Semantic Body Browser

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

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Semantic Body Browser

  1. 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. 2. CONTENTS1.  Overview CellFinder & CELDA2.  Motivation3.  Application Live Presentation4.  Application Design5.  Lookout6.  Questions10.12.12 Fritz Lekschas 2
  3. 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. 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. 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. 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. 7. LIVE EXAMPLE•  What can be done with the Semantic Body Browser?10.12.12 Fritz Lekschas 7
  8. 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. 9. AVAILABLE BROWSING VIEWS10.12.12 Fritz Lekschas 9
  10. 10. APPLICATION ARCHITECTURE10.12.12 Fritz Lekschas 10
  11. 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. 12. ANGULARJS MVC INTERPRETATION10.12.12 Fritz Lekschas 12
  13. 13. DATABASE DESIGN10.12.12 Fritz Lekschas 13
  14. 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. 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. 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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