Semantic Body Browser

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

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Fritz Lekschas

December 10, 2012
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  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  
  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
  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
  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
  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
  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
  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 pictures 10.12.12 Fritz Lekschas 8
  9. AVAILABLE BROWSING VIEWS 10.12.12 Fritz Lekschas 9

  10. APPLICATION ARCHITECTURE 10.12.12 Fritz Lekschas 10

  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
  12. ANGULARJS MVC INTERPRETATION 10.12.12 Fritz Lekschas 12

  13. DATABASE DESIGN 10.12.12 Fritz Lekschas 13

  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
  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
  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