The MGED Ontology: A framework for describing functional genomics experiments SOFG Nov. 19, 2002...
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Transcript of The MGED Ontology: A framework for describing functional genomics experiments SOFG Nov. 19, 2002...
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 GinsburgJonathan 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
MAGEMIAMEDB
MIAMEDBExternal
Ontologies/CVs
MGED Ontology
Software and database developers
Investigators annotating experiments
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
ArrayExpress
MIAMExpress
RADMAGE-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
SexC
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
ElementAnnotation
Analysis
AnalysisImplementationParam
AnalysisInput
AnalysisImplementation1
0..*1
0..*
1 0..*1 0..*
AnalysisInvocationParamAnalysisInvocation1
0..*1
0..*
1
0..*
1
0..*
1 0..*1 0..*
AnalysisOutput
1
0..*
1
0..*
CompositeElementAnnotation
ArrayAnnotation
CompositeElementImp
0..*0..1 0..*0..1
1
0..*
1
0..*
ElementResultImp CompositeElementResultImp
1
0..*
1
0..*
0..10..* 0..10..*
QuantificationParam
RelatedQuantification
Study
StudyDesignDescription
StudyAssay10..* 10..*
StudyDesignAssay
StudyFactorValueAssayLabeledExtract
BioMaterialImp1
0..*
1
0..*
LabelMethod
0..1
0..*
0..1
0..*
ProtocolParam
MAGEDocumentation
MAGE_ML
0..*
1
0..*
1
AcquisitionParam
Assay
1
0..*
1
0..*
1
0..*
1
0..*
1
0..*
1
0..*
1
0..*
1
0..*
Channel
1
0..*
1
0..*
0..*0..1
0..*0..1
Quantification1
0..*
1
0..*1
0..*
1
0..*
10..*
10..*
1 0..*1 0..*1 0..*1 0..*
Acquisition1
0..*
1
0..*
1
0..*
1
0..*
1
0..*
1
0..*
1
0..*
1
0..*
RelatedAcquisition1 0..*1 0..*1 0..*1 0..*
ProcessImplementationParam
ProcessIO
ProcessInvocation
1
0..*
1
0..*
ProcessInvocationParam10..* 10..*
Array
1
0..*
1
0..*
10..*
10..* 1 0..*1 0..*
BioMaterialMeasurement1 0..*1 0..*
Protocol
1
0..*
1
0..*
1
0..*
1
0..*
0..1
0..*
0..1
0..*
0..1
0..*
0..1
0..*Treatment
1
0..*
1
0..*
1
0..*
1
0..*
0..1
0..*
0..1
0..*
StudyDesign
1
0..*
1
0..*10..* 10..*
1 0..*1 0..*
BioMaterialCharacteristic1
0..*1
0..*
ProcessImplementation10..* 10..*
1
0..*
1
0..*
ElementImp
0..10..* 0..10..*
1
0..*
1
0..*
1
0..*
1
0..*
1
0..*
1
0..*
Control
1
0..*
1
0..*
ProcessResult1 0..*1 0..*
StudyFactor
1
0..*
1
0..*
10..* 10..*
OntologyEntry10..* 10..*
0..*0..1
0..*0..1
1
0..*
1
0..*
RAD schema uses MAGE/MIAMEMAGE
ExperimentArray
BioMaterialBioAssay
BioAssayData Protocol, Descr.
HigherLevelAnalysis
MAGEExperiment
ArrayBioMaterial
BioAssayBioAssayData
Protocol, Descr.HigherLevelAnalysis
MIAMEExperimental Design
Array designSamples
Hybridization, MeasureNormalization
.
MIAMEExperimental Design
Array designSamples
Hybridization, MeasureNormalization
.
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
Add term from an External Database
OR
Generating Forms from the MGED Ontology
OntologyEntry
ExternalDatabases
PHP/SQL WWW
RAD Forms
MGED OntologyAnatomy
DevelopmentalStageDiseaseLineage
PATOAttributePhenotype
Taxon
SRES
RAD3
MGED Ontology
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
DoTSsequence and
annotationCentral dogma
RAD Gene expresssion MIAME/MAGE
TESS Gene regulation Grammars
GUS Supports Multiple ProjectsAllGenesAllGenes PlasmoDBPlasmoDB
EPConDBEPConDB
CoreSRESTESSRADDoTS
Oracle RDBMS Object Layer for Data Loading
Java ServletsOther sites,Other projects,e.g. GeneDB
Other sites,Other projects,e.g. GeneDB
Available at http://www.gusdb.org
http://www.gusdb.org
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