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Background  Electronic Medical Records(EMRs) contain much medical information about patients. Medical named entity extracting from EMRs can provide value information to support doctors’ decision making. The research on information extraction of Chinese Electronic Medical Records is still behind that has done in English.    Methods  This paper proposed a practical annotation scheme for medical entity extraction on Resident Admit Notes (RANs), and a model which can automatic extract medical entity. Nine types of clinical entities, four types of clinical relationships were defined in our annotation scheme. An end-to-end deep neural network with convolution neural network and long-short term memory units was applied in our model for the medical named entity recognition(NER).    Result  We annotated RANs in three rounds. The overall F-score of annotation consistency was up to 97.73%. And our NER model on the 255 annotated RANs achieved the best F-score of 91.08%.    Conclusion  The annotation scheme and the model for NER in this paper are effective to extract medical named entity from RANs and provide the basis for fully excavating the patient’s information.

Constructing a Chinese electronic medical record corpus for named entity recognition on resident admit notes