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

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
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2. CONTENTS
1. Overview CellFinder & CELDA
2. Motivation
3. Application Live Presentation
4. Application Design
5. Lookout
6. Questions
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3. 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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4. CELDA ONTOLOGY
• Data structure behind CellFinder
• Describes / organizes cells
– Expression
– Localization
– Development
– Anatomy
• Integrates 8 ontologies + 11 bridges
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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
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6. CONCEPT
• Provide intuitive model for browsing
– Map of an organism‘s body
– 3 Dimensions
• Resolution
• Development
• Species
– Easy extendibility
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7. LIVE EXAMPLE
• What can be done with the Semantic Body Browser?
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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
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9. AVAILABLE BROWSING VIEWS
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10. APPLICATION ARCHITECTURE
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11. TECHNOLOGIES
CLIENT-SIDE
SERVER-SIDE
• JavaScript
• PHP
– AngularJS
– SlimPHP
– Raphaël
• MySQL
– jQuery
– Hammer.JS
– Grunt
• HTML5 & CSS 3
• SVG (Converted to JSON)
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12. ANGULARJS MVC INTERPRETATION
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13. DATABASE DESIGN
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14. COMPATABILITY
DESKTOP
APPLE iOS
• All modern web • Mobile Safari iOS
browser
5.1+
– Chrome 11+
– Safari 5+
– Firefox 3.6+
– Opera 11.6+
– Internet Explorer 9+
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15. 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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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
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