Natural Products (NPs) are behind more than half of newly approved drugs. But beyond those medical benefits lie a myriad of other uses. Flavors, colors, medical devices, technical oils, fibers, polymers the list of the applications of substances extracted from plants, fungi, or bacteria is long. The openly accessible body of knowledge behind NPs is colossal. But we scattered this information across a myriad of databases. Thus making it difficult to cross sub-disciplines or interests boundaries. The summarized information that populates public databases comes from publications, patents, and clinical trials. The parallel development of computers and efficient research tools helped the body of knowledge to increase rapidly since the 1960s. This led to an explosion of new databases, creating their own set of issues from databases going extinct to the lack of links and annotations that are precious to navigate complex information. The LOTUS initiative, composed of an international team of researchers across various disciplines, aims to liberate NPs related information. LOTUS hosts this information on Wikidata, a collectively edited public domain Knowledge Base behind Wikimedia projects such as Wikipedia. Wikidata provides LOTUS with its wide and active community, data in the public domain and links to other resources. It also provides tools to search, access and change information. Wikidata has 95 millions of items linked and described by over 1 billion statements. Humans and their “robots”, assisting them with complex or repetitive edition tasks, both manage these statements. The LOTUS project contributes to Wikidata by linking chemical, taxonomical and bibliographical information. As a result, we can describe what organism produces a molecule and which publications reported that discovery and link to other entries in Wikidata and external databases. To carry this out, LOTUS comprises a processing pipeline and its associated tools. This pipeline extracts information from databases, cleans it, validates it and links it to other resources. Then our “robot" updates Wikidata with this new information. The millions of statements we added so far make Wikidata the largest NPs knowledge base, combining chemical, taxonomical and bibliographical information. And this provides new usages by bringing this information to other communities. This presentation will first introduce the LOTUS project, present non drug-related applications and examine future directions.

Beyond drug discovery: Breaking the boundaries of natural products information

ACS Spring 2022

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