KEGGtranslator

KEGGtranslator converts and visualizes KEGG KGML-formatted pathway XML files into multiple output formats to support pathway analysis, metabolic and nonmetabolic network modeling, and integration with computational biology tools.

Key Features:

• Multi-Format Conversion: Converts KGML-formatted XML files into a wide array of output formats for integration with various bioinformatics software.
• Visualization: Renders KEGG PATHWAY KGML pathway maps showing genes, reactions, and their interrelations.
• Augmentation of Information: Adds annotations such as MIRIAM identifiers to extend the information encoded in KGML files.
• Amendment of Fragmentary Reactions: Identifies and amends incomplete reactions by adding missing components to enable more accurate simulations and analyses.
• KGML Parsing: Parses KGML-formatted XML from the KEGG PATHWAY database to extract pathway entities and relations.

Scientific Applications:

• Metabolic network modeling: Provides converted and annotated KEGG pathway data for construction and analysis of metabolic network models.
• Simulation studies: Supplies amended and annotated reaction information to support accurate dynamic and stoichiometric simulations.
• Integration with computational biology tools: Enables interoperability with other computational biology software via multiple output formats and MIRIAM annotations.

Methodology:

Parses KGML-formatted XML files from the KEGG PATHWAY database, visualizes pathway maps, converts them into various output formats, augments translations with annotations such as MIRIAM, and amends incomplete reactions.