Building the KOMODO media database

Abstract

This protocol describes the process used to convert >1300 microbial media recipes, listed on the website of the Leibniz Institute DSMZ \(see: https://www.dsmz.de/?id=441), into a machine readable format, and then to read them into a SQL database. In the process, we combine compounds with degenerate names and include concentrations of all compounds in standard units. The protocol includes steps for error-checking, as well as a process to recursively add media when they cross-reference each other. The protocol might be useful in other, similar database building tasks, and especially might help in efforts to incorporate other microbial media recipes from literature into this or another database.