OntoCR: A CEN/ISO-13606 clinical repository based on ontologies

Objective: To design a new semantically interoperable clinical repository, based on ontologies, conforming to CEN/ISO 13606 standard. Materials and Methods: The approach followed is to extend OntoCRF, a framework for the development of clinical repositories based on ontologies. The meta-model of OntoCRF has been extended by incorporating an OWL model integrating CEN/ISO 13606, ISO 21090 and SNOMED CT structure. Results: This approach has demonstrated a complete evaluation cycle involving the creation of the meta-model in OWL format, the creation of a simple test application, and the communication of standardized extracts to another organization. Discussion: Using a CEN/ISO 13606 based system, an indefinite number of archetypes can be merged (and reused) to build new applications. Our approach, based on the use of ontologies, maintains data storage independent of content specification. With this approach, relational technology can be used for storage, maintaining extensibility capabilities. Conclusions: The present work demonstrates that it is possible to build a native CEN/ISO 13606 repository for the storage of clinical data. We have demonstrated semantic interoperability of clinical information using CEN/ISO 13606 extracts

TransformEHRs: a flexible methodology for building transparent ETL processes for EHR reuse

Background: During the COVID-19 pandemic, several methodologies were designed for obtaining electronic health record (EHR)-derived datasets for research. These processes are often based on black boxes, on which clinical researchers are unaware of how the data were recorded, extracted, and transformed. In order to solve this, it is essential that extract, transform, and load (ETL) processes are based on transparent, homogeneous, and formal methodologies, making them understandable, reproducible, and auditable. Objectives: This study aims to design and implement a methodology, according with FAIR Principles, for building ETL processes (focused on data extraction, selection, and transformation) for EHR reuse in a transparent and flexible manner, applicable to any clinical condition and health care organization. Methods: The proposed methodology comprises four stages: (1) analysis of secondary use models and identification of data operations, based on internationally used clinical repositories, case report forms, and aggregated datasets; (2) modeling and formalization of data operations, through the paradigm of the Detailed Clinical Models; (3) agnostic development of data operations, selecting SQL and R as programming languages; and (4) automation of the ETL instantiation, building a formal configuration file with XML. Results: First, four international projects were analyzed to identify 17 operations, necessary to obtain datasets according to the specifications of these projects from the EHR. With this, each of the data operations was formalized, using the ISO 13606 reference model, specifying the valid data types as arguments, inputs and outputs, and their cardinality. Then, an agnostic catalog of data was developed through data-oriented programming languages previously selected. Finally, an automated ETL instantiation process was built from an ETL configuration file formally defined. Conclusions: This study has provided a transparent and flexible solution to the difficulty of making the processes for obtaining EHR-derived data for secondary use understandable, auditable, and reproducible. Moreover, the abstraction carried out in this study means that any previous EHR reuse methodology can incorporate these results into them.Ministerio de Economía y Competitividad Instituto de Salud Carlos III PI18/00981, PI18/01047, PI18CIII/00019.S

Machine learning-based model for prediction of clinical deterioration in hospitalized patients by COVID 19

[EN] Despite the publication of great number of tools to aid decisions in COVID-19 patients, there is a lack of good instruments to predict clinical deterioration. COVID19-Osakidetza is a prospective cohort study recruiting COVID-19 patients. We collected information from baseline to discharge on: sociodemographic characteristics, comorbidities and associated medications, vital signs, treatment received and lab test results. Outcome was need for intensive ventilatory support (with at least standard high-flow oxygen face mask with a reservoir bag for at least 6 h and need for more intensive therapy afterwards or Optiflow high-flow nasal cannula or noninvasive or invasive mechanical ventilation) and/or admission to a critical care unit and/or death during hospitalization. We developed a Catboost model summarizing the findings using Shapley Additive Explanations. Performance of the model was assessed using area under the receiver operating characteristic and prediction recall curves (AUROC and AUPRC respectively) and calibrated using the Hosmer-Lemeshow test. Overall, 1568 patients were included in the derivation cohort and 956 in the (external) validation cohort. The percentages of patients who reached the composite endpoint were 23.3% vs 20% respectively. The strongest predictors of clinical deterioration were arterial blood oxygen pressure, followed by age, levels of several markers of inflammation (procalcitonin, LDH, CRP) and alterations in blood count and coagulation. Some medications, namely, ATC AO2 (antiacids) and N05 (neuroleptics) were also among the group of main predictors, together with C03 (diuretics). In the validation set, the CatBoost AUROC was 0.79, AUPRC 0.21 and Hosmer-Lemeshow test statistic 0.36. We present a machine learning-based prediction model with excellent performance properties to implement in EHRs. Our main goal was to predict progression to a score of 5 or higher on the WHO Clinical Progression Scale before patients required mechanical ventilation. Future steps are to externally validate the model in other settings and in a cohort from a different period and to apply the algorithm in clinical practice. Registration: ClinicalTrials.gov Identifier: NCT04463706.This work was supported in part by grants from the Instituto de Salud Carlos III and the European Regional Development Fund COVID20/00459; the health outcomes group from Galdakao-Barrualde Health Organization; the Kronikgune Institute for Health Service Research; and the thematic network–REDISSEC (Red de Investigación en Servicios de Salud en Enfermedades Crónicas)–of the Instituto de Salud Carlos III. The funder of the study had no role in study design, data collection, analysis, management or interpretation, or writing of the report

EXTRAE: EXTRaction of Associations between Diseases and Other Medical Concepts

El propósito de este proyecto es investigar en la mejora de las técnicas de extracción de Reglas de Asociación (RA) entre enfermedades, o entre enfermedades y otros conceptos médicos. Estas reglas permiten representar el conocimiento médico subyacente a un conjunto de Historias Clínica Electrónica (HCE). Concretamente nos planteamos explorar técnicas semisupervisadas que nos permitan alcanzar resultados equiparables a los de las técnicas supervisadas con una mínima supervisión. El proyecto se propone realizar avances significativos en la selección de reglas de asociación relevantes en el dominio de la salud, que pueden tener una alta aplicabilidad en la ayuda al diagnóstico y en la prevención de enfermedades.This project aims to improve the techniques for extracting Association Rules (AR) between diseases, or between diseases and other medical concepts. These rules allow the representation of medical knowledge underlying a set of Electronic Medical Records (EHR). Particularly, we plan to explore semi-supervised techniques that allow us to achieve similar results to those obtained using supervised techniques, but requiring minimal supervision. The project intends to make significant progress in the selection of relevant AR, which may be applied in the health domain for developing diagnostic help systems, or for disease prevention.Este trabajo ha sido parcialmente financiado por los proyectos EXTRAE (IMIENS 2017) y PROSA-MED (TIN2016-77820-C3-2-R)

HAZLO: Plataforma de telesalud basada en tecnologías mhealth para el despliegue de programas personalizados de rehabilitación cardiaca fase II

CASEIB 2015. XXXIII Congreso Anual de la Sociedad Española de Ingeniería Biomédica. Madrid 4, 5 y 6 de noviembre 2015.Actualmente, los Programas de Rehabilitación Cardiaca, tanto en provisión presencial como domiciliaria, afrontan la necesidad de incrementar sus tasas de adopción y adherencia, y en estos retos, los servicios de telesalud basados en mhealth comienzan a jugar un papel relevante, aunque la evidencia es fragmentada y de baja calidad. Se ha implementado un servicio de telesalud que despliega un programa basado en actividades terapéuticas de rehabilitación física (marcha) y psicológica (relajación), contenidos educativos para la autogestión, y herramientas para la interacción virtual (mensajería, videollamada y foros). Se presenta en este trabajo la descripción del servicio y los resultados del pilotaje (41 pacientes, 5 meses), para evaluar la viabilidad en términos de operatividad-funcionalidad en cada uno de sus componentes y adherencia a los protocolos por parte de los pacientes. Se ha iniciado un ensayo aleatorizado controlado (128+128 pacientes) para estudiar la no inferioridad en resultados clínicos del modelo de provisión basado en telesalud frente al tradicional; adicionalmente, se estudiarán la mejora en calidad de vida, satisfacción y usabilidad.Este trabajo está siendo financiado por la AES 2012, PI12/00389 y PI12/00585 (coordinados), y PI12/00508, y la colaboración de REDISSEC RD12/0001/0001.N

OntoCR: A CEN/ISO-13606 clinical repository based on ontologies

Objective: To design a new semantically interoperable clinical repository, based on ontologies, conforming to CEN/ISO 13606 standard. Materials and Methods: The approach followed is to extend OntoCRF, a framework for the development of clinical repositories based on ontologies. The meta-model of OntoCRF has been extended by incorporating an OWL model integrating CEN/ISO 13606, ISO 21090 and SNOMED CT structure. Results: This approach has demonstrated a complete evaluation cycle involving the creation of the meta-model in OWL format, the creation of a simple test application, and the communication of standardized extracts to another organization. Discussion: Using a CEN/ISO 13606 based system, an indefinite number of archetypes can be merged (and reused) to build new applications. Our approach, based on the use of ontologies, maintains data storage independent of content specification. With this approach, relational technology can be used for storage, maintaining extensibility capabilities. Conclusions: The present work demonstrates that it is possible to build a native CEN/ISO 13606 repository for the storage of clinical data. We have demonstrated semantic interoperability of clinical information using CEN/ISO 13606 extracts

CAREVID+: Plataforma web para la evaluación de la implantación de buenas prácticas en cuidados

El objetivo de este trabajo es presentar la plataforma web CAREVID+, como una herramienta para el soporte de: (1) la implantación de guías de e buenas prácticas (BBPP) en aquellas entidades sanitarias adheridas al Programa de Implantación de Guías de Buenas Prácticas en Centros Comprometidos con la Excelencia en Cuidados (CCEC®); y (2) la evaluación continuada del proceso de implantación de las guías de BBPP, a través del análisis de una serie de indicadores definidos en cada guía.Trabajo financiado por: proyecto de investigación PI15CIII-00003 de la Acción Estratégica de Salud Intramural 2015; CIBERFES; y RETIC REDISSEC RD16/0001/0016S

Desarrollo y evaluación de un repositorio para usos secundarios conforme a OMOP-CDM para la cohorte CoRIS

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Transformación OMOP-CDM del repositorio para usos secundarios de la cohorte de la Red Española de Investigación en SIDA (CoRIS)

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Educar por una cultura de paz y convivencia : actas

Además de artículos realizados por los autores citados cuenta con artículos de los siguientes autores: Jonan Fernández Erdozia, Carme Orte Socías, Javier ElzoActas del curso en que se analizaron las bases de una educación para la paz, la situación actual (con los conflictos y desequilibrios existentes) y las posibles estrategias para afrontar esta realidad.BalearesES