Transcript MGED Ontology Working Group - University of Pennsylvania

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
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
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
Figure from:
David J. Duggan et al. (1999) Expression Profiling using cDNA microarrays. Nature Genetics 21: 10-14
The Computational View of Microarray Information
Need an ontology to unambiguously represent this information.
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
Relationship of MGED Efforts
Software and database developers
MIAME
DB
MAGE
MGED Ontology
External
Ontologies/CVs
Investigators annotating experiments
MIAME
DB
The MGED Ontology Home Page
http://mged.sourceforge.net/ontologies/
The MGED Ontology Provides a Listing of Resources for Many Species
The MGED Ontology Organizes the Resources According to Concepts
The MGED Ontology is Structured in
DAML+OIL using OILed 3.4
MGED Ontology: BiomaterialDescription:
BiosourceProperty: Age
MGED Ontology: BiosourceOntologyEntry:
DiseaseState
C
MGED Ontology
C BiomaterialDescription
Sex
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:
Curation of
user defined
terms, before
inclusion in
the ontology
female, hermaphrodite,male,mixed_sex,unknown_sex
Ontology instances propagated to
submission/annotation web forms
User defined terms
collected via forms
MIAMExpress
ArrayExpress
MAGE-ML data exchange
RAD
The MGED Ontology in Action: MIAMExpress
RAD schema uses MAGE/MIAME
0..*
MAGE
Experiment
Array
BioMaterial
BioAssay
BioAssayData
Protocol, Descr.
HigherLevelAnalysis
StudyAssay
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Array
1
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1
Assay
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1
1
0..*
Study
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1
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1
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1
StudyDesignAssay
ArrayAnnotation
StudyDesign
1
0..*
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0..*
Control
ElementAnnotation
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0..1
0..*
1
1
BioMaterialCharacteristic
0..*
BioMaterialImp
1
ElementImp
1
StudyFactor
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StudyDesignDescription
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StudyFactorValue
AssayLabeledExtract
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1
Channel
CompositeElementImp
1
1
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0..*
BioMaterialMeasurement
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1
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1
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1
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Acquisition
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LabelMethod
RelatedAcquisition
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CompositeElementAnnotation
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OntologyEntry
Treatment
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AcquisitionParam
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ElementResultImp
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CompositeElementResultImp
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1
ProcessResult
Quantification
0..*
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1
1
1
MAGEDocumentation
RelatedQuantification
0..*
ProtocolParam
0..*
ProcessIO
1
MAGE_ML
QuantificationParam
0..*
1
0..1
0..*
1
MIAME
Protocol
1
0..*
Experimental Design
Array design
Samples
Hybridization, Measure
Normalization
.
0..*
1
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0..*
1
AnalysisInput
0..*
1
1
ProcessInvocation
ProcessInvocationParam
ProcessImplementationParam
1
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AnalysisInvocation
AnalysisInvocationParam
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AnalysisOutput
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ProcessImplementation
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Analysis
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AnalysisImplementation
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0..*AnalysisImplementatio
nParam
0..*
The MGED Ontology in Action: RAD
• Add screen shot of
study factor
RAD Generic Form for
BioMaterial Characteristics
RAD Project-Specific Form PlasmoDB
Acquiring New Terms
Add term from SRes
OR
Add term from an External Database
Generating Forms from the MGED Ontology
PHP/SQL WWW
RAD3
OntologyEntry
RAD Forms
SRES
MGED Ontology
ExternalDatabases
MGED Ontology
Anatomy
DevelopmentalStage
Disease
Lineage
PATOAttribute
Phenotype
Taxon
RAD is now part of GUS-3.0
GUS has 5 name spaces compartmentalizing different
types of information.
Namespace
Domain
Features
Core
Data Provenance
Workflows
Sres
Shared resources
Ontologies
DoTS
sequence and
annotation
Central dogma
RAD
Gene expresssion
MIAME/MAGE
TESS
Gene regulation
Grammars
GUS Supports Multiple Projects
AllGenes
PlasmoDB
EPConDB
Java Servlets
DoTS RAD TESS SRES Core
Oracle RDBMS
Object Layer for Data Loading
Other sites,
Other projects,
e.g. GeneDB
Available at http://www.gusdb.org
http://www.gusdb.org
Acknowledgements
• RAD/GUS
• MGED Ontology
– Helen Parkinson (EBI)
– Trish Whetzel
– The MGED Ontology Working
Group
– MAGE working group
– Angel Pizarro
– Nelson Axelrod
www.mged.org
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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.cbil.upenn.edu