6.3 Database Search

6.3 Database Search

This section introduce you to the database search procedures. You can perform a database search to locate any type of objects stored in the database. In general, the software supports two types of searches:

  • Context search

  • Search by attributes



6.3.1 Context Search


The context index provides the retrieval of sets of objects that have attributes containing the specified query phrase (string) partially or completely. The text fields are broken into words according to a conventional manner. The quick context search is optimized for speed of retrieval.
Fig.6.3.1 Search database by string values.
Fig.6.3.1 Search database by string values.


The Context Search icon is located at the top of the Project Pane. See Figure 6.3.1
To call a context search:

  • Click Context Search Icon;

  • The Find dialog box appears;

  • Choose a type of node for selection; it may be CellObject, CellProcess,Protein and others;

  • Enter the text. Click OK;

  • The search result appears in the Search Result List Pane;


Fig.6.3.2 Search database by string values.
Fig.6.3.2 Search database by string values.


The search results are displayed in a separate Search Result List Pane and can be added to a pathway (or a group) by Copy and paste or a drag and drop operation.

6.3.2 Search by Attributes


The search by attributes allows you to search database objects using many types of data as search conditions. These include, for example, node type, effect (positive, negative, unknown), mechanism (transcription, phosphorylation), tissue type, description/userdefined attributes text, and so forth.

Fig.6.3.3 Search database by property values.
Fig.6.3.3 Search database by property values.


The Property Search icon is located at the top of the Project Pane. See Figure 6.3.3
To call a property search:

  • Click Property Search Icon;

  • The Find dialog box appears;

  • Choose where you want to make a search: on the Table Query Interface or on the Advanced Tree Interface;

  • Choose where you want to make a search: in the entire Workspace or in the active pathway only;

  • Choose a type of node for selection; it may be CellObject, CellProcess, Protein and others;

  • Select an attribute type in the Attribute field or in the Attribute Tree;

  • Select an operation type in the Operation field, it may be equals, not equal, includes, and starts with.

  • Specify value in the Value field. Some attributes contain dictionary values. For such attributes the software will display the list of the dictionary terms. For all other attributes, you must to type in the value. For example, if you choose CellObject in the Attribute field, you can see in the Value field the names the allowed names of cell objects such as chloroplast, liposome, DNA, and others.

  • Select the type to combine search parameters in the Logic field.

  • The query creation is complete;

  • To add the query in the Query list press the Add button. On the Tree interface conditions are added automatically to your query list ;

  • Click OK to run the query;


Fig.6.3.4 Search database by property values through Table Query Interface.
Fig.6.3.4 Search database by property values.


Fig.6.3.5 Search by Attribute and Node type window.
Fig.6.3.5 Search by Attribute and Node types through Advanced Tree Interface.


The search results are displayed in a separate Search Result List Pane and can be added to a pathway or a group by Copy and paste or a drag and drop operation.

6.3.3 Quick Search

You can perform a quick search for any object type stored in the Workspace. In the Quick Search window, you can set the search text and press the Start Quick Search button to start the Quick Search algorithm. All objects found will be placed in the separate list in the Search Result List Pane. You can save the search results as a individual group in the Groups folder, or as a search in the Searches folder (by default).


The Quick Search box is located at the top of the Project Pane. See Figure 6.3.6

Fig. 6.3.6 Quick search field.
Fig. 6.3.6 Quick search field.

Type your favorite gene name or keywords to search for all available information about it presented in our database.

Your search results will be listed in the Search Result List Pane. See Figure 6.3.7

Fig.6.3.7 Search Result List Pane: quick search results.
Fig.6.3.7 Search Result List Pane: quick search results.



6.3.4 Querying database to explore gene relationships

You can drag and drop rows from the Search Result List Pane to your active pathway, or Build a Pathway from selected group of bioentities by right clicking on the chosen group of bioentities. See Figure 6.3.8

Fig.6.3.8 Search Result List Pane context menu.
Fig.6.3.8 Search Result List Pane context menu.

Choosing Build Pathway opens PathwayWizard Panel. See Figure 6.3.9

Check starting entities for your pathway, See Figure 6.3.10

Choose an algorithm for pathway building, See Figure 6.3.10

Fig.6.3.9 Build Pathway Wizard Window.
Fig.6.3.9 Build Pathway Wizard Window.

Pathway Wizard

PathwayWizard allows you to create pathways, using molecular interaction data from the database. It starts by suggesting several ways to determine starting entities, and then opens the Build Pathway dialog box. See Figure 6.3.10

Fig.6.3.10 Build Pathway Wizard Window.
Fig.6.3.10 Build Pathway Wizard Window.

Check the Filter option and set up the filter, if needed, See Figure 6.3.11.see (3)
Refer to the User Manual to learn more about the BuildPathway Wizard

Fig.6.3.11 Build Pathway Filters Wizard.
Fig.6.3.11 Build Pathway Filters Wizard.

Apply advanced attributes search to specify any logical combination of searched bioentities and bioprocesses properties. See Figure 6.3.12

Fig.6.3.12 Search by Attribute and Node type window.
Fig.6.3.12 Search by Attribute and Node type window.

Press the Start button to start data mining, and then click OK when done (4). The new pathway diagram appears in the Pathway Pane.