MedLexSp - a medical lexicon for Spanish medical natural language processing.

BACKGROUND: Medical lexicons enable the natural language processing (NLP) of health texts. Lexicons gather terms and concepts from thesauri and ontologies, and linguistic data for part-of-speech (PoS) tagging, lemmatization or natural language generation. To date, there is no such type of resource for Spanish. CONSTRUCTION AND CONTENT: This article describes an unified medical lexicon for Medical Natural Language Processing in Spanish. MedLexSp includes terms and inflected word forms with PoS information and Unified Medical Language System[Formula: see text] (UMLS) semantic types, groups and Concept Unique Identifiers (CUIs). To create it, we used NLP techniques and domain corpora (e.g. MedlinePlus). We also collected terms from the Dictionary of Medical Terms from the Spanish Royal Academy of Medicine, the Medical Subject Headings (MeSH), the Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT), the Medical Dictionary for Regulatory Activities Terminology (MedDRA), the International Classification of Diseases vs. 10, the Anatomical Therapeutic Chemical Classification, the National Cancer Institute (NCI) Dictionary, the Online Mendelian Inheritance in Man (OMIM) and OrphaData. Terms related to COVID-19 were assembled by applying a similarity-based approach with word embeddings trained on a large corpus. MedLexSp includes 100 887 lemmas, 302 543 inflected forms (conjugated verbs, and number/gender variants), and 42 958 UMLS CUIs. We report two use cases of MedLexSp. First, applying the lexicon to pre-annotate a corpus of 1200 texts related to clinical trials. Second, PoS tagging and lemmatizing texts about clinical cases. MedLexSp improved the scores for PoS tagging and lemmatization compared to the default Spacy and Stanza python libraries. CONCLUSIONS: The lexicon is distributed in a delimiter-separated value file; an XML file with the Lexical Markup Framework; a lemmatizer module for the Spacy and Stanza libraries; and complementary Lexical Record (LR) files. The embeddings and code to extract COVID-19 terms, and the Spacy and Stanza lemmatizers enriched with medical terms are provided in a public repository.

Lessons Learned from the Usability Evaluation of a Simulated Patient Dialogue System.

Simulated consultations through virtual patients allow medical students to practice history-taking skills. Ideally, applications should provide interactions in natural language and be multi-case, multi-specialty. Nevertheless, few systems handle or are tested on a large variety of cases. We present a virtual patient dialogue system in which a medical trainer types new cases and these are processed without human intervention. To develop it, we designed a patient record model, a knowledge model for the history-taking task, and a termino-ontological model for term variation and out-of-vocabulary words. We evaluated whether this system provided quality dialogue across medical specialities (n = 18), and with unseen cases (n = 29) compared to the cases used for development (n = 6). Medical evaluators (students, residents, practitioners, and researchers) conducted simulated history-taking with the system and assessed its performance through Likert-scale questionnaires. We analysed interaction logs and evaluated system correctness. The mean user evaluation score for the 29 unseen cases was 4.06 out of 5 (very good). The evaluation of correctness determined that, on average, 74.3% (sd = 9.5) of replies were correct, 14.9% (sd = 6.3) incorrect, and in 10.7% the system behaved cautiously by deferring a reply. In the user evaluation, all aspects scored higher in the 29 unseen cases than in the 6 seen cases. Although such a multi-case system has its limits, the evaluation showed that creating it is feasible; that it performs adequately; and that it is judged usable. We discuss some lessons learned and pivotal design choices affecting its performance and the end-users, who are primarily medical students.

A clinical trials corpus annotated with UMLS entities to enhance the access to evidence-based medicine.

BACKGROUND: The large volume of medical literature makes it difficult for healthcare professionals to keep abreast of the latest studies that support Evidence-Based Medicine. Natural language processing enhances the access to relevant information, and gold standard corpora are required to improve systems. To contribute with a new dataset for this domain, we collected the Clinical Trials for Evidence-Based Medicine in Spanish (CT-EBM-SP) corpus. METHODS: We annotated 1200 texts about clinical trials with entities from the Unified Medical Language System semantic groups: anatomy (ANAT), pharmacological and chemical substances (CHEM), pathologies (DISO), and lab tests, diagnostic or therapeutic procedures (PROC). We doubly annotated 10% of the corpus and measured inter-annotator agreement (IAA) using F-measure. As use case, we run medical entity recognition experiments with neural network models. RESULTS: This resource contains 500 abstracts of journal articles about clinical trials and 700 announcements of trial protocols (292 173 tokens). We annotated 46 699 entities (13.98% are nested entities). Regarding IAA agreement, we obtained an average F-measure of 85.65% (±4.79, strict match) and 93.94% (±3.31, relaxed match). In the use case experiments, we achieved recognition results ranging from 80.28% (±00.99) to 86.74% (±00.19) of average F-measure. CONCLUSIONS: Our results show that this resource is adequate for experiments with state-of-the-art approaches to biomedical named entity recognition. It is freely distributed at: http://www.lllf.uam.es/ESP/nlpmedterm_en.html . The methods are generalizable to other languages with similar available sources.

Initial Experiments for Pharmacovigilance Analysis in Social Media Using Summaries of Product Characteristics.

We report initial experiments for analyzing social media through an NLP annotation tool on web posts about medications of current interests (baclofen, levothyroxine and vaccines) and summaries of product characteristics (SPCs). We conducted supervised experiments on a subset of messages annotated by experts according to positive or negative misuse; results ranged from 0.62 to 0.91 of F-score. We also annotated both SPCs and another set of posts to compare MedDRA annotations in each source. A pharmacovigilance expert checked the output and confirmed that entities not found in SCPs might express drug misuse or unknown ADRs.