SATORI - A System for Ontology-Guided Visual Exploration of Biomedical Data Repositories

These are the slides from my master thesis presentation. SATORI is an ontology-guided visual exploration system for data repositories, which combines powerful metadata search with a treemap and a node-link diagram that visualize the repository structure, provide context to retrieved data sets, and serve as an interface to drive semantic querying and exploration, and thereby support the information foraging loop. SATORI is web-based, open-source, and integrated in the Refinery Platform – an application for biomedical data management, analysis, and visualization.

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1. Fritz Lekschas SATORI Apr 15, 2016 !1 A System for Ontology-Guided Visual Exploration of Biomedical Data Repositories
2. Fritz Lekschas 

   “Seeing into one's true nature” Apr 15, 2016 !2
3. Fritz Lekschas GOAL A System for Ontology-guided Visual Exploration of Biomedical Data Repositories » Refinery » Biological Context » Search & Visualization
 » RNA-Seq, ChIP-Seq, … » Stem Cell Commons, … Apr 15, 2016 !3
4. Fritz Lekschas WHY? Apr 15, 2016 !4
5. Jules J. Berman, 2013 “BIG DATA” Volume—Larger studies Variety—More studies Velocity—Constantly changing data Apr 15, 2016 !5
6. Fritz Lekschas BIG DATA Opportunities • Test hypothesis without data generation • Enrich in-house generated data • Meta analysis • Large scale data mining Challenges ➢ Find relevant data Apr 15, 2016 !6
7. Fritz Lekschas USER ROLES Data Analyst Analysing raw data to test a specific hypothesis Data Curator Develop and maintain annotation strategies Apr 15, 2016 !7 Project Leader Propose ideas to address challenges and foresee trends
8. Fritz Lekschas WHAT? Apr 15, 2016 !8
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12. Fritz Lekschas HOW? Apr 15, 2016 !12
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18. Fritz Lekschas LIVE DEMO *All bugs have been introduced for the sake of entertainment only. Please do not report them. Apr 15, 2016 !18
19. Fritz Lekschas WRAP UP Apr 15, 2016 !19
20. Fritz Lekschas CONCLUSION • Ontology-guided visualizations enrich exploration: overview & higher-level terms • Users need initial training or guidance • Need unified query interface • Utility of ontologies crucially depend on the annotation quality Apr 15, 2016 !20
21. Fritz Lekschas FUTURE WORK • Evaluate generality of SATORI • Unified query interface • Invert order nodes in the graph • Unify concept of the graph with faceted browsing Apr 15, 2016 !21
22. Fritz Lekschas THANK YOU! http://satori.refinery-platform.org Apr 15, 2016 !22
23. Fritz Lekschas APPENDIX Apr 15, 2016 !23
24. Fritz Lekschas PRECISION & RECALL Apr 15, 2016 !24
25. Fritz Lekschas PRECISION & RECALL Data Set Organism Cell Type Disease Seq. Techno. 1 Human Hepatocyte Healthy RNA-Seq Mouse Hepatocyte Healthy RNA-Seq 2 Human Podocyte Healthy RNA-Seq Human Podocyte Congenital nephrotic syndrome RNA-Seq 3 Human Fibroblast Healthy Microarray C57BL/6 Fibroblast Healthy Microarray 4 Human Fibroblast Cardiac fibrosis Microarray 5 Human Fibroblast Healthy RNA-Seq Charact. Value Precision Recall Charact. Value Precision Recall Organism Human 2 / 2 2 / 5 Disease Healthy 2 / 2 2 / 5 Mouse 1 / 2 1 / 2 Cardiac Fibrosis 1 / 2 1 / 1 Cell Type Fibroblast 2 / 2 2 / 3 Seq. Techno. Microarray 2 / 2 2 / 2 Apr 15, 2016 !25 Search: “Human Fibroblast Microarray”
26. Fritz Lekschas PRECISION & RECALL Apr 15, 2016 !26
27. Fritz Lekschas SATORI Semantic Annotation Tool and Ontological Relations Interface Apr 15, 2016 !27
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    “Enlightenment, Awakening, Comprehension & Understanding” Apr 15, 2016 !28