign Object
• Create a blank Experiment object, and add the
  ExperimentDesign, and pass the Experiment object
  to the MAGE object.

6
Where to start Work Flow

• Paying attention to the intended use case
  actually helped!
• Additional workflows and use cases would be
  appreciated.

7
General Approach

• Perl MAGE-stk
• Package and object-level exporter classes, as
  appropriate
• Print ? ArrayManufacture PhysicalArrayDesign
• User ? Person
• OntologyEntry exporter for CV objects
• SeqType ? biosequencetype OntologyEntry
• Utility module to export static objects
  (SMDUtils.pm)
• Channels
• QuantitationTypes
• Databases
• Generic method for generating identifiers

8
Identifiers

• Roughly adhere to LSID standard
• Generated by single method to ensure uniformity
• For machine parsing (name attribute is for human
  readers)
• Namespace identifier
• smd.stanford.edu for SMD objects
• Other for Database objects, as appropriate
• URNLSIDebi.ac.ukdatabaseEBI
• Object identifier
• Contains one or more SMD object attributes
• May contain non-database human information
• MAGE-OM object appended, to escape degeneracy
• Examples (URNLSIDsmd.stanford.edu)
• print.printid802/MAGE.PhysicalArrayDesign
• spotlist.printid_spotlist.spot802_17/MAGE.Feature
  
• print.printid_at.gene model802_At3g9247/MAGE.Comp
  ositeSequence

9
Wisdom, Painfully Gained

• Memory usage is high remove limits.
• Performance is low report progress and dont
  run over the web! (XMLWriter could usefully
  become verbose)
• Ontologies and best practices need some community
  effort (but for now, were doing what EBI tells
  us to do).