Inferring over and extracting information from Large Language Models (LLMs) trained on a large corpus of scientific literature can potentially drive a new era in biomedical research, reducing the barriers for accessing existing medical evidence. This work examines the potential of LLMs for dialoguing with biomedical background knowledge, using the context of antibiotic discovery as an exemplar motivational scenario. The context of biomedical discovery from natural products entails understanding the relational evidence between an organism, an associated chemical and its associated antibiotic properties. We provide a systematic assessment on the ability of LLMs to encode and express these relations, verifying for fluency, prompt-alignment, semantic coherence, factual knowledge and specificity of generated responses. The systematic analysis is applied to nine state-of-the-art models (including ChatGPT and GPT-4) in two prompting-based tasks: chemical compound definition generation and chemical compound-fungus relation determination. Results show that while recent models have improved in fluency, factual accuracy is still low and models are biased towards over-represented entities. The ability of LLMs to serve as biomedical knowledge bases is questioned, and the need for additional systematic evaluation frameworks is highlighted. The best performing GPT-4 produced a factual definition for 70% of chemical compounds and 43.6% factual relations to fungi, whereas the best open source model BioGPT-large 30% of the compounds and 30% of the relations for the best-performing prompt. The results show that while LLMs are currently not fit for purpose to be used as biomedical factual knowledge bases, there is a promising emerging property in the direction of factuality as the models become domain specialised, scale-up in size and level of human feedback.

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