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Durango MC, Torres-Silva EA, Orozco-Duque A. Named Entity Recognition in Electronic Health Records: A Methodological Review. Healthc Inform Res 2023; 29:286-300. [PMID: 37964451 PMCID: PMC10651400 DOI: 10.4258/hir.2023.29.4.286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/29/2023] [Accepted: 09/03/2023] [Indexed: 11/16/2023] Open
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.
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Affiliation(s)
- María C. Durango
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Antioquia,
Colombia
| | - Ever A. Torres-Silva
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Antioquia,
Colombia
| | - Andrés Orozco-Duque
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Antioquia,
Colombia
- Facultad de Ingenierías, Universidad de Medellín, Antioquia,
Colombia
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Fernandes MB, Valizadeh N, Alabsi HS, Quadri SA, Tesh RA, Bucklin AA, Sun H, Jain A, Brenner LN, Ye E, Ge W, Collens SI, Lin S, Das S, Robbins GK, Zafar SF, Mukerji SS, Westover MB. Classification of neurologic outcomes from medical notes using natural language processing. EXPERT SYSTEMS WITH APPLICATIONS 2023; 214:119171. [PMID: 36865787 PMCID: PMC9974159 DOI: 10.1016/j.eswa.2022.119171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Neurologic disability level at hospital discharge is an important outcome in many clinical research studies. Outside of clinical trials, neurologic outcomes must typically be extracted by labor intensive manual review of clinical notes in the electronic health record (EHR). To overcome this challenge, we set out to develop a natural language processing (NLP) approach that automatically reads clinical notes to determine neurologic outcomes, to make it possible to conduct larger scale neurologic outcomes studies. We obtained 7314 notes from 3632 patients hospitalized at two large Boston hospitals between January 2012 and June 2020, including discharge summaries (3485), occupational therapy (1472) and physical therapy (2357) notes. Fourteen clinical experts reviewed notes to assign scores on the Glasgow Outcome Scale (GOS) with 4 classes, namely 'good recovery', 'moderate disability', 'severe disability', and 'death' and on the Modified Rankin Scale (mRS), with 7 classes, namely 'no symptoms', 'no significant disability', 'slight disability', 'moderate disability', 'moderately severe disability', 'severe disability', and 'death'. For 428 patients' notes, 2 experts scored the cases generating interrater reliability estimates for GOS and mRS. After preprocessing and extracting features from the notes, we trained a multiclass logistic regression model using LASSO regularization and 5-fold cross validation for hyperparameter tuning. The model performed well on the test set, achieving a micro average area under the receiver operating characteristic and F-score of 0.94 (95% CI 0.93-0.95) and 0.77 (0.75-0.80) for GOS, and 0.90 (0.89-0.91) and 0.59 (0.57-0.62) for mRS, respectively. Our work demonstrates that an NLP algorithm can accurately assign neurologic outcomes based on free text clinical notes. This algorithm increases the scale of research on neurological outcomes that is possible with EHR data.
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Affiliation(s)
- Marta B. Fernandes
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Clinical Data Animation Center (CDAC), MGH, Boston, MA, United States
| | - Navid Valizadeh
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Haitham S. Alabsi
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Syed A. Quadri
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Clinical Data Animation Center (CDAC), MGH, Boston, MA, United States
| | - Ryan A. Tesh
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Clinical Data Animation Center (CDAC), MGH, Boston, MA, United States
| | - Abigail A. Bucklin
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Clinical Data Animation Center (CDAC), MGH, Boston, MA, United States
| | - Haoqi Sun
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Clinical Data Animation Center (CDAC), MGH, Boston, MA, United States
| | - Aayushee Jain
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Clinical Data Animation Center (CDAC), MGH, Boston, MA, United States
| | - Laura N. Brenner
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, MGH, Boston, MA, United States
- Division of General Internal Medicine, MGH, Boston, MA, United States
| | - Elissa Ye
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Clinical Data Animation Center (CDAC), MGH, Boston, MA, United States
| | - Wendong Ge
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Clinical Data Animation Center (CDAC), MGH, Boston, MA, United States
| | - Sarah I. Collens
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
| | - Stacie Lin
- Harvard Medical School, Boston, MA, United States
| | - Sudeshna Das
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Gregory K. Robbins
- Harvard Medical School, Boston, MA, United States
- Division of Infectious Diseases, MGH, Boston, MA, United States
| | - Sahar F. Zafar
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Shibani S. Mukerji
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Vaccine and Immunotherapy Center, Division of Infectious Diseases, MGH, Boston, MA, United States
| | - M. Brandon Westover
- Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Clinical Data Animation Center (CDAC), MGH, Boston, MA, United States
- McCance Center for Brain Health, MGH, Boston, MA, United States
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Xiu X, Qian Q, Wu S. Construction of a Digestive System Tumor Knowledge Graph Based on Chinese Electronic Medical Records: Development and Usability Study. JMIR Med Inform 2020; 8:e18287. [PMID: 33026359 PMCID: PMC7578820 DOI: 10.2196/18287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 08/23/2020] [Accepted: 09/22/2020] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND With the increasing incidences and mortality of digestive system tumor diseases in China, ways to use clinical experience data in Chinese electronic medical records (CEMRs) to determine potentially effective relationships between diagnosis and treatment have become a priority. As an important part of artificial intelligence, a knowledge graph is a powerful tool for information processing and knowledge organization that provides an ideal means to solve this problem. OBJECTIVE This study aimed to construct a semantic-driven digestive system tumor knowledge graph (DSTKG) to represent the knowledge in CEMRs with fine granularity and semantics. METHODS This paper focuses on the knowledge graph schema and semantic relationships that were the main challenges for constructing a Chinese tumor knowledge graph. The DSTKG was developed through a multistep procedure. As an initial step, a complete DSTKG construction framework based on CEMRs was proposed. Then, this research built a knowledge graph schema containing 7 classes and 16 kinds of semantic relationships and accomplished the DSTKG by knowledge extraction, named entity linking, and drawing the knowledge graph. Finally, the quality of the DSTKG was evaluated from 3 aspects: data layer, schema layer, and application layer. RESULTS Experts agreed that the DSTKG was good overall (mean score 4.20). Especially for the aspects of "rationality of schema structure," "scalability," and "readability of results," the DSTKG performed well, with scores of 4.72, 4.67, and 4.69, respectively, which were much higher than the average. However, the small amount of data in the DSTKG negatively affected its "practicability" score. Compared with other Chinese tumor knowledge graphs, the DSTKG can represent more granular entities, properties, and semantic relationships. In addition, the DSTKG was flexible, allowing personalized customization to meet the designer's focus on specific interests in the digestive system tumor. CONCLUSIONS We constructed a granular semantic DSTKG. It could provide guidance for the construction of a tumor knowledge graph and provide a preliminary step for the intelligent application of knowledge graphs based on CEMRs. Additional data sources and stronger research on assertion classification are needed to gain insight into the DSTKG's potential.
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Affiliation(s)
- Xiaolei Xiu
- Institute of Medical Information/Medical Library, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qing Qian
- Institute of Medical Information/Medical Library, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Sizhu Wu
- Institute of Medical Information/Medical Library, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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