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.
Table of contents
After installation, you can find the KEGG access in the File -> New menu.
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:
- by text search (left image) or
- by browsing organisms (right image)
The found reactions are listed on the right side. From there, add desired reactions 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.
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.
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.
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.
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.
- BioCyc Database Plug-In
- Reaction Equations Plug-In
- Kyoto Encyclopedia of Genes and Genomes
- KEGG licensing information