Assessing the ability of ChatGPT to extract natural product bioactivity and biosynthesis data from publications

Abstract

Natural products are an excellent source of therapeutics and are often discovered through the process of genome mining, where genomes are analyzed by bioinformatic tools to determine if they have the biosynthetic capacity to produce novel or active compounds. Recently, several tools have been reported for predicting natural product bioactivities from the sequence of the biosynthetic gene clusters that produce them. These tools have the potential to accelerate the rate of natural product drug discovery by enabling the prioritization of novel biosynthetic gene clusters that are more likely to produce compounds with therapeutically relevant bioactivities. However, these tools are severely limited by a lack of training data, specifically data pairing biosynthetic gene clusters with activity labels for their products. There are many reports of natural product biosynthetic gene clusters and bioactivities in the literature that are not included in existing databases. Manual curation of these data is time consuming and inefficient. Recent developments in large language models and the chatbot interfaces built on top of them have enabled automatic data extraction from text, including scientific publications. We investigated how accurate ChatGPT is at extracting the necessary data for training models that predict natural product activity from biosynthetic gene clusters. We found that ChatGPT did well at determining if a paper described discovery of a natural product and extracting information about the product’s bioactivity. ChatGPT did not perform as well at extracting accession numbers for the biosynthetic gene cluster or producer’s genome although using an altered prompt improved accuracy.