On the Redundancy of Natural Products Public Databases and Where to Find Data in 2020 - A Review on Natural Products Databases

Abstract

Natural products (NPs) have been the centre of attention of the scientific community in the last decencies and the interest around them continues to grow incessantly. As a consequence, in the last 20 years, there was a rapid multiplication of various databases and collections as generalistic or thematic resources for NP information. In this review, we establish a complete overview of these resources, and the numbers are overwhelming: over 120 different NP databases and collections were published and re-used since 2000. 98 of them are still somehow accessible and only 50 are open access. The latter include not only databases but also big collections of NPs published as supplementary material in scientific publications and collections that were backed up in the ZINC database for commercially-available compounds. Some databases, even published relatively recently are already not accessible anymore, which leads to a dramatic loss of data on NPs. The data sources are presented in this manuscript, together with the comparison of the content of open ones. With this review, we also compiled the open-access natural compounds in one single dataset a COlleCtion of Open NatUral producTs (COCONUT), which is available on Zenodo and contains structures and sparse annotations for over 400000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date.

<strong></strong>LANaPD: Towards a Unified Latin America Natural Products Database

“…It is also available at ChemSpider and ZINC 15 [32] where it can be found, for instance, as a natural product catalog. NuBBEDB has been recently included the COCONUT database [22].…”

“…of the COCONUT database [22]. The second version of BIOFACQUIM is freely accessible at Fighsare [31] [38] and is part of the D-TOOLS initiative aimed to provide open databases and chemoinformatic resources [25].…”

“…It would be advisable that a research group would be in charge of this endeavor using publicly accessible tools and scripts or workflows available in public repositories [39,40]. COCONUT database (vide supra) is an example of a large-scale database assembled and curated from several different sources around the world [22].…”

“…One of the first reviews was published in 2012 [18] that included five NPs datasets (commercial and non-commercial with chemical structures available on the web). Recently, it was published the COlleCtion of Open NatUral producTs (COCONUT) database that collects over 120 databases collecting more than 400,000 non-redundant NPs and are freely accessible [22]. As part of the global efforts, different countries around the world are analyzing the information of NPs in their countries of origin.…”