Meijer David, Beniddir Mehdi A, Coley Connor W, Mejri Yassine M, Öztürk Meltem, van der Hooft Justin J J, Medema Marnix H, Skiredj Adam
Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands.
Equipe "Chimie des Substances Naturelles", Université Paris-Saclay, CNRS, BioCIS, 17 Avenue des Sciences, 91400 Orsay, France.
Nat Prod Rep. 2025 Apr 16;42(4):654-662. doi: 10.1039/d4np00008k.
Artificial intelligence (AI) is accelerating how we conduct science, from folding proteins with AlphaFold and summarizing literature findings with large language models, to annotating genomes and prioritizing newly generated molecules for screening using specialized software. However, the application of AI to emulate human cognition in natural product research and its subsequent impact has so far been limited. One reason for this limited impact is that available natural product data is multimodal, unbalanced, unstandardized, and scattered across many data repositories. This makes natural product data challenging to use with existing deep learning architectures that consume fairly standardized, often non-relational, data. It also prevents models from learning overarching patterns in natural product science. In this Viewpoint, we address this challenge and support ongoing initiatives aimed at democratizing natural product data by collating our collective knowledge into a knowledge graph. By doing so, we believe there will be an opportunity to use such a knowledge graph to develop AI models that can truly mimic natural product scientists' decision-making.
人工智能(AI)正在加速我们开展科学研究的方式,从利用AlphaFold折叠蛋白质、使用大语言模型总结文献发现,到注释基因组以及使用专门软件对新生成的分子进行筛选排序。然而,迄今为止,人工智能在天然产物研究中模拟人类认知的应用及其后续影响一直较为有限。造成这种有限影响的一个原因是,现有的天然产物数据是多模态的、不平衡的、未标准化的,并且分散在许多数据存储库中。这使得天然产物数据难以与现有的深度学习架构配合使用,因为这些架构通常需要相当标准化且往往是非关系型的数据。这也阻碍了模型学习天然产物科学中的总体模式。在本观点文章中,我们应对这一挑战,并支持正在进行的旨在通过将我们的集体知识整理到知识图谱中来实现天然产物数据民主化的倡议。我们相信,通过这样做,将有机会利用这样的知识图谱来开发能够真正模仿天然产物科学家决策过程的人工智能模型。