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BackgroundImages of anatomical regions and neuron type distribution, as well as their related literature are valuable assets for neuroscience research. They are vital evidence and vehicles in discovering new phenomena and knowledge refinement through image and text big data. The knowledge acquired from image data generally echoes with the literature accumulated over the years. The knowledge within the literature can provide a comprehensive context for a deeper understanding of the image data. However, it is quite a challenge to manually identify the related literature and summarize the neuroscience knowledge in the large‐scale corpus. Thus, neuroscientists are in dire need of an automated method to extract neuroscience knowledge from large‐scale literature.MethodsA proposed deep learning model named BioBERT‐CRF extracts brain region entities from the WhiteText dataset. This model takes advantage of BioBERT and CRF to predict entity labels while training.ResultsThe proposed deep learning model demonstrated comparable performance against or even outperforms the previous models on the WhiteText dataset. The BioBERT‐CRF model has achieved the best average precision, recall, and F1 score of 81.3%, 84.0%, and 82.6%, respectively. We used the BioBERT‐CRF model to predict brain region entities in a large‐scale PubMed abstract dataset and used a rule‐based method to normalize all brain region entities to three neuroscience dictionaries.ConclusionsOur work shows that the BioBERT‐CRF model can be well‐suited for brain region entity extraction. The rankings of different brain region entities by their appearance in the large‐scale corpus indicate the anatomical regions that researchers are most concerned about.