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.RegulonDB是收录大肠杆菌（Escherichia coli, E. coli）K-12转录起始调控领域最全面知识的数据库，涵盖经典分子生物学与高通量实验技术产生的相关数据。本文详述了转录调控各核心概念的生物学与计算学研究进展。这些基础概念最初于上世纪下半叶被提出并定义。此后，大量不符合原始定义的转录调控机制被陆续揭示，促使我们联合一众领域专家对原有定义进行更新，以涵盖当前转录调控领域的最新认知。本次更新后的定义将作为参照标准，用于阐述RegulonDB的发展历程、核心概念的关键演变以及当前数据内容概览。本研究同时完成了RegulonDB计算基础设施的全面重构，大幅优化了数据存储、检索与可访问性，为用户带来更直观、易用的使用体验。图形化工具的整合实现了遗传调控数据的清晰可视化，有效助力数据解读与知识整合。在补充材料中，我们总结了自上一篇发表于《核酸研究（Nucleic Acids Research, NAR）》的论文以来，RegulonDB在生物学内容上的主要更新。用户可通过以下网址访问RegulonDB：https://regulondb.ccg.unam.mx。