The LOTUS initiative for open knowledge management in natural products research

@article{Rutz2022TheLI,
  title={The LOTUS initiative for open knowledge management in natural products research},
  author={Adriano Rutz and Maria Sorokina and Jakub Galgonek and Daniel Mietchen and Egon L. Willighagen and Arnaud Gaudry and James G. Graham and Ralf Stephan and Roderic D. M. Page and Jiř{\'i} Vondr{\'a}{\vs}ek and Christoph Steinbeck and Guido F. Pauli and Jean‐Luc Wolfender and Jonathan Bisson and Pierre-Marie Allard},
  journal={eLife},
  year={2022},
  volume={11}
}
Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish… 

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SHOWING 1-10 OF 175 REFERENCES
The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
TLDR
The Natural Products Atlas is designed as a community-supported resource to provide a central repository for known natural product structures from microorganisms and is the first comprehensive, open access resource of this type.
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research
TLDR
There is a doubling of the number of annotated metabolite nodes in WikiPathways and an OpenAPI documentation of the authors' web services and the FAIR annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data.
The Natural Products Atlas 2.0: a database of microbially-derived natural products
TLDR
A new version of the database is reported 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.
Review on natural products databases: where to find data in 2020
TLDR
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 400,000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date.
MIBiG 2.0: a repository for biosynthetic gene clusters of known function
TLDR
MIBiG 2.0 is presented, which encompasses major updates to the schema, the data, and the online repository itself, and improves the user experience by adding new features such as query searches and a statistics page, and enabled direct link-outs to chemical structure databases.
Interoperable chemical structure search service
TLDR
This work presents a SPARQL service that augments existing semantic services by making interoperable substructure and similarity searches in small-molecule databases possible, and offers new possibilities for querying interoperable databases, and simplifies writing of heterogeneous queries that include chemical-structure search terms.
NuBBEDB: an updated database to uncover chemical and biological information from Brazilian biodiversity
TLDR
The latest advancements concerning the interface, content and functionality of the NuBBEDB are reported and a preliminary study on the current profile of the compounds present in Brazilian territory is presented.
WikiPathways: connecting communities
TLDR
The growth of WikiPathways over the last three years is shown, the new communities and collaborations of pathway authors and curators are highlighted, and various technologies to connect to external resources and initiatives are described.
SANCDB: a South African natural compound database
TLDR
SANCDB is currently the only web-based NP database in Africa and aims to provide a useful resource for the in silico screening of South African NPs for drug discovery purposes.
Wikidata as a knowledge graph for the life sciences
TLDR
The breadth and depth of the biomedical knowledge contained within Wikidata is described, and the open-source tools built to add information toWikidata and to synchronize it with source databases are discussed.
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