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.

Transcript

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

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2. Fritz Lekschas
   

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

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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
   

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4. Fritz Lekschas
   WHY?
   Apr 15, 2016 !4
   

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

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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
   

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8. Fritz Lekschas
   WHAT?
   Apr 15, 2016 !8
   

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9. Fritz Lekschas
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10. Fritz Lekschas
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11. Fritz Lekschas
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12. Fritz Lekschas
    HOW?
    Apr 15, 2016 !12
    

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13. Fritz Lekschas
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14. Fritz Lekschas
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15. Fritz Lekschas
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16. Fritz Lekschas
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17. Fritz Lekschas
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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
    

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19. Fritz Lekschas
    WRAP UP
    Apr 15, 2016 !19
    

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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
    

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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
    

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

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23. Fritz Lekschas
    APPENDIX
    Apr 15, 2016 !23
    

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24. Fritz Lekschas
    PRECISION & RECALL
    Apr 15, 2016 !24
    

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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”
    

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26. Fritz Lekschas
    PRECISION & RECALL
    Apr 15, 2016 !26
    

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

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28. Fritz Lekschas
    

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

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