March 24, Integrating genomic knowledge sources through an anatomy ontology Gennari JH, Silberfein A, and Wiley JC Pac Symp Biocomputing 2005: Presented by Morgan Langille MEDG 505

March 24, 2005Morgan Langille2 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, Hawaii

March 24, 2005Morgan Langille3 Outline Gene Ontology Gene Expression Data Foundational Model of Anatomy Integrated Knowledge Base!

March 24, 2005Morgan Langille4 Foundational Model of Anatomy (FMA)  FMA describes all of human anatomy (even sub- cellular) 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

March 24, 2005Morgan Langille5 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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March 24, 2005Morgan Langille7 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)

March 24, 2005Morgan Langille8 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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March 24, 2005Morgan Langille10 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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March 24, 2005Morgan Langille12 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

March 24, 2005Morgan Langille13 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

March 24, 2005Morgan Langille14 Overview of MGD, GO, and FMA data integration

March 24, 2005Morgan Langille15 Example

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March 24, 2005Morgan Langille17 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

March 24, 2005Morgan Langille18 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

March 24, 2005Morgan Langille19 Questions?  Is anatomy the best knowledge hub?