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Database Components
Pathways databases can be accessed in the left panel of main Cellware user interface. In the Database tab pane, there are two visual components: a database tree panel and a description panel.
Figure 5-1: Database Browser
To access KEGG, click ‘Databases’ tab in left panel (See Figure 5-1). Under the root node “Databases’, ‘KEGG’ node appears. Double-click to expend the node. It will take several seconds to download the data. Once the data have been downloaded, it will be cached permanently for future access.
The KEGG pathways database is organized as a tree rooted from source of database server to its contents. There are 6 types of nodes in the tree and they are described in following sections.
5.1.1 Database node
A database node represents a data server. Currently KEGG is connected and the database node appears as “KEGG” under the root of database tree. The available organisms listed in KEGG are child nodes.
5.1.2 Organism node 
A organism node represents a top level pathway group belongs to the organism. Selecting a organism node shows related information such as name, data source, and releasing date as well. Currently 213 organism nodes are available. Pathways associated with each organism are listed as child nodes.
5.1.3 Pathways node 
A pathway node represents a biochemical pathway containing related chemical reactions appeared as a child node.
5.1.4 Reaction node 
A reaction node represents a reaction, which is composed of reactants, products and enzymes. Description panel shows stoichiometric equations indicating reversibility by “<=>” and irreversible by “–>”. A reaction importing from database will be intelligently transformed into Cellware model.
5.1.5 Compound node 
Reactants and products of reactions are represented as compound nodes under a reaction node. Names, molecular formula and molecular mass will be shown in the description panel.
5.1.6 Enzyme node 
An enzyme node is under the reaction node. Annotation of an enzyme includes reference lists, comments and various names.
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