Graph search - Revision history

Stan.lo@dote.ru at 08:16, 19 June 2013

2013-06-19T08:16:46Z

Stan.lo@dote.ru at 07:50, 19 June 2013

2013-06-19T07:50:59Z

Stan.lo@dote.ru at 07:50, 19 June 2013

2013-06-19T07:50:24Z

Stan.lo@dote.ru at 07:47, 19 June 2013

2013-06-19T07:47:00Z

Lan@dote.ru: /* See also */

2013-06-19T07:17:47Z

‎See also

Stan.lo@dote.ru at 06:17, 19 June 2013

2013-06-19T06:17:48Z

Stan.lo@dote.ru: from GX manual

2013-06-18T11:57:12Z

from GX manual

New page

The graph search finds pathway components interacting with the selected graph element. This search option allows the user to extend diagrams, e.g. to add interactions around the molecules in focus. Whenever a diagram is opened in the [[document pane]] different features of the graph search can be used to add elements (genes or proteins or reactions) to a diagram.
[[File:Graph_search_viewpart.png|thumb]]

The '''graph search''' tab can be found in the [[viewpart|viewparts area]]. It contains the element pane (right) and the search parameters dialog (left). The grey fields of the dialog cannot be edited. The user has options to change the '''direction''' of search (upstream of the molecule in focus, or downstream, or both directions), the number of steps ('''depth''') and also specify search engines associated with the target databases in the drop-down menus.

To run a graph search the following steps are recommended:

* [[Repository_pane#Handling files|Open]] a diagram in the [[document pane]].
* Click on the graph element (gene or protein or reaction) for which you want to perform the search - the node will fade encompassed by a dotted rectangle and the [[Information_box#Property inspector|property inspector]] will display its description.
* Click on the icon [[File:Add_element_icon.png]] to add the element to the elements pane.
* As per your requirements you can change the direction, depth, and the target databases in the search parameters dialog. By default the tool sets the search for the database from which the element originates.
* Press [[File:Search_icon.png]] to start the search. Once the search is finished you the search results will be displayed in tabular form in the elements pane.
* Items selected from the results can be added to the current diagram by pressing the [[File:Add2docpane_icon.png]] icon. The user can decide which terms to add to the diagram by clicking the ‘Add’ box near the search elements.
* You can also add the search results to a new diagram by pressing [[File:Add2newdia_icon.png]] icon.

==See also==
*[[Search tools]]
*[[Diagram document]]
*[[BioUML_user_interface]]

@@ Line 13: / Line 13: @@
 # Press [[File:Search_icon.png]] to start the search. Once the search is finished, the search results will be displayed in tabular form in the elements pane.
 # Items selected from the results can be added to the current diagram by pressing the  [[File:Add2docpane_icon.png]] icon. The user can decide which terms to add to the diagram by (un)checking the ‘Add’ boxes next to the search elements.
-# You can also add the search results to a new diagram by pressing [[File:Add2newdia_icon.png]] icon.
+# You can also add the search results to a new diagram by pressing the[[File:Add2newdia_icon.png]] icon.
 ==See also==

@@ Line 12: / Line 12: @@
 # As per your requirements you can change the direction, depth, and the target databases in the search parameters dialog. By default the tool sets the search for the database from which the element originates.
 # Press [[File:Search_icon.png]] to start the search. Once the search is finished, the search results will be displayed in tabular form in the elements pane.
-# Items selected from the results can be added to the current diagram by pressing the  [[File:Add2docpane_icon.png]] icon. The user can decide which terms to add to the diagram by clicking the ‘Add’ box near the search elements.
+# Items selected from the results can be added to the current diagram by pressing the  [[File:Add2docpane_icon.png]] icon. The user can decide which terms to add to the diagram by (un)checking the ‘Add’ boxes next to the search elements.
 # You can also add the search results to a new diagram by pressing [[File:Add2newdia_icon.png]] icon.

← Older revision		Revision as of 06:17, 19 June 2013
Line 3:		Line 3:

	The '''graph search''' tab can be found in the [[viewpart\|viewparts area]]. It contains the element pane (right) and the search parameters dialog (left). The grey fields of the dialog cannot be edited. The user has options to change the '''direction''' of search (upstream of the molecule in focus, or downstream, or both directions), the number of steps ('''depth''') and also specify search engines associated with the target databases in the drop-down menus.		The '''graph search''' tab can be found in the [[viewpart\|viewparts area]]. It contains the element pane (right) and the search parameters dialog (left). The grey fields of the dialog cannot be edited. The user has options to change the '''direction''' of search (upstream of the molecule in focus, or downstream, or both directions), the number of steps ('''depth''') and also specify search engines associated with the target databases in the drop-down menus.
		+	[[File:Graph_search_steps.png\|thumb\|Basic steps to run a graph search]]

	To run a graph search the following steps are recommended:		To run a graph search the following steps are recommended:

@@ Line 17: / Line 17: @@
 ==See also==
 *[[Search tools]]
 *[[Diagram document]]
 *[[BioUML user interface]]

@@ Line 7: / Line 7: @@
 To run a graph search the following steps are recommended:
-* [[Repository_pane#Handling files|Open]] a diagram in the [[document pane]].
+# [[Repository_pane#Handling files|Open]] a diagram in the [[document pane]].
-* Click on the graph element (gene or protein or reaction) for which you want to perform the search - the node will fade encompassed by a dotted rectangle and the [[Information_box#Property inspector|property inspector]] will display its description.
+# Click on the graph element (gene or protein or reaction) for which you want to perform the search - the node will fade encompassed by a dotted rectangle and the [[Information_box#Property inspector|property inspector]] will display its description.
-* Click on the icon [[File:Add_element_icon.png]] to add the element to the elements pane.
+# Click on the icon [[File:Add_element_icon.png]] to add the element to the elements pane.
-* As per your requirements you can change the direction, depth, and the target databases in the search parameters dialog. By default the tool sets the search for the database from which the element originates.
+# As per your requirements you can change the direction, depth, and the target databases in the search parameters dialog. By default the tool sets the search for the database from which the element originates.
-* Press [[File:Search_icon.png]] to start the search. Once the search is finished you the search results will be displayed in tabular form in the elements pane.
+# Press [[File:Search_icon.png]] to start the search. Once the search is finished, the search results will be displayed in tabular form in the elements pane.
-* Items selected from the results can be added to the current diagram by pressing the  [[File:Add2docpane_icon.png]] icon. The user can decide which terms to add to the diagram by clicking the ‘Add’ box near the search elements.
+# Items selected from the results can be added to the current diagram by pressing the  [[File:Add2docpane_icon.png]] icon. The user can decide which terms to add to the diagram by clicking the ‘Add’ box near the search elements.
-* You can also add the search results to a new diagram by pressing [[File:Add2newdia_icon.png]] icon.
+# You can also add the search results to a new diagram by pressing [[File:Add2newdia_icon.png]] icon.
 ==See also==