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The MGED Ontology

The MGED Ontology. W3C Workshop on Semantic Web for life Sciences October 27, 2004 Presented by Liju Fan MGED Ontology Working Group Senior Scientist, KEVRIC. International organization Comprised of biologists, computer scientists, and data analysts

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The MGED Ontology

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  1. The MGED Ontology W3C Workshop on Semantic Web for life Sciences October 27, 2004 Presented by Liju Fan MGED Ontology Working Group Senior Scientist, KEVRIC

  2. International organization Comprised of biologists, computer scientists, and data analysts Aims to facilitate the sharing and evaluation of microarray data Establish standards for microarray data annotation Create microarray databases Promote sharing of high quality, well-annotated data Extends to cover data generated by functional genomics and proteomics experiments MGED Society http://www.mged.org

  3. MGED Standardization Efforts • MIAME • The formulation of the minimum information about a microarray experiment required to interpret and verify the results. • MAGE • The establishment of a data exchange format (MAGE-ML) and object model (MAGE-OM) for microarray experiments. • MGED Ontology • The development of an ontology for microarray experiment description, with particular emphasis on biological material (biomaterial) annotation. • Data Transformation and Normalization • The development of recommendations regarding microarray data transformations and normalization methods. • RSBI • The development of a public and compatible reporting structure for biological investigations (array-based data of Toxicogenomics, Nutrigenomics, and Environmental Genomics)

  4. MGED Ontology (MO) • Purpose • Provide standard terms for the annotation of microarray experiments • Not to model biology but to provide descriptors for experiment components • Benefits • Unambiguous description of how the experiment was performed • Structured queries can be generated • Ontology concepts derived from the MIAME guidelines/MAGE-OM • Also incorporating concepts from Transformations and RSBI

  5. MGED Ontology developmenthttp://mged.sourceforge.net/ontologies/MGEDontology.php • OilEd • File formats • DAML file • HTML file • NCI DTS Browser • Changes • Notes • Term Tracker

  6. MGED Ontology Class Hierarchy • MGED CoreOntology • Coordinated development with MAGE-OM • Ease of locating appropriate class to select terms from • MGED ExtendedOntology • Classes for additional terms as the usage of genomics technologies expand

  7. Relationship of MO 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

  8. MO and MAGE

  9. MO and References to External Ontologies

  10. MO and references to External Ontologies

  11. MO and Structured Queries

  12. Other Sites Using MO

  13. Future Development of MO • Areas of Development • Ongoing maintenance • Ontology language • Non-array technologies • Biological domain extensions • MO v2. development

  14. Proposed Development of MGED Ontology MO 1.x Move to OWL/Protege Proteomics in ExtendedOntology RSBI in ExtendedOntology RSBI in CoreOntology MO 2.x Sept. 2004 Jan. 2005 March 2005 Sept. 2005

  15. Acknowledgements • MGED Ontology Working Group • Chris Stoeckert, Trish Whetzel (Penn) • Helen Parkinson (EBI) • Joe White (TIGR) • Gilberto Fragoso, Mervi Heiskanen (NCI) • Many others! • MGED Ontology mailing list

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