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

by Fritz Lekschas

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

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Fritz Lekschas   “Seeing into one's true nature” Apr 15, 2016 !2

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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

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Fritz Lekschas WHY? Apr 15, 2016 !4

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Jules J. Berman, 2013 “BIG DATA” Volume—Larger studies Variety—More studies Velocity—Constantly changing data Apr 15, 2016 !5

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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

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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

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Fritz Lekschas WHAT? Apr 15, 2016 !8

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Fritz Lekschas HOW? Apr 15, 2016 !12

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Fritz Lekschas LIVE DEMO *All bugs have been introduced for the sake of entertainment only. Please do not report them. Apr 15, 2016 !18

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Fritz Lekschas WRAP UP Apr 15, 2016 !19

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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

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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

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Fritz Lekschas THANK YOU! http://satori.refinery-platform.org Apr 15, 2016 !22

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Fritz Lekschas APPENDIX Apr 15, 2016 !23

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Fritz Lekschas PRECISION & RECALL Apr 15, 2016 !24

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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”

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Fritz Lekschas PRECISION & RECALL Apr 15, 2016 !26

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Fritz Lekschas SATORI Semantic Annotation Tool and Ontological Relations Interface Apr 15, 2016 !27

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Fritz Lekschas   “Enlightenment, Awakening, Comprehension & Understanding” Apr 15, 2016 !28