RegulonDB v12.0.0

RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of E.coli K-12, including data from both classical molecular biology and high throughput methodologies. Here we describe biological and computational advances for each of the major concepts of transcriptional regulation. These fundamental concepts were initially defined in the second half of last century. Since then, there have been huge advances describing regulatory mechanisms that do not fit with the original definitions, motivating some of us with a group of experts to update definitions that capture current knowledge of transcriptional regulation. These are used here as the reference to describe the historical progress in RegulonDB, its conceptual key changes, together with its current content overview. We also present a full reconstruction of RegulonDB computational infrastructure, significantly improving data storage, retrieval, and accessibility supporting a more intuitive and user-friendly experience. The integration of graphical tools provides clear visual representations of genetic regulation data, facilitating data interpretation and knowledge integration. In supplementary material we summarize the major additions to the biological content since our last NAR paper. RegulonDB can be accessed at: https://regulondb.ccg.unam.mx.