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  

CONTENTS

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

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CELLFINDER

•  Web-based data repository on cell types –  Systematic / structural information

•  CELDA

–  Images –  Expression

•  Protein •  RNA

–  Text mining •  Automated retrieval of information

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CELDA ONTOLOGY

•  Data structure behind CellFinder •  Describes / organizes cells –  Expression –  Localization –  Development –  Anatomy

•  Integrates 8 ontologies + 11 bridges

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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

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CONCEPT

•  Provide intuitive model for browsing –  Map of an organism‘s body –  3 Dimensions

•  Resolution •  Development •  Species

–  Easy extendibility

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LIVE EXAMPLE

•  What can be done with the Semantic Body Browser?

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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

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AVAILABLE BROWSING VIEWS

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APPLICATION ARCHITECTURE

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TECHNOLOGIES CLIENT-SIDE

•  JavaScript –  AngularJS –  Raphaël –  jQuery –  Hammer.JS –  Grunt

•  HTML5 & CSS 3 •  SVG (Converted to JSON)

SERVER-SIDE

•  PHP –  SlimPHP

•  MySQL

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ANGULARJS MVC INTERPRETATION

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DATABASE DESIGN

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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+

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LOOKOUT

•  Upcoming update –  Liver (7 levels of resolution) –  RDFA integration

•  Linking expression data –  Dynamic heat maps

•  More organs, species & microscopic pictures

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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

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