1. Ontologies for Knowledge Sharing in Neuroanatomy John Gennari Informatics in Biology & Medicine Information & Computer Science Department University of California, Irvine This work developed in collaboration with the UCI Transdisciplinary Tobacco Use Research Center (TTURC)

2. San Diego, Aug 24 The TTURC project At UCI, a Transdisciplinary Tobacco Use Research Center (an NIH project) Researchers from: –Cognitive Science –Neuroanatomy –Pharmacology –Psychiatry –Computer Science (informatics)

3. San Diego, Aug 24 The big picture Transdisciplinary scientific research –Holistic science –Cross-field fertilization of scientific ideas Transdisciplinary knowledge sharing and ontologies –Abstraction –Visualization –Modeling –Terminology management –Easier access to experimental results Gruber: Ontologies for knowledge sharing -- Ontologies as a social contract for communication

4. San Diego, Aug 24 The long-term objectives Use Protégé-2000 for TTURC knowledge representation and sharing Protégé-2000 research question: Are our tools effective and useful? TTURC research question: Can transdisciplinary work accelerate or facilitate research in tobacco use?

5. San Diego, Aug 24 A knowledge sharing problem 1. Researchers in animal studies (rat) are measuring brain activity via CFOS staining 2. Social science researchers are studying tobacco use among (human) adolescents 3. Researchers in psychiatry are measuring brain activity (human) via MRI and PET scans Challenge: How can we combine research results?

6. San Diego, Aug 24 Knowledge combining scenario If we had… Knowledge about correspondences between rat brain regions and human brain regions Knowledge about the function of brain regions Knowledge about the connectivity of brain regions Then we could… Test theories about the effect of nicotine on cognitive function in rats and humans

7. San Diego, Aug 24 Knowledge requirements Ontologies (& knowledge bases) for: Definitions of brain regions: Neuroanatomy Brain region cross-species correspondences Brain region functionality Brain region connectivity

8. San Diego, Aug 24 Roadblocks (or challenges) The boundaries and definitions of brain regions are (sometimes) approximate The topology of brain regions is complex Terminologies conflict, even within species Functional knowledge is very limited Knowledge about brain region connectivity is not complete

9. San Diego, Aug 24 Ontologies(?) for neuroanatomy The USC Brain Project and the Human Brain Project consortium (NIH) NeuroScholar (USC) BrainMap (U Texas, San Antonio) Digital Anatomist (U Washington) NeuroNames (U Washington)

10. San Diego, Aug 24 Project status Strategy: bottom up, from experimental data –Built ontology for rat brain regions where CFOS expression is measured –Developed tool for describing brain region connectivity Next steps: –Adding human brain regions and PET scan data –Building tools for describing cross-species correspondences –Storing functional knowledge for brain regions

11. San Diego, Aug 24 Rat brain region ontology

12. San Diego, Aug 24 Brain region connectivity diagram

13. San Diego, Aug 24 Acknowledgements The Protégé team: Monica Crubezy Ray Fergerson William Grosso John Gennari Some TTURC investigators Francis Leslie James Beluzzi Rodham Shankle Mark Musen Natasha Noy Samson Tu …plus students & others James Fallon Larry Jamner Carol Whalen

14. San Diego, Aug 24