Here's a working page for brainstorming improvements for NCI-OWL in Jambalaya.

• when changing the hierarchy, for example to Chemical_or_drug_FDA_Approved_For_Disease, we should warn users how long this might take. For example, precalculate statistics and inform them displaying this will take x seconds. Also, we should give an option to cancel the change and revert what we are doing. When I tried this, it took 5 minutes to fetch the data for the operation, and then (only then) did it show the dialog saying "there are 31,420 children of root" and allowing me to cancel. This is too late.
• I don't think showing all the nodes is a good idea when changing a hierarchy. Related to the first point, we should only show the first levels of the ontology , such as 3 layers. Then, we should use some sort of hint mechanism indicating where metrics are greatest. This is the SpaceTree approach.
• show me all overrides of property "X" - in the NCI ontology, there are high-level properties that exist between 'roles' eg. Gene_Kind and Protein_Kind, and those properties are then 'restricted' to redefine the values for the range of that property - the OWL construct "someValuesFrom". So I think it would be useful to show these overrides.
• We could add scripts that would do a lot of these things, but metrics should be easily accessible to the script. Perhaps a default variable like that a script could use in conditionals and loops.
• Central to these improvements is the notion of metrics, particularly pre-computed metrics. We need a way of storing these per node when the ontology is first loaded into the database, or running in the background with low priority, and then saving them to a file or database table. This calls for some thinking, perhaps integrating with the Protege team?