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

3. MGED Standardization Efforts MIAME MIAME The formulation of the minimum information about a microarray experiment required to interpret and verify the results. The formulation of the minimum information about a microarray experiment required to interpret and verify the results. MAGE MAGE The establishment of a data exchange format (MAGE-ML) and object model (MAGE-OM) for microarray experiments. The establishment of a data exchange format (MAGE-ML) and object model (MAGE-OM) for microarray experiments. MGED Ontology MGED Ontology The development of an ontology for microarray experiment description, with particular emphasis on biological material (biomaterial) annotation. The development of an ontology for microarray experiment description, with particular emphasis on biological material (biomaterial) annotation. Data Transformation and Normalization Data Transformation and Normalization The development of recommendations regarding microarray data transformations and normalization methods. The development of recommendations regarding microarray data transformations and normalization methods. RSBI RSBI The development of a public and compatible reporting structure for biological investigations (array-based data of Toxicogenomics, Nutrigenomics, and Environmental Genomics) 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 Purpose Provide standard terms for the annotation of microarray experiments Provide standard terms for the annotation of microarray experiments Not to model biology but to provide descriptors for experiment components Not to model biology but to provide descriptors for experiment components Benefits Benefits Unambiguous description of how the experiment was performed Unambiguous description of how the experiment was performed Structured queries can be generated Structured queries can be generated Ontology concepts derived from the MIAME guidelines/MAGE-OM Ontology concepts derived from the MIAME guidelines/MAGE-OM Also incorporating concepts from Transformations and RSBI Also incorporating concepts from Transformations and RSBI

5. MGED Ontology development http://mged.sourceforge.net/ontologies/MGEDontology.php OilEd OilEd File formats File formats DAML file DAML file HTML file HTML file NCI DTS Browser NCI DTS Browser Changes Changes Notes Notes Term Tracker 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 MO class hierarchy follows that of MAGE-OM Association to OntologyEntry Association to OntologyEntry MO provides terms for these associations by: MO provides terms for these associations by: Instances internal to MO Instances internal to MO Instances from external ontologies Instances from external ontologies Take advantage of existing 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 Areas of Development Ongoing maintenance Ongoing maintenance Ontology language Ontology language Non-array technologies Non-array technologies Biological domain extensions Biological domain extensions MO v2. development MO v2. development

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

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