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Semantic Body Browser

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Presentation of the Semantic Body Browser in the scope of Fritz Lekschas Bachelor Thesis.

Presentation of the Semantic Body Browser in the scope of Fritz Lekschas Bachelor Thesis.

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  • 1. Bachelor  Thesis   SEMANTIC BODY BROWSER A web-based tool for graphically exploring an organism‘s body in respect to the CELDA ontology Supervisor  &  Reviewer:  Prof.  Dr.  Andreas  Kurtz   Review:  Prof.  Dr.  Robert  Tolksdorf  10.12.12 Fritz Lekschas 1
  • 2. CONTENTS1.  Overview CellFinder & CELDA2.  Motivation3.  Application Live Presentation4.  Application Design5.  Lookout6.  Questions10.12.12 Fritz Lekschas 2
  • 3. CELLFINDER•  Web-based data repository on cell types –  Systematic / structural information •  CELDA –  Images –  Expression •  Protein •  RNA –  Text mining •  Automated retrieval of information10.12.12 Fritz Lekschas 3
  • 4. CELDA ONTOLOGY•  Data structure behind CellFinder•  Describes / organizes cells –  Expression –  Localization –  Development –  Anatomy•  Integrates 8 ontologies + 11 bridges10.12.12 Fritz Lekschas 4
  • 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 informationà Goal: Provide enhanced browsing experience10.12.12 Fritz Lekschas 5
  • 6. CONCEPT•  Provide intuitive model for browsing –  Map of an organism‘s body –  3 Dimensions •  Resolution •  Development •  Species –  Easy extendibility10.12.12 Fritz Lekschas 6
  • 7. LIVE EXAMPLE•  What can be done with the Semantic Body Browser?10.12.12 Fritz Lekschas 7
  • 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 pictures10.12.12 Fritz Lekschas 8
  • 9. AVAILABLE BROWSING VIEWS10.12.12 Fritz Lekschas 9
  • 10. APPLICATION ARCHITECTURE10.12.12 Fritz Lekschas 10
  • 11. TECHNOLOGIESCLIENT-SIDE SERVER-SIDE•  JavaScript •  PHP –  AngularJS –  SlimPHP –  Raphaël •  MySQL –  jQuery –  Hammer.JS –  Grunt•  HTML5 & CSS 3•  SVG (Converted to JSON)10.12.12 Fritz Lekschas 11
  • 12. ANGULARJS MVC INTERPRETATION10.12.12 Fritz Lekschas 12
  • 13. DATABASE DESIGN10.12.12 Fritz Lekschas 13
  • 14. COMPATABILITYDESKTOP APPLE iOS•  All modern web •  Mobile Safari iOS browser 5.1+ –  Chrome 11+ –  Safari 5+ –  Firefox 3.6+ –  Opera 11.6+ –  Internet Explorer 9+10.12.12 Fritz Lekschas 14
  • 15. LOOKOUT•  Upcoming update –  Liver (7 levels of resolution) –  RDFA integration•  Linking expression data –  Dynamic heat maps•  More organs, species & microscopic pictures10.12.12 Fritz Lekschas 15
  • 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.org10.12.12 Fritz Lekschas 16

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