SOFG

The MGED Ontology:A framework for describing functional genomics experiments: 

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

Slide2: 

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

Slide3: 

Desirable Microarray Queries : 

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?

Microarray Information to be Shared: 

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

The Computational View of Microarray Information : 

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

An Experimental Ontology: 

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

http://www.mged.org: 

http://www.mged.org

Relationship of MGED Efforts: 

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

The MGED Ontology Home Page: 

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

The MGED Ontology Provides a Listing of Resources for Many Species: 

The MGED Ontology Provides a Listing of Resources for Many Species

The MGED Ontology Organizes the Resources According to Concepts: 

The MGED Ontology Organizes the Resources According to Concepts

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

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

MGED Ontology: BiomaterialDescription: BiosourceProperty: Age: 

MGED Ontology: BiomaterialDescription: BiosourceProperty: Age

MGED Ontology: BiosourceOntologyEntry: DiseaseState: 

MGED Ontology: BiosourceOntologyEntry: DiseaseState

Slide16: 

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

The MGED Ontology in Action: MIAMExpress: 

The MGED Ontology in Action: MIAMExpress

Slide18: 

RAD schema uses MAGE/MIAME

The MGED Ontology in Action: RAD: 

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

RAD Generic Form for BioMaterial Characteristics: 

RAD Generic Form for BioMaterial Characteristics

RAD Project-Specific Form - PlasmoDB: 

RAD Project-Specific Form - PlasmoDB

Acquiring New Terms: 

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

Generating Forms from the MGED Ontology: 

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

RAD is now part of GUS-3.0 : 

RAD is now part of GUS-3.0 GUS has 5 name spaces compartmentalizing different types of information.

GUS Supports Multiple Projects: 

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

http://www.gusdb.org: 

http://www.gusdb.org

Acknowledgements: 

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