6. Data Management
The software database provides storage and organization functions for proteins, small molecules, cell processes, events of regulation, chemical reactions, and other objects used in studies of molecular networks and pathway analysis.

6.1 Pathway Representation

The pathway concept is central in the design of the system. The program stores pathway as a diagram with groups, annotations, and user settings.

The pathway stores not only the list of all proteins, small molecules, and cellular processes, but also, the links and relationships between them. Graphically, each pathway is shown in a separate window and serves the purpose of organizing the data and saving results of searches in underlying database. Pathways can be saved to the database, and the list of existing pathways is displayed in the Folder Pane.

Pathways can be exported as separate XML files, exchanged between researchers for collaboration purposes and reimported back into the database.

To create the new pathway:

  • Choose File>New >Project from the Main Menu;

  • The Pathway named New Pathway appears in the Pathways folder;

  • Rename the new pathway by typing the new name in the folder box.



To remove the pathway from the Workspace:

  • Select the pathway of interest;

  • Choose Delete from the context menu;

  • Press Yes.