Requirments

UX Requirments

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? - should be selectable

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 other gene association files
• Add links to the mapped GO terms

Backend DB Requirements

NeXO DAG and other network data sets will be stored in Neo4j graph database. Access to the database will be done through Rexter RESTful API.

The graph database should have the following indices:

• Term ID (NeXO:([0-9]+))
• Name generated from aligned GO terms
• Definition (description from GO)
• Assigned genes
  • ORF names
  • "Biologists-friendly" gene names
• Scores
  • Score for each GO category
  • Robustness
  • Bootstrap

Graphs

NeXO data should be stored in the following form

• Tree
• Filtered DAG
• Original DAG