The Natural Products Atlas 2.0: a database of microbially-derived natural products.

Jeffrey A Van Santen,Roger G Linington,Jeffrey D Rudolf,David P Fewer,Caitlin A Mccadden,Sylvia Soldatou,Alison H Hughes,Trevor N Clark,Jonathan Parra,Emily Mcmann,Katherine R Duncan,Claire H Fergusson,Ella F Poynton,Tyler A Alsup,Elisabeth M-L Janssen,Dasha Iskakova

doi:10.1093/nar/gkab941

Abstract

Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.

Highlights

Despite growing efforts to catalogue the known global secondary metabolome (e.g. COCONUT [1], LOTUS [2]), inconsistent dereplication methodologies and high rates of rediscovery still plague natural products discovery programs. [3]
The Natural Products Atlas aims to address these issues by collating a standardized database of all known microbial natural product structures, source organisms and citations
The original publication in 2019 describing the Natural Products Atlas contained 24 594 compounds and included a web interface for manual exploration of the data [8]. In this new release we have increased the size of the database to 32 552 compounds, created a new application programming interface (API) infrastructure and website to permit automated database queries, incorporated biosynthetic and small molecule ontology terms, and added full taxonomic descriptions of all source organisms, permitting filtering of the database at any taxonomic rank

Summary

Introduction

Despite growing efforts to catalogue the known global secondary metabolome (e.g. COCONUT [1], LOTUS [2]), inconsistent dereplication methodologies and high rates of rediscovery still plague natural products discovery programs. [3]. The Natural Products Atlas aims to address these issues by collating a standardized database of all known microbial natural product structures, source organisms and citations This resource provides new discovery tools for the natural products community, including a user-friendly open-access platform for compound dereplication, and a standardized dataset of microbial natural product structures for new tool development. The original publication in 2019 describing the Natural Products Atlas contained 24 594 compounds and included a web interface for manual exploration of the data [8] In this new release we have increased the size of the database to 32 552 compounds, created a new API infrastructure and website to permit automated database queries, incorporated biosynthetic and small molecule ontology terms, and added full taxonomic descriptions of all source organisms, permitting filtering of the database at any taxonomic rank. Together these advancements significantly improve the coverage, accuracy, and utility of this open access resource

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Conclusion