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ChEBI new ontology visualisation

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

Published in: Design, Technology, Spiritual
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ChEBI new ontology visualisation

  1. 1. ChEBI Ontology VisualisationPaula de Matos and VenkatMuthukrishnan
  2. 2. ChEBI Ontology? • Chemical entity • Subatomic particle • Role • Chemical role • Biological role • Application
  3. 3. The Problem
  4. 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. 5. Metabolomics?
  6. 6. Understanding the user?• Interviews• Lab visits• Piggy backed on a workshop
  7. 7. Analysing the results
  8. 8. Persona + Workflows• Barbera the biologist• Chris the chemist• Charlie the curator• Basil the bioinformatician
  9. 9. So what was wrong with the oldvisualisation?
  10. 10. Website Log Analysis
  11. 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. 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. 13. Designing – simplifying graph view
  14. 14. Designing – extracting relationships
  15. 15. Designing – handling roles
  16. 16. Designing – handling structural classes
  17. 17. Implementation• The JavaScript InfoVis Toolkit (The JIT) – graph view• DOJO - slider• Moo Tools – galleryCompromises:• Toolkit made us compromise on some functionality• Browser incompatibilities are a real headache
  18. 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

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