Semantic validation of the use of SNOMED CT in HL7 clinical documents

<p>Abstract</p> <p>Background</p> <p>The HL7 Clinical Document Architecture (CDA) constrains the HL7 Reference Information model (RIM) to specify the format of HL7-compliant clinical documents, dubbed <it>CDA documents</it>. The use of clinical terminologies such as SNOMED CT^®further improves interoperability as they provide a shared understanding of concepts used in clinical documents. However, despite the use of the RIM and of shared terminologies such as SNOMED CT^®, gaps remain as to how to use both the RIM and SNOMED CT^®in HL7 clinical documents. The HL7 implementation guide on <it>Using SNOMED CT in HL7 Version 3 </it>is an effort to close this gap. It is, however, a human-readable document that is not suited for automatic processing. As such, health care professionals designing clinical documents need to ensure validity of documents manually.</p> <p>Results</p> <p>We represent the CDA using the Ontology Web Language OWL and further use the OWL version of SNOMED CT^®to enable the translation of CDA documents to so-called OWL <it>ontologies</it>. We formalize a subset of the constraints in the implementation guide on <it>Using SNOMED CT in HL7 Version 3 </it>as OWL <it>Integrity Constraints </it>and show that we can automatically validate CDA documents using OWL reasoners such as Pellet. Finally, we evaluate our approach via a prototype implementation that plugs in the Open Health Workbench.</p> <p>Conclusions</p> <p>We present a methodology to automatically check the validity of CDA documents which make reference to SNOMED CT^®terminology. The methodology relies on semantic technologies such as OWL. As such it removes the burden from IT health care professionals of having to manually implement such guidelines in systems that use HL7 Version 3 documents.</p

Report on the EHCR (Deliverable 26.2)

This deliverable is the second for Workpackage 26. The first, submitted after Month 12, summarised the areas of research that the partners had identified as being relevant to the semantic indexing of the EHR. This second one reports progress on the key threads of work identified by the partners during the project to contribute towards semantically interoperable and processable EHRs. This report provides a set of short summaries on key topics that have emerged as important, and to which the partners are able to make strong contributions. Some of these are also being extended via two new EU Framework 6 proposals that include WP26 partners: this is also a measure of the success of this Network of Excellence

Next generation assisting clinical applications by using semantic-aware electronic health records

The health care sector is no longer imaginable without electronic health records. However; since the original idea of electronic health records was focused on data storage and not on data processing, a lot of current implementations do not take full advantage of the opportunities provided by computerization. This paper introduces the Patient Summary Ontology for the representation of electronic health records and demonstrates the possibility to create next generation assisting clinical applications based on these semantic-aware electronic health records. Also, an architecture to interoperate with electronic health records formatted using other standards is presented

Design and Implementation of a Collaborative Clinical Practice and Research Documentation System Using SNOMED-CT and HL7-CDA in the Context of a Pediatric Neurodevelopmental Unit

This paper introduces a prototype for clinical research documentation using the structured information model HL7 CDA and clinical terminology (SNOMED CT). The proposed solution was integrated with the current electronic health record system (EHR-S) and aimed to implement interoperability and structure information, and to create a collaborative platform between clinical and research teams. The framework also aims to overcome the limitations imposed by classical documentation strategies in real-time healthcare encounters that may require fast access to complex information. The solution was developed in the pediatric hospital (HP) of the University Hospital Center of Coimbra (CHUC), a national reference for neurodevelopmental disorders, particularly for autism spectrum disorder (ASD), which is very demanding in terms of longitudinal and cross-sectional data throughput. The platform uses a three-layer approach to reduce components’ dependencies and facilitate maintenance, scalability, and security. The system was validated in a real-life context of the neurodevelopmental and autism unit (UNDA) in the HP and assessed based on the functionalities model of EHR-S (EHR-S FM) regarding their successful implementation and comparison with state-of-the-art alternative platforms. A global approach to the clinical history of neurodevelopmental disorders was worked out, providing transparent healthcare data coding and structuring while preserving information quality. Thus, the platform enabled the development of user-defined structured templates and the creation of structured documents with standardized clinical terminology that can be used in many healthcare contexts. Moreover, storing structured data associated with healthcare encounters supports a longitudinal view of the patient’s healthcare data and health status over time, which is critical in routine and pediatric research contexts. Additionally, it enables queries on population statistics that are key to supporting the definition of local and global policies, whose importance was recently emphasized by the COVID pandemic.info:eu-repo/semantics/publishedVersio

Comparative study of healthcare messaging standards for interoperability in ehealth systems

Advances in the information and communication technology have created the field of "health informatics," which amalgamates healthcare, information technology and business. The use of information systems in healthcare organisations dates back to 1960s, however the use of technology for healthcare records, referred to as Electronic Medical Records (EMR), management has surged since 1990’s (Net-Health, 2017) due to advancements the internet and web technologies. Electronic Medical Records (EMR) and sometimes referred to as Personal Health Record (PHR) contains the patient’s medical history, allergy information, immunisation status, medication, radiology images and other medically related billing information that is relevant. There are a number of benefits for healthcare industry when sharing these data recorded in EMR and PHR systems between medical institutions (AbuKhousa et al., 2012). These benefits include convenience for patients and clinicians, cost-effective healthcare solutions, high quality of care, resolving the resource shortage and collecting a large volume of data for research and educational needs. My Health Record (MyHR) is a major project funded by the Australian government, which aims to have all data relating to health of the Australian population stored in digital format, allowing clinicians to have access to patient data at the point of care. Prior to 2015, MyHR was known as Personally Controlled Electronic Health Record (PCEHR). Though the Australian government took consistent initiatives there is a significant delay (Pearce and Haikerwal, 2010) in implementing eHealth projects and related services. While this delay is caused by many factors, interoperability is identified as the main problem (Benson and Grieve, 2016c) which is resisting this project delivery. To discover the current interoperability challenges in the Australian healthcare industry, this comparative study is conducted on Health Level 7 (HL7) messaging models such as HL7 V2, V3 and FHIR (Fast Healthcare Interoperability Resources). In this study, interoperability, security and privacy are main elements compared. In addition, a case study conducted in the NSW Hospitals to understand the popularity in usage of health messaging standards was utilised to understand the extent of use of messaging standards in healthcare sector. Predominantly, the project used the comparative study method on different HL7 (Health Level Seven) messages and derived the right messaging standard which is suitable to cover the interoperability, security and privacy requirements of electronic health record. The issues related to practical implementations, change over and training requirements for healthcare professionals are also discussed

Archetype development and governance methodologies for the electronic health record

[ES] La interoperabilidad semántica de la información sanitaria es un requisito imprescindible para la sostenibilidad de la atención sanitaria, y es fundamental para afrontar los nuevos retos sanitarios de un mundo globalizado. Esta tesis aporta nuevas metodologías para abordar algunos de los aspectos fundamentales de la interoperabilidad semántica, específicamente aquellos relacionados con la definición y gobernanza de modelos de información clínica expresados en forma de arquetipo. Las aportaciones de la tesis son: - Estudio de las metodologías de modelado existentes de componentes de interoperabilidad semántica que influirán en la definición de una metodología de modelado de arquetipos. - Análisis comparativo de los sistemas e iniciativas existentes para la gobernanza de modelos de información clínica. - Una propuesta de Metodología de Modelado de Arquetipos unificada que formalice las fases de desarrollo del arquetipo, los participantes requeridos y las buenas prácticas a seguir. - Identificación y definición de principios y características de gobernanza de arquetipos. - Diseño y desarrollo de herramientas que brinden soporte al modelado y la gobernanza de arquetipos. Las aportaciones de esta tesis se han puesto en práctica en múltiples proyectos y experiencias de desarrollo. Estas experiencias varían desde un proyecto local dentro de una sola organización que requirió la reutilización de datos clínicos basados en principios de interoperabilidad semántica, hasta el desarrollo de proyectos de historia clínica electrónica de alcance nacional.[CA] La interoperabilitat semàntica de la informació sanitària és un requisit imprescindible per a la sostenibilitat de l'atenció sanitària, i és fonamental per a afrontar els nous reptes sanitaris d'un món globalitzat. Aquesta tesi aporta noves metodologies per a abordar alguns dels aspectes fonamentals de la interoperabilitat semàntica, específicament aquells relacionats amb la definició i govern de models d'informació clínica expressats en forma d'arquetip. Les aportacions de la tesi són: - Estudi de les metodologies de modelatge existents de components d'interoperabilitat semàntica que influiran en la definició d'una metodologia de modelatge d'arquetips. - Anàlisi comparativa dels sistemes i iniciatives existents per al govern de models d'informació clínica. - Una proposta de Metodologia de Modelatge d'Arquetips unificada que formalitza les fases de desenvolupament de l'arquetip, els participants requerits i les bones pràctiques a seguir. - Identificació i definició de principis i característiques de govern d'arquetips. - Disseny i desenvolupament d'eines que brinden suport al modelatge i al govern d'arquetips. Les aportacions d'aquesta tesi s'han posat en pràctica en múltiples projectes i experiències de desenvolupament. Aquestes experiències varien des d'un projecte local dins d'una sola organització que va requerir la reutilització de dades clíniques basades en principis d'interoperabilitat semàntica, fins al desenvolupament de projectes d'història clínica electrònica d'abast nacional.[EN] Semantic interoperability of health information is an essential requirement for the sustainability of healthcare, and it is essential to face the new health challenges of a globalized world. This thesis provides new methodologies to tackle some of the fundamental aspects of semantic interoperability, specifically those aspects related to the definition and governance of clinical information models expressed in the form of archetypes. The contributions of the thesis are: - Study of existing modeling methodologies of semantic interoperability components that will influence in the definition of an archetype modeling methodology. - Comparative analysis of existing clinical information model governance systems and initiatives. - A proposal of a unified Archetype Modeling Methodology that formalizes the phases of archetype development, the required participants, and the good practices to be followed. - Identification and definition of archetype governance principles and characteristics. - Design and development of tools that provide support to archetype modeling and governance. The contributions of this thesis have been put into practice in multiple projects and development experiences. These experiences vary from a local project inside a single organization that required a reuse on clinical data based on semantic interoperability principles, to the development of national electronic health record projects.This thesis was partially funded by the Ministerio de Economía y Competitividad, ayudas para contratos para la formación de doctores en empresas “Doctorados Industriales”, grant DI-14-06564 and by the Agencia Valenciana de la Innovación, ayudas del Programa de Promoción del Talento – Doctorados empresariales (INNODOCTO), grant INNTA3/2020/12.Moner Cano, D. (2021). Archetype development and governance methodologies for the electronic health record [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/16491

SNOMED2HL7: a tool to normalize and bind SNOMED CT concepts to the HL7 Reference Information Model

[Abstract] BACKGROUND: Current clinical research and practice requires interoperability among systems in a complex and highly dynamic domain. There has been a significant effort in recent years to develop integrative common data models and domain terminologies. Such efforts have not completely solved the challenges associated with clinical data that are distributed among different and heterogeneous institutions with different systems to encode the information. Currently, when providing homogeneous interfaces to exploit clinical data, certain transformations still involve manual and time-consuming processes that could be automated. OBJECTIVES: There is a lack of tools to support data experts adopting clinical standards. This absence is especially significant when links between data model and vocabulary are required. The objective of this work is to present SNOMED2HL7, a novel tool to automatically link biomedical concepts from widely used terminologies, and the corresponding clinical context, to the HL7 Reference Information Model (RIM). METHODS: Based on the recommendations of the International Health Terminology Standards Development Organisation (IHTSDO), the SNOMED Normal Form has been implemented within SNOMED2HL7 to decompose and provide a method to reduce the number of options to store the same information. The binding of clinical terminologies to HL7 RIM components is the core of SNOMED2HL7, where terminology concepts have been annotated with the corresponding options within the interoperability standard. A web-based tool has been developed to automatically provide information from the normalization mechanisms and the terminology binding. RESULTS: SNOMED2HL7 binding coverage includes the majority of the concepts used to annotate legacy systems. It follows HL7 recommendations to solve binding overlaps and provides the binding of the normalized version of the concepts. The first version of the tool, available at http://kandel.dia.fi.upm.es:8078, has been validated in EU funded projects to integrate real world data for clinical research with an 88.47% of accuracy. CONCLUSIONS: This paper presents the first initiative to automatically retrieve concept-centered information required to transform legacy data into widely adopted interoperability standards. Although additional functionality will extend capabilities to automate data transformations, SNOMED2HL7 already provides the functionality required for the clinical interoperability community.Instituto de Salud Carlos III; PI13/0202

Combining semantic web technologies with evolving fuzzy classifier eClass for EHR-based phenotyping : a feasibility study

In parallel to nation-wide efforts for setting up shared electronic health records (EHRs) across healthcare settings, several large-scale national and international projects are developing, validating, and deploying electronic EHR oriented phenotype algorithms that aim at large-scale use of EHRs data for genomic studies. A current bottleneck in using EHRs data for obtaining computable phenotypes is to transform the raw EHR data into clinically relevant features. The research study presented here proposes a novel combination of Semantic Web technologies with the on-line evolving fuzzy classifier eClass to obtain and validate EHR-driven computable phenotypes derived from 1956 clinical statements from EHRs. The evaluation performed with clinicians demonstrates the feasibility and practical acceptability of the approach proposed

Archetype Modeling Methodology

[EN] Clinical Information Models (CIMs) expressed as archetypes play an essential role in the design and development of current Electronic Health Record (EHR) information structures. Although there exist many experiences about using archetypes in the literature, a comprehensive and formal methodology for archetype modeling does not exist. Having a modeling methodology is essential to develop quality archetypes, in order to guide the development of EHR systems and to allow the semantic interoperability of health data. In this work, an archetype modeling methodology is proposed. This paper describes its phases, the inputs and outputs of each phase, and the involved participants and tools. It also includes the description of the possible strategies to organize the modeling process. The proposed methodology is inspired by existing best practices of CIMs, software and ontology development. The methodology has been applied and evaluated in regional and national EHR projects. The application of the methodology provided useful feedback and improvements, and confirmed its advantages. The conclusion of this work is that having a formal methodology for archetype development facilitates the definition and adoption of interoperable archetypes, improves their quality, and facilitates their reuse among different information systems and EHR projects. Moreover, the proposed methodology can be also a reference for CIMs development using any other formalism.This work was partially funded by grant DI-14-06564 (Doctorados Industriales) of the Ministerio de Economia y Competitividad of Spain. The authors would also thank the participants of all R&D projects that have served to evaluate and improve the presented methodology.Moner Cano, D.; Maldonado Segura, JA.; Robles Viejo, M. (2018). Archetype Modeling Methodology. Journal of Biomedical Informatics. 79:71-81. https://doi.org/10.1016/j.jbi.2018.02.003S71817

Workshop on the EHCR

This deliverable provides a summary report of a workshop on Electronic Health Records that was organised and delivered as the main focus of Workpackage 16 of the Semantic Mining project. The workshop was held as day three of a three-day series of events held in Brussels in late November 2004, under the umbrella and with kind support of the EUROREC organisation. This report provides a brief summary of that event, and includes in Annex 1 the complete delegate pack as printed and issued to all persons attending the event, This delegate pack included printed copies of all slides and screenshots used throughout the day. The workshop was well attended, and in particular the organisers are pleased to report that some very productive discussions took place that will act as the stimulus for new threads of research collaboration between various Semantic Mining partners, under the work plan of Workpackage 26. The organisers are grateful for the support of the EUROREC organisation in facilitating the organisation of this workshop and for lending their support to it through their web site and a personal endorsement of the event