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DiscoverySpace Databank Primer

The Databank is the central file and tool management interface within DiscoverySpace 4. The Databank allows the user to create, modify and delete queries, datasets, comparisons and other definitions. The Databank also allows the user to analyze those definitions using DS4's inbuild tools. It is vital that new users acquaint themselves with this important tool.

The DiscoverySpace 4 Databank

Definition of Terms

The Databank allows the user to create, modify and delete definitions. Definitions are the collective term for user-defined objects within DiscoverySpace. A definition has a datatype which describes the kind of definition it is; for example a Query definition, a Comparison definition, a Template definition, etc. A definition may also have a class, which describes the class of resource that the definition contains; for example a set of Tag Sequences. The Databank also has a toolbar which displays the actions available to the user. Some actions can be executed as stand-alone actions and some are executed on the selected definitions.

Contents of the Databank

The Databank user interface displays the table of definitions that the user has available. Each definition has associated descriptive information such as a name, description, annotation, etc. The actions in the Databank toolbar become enabled and disabled based upon the status of the currently selected definitions. Some actions are always enabled, even without a current selection; for example, "New Query" or "New Data". Some actions such "Save" and "Save All" are enabled when definitions are created or modified. Some are enabled for a given class of Data or Query definition; for example, Venn Table is enabled only for sets of Tag Sequence. Figures 1a-1c (below) illustrate how actions are enabled and disabled based upon the selection.
Screenshot of databank - Taxon selected
Figure 1a) A detail from the Databank window. In the toolbar at the top of the Databank you will notice that the many of the icons are disabled (greyed out). The Databank only enables the actions available for the currently selected definition. In this image the user has selected the definition "Taxons of all GSC SAGE Libraries". This is a Query definition containing resources of class NCBI Taxonomy - this can be determined by the "Class" and the "Type" columns. Because this definition is a Query one can see that the Exploror icon is enabled.
Screenshot of databank - Comparison selected
Figure 1b) A detail from the Databank. In this image the user has changed the selected definition to "SHS04 vs S1881", a Comparison of Tag Sequences. This is the type required for the Scatter Plot tool and one can see that the Scatter Plot action has been enabled. Because this definition is not a Query or Data definition one can see that the Explorer icon has been disabled.
Screenshot of databank - Tag Sequence selected
Figure 1c) A detail from the Databank. In this screenshot the user has selected definition 'SHS04 0.99' which is a Query of Tag Sequences. This is the type and class of definition required by the Venn Table tool. Notice that the Venn Table action and the Explorer action are now enabled.

Loading and Modifying Definitions

In addition to displaying the properties of a definition the Databank shows its modification and load status. This is displayed on the two left hand columns of the Databank table. A definition is loaded if its data has been loaded into memory. This is particularly useful for large datasets which take time to load. Also, the user can unload the data of a definition (using the "Unload Data" action) if she finds her memory is starting to get low. A definition is modified if the user has edited and altered the definition without saving it. The modified flag helps the user to keep track of unsaved changes that she has made.
Screenshot of databank - One modified, one loaded
Figure 2) A detail from the Databank. Notice that the Data definition "SHS05 vs SHS04 selected Tags" is presently marked as loaded, meaning that the data is loaded into memory. The user has made some changes to Query "SHS05 0.99" without saving those changes. This definition is marked as  modified.

Editing Definitions

Databank definitions can edited by opening the properties window; either by double-clicking a definition entry itself or by selecting a definition and clicking the 'Edit' action. Each definition has a "General" panel which allows the user to edit common information such as name, description, annotation, etc. Each definition will also have other panels to edit, and these will be specific to the type of definition. For example, the Query has a "Query" panel. Please be sure to keep the properties of each definition accurate and up-to-date as these are your main methods of organizing your definitions.
Screenshot of General panel of Definition
Figure 3) The Definition Properties window. This window is opened by double-clicking a definition from the Databank. Using this window the user can edit the name, description and annotate the definition. Accurate names and descriptions are vital to good organization within the databank. Please keep spend the time to make your names useful.

 

 

N. R. ROBERTSON 05 APR 2005

Page last modified Jun 08, 2010