1. BBN Technologies Copyright 2009 Slide 1 The S*QL Plugin for Cytoscape Visual Analytics on the Web of Linked Data Rusty (Robert J.) Bobrow Jeff Berliner, Prakash Manghwani Eric Neumann – Clinical Semantics Group rusty@bbn.comrusty@bbn.com (617) 873-3601

2. BBN Technologies Copyright 2010 Slide 2 Biological Network Inference Genomics Pathways Regulatory Networks Anatomy and Tissue Diseases Therapeutics Experimental Data

3. BBN Technologies Copyright 2010 Slide 3 The Need for Visualization Example Text-Mined Data Set: Over 1000 nodes: genes, processes and compounds ~8000 links: inhibit, stimulate, interact Interactions occurring in hepatocytes and adipocytes -- from text-mining biological literature

4. BBN Technologies Copyright 2010 Slide 4 Proposed mechanism-derived gene expression signatures and predictive biomarkers; follow-up experiments. Biomarker Identification and Validation Multiple Condition Whole Genome Measurements Expression Analysis Interaction Pathways Regulatory Networks Interaction Pathways Regulatory Networks Nucleic Acids Research, 2008, Vol. 36 KEGG for linking genomes to life and the environment Integrate and interpret experimental data in the context of diverse sources of background knowledge Gene Disease Relations The human disease network www.pnas.orgcgidoi10.1073pnas.0701361104 Unsupervised discovery followed by supervised interpretation

5. BBN Technologies Copyright 2010 Slide 5 Knowledge Exploration & Discovery Framework Less Structured More Structured Users Analysis Search/Query, Navigation Search/Query, Navigation Hypothesis & Reasoning Tools Hypothesis & Reasoning Tools Data Resources Relational DBs, Knowledge Bases, … Spreadsheets, XML Docs, … Web Pages, Podcasts, … Documents, Images, Video, … Data & Distributed Operations Tools Data & Distributed Operations Tools Integration Semantic Web & Complementary Technologies Visualization BBN Kineti-Graph TM Dynamic Data Visualization Data Lenses Cytoscape, etc. Supporting the analytic process: - Visualize multiple data sources - Propose and examine patterns within a single data source - Examine implications of selected patterns across multiple displays, data tables - Export selection with descriptive (semantic) meta-data

6. BBN Technologies Copyright 2010 Slide 6 S*QL Plugin for Cytoscape SPARQL and SQL access to resources on the web Linked data visualization and analysis tools

7. BBN Technologies Copyright 2010 Slide 7 Cytoscape Open Source Graph Visualization Tool Large Community Involvement Multiple Applications Protein interactions Pathways Genes and diseases Social networks Plug-in architecture ~80 plugins Analysis, Network and Attribute I/O, Network Inference, Functional Enrichment, Communication/Scripting Filters Graph Analyses (cluster algorithms)

8. BBN Technologies Copyright 2010 Slide 8 Query over the Web

9. BBN Technologies Copyright 2010 Slide 9 Biopax Pathways

10. BBN Technologies Copyright 2010 Slide 10 Demonstration Architecture Users Analysis Visualization BBN Kineti-Graph TM Dynamic Data Visualization Cytoscape Network View Integration Data Resources SPARQL & SQL Query Data Selection SPARQL & SQL Query Data Selection SPARQL & SQL Query Data Access SPARQL & SQL Query Data Access Drug Indications Triple Store Clinical Trials Triple Store Analysis/Display Plugins

11. BBN Technologies Copyright 2010 Slide 11 S*QL Interface Data Source Navigation Query Edit Area Connection Parameters Destination Merge Operations Destination Network

12. BBN Technologies Copyright 2010 Slide 12 RDF Graph:Alternative Drug Applications 768 Entities 1050 Associations Angela Qu et al, 2008 Cincinnati Children’s Hospital Medical Center Systemic Lupus Erythematosus + Tamoxifen Genes Diseases Phenotypes Mechanisms Compounds