FuncFetch: an LLM-assisted workflow enables mining thousands of enzyme–substrate interactions from published manuscripts

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Abstract Motivation Thousands of genomes are publicly available, however, most genes in those genomes have poorly defined functions. This is partly due to a gap between previously published, experimentally characterized protein activities and activities deposited in databases. This activity deposition is bottlenecked by the time-consuming biocuration process. The emergence of large language models presents an opportunity to speed up the text-mining of protein activities for biocuration. Results We developed FuncFetch—a workflow that integrates NCBI E-Utilities, OpenAI’s GPT-4, and Zotero—to screen thousands of manuscripts and extract enzyme activities. Extensive validation revealed high precision and recall of GPT-4 in determining whether the abstract of a given paper indicates the presence of a characterized enzyme activity in that paper. Provided the manuscript, FuncFetch extracted data such as species information, enzyme names, sequence identifiers, substrates, and products, which were subjected to extensive quality analyses. Comparison of this workflow against a manually curated dataset of BAHD acyltransferase activities demonstrated a precision/recall of 0.86/0.64 in extracting substrates. We further deployed FuncFetch on nine large plant enzyme families. Screening 26 543 papers, FuncFetch retrieved 32 605 entries from 5459 selected papers. We also identified multiple extraction errors including incorrect associations, nontarget enzymes, and hallucinations, which highlight the need for further manual curation. The BAHD activities were verified, resulting in a comprehensive functional fingerprint of this family and revealing that ∼70% of the experimentally characterized enzymes are uncurated in the public domain. FuncFetch represents an advance in biocuration and lays the groundwork for predicting the functions of uncharacterized enzymes. Availability and implementation Code and minimally curated activities are available at: https://github.com/moghelab/funcfetch and https://tools.moghelab.org/funczymedb.