Unfortunately, the KGML-formatted pathways are primarily designed for visualization purposes and not directly usable as metabolic or signaling models.
This map was assembled in CellDesigner, a free process diagram editor for gene-regulatory and biochemical networks http://celldesigner.org/; it was then web-published using BioPP, a software suite which converts CellDesigner-SBML formatted pathways into a web-viewable format [ 16].
SBML is a major standard format for pathway representation and interchange, and its use assures compatibility with a large ecosystem of existing pathway curation tools and resources.
This sets it apart from existing exchange formats for pathways.
For this format of pathway data, the biochemical reactions were converted into binary interaction Simple Interaction Format (SIF).
BCML is our proposal to overcome this lack of flexibility in the current available data formats for pathways.
As a drawback, KGML-formatted KEGG pathways are primarily designed for visualization purposes and often omit important details for the sake of a clear arrangement of its entries.
Alternatively, data models can be defined using an ontology language, as exemplified by the BioMoby Object Ontology defining XML exchange formats within the BioMoby framework (Wilkinson et al., 2008), and the BioPAX exchange format for pathway data (Demir et al., 2010).
This format supports metabolic pathways, signaling pathways (including states of molecules and generic molecules), gene regulatory networks, molecular interactions and genetic interactions.
There are three main steps to run MESSI as follows: Two input formats, KEGG pathway names and KEGG compound IDs, are acceptable in MESSI.
