Graph search

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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.

Graph search viewpart.png

The graph search tab can be found in the 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.

Basic steps to run a graph search

To run a graph search the following steps are recommended:

  1. Open a diagram in the document pane.
  2. 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 property inspector will display its description.
  3. Click on the icon Add element icon.png to add the element to the elements pane.
  4. 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.
  5. Press 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.
  6. Items selected from the results can be added to the current diagram by pressing the 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.
  7. You can also add the search results to a new diagram by pressing theAdd2newdia icon.png icon.

See also

Personal tools

BioUML platform
Analysis & Workflows
Collaborative research
Virtual biology