March 24, 2005 1 Integrating genomic knowledge sources through an anatomy ontology Gennari JH,...

March 24, 2005March 24, 2005 11

Integrating genomic Integrating genomic knowledge sources through knowledge sources through

an anatomy ontologyan anatomy ontologyGennari JH, Silberfein A, and Wiley JCGennari JH, Silberfein A, and Wiley JCPac Symp Biocomputing 2005: 115-26Pac Symp Biocomputing 2005: 115-26

Presented by Morgan LangillePresented by Morgan LangilleMEDG 505MEDG 505

March 24, 2005March 24, 2005 Morgan LangilleMorgan Langille 22

Pac Symp Biocomputing?Pac Symp Biocomputing?

Proceedings of the Pacific Symposium on Proceedings of the Pacific Symposium on BiocomputingBiocomputing

“… “… research in the theory and application research in the theory and application of computational methods in problems of of computational methods in problems of biological significance”biological significance”

Jan, 2005 @ HawaiiJan, 2005 @ Hawaii


OutlineOutline

Gene Ontology

Gene Expression Data

Foundational Model of Anatomy

Integrated Knowledge

Base!


Foundational Model of Anatomy (FMA)Foundational Model of Anatomy (FMA)

FMA describes all of human anatomy (even sub-FMA describes all of human anatomy (even sub-cellular) as a symbolic ontology of concepts and cellular) as a symbolic ontology of concepts and relationshipsrelationships

Designed for the genomics domain not for a Designed for the genomics domain not for a certain type of usercertain type of user

Can be navigated by humans and machinesCan be navigated by humans and machines

No function or physiology of anatomyNo function or physiology of anatomy


Foundational Model of Anatomy (FMA)Foundational Model of Anatomy (FMA)

Implemented using ProtégéImplemented using Protégé Protégé Protégé

Authoring and editing environment for Authoring and editing environment for ontologiesontologies

Can be used to view the FMACan be used to view the FMA

Freely accessible since 2003Freely accessible since 2003 Can be viewed in a web browserCan be viewed in a web browser



Gene OntologyGene Ontology

Gene Ontology (GO) is a controlled Gene Ontology (GO) is a controlled vocabulary that can be used to annotate vocabulary that can be used to annotate genesgenes

Includes databases such as:Includes databases such as: FlyBase (Drosophila)FlyBase (Drosophila) Saccharomyces Genome Database (SGD)Saccharomyces Genome Database (SGD) Mouse Genome Database (MGD)Mouse Genome Database (MGD) WormBaseWormBase Rat Genome Database (RGD)Rat Genome Database (RGD)


Gene OntologyGene Ontology

The three organizing principles of GO:The three organizing principles of GO: molecular function - catalytic activity, molecular function - catalytic activity,

transporter activity, or binding, etc.transporter activity, or binding, etc. biological process - cell growth and biological process - cell growth and

maintenance or signal transduction, etc.maintenance or signal transduction, etc. cellular component - rough endoplasmic cellular component - rough endoplasmic

reticulum or nucleus, ribosome, proteasome, reticulum or nucleus, ribosome, proteasome, etc.etc.

No tissue specific informationNo tissue specific information



Integrating GO and FMAIntegrating GO and FMA

Connect GO with FMA via cellular Connect GO with FMA via cellular structurestructure

Hand built connections of 150 terms Hand built connections of 150 terms between FMA and GObetween FMA and GO

Built Protégé plugin to view the integrated Built Protégé plugin to view the integrated datadata



Gene Expression DataGene Expression Data

No standard source for anatomic knowledge for No standard source for anatomic knowledge for annotation of gene expression resultsannotation of gene expression results

Standards and Ontologies for Functional Standards and Ontologies for Functional Genomics (SOFG)Genomics (SOFG) Focused on integrating ontologies for mouse and Focused on integrating ontologies for mouse and

human anatomieshuman anatomies Devoloped “SOFG anatomy entry list” (SAEL)Devoloped “SOFG anatomy entry list” (SAEL) SAEL – 100 anatomic termsSAEL – 100 anatomic terms

Can be used to annotate gene expression dataCan be used to annotate gene expression data


Integrating Gene Expression DataIntegrating Gene Expression Data

Integrate the gene expression data from Integrate the gene expression data from the Mouse Genome Database (MGD)the Mouse Genome Database (MGD)

Built connections between anatomy terms Built connections between anatomy terms used in MGD to concepts defined in FMAused in MGD to concepts defined in FMA

Focused only on brain regionsFocused only on brain regions Few anatomic differences between human Few anatomic differences between human

and mouse brain regionsand mouse brain regions


Overview of MGD, GO, and FMA Overview of MGD, GO, and FMA data integrationdata integration


ExampleExample



Future Work/ProblemsFuture Work/Problems

Automation of connecting ontologiesAutomation of connecting ontologies Prompt Prompt

Plugin for ProtégéPlugin for Protégé Semi-automatic merging of ontologiesSemi-automatic merging of ontologies

BioMediatorBioMediator Dynamic connectionsDynamic connections

Anatomies will not always map between Anatomies will not always map between speciesspecies


ConclusionsConclusions

Many ontologies already exist in biology Many ontologies already exist in biology such as GO and the FMAsuch as GO and the FMA

Integration of multiple sources can be Integration of multiple sources can be based on anatomybased on anatomy

Future work is needed in automating Future work is needed in automating production of ontology connectionsproduction of ontology connections


Questions?Questions?

Is anatomy the best knowledge hub?Is anatomy the best knowledge hub?

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