1. The MGED Ontology: A framework for describing functional genomics experiments SOFG Nov. 19, 2002 Chris Stoeckert, Ph.D. Dept. of Genetics & Center for Bioinformatics University of Pennsylvania

2. Nature, October 3, 2002 http://plasmodb.org/ David Roos, Jessie Kissinger, Bindu Gajria, Martin Fraunholz, Jules Milgram, Phil Labo, Amit Bahl, Dave Pearson, Dinesh Gupta, Hagai Ginsburg Jonathan Crabtree, Jonathan Schug, Brian Brunk, Greg Grant, Trish Whetzel, Matt Mailman, Li Li

4. Desirable Microarray Queries Return all experiments using developmental stage X. –Sort by platform type –Which are untreated? Treated? Treated by what How comparable are these? What can these experiments tell me?

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

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

7. 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

8. http://www.mged.org

9. Relationship of MGED Efforts MAGE MIAME DB MIAME DB External Ontologies/CVs MGED Ontology Software and database developers Investigators annotating experiments

10. The MGED Ontology Home Page http://mged.sourceforge.net/ontologies/

11. The MGED Ontology Provides a Listing of Resources for Many Species

12. The MGED Ontology Organizes the Resources According to Concepts

13. The MGED Ontology is Structured in DAML+OIL using OILed 3.4

14. MGED Ontology: BiomaterialDescription: BiosourceProperty: Age

15. MGED Ontology: BiosourceOntologyEntry: DiseaseState

16. ArrayExpress MIAMExpress RAD MAGE-ML data exchange Ontology instances propagated to submission/annotation web forms Curation of user defined terms, before inclusion in the ontology User defined terms collected via forms MGED Ontology BiomaterialDescription Sex C C C C Gender documentation: Subclass of sex applicable to heterogametic species (i.e., those in which the sexes produce gametes of markedly different size). Males produce small numerous gametes. Females produce small numbers of large gametes. Hermaphrodites are individuals with both male and female characteristics. Mixed refers to a population of individuals with more than one type of gender. used in individuals: female, hermaphrodite,male,mixed_sex,unknown_sex

17. The MGED Ontology in Action: MIAMExpress

18. RAD schema uses MAGE/MIAME MAGE Experiment Array BioMaterial BioAssay BioAssayData Protocol, Descr. HigherLevelAnalysis MAGE Experiment Array BioMaterial BioAssay BioAssayData Protocol, Descr. HigherLevelAnalysis MIAME Experimental Design Array design Samples Hybridization, Measure Normalization. MIAME Experimental Design Array design Samples Hybridization, Measure Normalization.

19. The MGED Ontology in Action: RAD Add screen shot of study factor

20. RAD Generic Form for BioMaterial Characteristics

21. RAD Project-Specific Form - PlasmoDB

22. Acquiring New Terms Add term from SRes Add term from an External Database OR

23. Generating Forms from the MGED Ontology OntologyEntry ExternalDatabases PHP/SQL WWW RAD Forms MGED Ontology Anatomy DevelopmentalStage Disease Lineage PATOAttribute Phenotype Taxon SRES RAD3 MGED Ontology

24. RAD is now part of GUS-3.0 GUS has 5 name spaces compartmentalizing different types of information. NamespaceDomainFeatures CoreData ProvenanceWorkflows SresShared resourcesOntologies DoTS sequence and annotation Central dogma RADGene expresssionMIAME/MAGE TESSGene regulationGrammars

25. GUS Supports Multiple Projects AllGenes PlasmoDB EPConDB CoreSRESTESSRADDoTS Oracle RDBMS Object Layer for Data Loading Java Servlets Other sites, Other projects, e.g. GeneDB Other sites, Other projects, e.g. GeneDB Available at http://www.gusdb.org

26. http://www.gusdb.org

27. Acknowledgements MGED Ontology –Helen Parkinson (EBI) –Trish Whetzel –The MGED Ontology Working Group –MAGE working group –Angel Pizarro –Nelson Axelrod RAD/GUS –Brian Brunk –Jonathan Crabtree –Steve Fischer –Yongchang Gan –Greg Grant –Hongxian He –Li Li –Junmin Liu –Matt Mailman –Elizabetta Manduchi –Joan Mazzarelli –Shannon McWeeney (OHSU) –Debbie Pinney –Angel Pizarro –Jonathan Schug –Trish Whetzel www.mged.org www.cbil.upenn.edu