Browsing by Subject "Semantic interoperability"

Now showing 1 - 9 of 9
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    A semantic web based framework for the interoperability and exploitation of clinical models and EHR data
    (Elsevier Science BV, 2016-05-12) Legaz García, María del Carmen; Martínez Costa, Catalina; Menárguez Tortosa, Marcos; Fernández Breis, Jesualdo Tomás; Informática y Sistemas
    The advent of electronic healthcare records (EHR) systems has triggered the need for their semantic in- teroperability, which is reinforced by the opportunities for the secondary use of EHR data. The joint use of EHR standards and semantic resources has been identified as key for semantic interoperability. To date, existing tools focused on EHR standards permit to create, search, explore clinical models and to map data sources to clinical models, but do not provide an appropriate support and integration of semantic re- sources or permit the secondary use of EHR data. In this paper we describe an OWL-based framework that leverages EHR and Semantic Web technologies for the interoperability and exploitation of archetypes, EHR data and ontologies. It also enables the secondary use of clinical data. This framework has been im- plemented in the Archetype Management System (ArchMS). We also describe how ArchMS has been used in a real study in the colorectal cancer domain.
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    An approach for the semantic interoperability of ISO EN 13606 and OpenEHR archetypes
    (Elsevier, 2010-06) Martínez Costa, Catalina; Menárguez Tortosa, Marcos; Fernández Breis, Jesualdo Tomás; Informática y Sistemas
    The communication between health information systems of hospitals and primary care organizations is currently an important challenge to improve the quality of clinical practice and patient safety. However, clinical information is usually distributed among several independent systems that may be syntactically or semantically incompatible. This fact prevents healthcare professionals from accessing clinical information of patients in an understandable and normalized way. In this work, we address the semantic interoperability of two EHR standards: OpenEHR and ISO EN 13606. Both standards follow the dual model approach which distinguishes information and knowledge, this being represented through archetypes. The solution presented here is capable of transforming OpenEHR archetypes into ISO EN 13606 and vice versa by combining Semantic Web and Model-driven Engineering technologies. The resulting software implementation has been tested using publicly available collections of archetypes for both standards.
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    Open Access
    Clinical data interoperability based on archetype transformation
    (Elsevier, 2011-05) Martínez Costa, Catalina; Menárguez Tortosa, Marcos; Fernández Breis, Jesualdo Tomás; Informática y Sistemas
    The semantic interoperability between health information systems is a major challenge to improve the quality of clinical practice and patient safety. In recent years many projects have faced this problem and provided solutions based on specific standards and technologies in order to satisfy the needs of a particular scenario. Most of such solutions cannot be easily adapted to new scenarios, thus more global solutions are needed. In this work, we have focused on the semantic interoperability of electronic healthcare records standards based on the dual model architecture and we have developed a solution that has been applied to ISO 13606 and openEHR. The technological infrastructure combines reference models, archetypes and ontologies, with the support of Model-driven Engineering techniques. For this purpose, the interoperability infrastructure developed in previous work by our group has been reused and extended to cover the requirements of data transformation
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    HL7 FHIR: ontological reinterpretation of medication resources
    (IOS Press, 2017) Martínez Costa, Catalina; Schulz, Stefan; Informática y Sistemas
    A solid ontology-based analysis with a rigorous formal mapping for correctness" is one of the ten reasons why the HL7 standard Fast Healthcare Interoperability Resources (FHIR) is advertised to be better than other standards for EHR interoperability. In this paper, we aim at contributing to this formal analysis by proposing an RDF representation of a subset of FHIR resources based on a highly constrained top-level ontology and guided by the use of a set of Content Ontology Design Patterns (Content ODPs) for representing clinical information. We exemplify this by reinterpreting FHIR medication resources. Although a manual task now, we foresee a possible automatic translation by using RDF shapes
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    Performance assessment of ontology matching systems for FAIR data
    (2022-07-15) Van Damme, P.; Fernandez-Breis, J. T.; Benis, N.; Miñarro Giménez, José Antonio; De Keizer, N.; Cornet, R.; Informática y Sistemas
    Background: Ontology matching should contribute to the interoperability aspect of FAIR data (Findable, Accessible, Interoperable, and Reusable). Multiple data sources can use different ontologies for annotating their data and, thus, creating the need for dynamic ontology matching services. In this experimental study, we assessed the performance of ontology matching systems in the context of a real-life application from the rare disease domain. Additionally, we present a method for analyzing top-level classes to improve precision. Results: We included three ontologies (NCIt, SNOMED CT, ORDO) and three matching systems (AgreementMakerLight 2.0, FCA-Map, LogMap 2.0). We evaluated the performance of the matching systems against reference alignments from BioPortal and the Unified Medical Language System Metathesaurus (UMLS). Then, we analyzed the top-level ancestors of matched classes, to detect incorrect mappings without consulting a reference alignment. To detect such incorrect mappings, we manually matched semantically equivalent top-level classes of ontology pairs. AgreementMakerLight 2.0, FCA-Map, and LogMap 2.0 had F1-scores of 0.55, 0.46, 0.55 for BioPortal and 0.66, 0.53, 0.58 for the UMLS respectively. Using vote-based consensus alignments increased performance across the board. Evaluation with manually created top-level hierarchy mappings revealed that on average 90% of the mappings’ classes belonged to top-level classes that matched. Conclusions: Our findings show that the included ontology matching systems automatically produced mappings that were modestly accurate according to our evaluation. The hierarchical analysis of mappings seems promising when no reference alignments are available. All in all, the systems show potential to be implemented as part of an ontology matching service for querying FAIR data. Future research should focus on developing methods for the evaluation of mappings used in such mapping services, leading to their implementation in a FAIR data ecosystem.
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    Records in context: el camino de los archivos hacia la interoperabilidad semántica
    (Ediciones el Profesional de la Información, 2017) Pastor-Sánchez, Juan-Antonio; Llanes-Padrón, Dunia; Información y Documentación
    En los últimos años el proceso de descripción archivística ha experimentado cambios en su concepción teórica y metodológica. Las tecnologías y los nuevos usuarios han obligado a cambiar los métodos de concebir el proceso. El paradigma posmoderno ha influido en la representación de la información, disipando las líneas de separación entre los archivos, las bibliotecas y los museos. En este contexto, el Consejo Internacional de Archivos ha desarrollado un modelo conceptual para la descripción denominado Records in context, que unifica la normas ISAD(G), ISAAR(CPF), ISDF e ISDIAH y establece las entidades, atributos y relaciones que conforman las descripciones archivísticas. El modelo facilita la interoperabilidad semántica descentralizada y viabiliza el desarrollo de una ontología OWL para la representación y publicación de conjuntos de datos archivísticos mediante tecnologías de la web semántica. Records in context posiciona a los recursos archivísticos en la dinámica de la publicación directa en la Web y ofrece una gran oportunidad para adoptar nuevos enfoques en la búsqueda, el acceso y uso de la información archivística.
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    Records in Contexts: the road of archives to semantic interoperability
    (Emerald, 2017) Llanes-Padrón, Dunia; Pastor Sánchez, Juan Antonio; Información y Documentación
    Purpose - This paper examines the Records in Contexts proposal of a conceptual model (RiC-CM) from the International Council on Archives’ (ICA) archival description and proposes an OWL ontology for its implementation in the semantic web. Design/methodology/approach - The various elements of the model are studied and are related to earlier norms in order to understand their structure and the modeling of the ontology. Findings - The analysis reveals the integrating nature of RiC-CM and the possibilities it offers for greater interoperability of data from archival descriptions. Two versions of an OWL ontology were developed to represent the conceptual model. The first makes a direct transposition of the conceptual model; the second optimizes the properties and relations in order to simplify the use and maintenance of the ontology. Research limitations / implications - The proposed ontology will follow the considerations of the final version of the ICA’s RiC-CM. Practical implications - The analysis affords an understanding of the role of RiC-CM in publishing online archival datasets, while the ontology is an initial approach to the semantic web technologies involved. Originality/value - The paper offers an overview of Records in Contexts with respect to the advantages in the field of semantic interoperability, and supposes the first proposal of an ontology based on the conceptual model.
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    Using the ResearchEHR platform to facilitate the practical application of the EHR standards
    (Elsevier, 2012-08) Maldonado, Jose Alberto; Martínez Costa, Catalina; Moner, David; Menárguez Tortosa, Marcos; Boscá, Diego; Miñarro Giménez, José Antonio; Fernández Breis, Jesualdo Tomás; Robles, Montserrat; Informática y Sistemas
    Possibly the most important requirement to support co-operative work among health professionals and institutions is the ability of sharing EHRs in a meaningful way, and it is widely acknowledged that standardization of data and concepts is a prerequisite to achieve semantic interoperability in any domain. Different international organizations are working on the definition of EHR architectures but the lack of tools that implement them hinders their broad adoption. In this paper we present ResearchEHR, a software platform whose objective is to facilitate the practical application of EHR standards as a way of reaching the desired semantic interoperability. This platform is not only suitable for developing new systems but also for increasing the standardization of existing ones. The work reported here describes how the platform allows for the edition, validation, and search of archetypes, converts legacy data into normalized, archetypes extracts, is able to generate applications from archetypes and finally, transforms archetypes and data extracts into other EHR standards. We also include in this paper how ResearchEHR has made possible the application of the CEN/ISO 13606 standard in a real environment and the lessons learnt with this experience
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    Validating EHR clinical models using ontology patterns
    (Elsevier, 2017-12) Martínez Costa, Catalina; Schulz, Stefan; Informática y Sistemas
    Clinical models are artefacts that specify how information is structured in electronic health records (EHRs). However, the makeup of clinical models is not guided by any formal constraint beyond a semantically vague information model. We address this gap by advocating ontology design patterns as a mechanism that makes the semantics of clinical models explicit. This paper demonstrates how ontology design patterns can validate existing clinical models using SHACL. Based on the Clinical Information Modelling Initiative (CIMI), we show how ontology patterns detect both modeling and terminology binding errors in CIMI models. SHACL, a W3C constraint language for the validation of RDF graphs, builds on the concept of “Shape”, a description of data in terms of expected cardinalities, datatypes and other restrictions. SHACL, as opposed to OWL, subscribes to the Closed World Assumption (CWA) and is therefore more suitable for the validation of clinical models. We have demonstrated the feasibility of the approach by manually describing the correspondences between six CIMI clinical models represented in RDF and two SHACL ontology design patterns. Using a Java-based SHACL implementation, we found at least eleven modeling and binding errors within these CIMI models. This demonstrates the usefulness of ontology design patterns not only as a modeling tool but also as a tool for validation.