Maria C. Durango

Early detection of morbidities that complicate pregnancy improves health outcomes in low- and middle-income countries. Automatic revision of electronic health records (EHRs) can help identify such morbidity risks. There is a lack of corpora to train models in Spanish in specific domains, and there are no models specialized in maternal EHRs. This study aims to develop a fine-tuned model that detects clinical concepts using a built database with text extracted from maternal EHRs in Spanish. We created a corpus with 13.998 annotations from 200 clinical notes in Spanish associated with EHRs obtained from a reference institution of high obstetric risk in Colombia. Using the Beginning–Inside–Outside tagging scheme, we fine-tuned five different transformer-based models to classify between 16 classes associated with eight entities. The best model achieved a macro F1 score of 0.55 ± 0.03. The entities with the best performance were signs, symptoms, and negations, with exact F1 scores of 0.714 and 0.726, respectively. The lower scores were associated with those classes with fewer observations. Even though our dataset is shorter in size and more diverse in entity types than other datasets in Spanish, our results are comparable to other state-of-the-art named entity recognition models fine-tuned in Spanish and the biomedical domain. This work introduces the first fine-tuning of a model for named entity recognition specifically designed for maternal EHRs. Our results can be used as a base to develop new models to extract concepts in the maternal–fetal domains and help healthcare providers detect morbidities that complicate pregnancy early.

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.