Introduction

NPBS (Natural Product & Biological Source) database is a biochemical data resource with relational data between natural products and biological sources, manually curated from literatures of natural products research. The relational data links a specific species and all the natural products derived from it, contrarily, links a specific natural product and all the biological sources.

Aims

Besides mining information from literatures, to make published data quickly accessible and to combine them logically for further applications, the main purpose or destination of this database is clarifying about the relationships between natural products and biological sources, since the relationships are intersecting. For example, the same natural product and its homologues can originate from various biological sources, adopters can have a wider choice on biological sources from their own concerns. On the other hand, integrated constituent information from a specific biological source, can inspire novel applications of the biological source, for example, adopters can use the natural product structures from a specific biological source for dereplication with experimental data (MS, NMR), to prevent re-isolation and re-characterization of already known molecules.

Data source

The data of NPBS is manually curated from literatures with a mining system. The literatures involved in this database are from publications of natural product deriving researches both domestic(Chinese) and international(English). See database Coverage.

A neural machine translation tool of chemical nomenclature has been used for Chinese compound names to English translation.(https://doi.org/10.1186/s13321-020-00457-0)

The structures of the molecules are generated by “name to structure module” of ACDLabs, ChemOffice and OPSIN, we use ChemDraw and Reaxys for drawing and searching the structures manually. RDKit has been applied in Python for molecular properties computing.

We update and expand NPBS according to the project schedule.

Last update: July.13.2020

Database features

NPBS database includes relational data, biological sources data and molecules data of natural products. The biological sources cover diverse species of plant, bacterial, fungal and marine organism, the natural molecules have proper chemical structure data and computable molecular properties, and all the relational data have corresponding references.

Data use

The data of NPBS can be used for noncommercial purposes under the condition of proper citation:

Xu, T., Chen, W., Zhou, J. et al.
NPBS database: a chemical data resource with relational data between natural products and biological sources. Database. 2020, baaa102.
https://doi.org/10.1093/database/baaa102