Microbial natural product databases: moving forward in the multi-omics era

Covering: 2010-2020 The digital revolution is driving significant changes in how people store, distribute, and use information. With the advent of new technologies around linked data, machine learning and large-scale network inference, the natural products research field is beginning to embrace real-time sharing and large-scale analysis of digitized experimental data. Databases play a key role in this, as they allow systematic annotation and storage of data for both basic and advanced applications. The quality of the content, structure, and accessibility of these databases all contribute to their usefulness for the scientific community in practice. This review covers the development of databases relevant for microbial natural product discovery during the past decade (2010-2020), including repositories of chemical structures/properties, metabolomics, and genomic data (biosynthetic gene clusters). It provides an overview of the most important databases and their functionalities, highlights some early meta-analyses using such databases, and discusses basic principles to enable widespread interoperability between databases. Furthermore, it points out conceptual and practical challenges in the curation and usage of natural products databases. Finally, the review closes with a discussion of key action points required for the field moving forward, not only for database developers but for any scientist active in the field.

Automated summary

From 2010 to 2020, significant changes in storing, distributing, and using information have been driven by the digital revolution. The natural products research field is beginning to embrace real-time sharing and large-scale analysis of digitized experimental data with the help of new technologies. Databases play a key role in this and their interoperability and data quality remain as challenges for database developers and scientists.