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

Caso de Uso Comunidad Autónoma1: Interoperabilidad de sistemas y datos en Salud Digital para la Medicina de Precisión.

Sesión 3. Medicina de Precisión y Transformación Digital del Sistema Nacional de Salud.Trayectoria de proyectos. Registro y uso primario de la información. Modelo de información COVID-19 del H120. Historia Persona de Salud y registros del paciente. Estrategia: un registro, múltiples usos secundarios Models normalization in EHR data reuse process. Modelos de información de salud. Modelo y significado de los datos. Ecosistema Uso secundario del H120.Proyectos de información de salud y casos de éxito Repositorio i2b2 y plataforma Insite/Tri/NetX. Referencia nacional en Portal COVID19 europeo. IMPaCT.N

Hacia la gestión del conocimiento hospitalario desde la biblioteca: gestión de la producción científica del hospital universitario de Fuenlabrada [PÓSTER]

Incluye resumen y pósterDesde 2009, la Biblioteca del Hospital Universitario de Fuenlabrada (HUF) integra entre sus servicios la gestión de la producción científica de los profesionales del Hospital dando apoyo a los investigadores (elaboración de su Curriculum Vitae) y a la propia organización (elaboración de la Memoria Científica). Dicho apoyo se concreta en cuatro líneas de actuación de la biblioteca: 1. Informar y alertar sobre la actualidad del mundo de la investigación. 2. Recopilar la producción científica realizada por profesionales del hospital. 3. Apoyar a los investigadores a través de los servicios de Atención Bibliográfica Personalizada (SABP) y Formación de Usuarios (SFU). 4. Analizar los datos recopilados y difundirlos a través de la Memoria Científica del HUF.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

Patient summary and medicines reconciliation: application of the ISO/CEN EN 13606 standard in clinical practice

The comparison of the patient's current medication list with the medication being ordered when admitted to Hospital, identifying omissions, duplications, dosing errors, and potential interactions, constitutes the core process of medicines reconciliation. Access to the medication the patient is taking at home could be unfeasible as this information is frequently stored in various locations and in diverse proprietary formats. The lack of interoperability between those information systems, namely the Primary Care and the Specialized Electronic Health Records (EHRs), facilitates medication errors and endangers patient safety. Thus, the development of a Patient Summary that includes clinical data from different electronic systems will allow doctors access to relevant information enabling a safer and more efficient assistance. Such a collection of data from heterogeneous and distributed systems has been achieved in this Project through the construction of a federated view based on the ISO/CEN EN13606 Standard for architecture and communication of EHRsThis Project has been funded by the Spanish Health Ministry (Convenio de colaboración para el impulso de prácticas seguras en Centros Sanitarios 2008) and has been awarded with one of the Quality within the Spanish National Health System Prizes 2009.Farfán Sedano, FJ.; Terrón Cuadrado, M.; Castellanos Clemente, Y.; Serrano Balazote, P.; Moner Cano, D.; Robles Viejo, M. (2011). Patient summary and medicines reconciliation: application of the ISO/CEN EN 13606 standard in clinical practice. En Patient Safety Informatics: adverse drug events, human factors and IT tools for patient medication safety. IOS Press. 189-196. doi:10.3233/978-1-60750-740-6-189S18919

Examining database persistence of ISO/EN 13606 standardized electronic health record extracts: relational vs. NoSQL approaches

Background: The objective of this research is to compare the relational and non-relational (NoSQL) database systems approaches in order to store, recover, query and persist standardized medical information in the form of ISO/EN 13606 normalized Electronic Health Record XML extracts, both in isolation and concurrently. NoSQL database systems have recently attracted much attention, but few studies in the literature address their direct comparison with relational databases when applied to build the persistence layer of a standardized medical information system. Methods: One relational and two NoSQL databases (one document-based and one native XML database) of three different sizes have been created in order to evaluate and compare the response times (algorithmic complexity) of six different complexity growing queries, which have been performed on them. Similar appropriate results available in the literature have also been considered. Results: Relational and non-relational NoSQL database systems show almost linear algorithmic complexity query execution. However, they show very different linear slopes, the former being much steeper than the two latter. Document-based NoSQL databases perform better in concurrency than in isolation, and also better than relational databases in concurrency. Conclusion: Non-relational NoSQL databases seem to be more appropriate than standard relational SQL databases when database size is extremely high (secondary use, research applications). Document-based NoSQL databases perform in general better than native XML NoSQL databases. EHR extracts visualization and edition are also document-based tasks more appropriate to NoSQL database systems. However, the appropriate database solution much depends on each particular situation and specific problem

Supplementary files for Examining database persistence of ISO/EN 13606 standardized Electronic Health Record extracts: relational vs. noSQL approaches

3 code files written in sql, java and xquery performing six queries on mysql, mongodb and eXist databases respectively described in the paper entitled "Examining database persistence of ISO/EN 13606 standardized Electronic Health Record extracts: relational vs. noSQL approaches

Obtención de un conjunto de datos derivados de la HCE para investigación en VIH: prueba de concepto

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Students\u27 Perspectives and Experiences with the Interdisciplinary Community Engagement Pilot Project: Fair Housing 49507

PURPOSE: The purpose of this study is to assess the students’ perspectives and experiences with the interdisciplinary community learning pilot project: Fair Housing 49507. The study is important because it will inform the university/community about the opportunities and challenges of implementing interdisciplinary community engagement within the classroom environment. SUBJECTS: 40 undergraduate students enrolled in five courses across five different academic disciplines at GVSU. METHODS AND MATERIALS: An electronic survey administered in March 2014.ANALYSES: The survey asks about each student’s experience participating in the interdisciplinary community engagement pilot project: Fair Housing 49507. Analysis methods include frequencies and cross tabs analysis in SPSS. RESULTS: findings will be reported about students’ attitudes and learning experiences during the pilot. CONCLUSIONS: This study will then provide recommendations for future interdisciplinary community engagement efforts at GVSU