Purpose/Significance To analyze the research progress of assisted diagnosis of rare diseases, and to improve the ability to identify rare diseases.Method/Processs Through literature analysis, the paper expounds the research progress of rare disease knowledge system, and summarizes the research ideas and key technologies. Result/Conclusion It is proposed that the construction of the national rare disease diagnosis and treatment collaboration network should be enhanced, as well as the phenotype terminology recognition, rare disease knowledge integration, rare disease prediction model, semantic similarity algorithm improvement and other aspects in the collaboration network, so as to carry out technical exploration for the implementation of diagnostic tools in the collaboration network.