1. Contributions to mouse BIRN tools and resources Maryann Martone and Mark Ellisman University of California, San Diego 2008

2. Deliverables Continued population of CCDB –Improvement of upload tools –Integration of CCDB into BIRN Data Repository Improved access of CCDB data through MBAT –Spatial registration pipeline Query of CCDB through BIRN mediator –Mapping of content to BIRNLex Development of ontologies –Subcellular anatomy ontology –Ontologies for disease Integration of ontologies with annotation and segmentation tools

3. Population of CCDB Over 300 datasets are now available through public CCDB and MBAT Added DATKO and synuclein data to public CCDB -released over 60 data sets Improved upload tools to support bulk upload of files to CCDB –Minimal metadata for experimental data for BIRN BDR –Streamlining upload for BIRN BDR Redesigned data input forms available through portal Willy Wong, Diana Price, Monica Berlanga, Brad Vesely, Maryann Martone

4. Atlasing Tools Improved spatial registration pipeline for NCMIR data –Deployed production version within BIRN portal Improved web services for access of CCDB through MBAT –Worked to provide better characterization of content of CCDB in MBAT –Large scale images are now available Developed multiscale visualization using Image Services Developed wrappers and created web services for other application such as MBAT from UCLA for accessing spatial data from SmartAtlas Asif Memon and Willy Wong

5. Multiscale Image Services Asif Memon; Ilya Zaslavsky

6. Data Integration Worked with BIRN CC on data federation registration tools, particularly the Concept Mapper

7. Query of CCDB through Mediator

8. Ontologies Updated Subcellular Anatomy Ontology with entities relevant to neurodegenerative disease –e.g., plaques, Lewy bodies, protein aggregates Submitted SAO to NCBO BioPortal Integrated SAO into BIRNLex Worked with NCBO on “Neurodegenerative disease phenotype ontology” Integrated BIRNLex into annotation and segmentation tools –Jinx –Smart Atlas Lisa Fong, Sarah Maynard, Bill Bug, Stephen Larson, Stephan Lamont

9. Expansion of BIRNLex BIRNLex Common Anatomy Referece Ontology (CARO) Phenotypic Qualities (PATO) Subcellular Anatomy Ontology OBO Cell Type NIF Nerve Cell OBI NIF Molecule OBO Sequence Organism Taxonomy Sensory Behavior Cognition Disease Investigation Anatomy Bill Bug

10. Jessica Turner, Angie Laird, Bill Bug UCI, UT, UCSD Assessments, Behaviors and Stimuli

11. Ontology-based Annotation Jinx: “Deep” annotation using BIRNLex

12. Integration of ontologies into existing tools

13. Ontology + instances Semantic web technologies Knowledge-based queries Content-based retrieval Contains knowledge from literature, CCDB CCDB: data properties and experimental details CKB: Biological view Willy Wong, Amarnath Gupta, Bill Bug Find all instances of spines that contain membrane bound organelles Cellular Knowledge Base Willy Wong

14. Disease Phenotypes Lewy bodies are found in increased numbers in cerebral cortex of Parkinson’s disease patients Aggregates containing alpha-synuclein are found in cerebral cortex of mice overexpressing human alpha synuclein substantia nigra neurons decrease in number in Parkinson’s disease Working with autism and schizophrenia groups to coordinate efforts

15. Disease Phenotypes Using the PATO ontology of qualities Phenotype = Entity + Quality

16. “Find all regions that have high levels of alpha synuclein aggregates” Asif Memon, Willy Wong, Sarah Maynard, Stephen Larson, Bill Bug