Requirments

Details

Search UI

Search page should be simple. It should take search term(s) in the following form:

• Term IDs
• Keywords
  • Keyword should search Name and Definition
• Gene Names
  • Human-readable symbols (e.g. YAP1)
  • ORF names
• By Score (?)
  • Need to discuss details about UI
  • Probably different UI

Search Options

• Use DAG or Tree?

Search Result Table

The result table should display the following data:

• Term ID
• Name - This will be used as label in the visualization
  • Three separate fields - CC, BP, MF
  • Use ID if there is no mapping
• Definition
  • Three fields - CC, BP, MF
• Score
  • Robustness
  • Density
  • Bootstrap
  • GO term mappings
    • Use highest as term name
• Mapped Gene List

Summary View

The summary has two main blocks:

• Visualization
• Summary Table

Visualization

Visualization should be similar to the one in the Cytoscape session file distributed with the original paper. To achieve it, the renderer needs Google Map-like zoom-in/zoom out function.

• Visualization should be user selectable.
  • D3.js view - term to root
  • cytoscape.js view
  • Sigma.js View - example
    • This library already implements "smarter" zooming.
  • ? (extra renderes will be added later)

Summary Table

• Protein Association table should include more information
  • Taken from
• Add links to the mapped GO terms