MGED Ontology MO

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MGED Ontology (MO)

• A resource for creation of MAGE-ML documents that
  are MIAME Compliant

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The MGED Ontology Home Page
http//mged.sourceforge.net/ontologies/
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The Computational View of Microarray Information
Need an ontology to unambiguously represent this
information.
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An Experimental Ontology

• An ontology for microarray experiments
• Not an ontology of life but of experiments
• Parts are applicable to describing experiments in
  general
• Our approach to interfacing with other ontologies
  is experimental
• Not mapping terms from related ontologies
• Provide a framework to hang other ontologies off
  of
• Know where to find different types of annotation
• How to interpret that annotation

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The MGED Ontology is Structured in DAMLOIL using
OILed 3.4
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MGED Ontology BiosourceOntologyEntry
DiseaseState
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How do you use it?

• Currently it is only a term dictionary
• Reference the terms via MAGE OntologyEntry class
  through a stable URI
• To direct development and population of web-entry
  forms
• MIAME Express (EBI)
• RAD Forms (CBIL)

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The MGED Ontology in Action MIAMExpress
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RAD schema uses MAGE/MIAME
MAGE Experiment Array BioMaterial BioAssay BioAssa
yData Protocol, Descr. HigherLevelAnalysis
MIAME Experimental Design Array
design Samples Hybridization, Measure Normalizatio
n .
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The MGED Ontology in Action RAD

• Add screen shot of study factor

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RAD Generic Form for BioMaterial Characteristics
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Summary of the history

• The MGED Ontology Working Group exists
• Have released Version 1.6
• Using OILed ontology editor
• http//mged.sf.net/ontologies
• Journals are starting to recommend MIAME
  information as part of a submission
• See Nature article
• Hard to find what you need and how this relates
  to a MAGE document

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A new mission

• Produce a Core Ontology
• Organize ontology according to MAGE packages
• Class names have been changed to facilitate
  mapping and properties adjusted to avoid
  conflicts.
• Core ontology does not cover all of MAGE or
  contain all MAGE associations. Scope of ontology
  is supporting MAGE ontology entry associations,
  adding constraints within MAGE structure, and
  adding further structure and depth to MAGE
  classes without changing base classes.
• Definitions are derived from MAGE OMG
  specification where appropriate and available.
• Enumerated lists are represented as instances of
  a class where these lists are open ended.

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The new hierarchy
Screen shot of package hierarchy
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Why the redundancy with MAGE?

• Easier to find what you need
• The structure gives a concrete context to terms
• Translation between MAGE and MGED Ontology (MO)
  instances will be easier
• Possibly through use of ObjectMap
• We can use the MO to test for MIAME compliance of
  MAGE docs

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Future directions

• Stabilize the Core ontology and coordinate this
  closely to MAGE-ML 1.0
• Move to using OWL for transfer of the ontology
  and do integrity checks
• Tools for translation between MAGE MO
• EBI ArrayExpress has plans for this, as does CBIL
• Provide a better input method for the community
• Web submissions for new terms and extensions
• Voting scheme for alternate definitions?

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Acknowledgements

• MGED Ontology
• The MGED Ontology Working Group
• Chris Stoeckert
• Helen Parkinson (EBI)
• Trish Whetzel
• Nelson Axelrod
• MAGE working group

www.mged.org
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Acknowledgements

• Chris Stoeckert (UPENN)
• Trish whetzel (UPENN)
• Helen Parkinson (EBI)

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MGED Ontology BiomaterialDescription
BiosourceProperty Age