Generation of systems biology models from KEGG pathways. The flowchart shows all major steps involved in the creation of initial systems biology models from KEGG pathways. The whole method requires two sources: a KGML-formatted KEGG pathway and access to other KEGG databases, e.g., via the KEGG API. The preprocessing steps, depicted on the top, involve mainly the removal of inappropriate nodes and processing of reactions. An important step is the removal of duplicate entries. However, some further steps require information about these duplicates (e.g., when using the layout extension package for SBML) and thus, it is not always part of the preprocessing and may be performed at a later stage. Depending on the desired output format, separate processing steps are executed that involve appropriate conversion and annotation of the initial model.