Semantic Body Browser

A web-based tool for graphically exploring an organism‘s body in respect to the CELDA ontology.

Author: Fritz Lekschas

Website: http://sbb.cellfinder.org

Transcript

1. SEMANTIC BODY BROWSER
   A web-based tool for graphically exploring
   an organism‘s body in respect to the CELDA
   ontology
   10.12.12 Fritz Lekschas 1
   Bachelor  Thesis  
   Supervisor  &  Reviewer:  Prof.  Dr.  Andreas  Kurtz  
   Review:  Prof.  Dr.  Robert  Tolksdorf  
   

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2. CONTENTS
   1.  Overview CellFinder & CELDA
   2.  Motivation
   3.  Application Live Presentation
   4.  Application Design
   5.  Lookout
   6.  Questions
   10.12.12 Fritz Lekschas 2
   

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3. CELLFINDER
   •  Web-based data repository on cell types
   –  Systematic / structural information
   •  CELDA
   –  Images
   –  Expression
   •  Protein
   •  RNA
   –  Text mining
   •  Automated retrieval of information
   10.12.12 Fritz Lekschas 3
   

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4. CELDA ONTOLOGY
   •  Data structure behind CellFinder
   •  Describes / organizes cells
   –  Expression
   –  Localization
   –  Development
   –  Anatomy
   •  Integrates 8 ontologies + 11 bridges
   10.12.12 Fritz Lekschas 4
   

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5. MOTIVATION
   •  Two general ways of finding data
   1.  Search (text based, straight forward)
   •  Term is known by name
   2.  Browsing (fuzzy process of information retrieval)
   •  Term is not known by name
   •  Search via related information
   à Goal: Provide enhanced browsing experience
   10.12.12 Fritz Lekschas 5
   

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6. CONCEPT
   •  Provide intuitive model for browsing
   –  Map of an organism‘s body
   –  3 Dimensions
   •  Resolution
   •  Development
   •  Species
   –  Easy extendibility
   10.12.12 Fritz Lekschas 6
   

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7. LIVE EXAMPLE
   •  What can be done with the Semantic Body Browser?
   10.12.12 Fritz Lekschas 7
   

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8. SEMANTIC BODY BROWSER
   •  What can be done with the Semantic Body Browser?
   1.  Browsing organism
   •  Resolution: body à cellular level
   •  Development: nephron
   •  Species: homo sapiens & mus musculus
   2.  Retrieve information
   •  Definition
   •  Synonyms
   •  Find CellFinder page
   3.  Compare
   •  Microscopic pictures
   10.12.12 Fritz Lekschas 8
   

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9. AVAILABLE BROWSING VIEWS
   10.12.12 Fritz Lekschas 9
   

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10. APPLICATION ARCHITECTURE
    10.12.12 Fritz Lekschas 10
    

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11. TECHNOLOGIES
    CLIENT-SIDE
    •  JavaScript
    –  AngularJS
    –  Raphaël
    –  jQuery
    –  Hammer.JS
    –  Grunt
    •  HTML5 & CSS 3
    •  SVG (Converted to JSON)
    SERVER-SIDE
    •  PHP
    –  SlimPHP
    •  MySQL
    10.12.12 Fritz Lekschas 11
    

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12. ANGULARJS MVC INTERPRETATION
    10.12.12 Fritz Lekschas 12
    

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13. DATABASE DESIGN
    10.12.12 Fritz Lekschas 13
    

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14. COMPATABILITY
    DESKTOP
    •  All modern web
    browser
    –  Chrome 11+
    –  Safari 5+
    –  Firefox 3.6+
    –  Opera 11.6+
    –  Internet Explorer 9+
    APPLE iOS
    •  Mobile Safari iOS
    5.1+
    10.12.12 Fritz Lekschas 14
    

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15. LOOKOUT
    •  Upcoming update
    –  Liver (7 levels of resolution)
    –  RDFA integration
    •  Linking expression data
    –  Dynamic heat maps
    •  More organs, species & microscopic pictures
    10.12.12 Fritz Lekschas 15
    

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16. QUESTIONS
    Thank you!
    •  Special thanks
    –  Prof. Dr. Andreas Kurtz
    –  Prof. Dr. Robert Tolksdorf
    –  Dr. Harald Stachelscheid
    –  Stefanie Seltmann
    •  Website
    –  Integrated: http://cellfinder.org/browse
    –  Stand alone: http://sbb.cellfinder.org
    10.12.12 Fritz Lekschas 16
    

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