Biological knowledgebases facilitate discovery across the life sciences by structuring experimental findings into human-readable and computable formats. These essential resources are maintained by a small number of professional biocurators worldwide and face combined chronic underfunding and the exponential growth of the literature. In this perspective, we review how artificial intelligence, particularly large language models and agentic systems, can augment literature-curation workflows. Applications include literature recommendation, entity recognition, data extraction, summarization, ontology development, and quality control with emphasis on published use cases at Global Core BioData Resources and ELIXIR Core Data Resources. We identify key challenges, including the scarcity of training data, difficulty in extracting complex relationships, and concerns about error propagation. To address these challenges, we propose a human-in-the-loop framework where generative artificial intelligence approaches accelerate routine tasks while curators provide critical evaluation and domain expertise. We also propose practical recommendations for the community, including the creation of shared benchmark datasets, harmonized evaluation frameworks, and best-practice guidelines for transparent human-in-the-loop AI deployment in biocuration. These synergistic partnerships will be critical to ensure biological rigour, accelerating knowledge integration while maintaining the quality essential for trusted biological resources.

Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature curation

Panni, Simona;
2026-01-01

Abstract

Biological knowledgebases facilitate discovery across the life sciences by structuring experimental findings into human-readable and computable formats. These essential resources are maintained by a small number of professional biocurators worldwide and face combined chronic underfunding and the exponential growth of the literature. In this perspective, we review how artificial intelligence, particularly large language models and agentic systems, can augment literature-curation workflows. Applications include literature recommendation, entity recognition, data extraction, summarization, ontology development, and quality control with emphasis on published use cases at Global Core BioData Resources and ELIXIR Core Data Resources. We identify key challenges, including the scarcity of training data, difficulty in extracting complex relationships, and concerns about error propagation. To address these challenges, we propose a human-in-the-loop framework where generative artificial intelligence approaches accelerate routine tasks while curators provide critical evaluation and domain expertise. We also propose practical recommendations for the community, including the creation of shared benchmark datasets, harmonized evaluation frameworks, and best-practice guidelines for transparent human-in-the-loop AI deployment in biocuration. These synergistic partnerships will be critical to ensure biological rigour, accelerating knowledge integration while maintaining the quality essential for trusted biological resources.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.11770/399580
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