1. March 24, 2005 1 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

2. 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, 2005 @ Hawaii

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

4. 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

5. 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

6. March 24, 2005Morgan Langille6

7. 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)

8. 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

9. March 24, 2005Morgan Langille9

10. 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

11. March 24, 2005Morgan Langille11

12. 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

13. 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

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

15. March 24, 2005Morgan Langille15 Example

16. March 24, 2005Morgan Langille16

17. 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

18. 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

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