MOSES: combining automated ontology construction with a multi-agent system for explainable chemical knowledge reasoning

The vast and multiscale nature of chemical knowledge—from molecular structures to material properties—presents significant challenges for both human researchers and artificial intelligence (AI) systems. While large language models (LLMs) can process chemical information, they operate as black boxes without transparent reasoning. Here, we present our multi-agent ontology system for explainable knowledge synthesis (MOSES), a framework that combines automated knowledge organization with multi-agent collaboration to create an AI system for interpretable chemical knowledge reasoning. Using supramolecular chemistry as a testbed, we automatically constructed an ontology of over 10 000 classes from 52 publications and developed a multi-agent system that enables transparent knowledge retrieval and reasoning. Evaluations by human experts and LLMs show that MOSES significantly outperforms chemistry-oriented LLMs and leading general-purpose LLMs—including GPT-4.1 and o3—as well as GraphRAG-augmented GPT-4.1 models, on complex chemical questions, achieving superior scores in both direct assessments and Elo ratings. MOSES’s traceable reasoning paths reveal how it constructs answers through iterative refinement rather than probabilistic generation. However, we observe an asymmetry in handling positive versus negative knowledge claims, underscoring fundamental challenges in open-world reasoning. Our work demonstrates a pathway toward AI systems that can reason over complex scientific knowledge in a transparent and explainable manner.