Download Integrating genomic knowledge sources through an anatomy ontology

Integrating genomic
knowledge sources through
an anatomy ontology
Gennari JH, Silberfein A, and Wiley JC
Pac Symp Biocomputing 2005: 115-26
Presented by Morgan Langille
MEDG 505
March 24, 2005
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Pac Symp Biocomputing?
 Proceedings of the Pacific Symposium on
Biocomputing
 “… research in the theory and application
of computational methods in problems of
biological significance”
 Jan, 2005 @ Hawaii
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Outline
Gene Ontology
IntegratedGene Expression
Data
Knowledge
Base!
Foundational Model of
Anatomy
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Foundational Model of Anatomy (FMA)
 FMA describes all of human anatomy (even subcellular) as a symbolic ontology of concepts and
relationships
 Designed for the genomics domain not for a
certain type of user
 Can be navigated by humans and machines
 No function or physiology of anatomy
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Foundational Model of Anatomy (FMA)
 Implemented using Protégé
 Protégé
 Authoring and editing environment for
ontologies
 Can be used to view the FMA
 Freely accessible since 2003
 Can be viewed in a web browser
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Gene Ontology
 Gene Ontology (GO) is a controlled
vocabulary that can be used to annotate
genes
 Includes databases such as:
 FlyBase (Drosophila)
 Saccharomyces Genome Database (SGD)
 Mouse Genome Database (MGD)
 WormBase
 Rat Genome Database (RGD)
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Gene Ontology
 The three organizing principles of GO:
 molecular function - catalytic activity,
transporter activity, or binding, etc.
 biological process - cell growth and
maintenance or signal transduction, etc.
 cellular component - rough endoplasmic
reticulum or nucleus, ribosome, proteasome,
etc.
 No tissue specific information
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Integrating GO and FMA
 Connect GO with FMA via cellular
structure
 Hand built connections of 150 terms
between FMA and GO
 Built Protégé plugin to view the integrated
data
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Gene Expression Data
 No standard source for anatomic knowledge for
annotation of gene expression results
 Standards and Ontologies for Functional
Genomics (SOFG)
 Focused on integrating ontologies for mouse and
human anatomies
 Devoloped “SOFG anatomy entry list” (SAEL)
 SAEL – 100 anatomic terms
 Can be used to annotate gene expression data
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Integrating Gene Expression Data
 Integrate the gene expression data from
the Mouse Genome Database (MGD)
 Built connections between anatomy terms
used in MGD to concepts defined in FMA
 Focused only on brain regions
 Few anatomic differences between human
and mouse brain regions
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Overview of MGD, GO, and FMA
data integration
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Example
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Future Work/Problems
 Automation of connecting ontologies
 Prompt
 Plugin for Protégé
 Semi-automatic merging of ontologies
 BioMediator
 Dynamic connections
 Anatomies will not always map between
species
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Conclusions
 Many ontologies already exist in biology
such as GO and the FMA
 Integration of multiple sources can be
based on anatomy
 Future work is needed in automating
production of ontology connections
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Questions?
 Is anatomy the best knowledge hub?
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