Table 1.
Outline of solutions employed by the iRefScape plug-in
| Challenge/Need | Solution | See: |
|---|---|---|
| Data content and delivery | ||
| Multiple source databases with redundant and non-homogenous data. | Consolidation and normalization of data. | 1.1 |
| Need to retrieve a large dataset for subsequent visualization and filtering. Need for a private and static data set. | Operate on a local data set. Use of file system and collision-proof identifiers for storage and retrieval of meta-data. |
1.2 |
| Search | ||
| Need to support searching on multiple accession systems for proteins. | Use of universal ROGIDs and RIGIDs. | 2.1 |
| Differential choice of splice isoforms when curating interaction data. | Use of canonical expansion during search. | 2.2 |
| First order neighbours do not accurately reflect the neighbourhood of a protein. | Use of neighbourhood completion for query results. | 2.3 |
| Visualization | ||
| Need to track search result provenance. | Use of features and colour to indicate result level. Use of "Grid" layout for initial results. | 3.1 |
| Need to visualize all evidence supporting a given interaction. | Use of a multigraph representation | 3.2 |
| Need to distinguish between binary and n-ary interaction data. | Use of bipartite model to visualize n-ary data. | 3.3 |
| Need to view/filter search results on multiple node and edge attributes. | Distribution of rich and normalized attribute set. Advanced filter function. Dedicated "between-nodes" search. |
3.4 |
| Data discovery and navigation | ||
| Need to identify potential spoke-represented complexes. | Dedicated search tool. | 4.1 |
| Need to search on groups of genes related to a disease. | Dedicated disease-group search. | 4.2 |
| Need to explore connection between two groups of genes. | Use of synchronized adjacency-matrix viewer. | 4.3 |
| Need for interoperability with other plug-ins. | Export functionality. | 4.4 |
| Need for user to navigate a complex interface. | Use of wiki-documentation, in-line help and macros. | 4.5 |