Abstract
Literature-based discovery (LBD) mines existing literature in order to generate new hypotheses by finding links between previously disconnected pieces of knowledge. Although automated LBD systems are becoming widespread and indispensable in a wide variety of knowledge domains, little has been done to introduce LBD to the field of natural products research. Despite growing knowledge in the natural product domain, most of the accumulated information is found in detached data pools. LBD can facilitate better contextualization and exploitation of this wealth of data, for example by formulating new hypotheses for natural product research, especially in the context of drug discovery and development. Moreover, automated LBD systems promise to accelerate the currently tedious and expensive process of lead identification, optimization, and development. Focusing on natural product research, we briefly reflect the development of automated LBD and summarize its methods and principal data sources. In a thorough review of published use cases of LBD in the biomedical domain, we highlight the immense potential of this data mining approach for natural product research, especially in context with drug discovery or repurposing, mode of action, as well as drug or substance interactions. Most of the 91 natural product-related discoveries in our sample of reported use cases of LBD were addressed at a computer science audience. Therefore, it is the wider goal of this review to introduce automated LBD to researchers who work with natural products and to facilitate the dialogue between this community and the developers of automated LBD systems.
Highlights
Literature-based discovery (LBD) is a form of knowledge extraction
Focusing on the biomedical domain, the primary aim of this review is to provide an overview of published use cases of LBD linked with natural products
We argue that LBD is a powerful emerging computational approach for natural product research or in particular drug discovery
Summary
Literature-based discovery (LBD) is a form of knowledge extraction. It aims at discovering new knowledge that is implicitly present in scientific literature. This study is focused on natural products of non-mammalian origin and encompasses, 1) secondary metabolites or small molecules from plants, microorganisms, and higher fungi, including both isolated compounds, and complex mixtures such as herbal extracts or botanicals in general, 2) derivatives of the above group of natural products including semi-synthetic compounds, 3) animal venoms, 4) minerals and vitamins. Numerous natural products of botanical origin were discovered by studying traditionally used medicinal plants, which is regarded as the ethnopharmacological approach (Fabricant and Farnsworth, 2001; Heinrich, 2010) In addition to these established approaches in bioprospecting, biological, molecular, and or pharmacological information on the various organisms or their components can be used as starting points for research. After a general review in the biomedical domain, we focus on natural products and assess the potential of LBD for future discoveries
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