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  
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