A Simple Standard for Sharing Ontological Mappings (SSSOM).

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec

The Ligurian HIV network: How medical informatics standards can help clinical research

open11noIntegrating evidence from systematic research in daily clinical practice is one of the pillars of evidence-based medicine. Electronic data capture tools simplify data collection from different centers and supports the management of multicenter clinical trials. The Ligurian HIV Network (LHN) is one such tool, originating from a regional effort to integrate clinical trial capabilities for HIV and other chronic infectious diseases. In order to manually collect a complete report of all clinical tests on patients enrolled in a trial, a strenuous human effort and the allocation of great resources would be necessary. Moreover, the risk of error in a manual system is very high. The proposed system automatically extracts clinical data from the EHR of three hospitals of the LHN in a standardized way, and enhance their re-use in clinical trials. Through dedicated questionnaires, physicians reported a strongly positive feedback about the efficacy of the platform in supporting clinical research.openGiannini B.; Mora S.; Gazzarata R.; Di Biagio A; Cenderello G.; Dentone C.; Setti M.; Fenoglio D.; Cassola G.; Viscoli C.; Giacomini M.Giannini, B.; Mora, S.; Gazzarata, R.; Di Biagio, A; Cenderello, G.; Dentone, C.; Setti, M.; Fenoglio, D.; Cassola, G.; Viscoli, C.; Giacomini, M

The application of medical terminologies to free-text in routine databases using the example of strategies to reduce infant mortality

Hintergrund Die Säuglingssterblichkeitsrate (IMR), ein wichtiger Indikator für die Qualität eines Gesundheitssystems, liegt in Deutschland seit 10 Jahren bei rund 3.5‰. Generische Qualitätsindikatoren (QIs), wie sie seit 2010 in Deutschland verwendet werden, tragen wesentlich zu einem so guten Wert bei, scheinen aber nicht in der Lage zu sein, den IMR weiter zu reduzieren. Die neonatale Sterblichkeitsrate (NMR) trägt zu 65-70% der IMR bei. Der vorgestellte Ansatz schlägt daher eine Einzelfallanalyse neonataler Todesfälle auf der Grundlage von Krankenakten vor. Die meisten elektronischen Krankenakten enthalten noch immer große Mengen an Freitextdaten. Die semantische Auswertung solcher Daten erfordert, dass die Daten mit ausreichenden Klassifizierungen kodiert oder in eine wissensbasierte Datenbank umgewandelt werden. Methodik Die Nordic-Baltic-Classification (NBC) wurde zur Erkennung vermeidbarer neonataler Todesfälle verwendet. Diese Klassifikation wurde auf eine Stichprobe von 1.968 neonatalen Todesfällen angewandt, die über 90% aller neonatalen Todesfälle in Ost-Berlin von 1973 bis 1989 darstellen. Alle Fälle wurden damals von einer speziellen Kommission verschiedener Experten auf der Grundlage der vollständigen perinatalen und klinischen Daten auf ihre Vermeidbarkeit hin analysiert. Der entwickelte Ansatz ermöglicht es, Datenbanken, die über SQL (Structured Query Language) zugänglich sind, direkt über semantische Abfragen zu durchsuchen, ohne dass weitere Transformationen erforderlich sind. Dazu wurden 1.) eine Erweiterung von SQL „Ontology-SQL“ (O-SQL) entwickelt, die es ermöglicht, semantische Ausdrücke zu verwenden, 2.) ein Framework entwickelt, das einen Standardterminologieserver verwendet, um Freitext enthaltende Datenbanktabellen zu annotieren und 3.) ein Parser entwickelt, der O-SQL Ausdrücke in SQL konvertiert, so dass semantische Abfragen direkt an den Datenbankserver weitergeleitet werden können. Ergebnisse Die NBC wurde verwendet, um die Gruppe der Fälle auszuwählen, die ein hohes Vermeidungspotenzial hatten. Die ausgewählte Gruppe stellte 6,0% aller Fälle dar und 60,4% der Fälle innerhalb dieser Gruppe wurden tatsächlich als vermeidbar oder bedingt vermeidbar beurteilt. Die automatische Erkennung von Fehlbildungen ergab einen F1-Wert von 0,94. Darüber hinaus wurde die Verallgemeinerbarkeit des Ansatzes mit verschiedenen semantischen Abfragen nachgewiesen und dessen Güte mit F1-Werten von 0,91 bis 0,98 gemessen. Zusammenfassung Die Ergebnisse zeigen, dass die vorgestellte Methode automatisch anwendbar ist und ein leistungsfähiges und hochsensitives und -spezifisches Werkzeug zur Auswahl potenziell vermeidbarer neonataler Todesfälle und damit zur Unterstützung einer effizienten Einzelfallanalyse darstellt. Die nahtlose Verknüpfung von Ontologien und Standardtechnologien aus dem Datenbankbereich stellt einen wichtigen Bestandteil der unstrukturierten Datenanalyse dar. Die entwickelte Technologie lässt sich problemlos auf aktuelle Daten anwenden und unterstützt das immer wichtiger werdende Feld der translationalen Forschung.Background The infant mortality rate (IMR), a key indicator of the quality of a healthcare system, has remained at approximately 3.5‰ for the past 10 years in Germany. Generic quality indicators (QIs), as used in Germany since 2010, greatly help to ensure such a good value but do not seem to be able to further reduce the IMR. The neonatal mortality rate (NMR) contributes to 65-70% of the IMR. The presented approach therefore proposes single-case analysis of neonatal deaths on base of medical records. Most electronic medical records still contain large amounts of free-text data. Semantic evaluation of such data requires the data to be encoded with sufficient classifications or transformed into a knowledge-based database. Methods The Nordic-Baltic classification (NBC) was used to detect avoidable neonatal deaths. This classification has been applied to a sample of 1,968 neonatal death records, which represent over 90% of all neonatal deaths in East Berlin from 1973 to 1989. All cases were analyzed as to their preventability based on the complete perinatal and clinical data by a special commission of different experts. The developed approach allows databases accessible via SQL (Structured Query Language) to be searched directly through semantic queries without the need for further transformations. Therefore, I) an extension to SQL named Ontology-SQL (O-SQL) that allows to use semantic expressions, II) a framework that uses a standard terminology server to annotate free-text containing database tables and III) a parser that rewrites O-SQL to SQL, so that such queries can be passed to the database server, have been developed. Results The NBC was used to select the group of cases that had a high potential of avoidance. The selected group represented 6.0% of all cases, and 60.4% of the cases within that group were judged avoidable or conditionally avoidable. The automatic detection of malformations showed an F1 score of 0.94. Furthermore, the generability has been proved with different semantic queries and was measured with between 0.91 and 0.98. Conclusion The results show, that the presented method can be applied automatically and is a powerful and highly specific tool for selecting potentially avoidable neonatal deaths and thus for supporting efficient single case analysis. The seamless connection of ontologies and standard technologies from the database field represents an important constituent of unstructured data analysis. The developed technology can be readily applied to current data and supports the increasingly important field of translational research

Beyond the prototypical: Developing a behavioral screening tool of same-gender male intimate partner violence.

In the United States, intimate partner violence (IPV) is estimated to be among the top three health issues impacting gay and bisexual males. Previous studies of IPV prevalence in this population result in epidemiological inconsistencies largely due to unreliable measurement. Behavioral tools employed in research and in clinical settings often apply a heterosexist and prototypical model to IPV screening; thereby, failing to contextualize occurrences of violence in a same-gender IPV relationship. Despite the estimated impact of IPV among gay/bisexual men, no known literature has attempted to create a behavioral screening tool that accounts for contextual factors in same-gender relationships characterized by IPV. The current study determined the essential theoretical constructs of a clinical screening tool for males involved in same-gender IPV relationships. Two groups of key informants participated in the study – men who have been in same-gender relationships involving partner violence (MSRV) and community mental health providers (MHP) with varying degrees of experience treating this population. Qualitative data collection and analyses occurred in four stages, and were informed by a participatory action research framework. Key informants provided insights regarding how they defined same-gender IPV, their experiences screening or being screened for same-gender IPV, their recommendations for the effective screening of IPV in MSRV, and (in the final stage) feedback related to the preliminary screening tool’s content, format, and structure. Future research should focus on adapting this tool for research purposes

The Effect of Education on Elder Abuse

This study was designed examine the effect of education on prevention of abuse in a long term care center. Participants in this study included direct care worker staff at a nursing home and nursing home residents

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

Towards a Learning Health System: a SOA based platform for data re-use in chronic infectious diseases

Abstract Information and Communication Technology (ICT) tools can efficiently support clinical research by providing means to collect automatically huge amount of data useful for the management of clinical trials conduction. Clinical trials are indispensable tools for Evidence-Based Medicine and represent the most prevalent clinical research activity. Clinical trials cover only a restricted part of the population that respond to particular and strictly controlled requirements, offering a partial view of the overall patients\u2019 status. For instance, it is not feasible to consider patients with comorbidities employing only one kind of clinical trial. Instead, a system that have a comprehensive access to all the clinical data of a patient would have a global view of all the variables involved, reflecting real-world patients\u2019 experience. The Learning Health System is a system with a broader vision, in which data from various sources are assembled, analyzed by various means and then interpreted. The Institute of Medicine (IOM) provides this definition: \u201cIn a Learning Health System, progress in science, informatics, and care culture align to generate new knowledge as an ongoing, natural by-product of the care experience, and seamlessly refine and deliver best practices for continuous improvement in health and health care\u201d. The final goal of my project is the realization of a platform inspired by the idea of Learning Health System, which will be able to re-use data of different nature coming from widespread health facilities, providing systematic means to learn from clinicians\u2019 experience to improve both the efficiency and the quality of healthcare delivery. The first approach is the development of a SOA-based architecture to enable data collection from sparse facilities into a single repository, to allow medical institutions to share information without an increase in costs and without the direct involvement of users. Through this architecture, every single institution would potentially be able to participate and contribute to the realization of a Learning Health System, that can be seen as a closed cycle constituted by a sequential process of transforming patient-care data into knowledge and then applying this knowledge to clinical practice. Knowledge, that can be inferred by re-using the collected data to perform multi-site, practice-based clinical trials, could be concretely applied to clinical practice through Clinical Decision Support Systems (CDSS), which are instruments that aim to help physicians in making more informed decisions. With 4 this objective, the platform developed not only supports clinical trials execution, but also enables data sharing with external research databases to participate in wider clinical trials also at a national level without effort. The results of these studies, integrated with existing guidelines, can be seen as the knowledge base of a decision support system. Once designed and developed, the adoption of this system for chronical infective diseases management at a regional level helped in unifying data all over the Ligurian territory and actively monitor the situation of specific diseases (like HIV, HCV and HBV) for which the concept of retention in care assumes great importance. The use of dedicated standards is essential to grant the necessary level of interoperability among the structures involved and to allow future extensions to other fields. A sample scenario was created to support antiretroviral drugs prescription in the Ligurian HIV Network setting. It was thoroughly tested by physicians and its positive impact on clinical care was measured in terms of improvements in patients\u2019 quality of life, prescription appropriateness and therapy adherence. The benefits expected from the employment of the system developed were verified. Student\u2019s T test was used to establish if significant differences were registered between data collected before and after the introduction of the system developed. The results were really acceptable with the minimum p value in the order of 10 125 and the maximum in the order of 10 123. It is reasonable to assess that the improvements registered in the three analysis considered are ascribable to this system introduction and not to other factors, because no significant differences were found in the period before its release. Speed is a focal point in a system that provides decision support and it is highly recognized the importance of velocity optimization. Therefore, timings were monitored to evaluate the responsiveness of the system developed. Extremely acceptable results were obtained, with the waiting times of the order of 10 121 seconds. The importance of the network developed has been widely recognized by the medical staff involved, as it is also assessed by a questionnaire they compiled to evaluate their level of satisfaction

Comparison of european health related ICT projects

Introdução: No mundo globalizado dos nossos dias, é expectável que os profissionais de saúde prestem os seus serviços a pacientes estrangeiros nalgum ponto das suas carreiras. A diferença de idiomas, sistemas de saúde e infraestruturas são barreiras para uma prestação de cuidados semelhantes aos que os cidadãos conhecem nos seus países de origem. Novas soluções interoperáveis para a partilha de informação clínica a níveis transfronteiriços figuram, por isso, na lista das prioridades digitais da agenda política dos Estados-Membros da União Europeia (UE) (1). A adoção da Diretiva 2011/24/UE do Parlamento Europeu e do Conselho, de Março de 2011, sobre os Direitos dos Pacientes nos cuidados de saúde transfronteiriços, representa o auge da liberdade dos cidadãos para receberem cuidados de saúde noutros Estados-Membros da União Europeia, com qualidade e segurança (2). Com o objetivo de facilitar ‘a prestação de serviços públicos Europeus, promovendo a interoperabilidade transfronteiriça e inter-sectorial’ (7), a European Interoperability Framework (EIF) estabelece uma série de recomendações que promovem várias políticas e iniciativas na UE, ao mesmo tempo que define quatro dimensões para a interoperabilidade: legal, organizacional, semântica e técnica. Objetivo: O objetivo do presente estudo é abordar o desafio da transição de soluções-piloto para uma infraestrutura transfronteiriça de larga-escala, que apoie os Estados-Membros da União Europeia na prestação de serviços públicos, especialmente no setor de saúde. Metodologias: Esta revisão aborda, empiricamente, informação publicada e não-publicada sobre eHealth e sistemas de partilha de dados clínicos, resumindo e correlacionando as conclusões mais importantes de diferentes fontes. É particularmente centrada na análise transversal de quatro projetos Europeus: epSOS, eSENS, Trillium Bridge e EXPAND. Resultados: As Diretivas de Proteção de Dados 95/46/CE e dos Direitos dos Pacientes nos cuidados de saúde transfronteiriços 2011/24/UE são os principais instrumentos legais abordados em todas as iniciativas, não obstante da existência de legislações nacionais. Métodos de trabalho estabelecidos no âmbito das organizações de saúde necessitam de ser adaptados e otimizados, de acordo com as novas arquiteturas de comunicação, mas serão os usuários os principais responsáveis pela sua integração nos seus próprios sistemas, procedimentos e culturas de trabalho. A interpretação universal de dados em saúde pode ser alcançada com terminologias mutuamente aceites, sistemas de codificação e criação de meta-informação, como o mapeamento da Health Level Seven Release 2 (HL 7 R2). O padrão de comunicação Clinical Document Architecture (CDA) estabelece uma estrutura consistente entre sistemas de informação clínica utilizados na Europa. Conclusões: Ainda existem inúmeras barreiras para uma prestação transeuropeia eficaz de serviços públicos. Apesar de um certo nível de complexidade que ainda marca os sistemas de informação em saúde, são várias as vantagens da sua utilização: o acesso rápido e seguro a dados de saúde relevantes para as decisões clínicas, confidencialidade dos mesmos, centralização e organização de acordo com classificações médicas internacionais, bem como a promoção de controlo estatístico e otimização de desempenho (12). A interoperabilidade não é uma finalidade ou uma questão de presença ou ausência, é antes um processo que poderá ser melhorado ao longo do tempo (59). Mais estudos serão necessários para entender como poderemos melhorar os nossos sistemas de informação, para uma partilha sustentável de dados cada vez mais complexos, como a informação em saúde.Introduction: With the globalized world of our days, health professionals are expected to provide their services to foreign patients at some point in their careers. Different languages, health systems and infrastructures are barriers to a sound provision of health care as people have been used to in their home countries. New interoperable solutions for the exchange of clinical data at cross-border levels are now listed as new digital priorities in the political agenda of the European Union (EU) Member States (MS) (1). The adoption of the Directive 2011/24/EU of the European Parliament and the Council of March 2011 on Patient’s Rights in cross-border health care was the pinnacle to assure citizen’s freedom to receive health care in another EU Member State, with quality and safety (2). With the purpose of facilitating ‘the delivery of European public services by fostering cross-border and cross-sectoral interoperability’ (7), the European Interoperability Framework (EIF) establishes a series of recommendations that promote several EU policy initiatives, while defining four dimensions for interoperability: legal, organizational, semantic, and technical. Objective: The purpose of the present review is to address the challenge of stirring from point-solution pilots to a large-scale deployment of cross-border facilities that support EU Member States in delivering public services, especially in health sector. Methodologies: This study empirically addresses published and unpublished information in eHealth and clinical data exchange systems, summarizing and correlating the most important conclusions of different sources. Particularly, it is centered in a transversal analysis of four different European projects focused on providing solutions for cross-border health care services: epSOS, eSENS, Trillium Bridge and EXPAND. Results: The Data Protection Directive 95/46/EC and the Patient’s Rights in cross-border health care Directive 2011/24/EU are the major legal instruments to comply with by all initiatives, notwithstanding the existence of national legislations. Established workflows within heath organizations need to be adapted and optimized according to new communication architectures, but users are ultimately responsible for integrating them in their own systems, procedures and working cultures. A universal interpretation of health data can be achieved with mutually accepted terminologies, coding systems and creation of metadata, such as Health Level Seven Release 2 (HL 7 R2) mapping. The Clinical Document Architecture (CDA) communication standard establishes structure consistency among health IT systems used in Europe. Conclusions: There are still numerous barriers in effective delivery of public services in a pan-European setting. Although a certain level of complexity is still present in health information systems, several advantages can still be highlighted such as rapid and secure access to health data relevant for the decision-making at the care point, confidentiality promotion, centralization and structuring according with medical standards and the promotion of statistical control and performance optimization (12). Interoperability is not an ending or a question of being present or absent, but rather a process that can be improved over time (59). More studies are needed to understand how we can better connect our IT systems towards a sustainable exchange route of richer and even more intricate data, as sensitive as health information