RESUMO
Detecting patients with a high-risk profile for treatment-resistant schizophrenia (TRS) can be beneficial for implementing individually adapted therapeutic strategies and better understanding the TRS etiology. The aim of this study was to explore, with machine learning methods, the impact of demographic and clinical patient characteristics on TRS prediction, for already established risk factors and unexplored ones. This was a retrospective study of 500 patients admitted during 2020 to the University Hospital Group for Paris Psychiatry. We hypothesized potential TRS risk factors. The selected features were coded into structured variables in a new dataset, by processing patients discharge summaries and medical narratives with natural-language processing methods. We compared three machine learning models (XGBoost, logistic elastic net regression, logistic regression without regularization) for predicting TRS outcome. We analysed feature impact on the models, suggesting the following factors as markers of a high-risk TRS profile: early age at first contact with psychiatry, antipsychotic treatment interruptions due to non-adherence, absence of positive symptoms at baseline, educational problems and adolescence mental disorders in the personal psychiatric history. Specifically, we found a significant association with TRS outcome for age at first contact with psychiatry and medication non-adherence. Our findings on TRS risk factors are consistent with the review of the literature and suggest potential in using early pathophysiologic features for TRS prediction. Results were encouraging with the use of natural-langage processing techniques to leverage raw data provided by discharge summaries, combined with machine leaning models. These findings are a promising step for helping clinicians adapt their guidelines to early detection of TRS.
Assuntos
Aprendizado de Máquina , Esquizofrenia Resistente ao Tratamento , Humanos , Masculino , Feminino , Adulto , Estudos Retrospectivos , Esquizofrenia Resistente ao Tratamento/tratamento farmacológico , Esquizofrenia Resistente ao Tratamento/fisiopatologia , Antipsicóticos/farmacologia , Fatores de Risco , Adulto Jovem , Pessoa de Meia-Idade , Adesão à Medicação , Adolescente , Prognóstico , Esquizofrenia/tratamento farmacológico , Esquizofrenia/fisiopatologiaRESUMO
AIMS: The global older population is growing rapidly, and the rise in polypharmacy has increased potentially inappropriate medication (PIM) encounters. PIMs pose health risks, but detecting them automatically in large medical databases is complex. This review aimed to uncover PIM prevalence in individuals aged 65 years or older using health databases and emphasized the risk of underestimating PIM prevalence due to underutilization of detection tools. METHODS: This study conducted a broad search on the Medline database to identify articles about the prevalence of PIMs in older adults using various databases. Articles published between January 2010 and June 2023 were included, and specific criteria were applied for study selection. Two literature reviews conducted before our study period were integrated to obtain a perspective from the 1990s to the present day. The selected papers were analysed for variables including database type, screening method, adaptations and PIM prevalence. The study categorized databases and original screening tools for clarity, examined adaptations and assessed concordance among different screening methods. RESULTS: This study encompassed 48 manuscripts, covering 58 sample evaluations. The mean prevalence of PIMs within the general population aged over 65 years was 27.8%. Relevant heterogeneity emerged in both the utilized databases and the detection methods. Adaptation of original screening tools was observed in 86.2% (50/58) of cases. Half of the original screening tools used for assessing PIMs belonged to the simple category. About a third of the studies employed less than half of the original criteria after adaptation. Only three studies used over 75% of the original criteria and more than 50 criteria. CONCLUSIONS: This extensive review highlights PIM prevalence among the older adults, emphasizing method intricacies and the potential for underestimation due to data limitations and algorithm adjustments. The findings call for enhanced methodologies, transparent algorithms and a deeper understanding of intricate rules' impact on public health implications.
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Bases de Dados Factuais , Prescrição Inadequada , Polimedicação , Lista de Medicamentos Potencialmente Inapropriados , Humanos , Idoso , Prescrição Inadequada/estatística & dados numéricos , Prevalência , Lista de Medicamentos Potencialmente Inapropriados/estatística & dados numéricos , Bases de Dados Factuais/estatística & dados numéricosRESUMO
AIMS: To describe the key elements of the interprofessional decision-making process in health, based on published scientific studies. To describe the authors, reviews and subject matter of those publications. DESIGN: Scoping review of the literature. DATA SOURCES: MEDLINE, APA Psycinfo OpenGrey, Lissa and Cochrane databases were searched in December 2019 and January 2023. REVIEW METHODS: References were considered eligible if they (i) were written in French or English, (ii) concerned health, (iii) studied a clinical decision-making process, (iv) were performed in an interprofessional context. 'PRISMA-scoping review' guidelines were respected. The eligible studies were analysed and classified by an inductive approach RESULTS: We identified 1429 sources of information, 145 of which were retained for the analysis. Based on these studies, we identified five key elements of interprofessional decision-making in health. The process was found to be influenced by group dynamics, the available information and consideration of the unique characteristics of the patient. An organizational framework and specific training favoured improvements in the process. CONCLUSION: Decision-making can be based on a willingness of the healthcare organization to promote models based on more shared leadership and to work on professional roles and values. It also requires healthcare professionals trained in the entire continuum of collaborative practices, to meet the unique needs of each patient. Finally, it appears essential to favour the sharing of multiple sources of accessible and structured information. Tools for knowledge formalization should help to optimize interprofessional decision-making in health. IMPACT: The quality of a team decision-making is critical to the quality of care. Interprofessional decision-making can be structured and improved through different levels of action. These improvements could benefit to patients and healthcare professionals in every settings of care involving care collaboration. IMPACT STATEMENT: Interprofessional decision-making in health is an essential lever of quality of care, especially for the most complex patients which are a contemporary challenge. This scoping review article offers a synthesis of a large corpus of data published to date about the interprofessional clinical decision-making process in healthcare. It has the potential to provide a global vision, practical data and a list of references to facilitate the work of healthcare teams, organizations and teachers ready to initiate a change.
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Comportamento Cooperativo , Relações Interprofissionais , Humanos , Atenção à Saúde , Papel Profissional , Tomada de Decisão ClínicaRESUMO
OBJECTIVES: To select, present, and summarize the best papers in 2022 for the Knowledge Representation and Management (KRM) section of the International Medical Informatics Association (IMIA) Yearbook. METHODS: We conducted PubMed queries and followed the IMIA Yearbook guidelines for performing biomedical informatics literature review to select the best papers in KRM published in 2022. RESULTS: We retrieved 1,847 publications from PubMed. We nominated 15 candidate best papers, and two of them were finally selected as the best papers in the KRM section. The topics covered by the candidate papers include ontology and knowledge graph creation, ontology applications, ontology quality assurance, ontology mapping standard, and conceptual model. CONCLUSIONS: In the KRM best paper selection for 2022, the candidate best papers encompassed a broad range of topics, with ontology and knowledge graph creation remaining a considerable research focus.
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Informática Médica , Gestão do ConhecimentoRESUMO
We present an ontology design pattern for modeling scientific experiments and examinations conducted in a clinical research study. Integrating heterogeneous data into a common ontological model is a challenge, redoubled if we want them to be explored later. In order to facilitate the development of dedicated ontological modules, this design pattern relies on invariants, is centered on the event of the experiment, and keeps the link to the original data.
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Exame Físico , RegistrosRESUMO
The use of eCRFs is now commonplace in clinical research studies. We propose here an ontological model of these forms allowing to describe them, to express their granularity and to link them to the relevant entities of the study in which they are used. It has been developed in a psychiatry project but its generality may allow a wider application.
RESUMO
Building a timeline of psychiatric patient profiles can answer many valuable questions, such as how important medical events affect the progression of psychosis in patients. However, the majority of text information extraction and semantic annotation tools, as well as domain ontologies, are only available in English and cannot be easily extended to other languages, due to fundamental linguistic differences. In this paper, we describe a semantic annotation system based on an ontology developed in the PsyCARE framework. Our system is being manually evaluated by two annotators on 50 patient discharge summaries, showing promising results.
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Idioma , Semântica , Humanos , Armazenamento e Recuperação da InformaçãoRESUMO
OBJECTIVES: To select, present, and summarize the best papers in the field of Knowledge Representation and Management (KRM) published in 2021. METHODS: Following the International Medical Informatics Association (IMIA) Yearbook guidelines, a comprehensive and standardized review of the biomedical informatics literature was performed to select the best KRM papers published in 2021, based on PubMed queries. RESULTS: A total of 1,231 publications were retrieved from PubMed. We nominated 15 candidate best papers, and four of them were finally selected as the best papers in the KRM section. The topics covered by these papers include knowledge graph, ontology development, ontology alignment, and the International Classification of Diseases. CONCLUSION: In the KRM best paper selection for 2021, the candidate best papers covered a wider spectrum of topics compared to the last year's significant focus on ontology curation. In particular, ontology development for specific domains (e.g., Alzheimer's disease, infectious diseases, bioethics) has received the most attention.
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Bioética , Informática Médica , Classificação Internacional de Doenças , Gestão do ConhecimentoRESUMO
BACKGROUND: Although the drug is finished, identifiable, there is no universally accepted standard for naming them. The objective of this work is to evaluate qualitatively the HeTOP drug terminology server by two categories of students: (a) pharmacy students and (b) a control group. METHODS: A formal evaluation was built to measure the perception of users about the HeTOP drug server, using the three mains questions about "teaching interest", "skill interest" (or competence) and "ergonomics". RESULTS: The three pharmacy student subgroups gave the best and the worst score to the same categories. CONCLUSION: All three criteria are rated above 6.5 out of 10. The HeTOP drug terminology server is freely available to "non drug" specialists (URL: www.hetop.eu/hetop/drugs/).
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Estudantes de Farmácia , Humanos , FarmacêuticosRESUMO
Representing temporal information is a recurrent problem for biomedical ontologies. We propose a foundational ontology that combines the so-called three-dimensional and four-dimensional approaches in order to be able to track changes in an individual and to trace his or her medical history. This requires, on the one hand, associating with any representation of an individual the representation of his or her life course and, on the other hand, distinguishing the properties that characterize this individual from those that characterize his or her life course.
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Ontologias Biológicas , Gestão do Conhecimento , Humanos , Fatores de TempoRESUMO
Biomedical ontologies define concepts having biomedical significance and the semantic relations among them. Developing high-quality and reusable ontologies in the biomedical domain is a challenging task. Pattern-based ontology design is considered a promising approach to overcome the challenges. Ontology Design Patterns (ODPs) are reusable modeling solutions to facilitate ontology development. This study relies on ODPs to semantically enrich biomedical ontologies by assigning logical definitions to ontological entities. Specifically, pattern-based logical definitions grounded on dispositions are given to prenatal disorders. The proposed approach is performed under the supervision of fetal domain experts.
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Ontologias Biológicas , Lógica , SemânticaRESUMO
Biomedical research data reuse and sharing is essential for fostering research progress. To this aim, data producers need to master data management and reporting through standard and rich metadata, as encouraged by open data initiatives such as the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines. This helps data re-users to understand and reuse the shared data with confidence. Therefore, dedicated frameworks are required. The provenance reporting throughout a biomedical study lifecycle has been proposed as a way to increase confidence in data while reusing it. The Biomedical Study - Lifecycle Management (BMS-LM) data model has implemented provenance and lifecycle traceability for several multimodal-imaging techniques but this is not enough for data understanding while reusing it. Actually, in the large scope of biomedical research, a multitude of metadata sources, also called Knowledge Organization Systems (KOSs), are available for data annotation. In addition, data producers uses local terminologies or KOSs, containing vernacular terms for data reporting. The result is a set of heterogeneous KOSs (local and published) with different formats and levels of granularity. To manage the inherent heterogeneity, semantic interoperability is encouraged by the Research Data Management (RDM) community. Ontologies, and more specifically top ontologies such as BFO and DOLCE, make explicit the metadata semantics and enhance semantic interoperability. Based on the BMS-LM data model and the BFO top ontology, the BioMedical Study - Lifecycle Management (BMS-LM) core ontology is proposed together with an associated framework for semantic interoperability between heterogeneous KOSs. It is made of four ontological levels: top/core/domain/local and aims to build bridges between local and published KOSs. In this paper, the conversion of the BMS-LM data model to a core ontology is detailed. The implementation of its semantic interoperability in a specific domain context is explained and illustrated with examples from small animal preclinical research.
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Ontologias Biológicas , Pesquisa Biomédica , Animais , Curadoria de Dados , Metadados , Projetos de Pesquisa , SemânticaRESUMO
OBJECTIVE: To select, present and summarize some of the best papers in the field of Knowledge Representation and Management (KRM) published in 2020. METHODS: A comprehensive and standardized review of the medical informatics literature was performed to select the most interesting papers of KRM published in 2020, based on PubMed queries. This review was conducted according to the IMIA Yearbook guidelines. RESULTS: Four best papers were selected among 1,175 publications. In contrast with the papers selected last year, the four best papers of 2020 demonstrated a significant focus on methods and tools for ontology curation and design. The usual KRM application domains (bioinformatics, machine learning, and electronic health records) were also represented. CONCLUSION: In 2020, ontology curation emerges as a significant topic of research interest. Bioinformatics, machine learning, and electronics health records remain significant research areas in the KRM community with various applications. Knowledge representations are key to advance machine learning by providing context and to develop novel bioinformatics metrics. As in 2019, representations serve a great variety of applications across many medical domains, with actionable results and now with growing adhesion to the open science initiative.
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Ontologias Biológicas , Interoperabilidade da Informação em Saúde , Gestão do Conhecimento , Genômica , Humanos , Informática Médica , Unified Medical Language SystemRESUMO
The objective of this study was to describe the care pathway of patients with amyotrophic lateral sclerosis (ALS) based on real-life textual data from a regional coordination network, the Ile-de-France ALS network. This coordination network provides care for 92% of patients diagnosed with ALS living in Ile-de-France. We developed a modular ontology (OntoPaRON) for the automatic processing of these unstructured textual data. OntoPaRON has different modules: the core, medical, socio-environmental, coordination, and consolidation modules. Our approach was unique in its creation of fully defined concepts at different levels of the modular ontology to address specific topics relating to healthcare trajectories. We also created a semantic annotation tool specific to the French language and the specificities of our corpus, the Ontology-Based Semantic Annotation Module (OnBaSAM), using the OntoPaRON ontology as a reference. We used these tools to annotate the records of 928 patients automatically. The semantic (qualitative) annotations of the concepts were transformed into quantitative data. By using these pipelines we were able to transform unstructured textual data into structured quantitative data. Based on data processing, semantic annotations, sociodemographic data for the patient and clinical variables, we found that the need and demand for human and technical assistance depend on the initial form of the disease, the motor state, and the patient age. The presence of exhaustion in care management, is related to the patient's motor and cognitive state.
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Esclerose Lateral Amiotrófica/terapia , Atenção à Saúde , Processamento de Linguagem Natural , França , Humanos , IdiomaRESUMO
OBJECTIVE: To select, present, and summarize the best papers in the field of Knowledge Representation and Management (KRM) published in 2019. METHODS: A comprehensive and standardized review of the biomedical informatics literature was performed to select the most interesting papers of KRM published in 2019, based on PubMed and ISI Web Of Knowledge queries. RESULTS: Four best papers were selected among 1,189 publications retrieved, following the usual International Medical Informatics Association Yearbook reviewing process. In 2019, research areas covered by pre-selected papers were represented by the design of semantic resources (methods, visualization, curation) and the application of semantic representations for the integration/enrichment of biomedical data. Besides new ontologies and sound methodological guidance to rethink knowledge bases design, we observed large scale applications, promising results for phenotypes characterization, semantic-aware machine learning solutions for biomedical data analysis, and semantic provenance information representations for scientific reproducibility evaluation. CONCLUSION: In the KRM selection for 2019, research on knowledge representation demonstrated significant contributions both in the design and in the application of semantic resources. Semantic representations serve a great variety of applications across many medical domains, with actionable results.
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Ontologias Biológicas , Registros Eletrônicos de Saúde , Gestão do Conhecimento , Bases de Dados Genéticas , Humanos , Bases de Conhecimento , Web SemânticaRESUMO
A lexical method was used to map ICD-11 to the terminologies included in the HeTOP server. About half of ICD-11 codes (47.76%) were mapped to at least one concept. The developed tool reached a global precision of 0.98 and a recall of 0.66. Lexical methods are powerful methods to map health terminologies. Supervised and manual mapping is still necessary to complete the mapping.
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Classificação Internacional de Doenças , Vocabulário ControladoRESUMO
OBJECTIVE: To select, present, and summarize the best papers published in 2018 in the field of Knowledge Representation and Management (KRM). METHODS: A comprehensive and standardized review of the medical informatics literature was performed to select the most interesting papers published in 2018 in KRM, based on PubMed and ISI Web Of Knowledge queries. RESULTS: Four best papers were selected among the 962 publications retrieved following the Yearbook review process. The research areas in 2018 were mainly related to the ontology-based data integration for phenotype-genotype association mining, the design of ontologies and their application, and the semantic annotation of clinical texts. CONCLUSION: In the KRM selection for 2018, research on semantic representations demonstrated their added value for enhanced deep learning approaches in text mining and for designing novel bioinformatics pipelines based on graph databases. In addition, the ontology structure can enrich the analyses of whole genome expression data. Finally, semantic representations demonstrated promising results to process phenotypic big data.
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Inteligência Artificial , Ontologias Biológicas , Mineração de Dados , Aprendizado Profundo , Estudos de Associação Genética , Big Data , Biologia Computacional , Análise de Dados , Genômica , Gestão do Conhecimento , SemânticaRESUMO
To understand the home-based difficulties encountered in the health care pathways of patients with Amyotrophic Lateral Sclerosis (ALS), we must annotate a large amount of textual data, from a database created by the ALS Île de France coordination network. For this purpose, we have developed a modular ontology, consisting of four modules, and a semantic annotation tool integrating the created ontology. The specificity of our approach is the creation of equivalent classes at different levels of the ontology. These equivalent classes represent variables of interest allowing a statistical approach and a clinical analysis of comprehension of care pathways ruptures causing.
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Esclerose Lateral Amiotrófica , Procedimentos Clínicos , Atenção à Saúde , Compreensão , França , Humanos , SemânticaRESUMO
BACKGROUND: Early pregnancy ultrasound scans are usually performed by nonexpert examiners in obstetrics/gynecology (OB/GYN) emergency departments. Establishing the precise diagnosis of pregnancy location is key for appropriate management of early pregnancies, and experts are usually able to locate a pregnancy in the first scan. A decision-support system based on a semantic, expert-validated knowledge base may improve the diagnostic performance of nonexpert examiners for early pregnancy transvaginal ultrasound. OBJECTIVE: This study aims to evaluate a novel Intelligent Scan Assistant System for early pregnancy ultrasound to diagnose the pregnancy location and determine the image quality. METHODS: Two trainees performed virtual transvaginal ultrasound examinations of early pregnancy cases with and without the system. The ultrasound images and reports were blindly reviewed by two experts using scoring methods. A diagnosis of pregnancy location and ultrasound image quality were compared between scans performed with and without the system. RESULTS: Each trainee performed a virtual vaginal examination for all 32 cases with and without use of the system. The analysis of the 128 resulting scans showed higher quality of the images (quality score: +23%; P<.001), less images per scan (4.6 vs 6.3 [without the CDSS]; P<.001), and higher confidence in reporting conclusions (trust score: +20%; P<.001) with use of the system. Further, use of the system cost an additional 8 minutes per scan. We observed a correct diagnosis of pregnancy location in 39 (61%) and 52 (81%) of 64 scans in the nonassisted mode and assisted mode, respectively. Additionally, an exact diagnosis (with precise ectopic location) was made in 30 (47%) and 49 (73%) of the 64 scans without and with use of the system, respectively. These differences in diagnostic performance (+20% for correct location diagnosis and +30% for exact diagnosis) were both statistically significant (P=.002 and P<.001, respectively). CONCLUSIONS: The Intelligent Scan Assistant System is based on an expert-validated knowledge base and demonstrates significant improvement in early pregnancy scanning, both in diagnostic performance (pregnancy location and precise diagnosis) and scan quality (selection of images, confidence, and image quality).
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Sistemas de Apoio a Decisões Clínicas/normas , Ultrassonografia/métodos , Diagnóstico Precoce , Feminino , Humanos , GravidezRESUMO
OBJECTIVES: To select, present, and summarize the best papers published in 2017 in the field of Knowledge Representation and Management (KRM). METHODS: A comprehensive and standardized review of the medical informatics literature was performed to select the most interesting papers of KRM published in 2017, based on a PubMed query. RESULTS: In direct line with the research on data integration presented in the KRM section of the 2017 edition of the International Medical Informatics Association (IMIA) Yearbook, the five best papers for 2018 demonstrate even further the added-value of ontology-based integration approaches for phenotype-genotype association mining. Additionally, among the 15 preselected papers, two aspects of KRM are in the spotlight: the design of knowledge bases and new challenges in using ontologies. CONCLUSIONS: Ontologies are demonstrating their maturity to integrate medical data and begin to support clinical practices. New challenges have emerged: the query on distributed semantically annotated datasets, the efficiency of semantic annotation processes, the semantic representation of large textual datasets, the control of biases associated with semantic annotations, and the computation of Bayesian indicators on data annotated with ontologies.