ChEBI Ontology Visualisation

Paula de Matos and Venkat Muthukrishnan

ChEBI Ontology?

• Chemical entity• Subatomic particle• Role

• Chemical role• Biological role• Application

The Problem

Who are our users?

• Text miners?• Ontologists?• Biocurators?• Bioinformaticians?• Chemoinformaticians?• Wet-lab biologists?• Chemists?

Decided to focus on • Metabolomics experimentalist (biologist or

chemist)

Metabolomics?

Understanding the user?

• Interviews

• Lab visits

• Piggy backed on a workshop

Analysing the results

Persona + Workflows

• Barbera the biologist

• Chris the chemist• Charlie the curator• Basil the bioinformatician

So what was wrong with the old visualisation?

Website Log Analysis

Requirements Specification

Functional RequirementsExample:•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…

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

Designing – simplifying graph view

Designing – extracting relationships

Designing – handling roles

Designing – handling structural classes

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

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