KEGG Database Plug-In

The KEGG Database Plug-In allows to search for organisms, pathways, enzymes and reactions in the KEGG databases and to load them as networks into Omix.

Using the Plug-In

After installation, you can find the KEGG access in the File -> New menu.

File menu containing access to KEGG
File menu containing access to KEGG

After choosing this option, the following dialog appears where you can search in the KEGG databases:

Screenshot of the KEGG browser

There are basically two ways to search for reactions in the database:
  1. by text search (left image) or
  2. by browsing organisms (right image)
Select the tab "Find Reactions". A text area appears where you can enter arbitrary content. Each line represents an expression that is searched for in the database. You can for instance search for reactions by name or enter a list of KEGG reaction identifiers. By changing the searched database to "Enzymes" you can also search for EC numbers.
The found reactions are listed on the right side. From there, add desired reactions to the list of selected reactions.

1.1.2. Browsing Organism

You can search for pathways in a specific organism on the "Browse Organisms" tab. Here, the first list contains all organisms provided by the KEGG databases. Select on of them in order to list the organisms metabolic pathways. Double click on a pathway lists all reactions in the right field. From here, you can select the desired reactions to be loaded. Alternatively, you can add an entire pathway to the list of selected reactions.

The bottom section shows all reaction selected to be downloaded from KEGG.
Many reactions provide a number of alternative names which you can select for each individual reaction in the bottom selection list. Likewise, you can specify, to which pathway the reaction shall belong in Omix.

Selecting reaction name
Selecting reaction name

After collecting an arbitrary number of reactions, the network can be finally assembled. You are asked how the reactions shall be named, if layout information shall be downloaded and if pathways shall be arranged in groups (see image below). Thereafter, the plug-in connects the database in order to download all necessary information about the reactions and reactants. This process can take several minutes. Finally, the network is loaded as new document in Omix.

Import settings
Import settings

After loading the network usually not all reactions and metabolites are drawn on the drawing area. Some elements might be just listed in the component view (highlighted red) because, positioning information is not available in KEGG or not chosen to be included. You can place the individual items on the drawing area by drag and drop, you can use the layout pattern and motif stamp feature of Omix (see User Manual) and/or you can use the AutoLayout Plug-In in order to arrange the network on the drawing area.

Network diagram imported from KEGG
Network diagram imported from KEGG

It is highly recommended not to load too many reactions in one step but to begin with a small selection (e.g. one pathway), finishing the diagram layout and then import further sets of reactions into the document.

1.2. Importing into other Documents

Instead of loading KEGG database content into new Omix documents as described, you can also choose to import content into existing documents. Therefore, choose the menu entry File -> Import... -> Import Network from KEGG.

1.3. Cache

By default, all content downloaded from the KEGG databases will be cached in your local user directory. This makes later access to the same data much faster. In the configuration window of Omix, you can enable/disable caching and specify how often the cache shall be updated (go to menu Extra -> Configure; on OS X go to menu Omix -> Preferences).

Configuring KEGG plug-in
Configuring KEGG plug-in

1.4. Chemical Structures and Atom Mappings

In case that the Chemical Structure Plug-In is installed in Omix, the KEGG Database Plug-In offers the option to import a network including the chemical structures available in the databases.
If the Atomic Layer Plug-In is installed, the KEGG plug-in can also download atom mappings for most of the reactions. Both options are provided for choice after collecting the list of reactions.

1.5. Further reading