Microarray and Gene Expression

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Microarray and Gene Expression Object
Model (MAGE-OM) Brief Overview
Michael Miller Senior Application
Developer Rosetta Biosoftware OMG/I3C Joint
Technical Meeting January 29, 2003
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Overview
Modeling of Gene Expression Experiments Organizat
ion of Gene Expression Experiment Structure of
Annotation in MAGE-OM Annotation
Elements OntologyEntry MAGE-ML Acknowledgments
Links
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Modeling of Gene Expression Experiments
BioMaterial
Protocol
Protocol
Protocol
Image Aquisition
BioAssay Treatment
Hyb
Physical BioAssay
Physical BioAssay
Array
Protocol
Feature Extraction
Mapping
Physical BioAssay
Measured BioAssay
Derived BioAssay
Transformation
Image
Derived BioAssayData
Measured BioAssayData
Protocol

• The Flow of the Experiment
• The objects of the experiment (Green and
  Purple).
• The transformation Bioaction (Blue) and the
  annotation of that action (Brown).

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Organization of Gene Expression Experiment

• Hierarchy of Experiment
• As BioAssays are produced and transformed, they
  fit into the Experiment Design.
• Each ExperimentFactor provides a Dimension,
  whose coordinates are its Factor Values.
• Each set of these coordinates then has a tree of
  BioAssays whose root is one of the
  topLevelBioAssays of the Experiment Design.

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Structure of Annotation in MAGE-OM

• All Classes in MAGE inherit from one of the three
  Abstract classes
• Identifiable provides the attributes for naming
  objects. This allows referencing an object in
  the DTD in a reference element.
• Describable objects have a rich set of
  associations to provide annotation.
• Extendable objects allow arbitrary Property Sets
  to be used to help in processing. These property
  sets have no biological relevance.

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Annotation Elements

• Audit
• Allows time stamps to be associated with the
  change of data or annotation.
• Security
• Allows description of SecurityGroups who have
  permission on an object.
• Not rich enough to specify the creation and
  rights of the groups.
• In general, these Groups would have to be
  pre-existing in the datastore the object is saved
  to.
• Description
• Allows comments, bibliographic references,
  ontology entries, and database entries.

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OntologyEntry

• Innocuous little class
• Appears many, many places in the model.
• Usually its role is a simple controlled
  vocabulary. In the datatype role of Parameter,
  the values are Integer, Float, Double, etc.
• Then there are some, like the characteristics
  role from BioMaterial which can be very rich. In
  fact, the Ontology for that role, if complete,
  would describe everything about every living
  organism (and probably a few dead ones).
• By using this class in the model, rather than
  try to 'guess' what people would use, leaves it
  open ended and expandable.

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MAGE-ML

• Generated Directly from the Model
• Rules described in Chapter 3 of the submission.

lt!-- Element and Attlist declarations for
Audit --gt lt!ELEMENT AuditTrail_assnlist (Audit)
gt lt!ELEMENT Audit ((Describable_content),
Performer_assnref?) gt lt!ATTLIST Audit
Describable_attrs date CDATA REQUIRED action
(creationmodification) REQUIRED gt lt!--
Element and Attlist declarations for
Security --gt lt!ELEMENT Security_assnlist
(Security) gt lt!ELEMENT Security_assnref
(Security_ref) gt lt!ELEMENT Security_ref EMPTY
gt lt!ATTLIST Security_ref identifier CDATA
REQUIRED name CDATA IMPLIED gt lt!ELEMENT
Security ((Identifiable_content),
Owner_assnreflist?, SecurityGroups_assnreflist?)
gt lt!ATTLIST Security Identifiable_attrs
gt lt!-- Element and Attlist declarations for
SecurityGroup --gt lt!ELEMENT SecurityGroup_assnlist
(SecurityGroup) gt lt!ELEMENT SecurityGroups_assn
reflist (SecurityGroup_ref) gt lt!ELEMENT
SecurityGroup_ref EMPTY gt lt!ATTLIST
SecurityGroup_ref identifier CDATA REQUIRED
name CDATA IMPLIED gt lt!ELEMENT SecurityGroup
((Identifiable_content), Members_assnreflist)
gt lt!ATTLIST SecurityGroup Identifiable_attrs gt
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Acknowledgments

• Bill Andreopoulos University of Toronto
• Cathy Ball Stanford University
• Doug Bassett Rosetta Biosoftware
• Derek Bernhart Affymetrix
• Alvis Brazma EBI
• Tina Boussard Stanford University
• Steve Chervitz Affymetrix
• Francisco De La Vega Applied Biosystems
• Eric Deutsch ISB
• Michael Dickson LION
• David Frankel IONA
• Jason Goncalves Iobion
• Ken Griffiths LION
• Robert Hubley ISB
• Brandon Hunt Rosetta Biosoftware
• Daniel Iordan Iobion
• Hilmar Lapp Novartis GNF
• Marc Lepage Molecular Mining

• Scott Markel LION
• W.L. Marks Iobion
• Douglas McArthur UC Santa Cruz
• Michael Miller Rosetta Biosoftware
• Helen Parkinson EBI
• Kjell Petersen University of Bergen
• Todd Peterson NCGR
• Angel Pizarro University of Pennsylvania
• Alan Robinson EBI
• Ugis Sarkans EBI
• Martin Senger EBI
• Paul Spellman UC Berkeley
• Jason Stewart Open Informatics
• Marcin Swiatek Imaging Research
• Charles Troup Agilent
• Joe White TIGR
• John Yost National Cancer Institute
• (and many more)

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Links

• OMG and Submitters
• Object Management Group www.omg.org
• Life Science Research Domain Task Force
  www.omg.org/lsr
• Rosetta Biosoftware www.rosettabio.com
• Microarray Gene Expression Data Group
  www.mged.org
• Open Source
• Download for reference implementations
• http//mged.sf.net/downloads.shtml
• Discussion group
• mged-mage http//lists.sourceforge.net/lists/lis
  tinfo/mged-mage
• Generating Code
• http//cvs.sourceforge.net/cgi-bin/viewcvs.cgi/mg
  ed