The MGED Ontology: Providing Descriptors for Microarray Data

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The MGED Ontology Providing Descriptors for
Microarray Data

• Trish Whetzel
• Department of Genetics
• Center for Bioinformatics
• University of Pennsylvania

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Acknowledgements

• CBIL
• Chris Stoeckert
• Angel Pizarro
• Elisabetta Manduchi
• EBI
• Helen Parkinson
• Susanna Sansone
• TIGR
• Joe White
• Stanford
• Cathy Ball

• NCICB
• Gilberto Fragoso
• Liju Fan
• Mervi Heiskanen
• Others
• Paul Spellman
• John Matese
• Helen Causton
• Ontology Mailing List

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MGED Society

• International organization
• Comprised of biologists computer scientists, and
  data analysts
• Aims to facilitate the sharing of functional
  genomics data generated by microarray and
  proteomics experiments
• Establish standards for microarray data
  annotation
• Create microarray databases
• Promote sharing of high quality, well-annotated
  data

www.mged.org
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MGED Standardization Efforts

• MIAME
• The formulation of the minimum information
  required about a microarray experiment in order
  to interpret and verify the results.
• MAGE
• The establishment of a data exchange format
  (MAGE-ML) and an object model (MAGE-OM) for
  microarray experiments.
• Ontololgy Working Group
• The development of an ontology to describe
  microarray experiments and in particular the
  biological material (biomaterial) used in these
  experiments.
• Transformations
• The development of recommendations regarding
  microarray data transformations and normalization
  methods.

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Microarray Information to be Shared
Figure from David J. Duggan et al. (1999)
Expression Profiling using cDNA microarrays.
Nature Genetics 21 10-14
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MGED Ontology (MO)

• Purpose
• Provide standard terms for the annotation of
  microarray experiments
• Benefits
• Unambiguous description of how the experiment was
  performed
• Structured queries can be generated
• MGED Ontology concepts derived from the MIAME
  guidelines/MAGE-OM

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MGED Ontology developmenthttp//mged.sourceforge.
net/ontologies/MGEDontology.php

• Oiled
• File formats
• Html file
• Daml file
• NCI DTS Browser

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MGED Ontology Class Hierarchy

• MGED CoreOntology
• In synch with MAGE v.1
• Stable class structure
• MGED ExtendedOntology
• Classes for additional terms as the usage of MO
  expands for genomics technologies

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Relationship ofMO to MAGE-OM

• MO class hierarchy follows that of MAGE-OM
• Association to OntologyEntry
• MO provides terms for these associations by
• Instances internal to MO
• Instances from external ontologies
• Take advantage of existing ontologies

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Relationship ofMO and MAGE-OM
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MO and References to External Ontologies
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MO and References to External Ontologies
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Desirable Microarray Queries

• Return all experiments with species X examined at
  developmental stage Y
• Sort by platform type
• Which are untreated? Treated?
• Treated with what compound?
• How comparable are these results?
• These questions can be asked of all experiments
  annotated using the MGED Ontology.

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MO and Structured Queries
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Future Work

• Convert to OWL
• W3C standard ontology language
• Expressivity
• Add terms to describe
• Data transformation and normalization methods
• Protocol types used by the Protein Data Bank

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Future Work cont.

• Expand the MGED Extended Ontology by adding
  classes and terms to describe new domains and
  technologies
• Toxicogenomics, ecotoxicogenomics and
  pharmacogenomics
• A public forum for developing internationally
  compatible and public infrastructure for
  reporting array-based toxicogenomics.
• Protein Standards Initiative
• Defines community standards for data
  representation in proteomics to facilitate data
  comparision, exchange and verification.

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Links

• mged.org
• http//mged.sourceforge.net/ontologies/MGEDontolog
  y.php

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The Computational View of Microarray Information
Need an ontology to unambiguously represent this
information.
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Issues to Discuss

• Burning Issues
• Developing MO in synch with related efforts
  (MAGE-OM v.2.0)
• Use/presentation in annotation forms
• Coverage of other technologies and biological
  domains
• Flame retardant structure
• ExtendedOntology
• Space to add new classes, terms and their
  relationship to one another

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Relationship of MO and MAGE-OM
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Microarray Information to be Shared
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Microarray Information to be Shared