Max-Planck-Institut für Informatik
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User manual, GOTaxExplorer, Version 1.0

Graphical User Interface (GUI)


The workplace

The workplace contains the query and the result frames. All frames can be hidden and made visible with options in the menu. All buttons and fields provide a tooltip that specifies their function.


The query frame

The query frame provides facilities to build a query and to submit it. The query can either be entered manually into the query field on top or build with the buttons provided. The query field serves also as query history and contains all former queries in a drop-down list.

Figure 6: The query frame. This frame contains facilities to incrementally build a query.

The query building facilities are divided into three parts. The results can be selected with the drop-down list and added to the query with the "Add result" button. The part to build the condition contains entity and operator selectors. An entity is specified with its database and the accession number. "DGO", "DPFAM" and "DSMART" specify that the direct mapping from the "pfam2go" or "smart2go" files are used to compute the results. The accession number can be inserted in the text field next to the database drop-down list and "Add entity" adds the entity to the query. "Add operator" adds the selected operator to the query. After either the "SIM" or the "FUNSIM" operator are entered, the selection buttons can be used to build the second query. GO results can be limited to an ontology or to specific evidence codes. It is also possible to exclude the selected ontology of the evidence codes. To this end, it is necessary to press the corresponding "exclude" button and to add the limits to the query. The tree view on the right allows to browse an ontology or the taxonomy for an entity. The menu can be used to select the tree to be displayed. A tooltip with the accession number is displayed after hovering the node with the mouse. Right-clicking a node opens a pop-up menu that allows access to the online databases.

The "search" button at the bottom submits the query and the "clear" button deletes the query and resets the query frame.


The SQL query frame

The SQL query frame is shown after entering the SQL mode through the menu. It contains a text area for entering a query. An arbitrary SQL query can be entered in this field. A button for submitting the query and a button for clearing the field are to the right of the text field. The results of SQL queries are also presented in a table in the results frame.

Figure 7: Frame for entering a SQL query.

The results frame

The results frame contains a tab for each query result. The query that returned the result is displayed in a tooltip after hovering over the tab. The results are formatted in tables that can be sorted by clicking on the header of the column. Holding the "Ctrl" key and clicking a column header specifies a secondary sorting which preserves the first order. The sorting is sustained if results are saved to text files. By right-clicking a row, a pop-up menu appears that allows to open a browser with the entry of the online database. If the results are from GO or the taxonomy and the 3D view is active, it is possible to center the corresponding node in the graph with an option in the pop-up menu. We also provide the possibility to search the tree representation for the results. The pop-up menu contains an option to search for the next occurrence of a node in the tree. This permits to find all occurrences of a node in the tree.

Figure 8: The results frame contains all query results in tabs.

The name search frame

The name search frame allows to search the database with the name of an entity. The search keyword can be entered into the text field on top. The domain to be searched is selected with a drop-down list below the text field. The query is submitted with the "Search" button and the results are shown in the result area at the bottom. A double-click on a row of the results table inserts the entity into the condition of the current query.

Figure 9: The name search frame provides the possibility to search for an entity with a part of its name.