I want to run simulations of various metabolic pathways – the project could end up becoming quite large, and having a machine readable chart would make thing a lot easier. Does anyone know if there is a machine readable file of Dr. Gerhard Michal's famous metabolic pathways chart?
Roche's Biochemical Pathways works as a big png image and just put labels on the map. But you could try to extract data using queries like http://biochemical-pathways.com/pol/fts/query?query=Glutarate It seems to be legal as it's not prohibited.
Escher is a good pathway visualization tool where you can save map in JSON or SVG.
Another choice is VMH (Virtual Metabolic Human) - the virtual metabolic human database provides literature-derived information on human metabolism, gut microbial metabolism, nutrition, and diseases.
Reactome has two layer map - first layer is biological interactions, second layer is pathways.