Named Entity Recognition in Electronic Health Records: A Methodological Review

Abstract

Objectives: A substantial portion of the data contained in Electronic Health Records (EHR) is unstructured, often appearing as free text. This format restricts its potential utility in clinical decision-making. Named entity recognition (NER) methods address the challenge of extracting pertinent information from unstructured text. The aim of this study was to outline the current NER methods and trace their evolution from 2011 to 2022.

Methods: We conducted a methodological literature review of NER methods, with a focus on distinguishing the classification models, the types of tagging systems, and the languages employed in various corpora.

Results: Several methods have been documented for automatically extracting relevant information from EHRs using natural language processing techniques such as NER and relation extraction (RE). These methods can automatically extract concepts, events, attributes, and other data, as well as the relationships between them. Most NER studies conducted thus far have utilized corpora in English or Chinese. Additionally, the bidirectional encoder representation from transformers using the BIO tagging system architecture is the most frequently reported classification scheme. We discovered a limited number of papers on the implementation of NER or RE tasks in EHRs within a specific clinical domain.

Conclusions: EHRs play a pivotal role in gathering clinical information and could serve as the primary source for automated clinical decision support systems. However, the creation of new corpora from EHRs in specific clinical domains is essential to facilitate the swift development of NER and RE models applied to EHRs for use in clinical practice.

Keywords: Clinical Decision Support System; Deep Learning; Electronic Health Records; Natural Language Processing; Supervised Machine Learning.

Figure 1

Flow diagram of the methodological review process. EHR: Electronic Health Record, NLP: natural language processing, NER: named entity recognition.

Figure 2

Timeline of named entity recognition models. ML: machine learning, LSTM: long short-term memory, BiLSTM: bidirectional long short-term memory, CNN: convolutional neural network, CRF: conditional random field, RNN: recurrent neural network, BiGRU: bidirectional gated recurrent unit, BERT: bidirectional encoder representations from transformers.

Figure 3

Named entity recognition approaches and types of tagging. GRU: gated recurrent unit, BiGUR: bidirectional gated recurrent unit, CNN: convolutional neural network, RNN: recurrent neural network, LSTM: long short-term memory, BiLSTM: bidirectional long short-term memory, ML: machine learning.

Figure 4

Corpus languages, types of models, and named entity recognition targets. ML: machine learning.