A presentation detailing the process used to develop the new ChEBI ontology visualisation.

1. ChEBI Ontology Visualisation
Paula de Matos and Venkat
Muthukrishnan

2. ChEBI Ontology?
• Chemical entity
• Subatomic particle
• Role
• Chemical role
• Biological role
• Application

3. The Problem

4. Who are our users?
• Text miners?
• Ontologists?
• Biocurators?
• Bioinformaticians?
• Chemoinformaticians?
• Wet-lab biologists?
• Chemists?
Decided to focus on
• Metabolomics experimentalist (biologist or
chemist)

5. Metabolomics?

6. Understanding the user?
• Interviews
• Lab visits
• Piggy backed on a workshop

7. Analysing the results

8. Persona + Workflows
• Barbera the biologist
• Chris the chemist
• Charlie the curator
• Basil the bioinformatician

9. So what was wrong with the old
visualisation?

10. Website Log Analysis

11. Requirements Specification
Functional Requirements
Example:
•The new design should offer a simplified view of the ontology.
•The new design should reduce prominence of less essential
data attributes in order not to continue cluttering of the core
data.
Data Requirements
•Chemical structure, definition, name, etc…

12. Designing – what have others done
• No clear winner - Katifori (2007)
• Indented list, node – link and tree, zoomable,
space filling, focus and context
• TreeMap works best for trees - Kobsa (2004)
• 3D visualisation not perfect or optimal - Wiss et. al.
(1998)
End conclusion:
A combination of visualisations is required depending
on the user and what information you are trying to
visualise

13. Designing – simplifying graph view

14. Designing – extracting relationships

15. Designing – handling roles

16. Designing – handling structural classes

17. Implementation
• The JavaScript InfoVis Toolkit (The JIT) – graph view
• DOJO - slider
• Moo Tools – gallery
Compromises:
• Toolkit made us compromise on some functionality
• Browser incompatibilities are a real headache

18. Thanks and Demo
• The users
• The MetaboLights team (Reza, Pablo and Ken)
• The ChEBI team (Gareth, Marcus, Steve, Adriano,
Venkat and Janna)
• The developer – Venkat