Inquiry on KEGG to SBML/SBGN Conversion and Boolean Modeling Workflows

[Muhammad Kabir]

Dear Members of the SBML Community,

I hope you are doing well.

I am currently working on constructing Boolean network models for pathway simulation (e.g., knock-in/knock-out analysis) using BoolNet. My goal is to derive these models from curated pathway resources.

More specifically, I am now focusing on pathways from the KEGG database (for example tyrosine_metabolism pathway at https://www.kegg.jp/pathway/map00350) and would like to convert KEGG pathway representations (KGML format) into either SBML (preferably SBML-qual) or SBGN formats, which are more suitable for downstream logical modeling.

I previously explored using KEGGtranslator for KGML to SBML/SBGN conversion; however, it appears to be outdated and no longer reliably supported. As a result, I am currently facing challenges in establishing a robust and reproducible workflow.

I would greatly appreciate your guidance on the following:

• Are there currently maintained tools or pipelines for converting KEGG KGML files into SBML (especially SBML-qual) or SBGN formats?

• Are there recommended best practices for transforming KEGG pathways into Boolean or logical models?

• Is there an alternative workflow (e.g., via BioPAX, Cytoscape, or other intermediate formats) that you would suggest for this purpose?

My overall aim is to establish a pipeline such as:

KGML (KEGG) → SBML/SBGN → Boolean network → simulation in BoolNet

If anyone has experience with a similar workflow or can recommend updated tools or strategies, I would be very grateful for your insights.

Thank you very much for your time and support.

Kind regards,
Muhammad Kabir