Network for Knowledge Organization (NEKO): an AI knowledge mining workflow for synthetic biology research

Abstract

Large language models (LLMs) can complete general scientific question-and-answer, yet they are constrained by their pretraining cut-off dates and lack the ability to provide specific, cited scientific knowledge. Here, we introduce Network for Knowledge Organization (NEKO), a workflow that uses LLM Qwen to extract knowledge through scientific literature text mining. When user inputs a keyword of interest, NEKO can generate knowledge graphs and comprehensive summaries from PubMed search. NEKO has immediate applications in daily academic tasks such as education of young scientists, literature review, paper writing, experiment planning/troubleshooting, and new hypothesis generation. We exemplified this workflows applicability through several case studies on yeast fermentation and cyanobacterial biorefinery. NEKOs output is more informative, specific, and actionable than GPT-4s zero-shot Q&A. NEKO offers flexible, lightweight local deployment options. NEKO democratizes artificial intelligence (AI) tools, making scientific foundation model more accessible to researchers without excessive computational power.