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

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

A NLP Pipeline for the Automatic Extraction of a Complete Microorganism’s Picture from Microbiological Notes

The Italian “Istituto Superiore di Sanità” (ISS) identifies hospital-acquired infections (HAIs) as the most frequent and serious complications in healthcare. HAIs constitute a real health emergency and, therefore, require decisive action from both local and national health organizations. Information about the causative microorganisms of HAIs is obtained from the results of microbiological cultures of specimens collected from infected body sites, but microorganisms’ names are sometimes reported only in the notes field of the culture reports. The objective of our work was to build a NLP-based pipeline for the automatic information extraction from the notes of microbiological culture reports. We analyzed a sample composed of 499 texts of notes extracted from 1 month of anonymized laboratory referral. First, our system filtered texts in order to remove nonmeaningful sentences. Thereafter, it correctly extracted all the microorganisms’ names according to the expert’s labels and linked them to a set of very important metadata such as the translations into national/international vocabularies and standard definitions. As the major result of our pipeline, the system extracts a complete picture of the microorganism

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

Identifying intimate partner violence in different ethnic groups in primary care - a systematic review and secondary data analysis

PhDBackground Intimate partner violence (IPV), including physical, sexual and emotional violence, causes short and long term ill-health. Brief questions that can identify women from different ethnic groups experiencing IPV who present in clinical settings are a prerequisite for an appropriate response from health services to this substantial public health problem. Aim: To examine the evidence for the validity of questions trying to identify IPV in different ethnic groups and to determine whether their validity varies between ethnic groups. Methods Design: A systematic review and the secondary data analysis of a cross-sectional survey of four questions (HARK) identifying IPV in a primary care sample. Main outcome measures: Systematic review - for each set of index questions identified, diagnostic accuracy indices, correlation coefficients, reliability measures, validity evidence based on response processes and test content were analysed and interpreted. Secondary data analysis - diagnostic indices for IPV and its dimensions in three ethnic groups were calculated for the four HARK questions combined and for the individual HARK questions. 4 Results Systematic review – there is no evidence of questions valid for identifying IPV in specific ethnic groups, including white groups. Secondary data analysis - the optimal HARK cut off score of ≥ 1 was unaffected by the participants‟ ethnicity. The diagnostic indices generated using the HARK cut off of ≥ 1 remained at a high level, in all three ethnic groups. There were no significant ethnic differences in the diagnostic indices of the four combined and individual HARK questions‟ ability at identifying either IPV or its dimensions. Conclusion From the systematic review and secondary data analysis, there is no evidence that questions‟ validity for identifying IPV varies significantly between different ethnic groups. The secondary data analysis does provide evidence that four questions (the HARK) can identify IPV in self-classified UK census categories of African- Caribbean, south Asian, and white groups

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

Intégration de ressources en recherche translationnelle : une approche unificatrice en support des systèmes de santé "apprenants"

Learning health systems (LHS) are gradually emerging and propose a complimentary approach to translational research challenges by implementing close coupling of health care delivery, research and knowledge translation. To support coherent knowledge sharing, the system needs to rely on an integrated and efficient data integration platform. The framework and its theoretical foundations presented here aim at addressing this challenge. Data integration approaches are analysed in light of the requirements derived from LHS activities and data mediation emerges as the one most adapted for a LHS. The semantics of clinical data found in biomedical sources can only be fully derived by taking into account, not only information from the structural models (field X of table Y), but also terminological information (e.g. International Classification of Disease 10th revision) used to encode facts. The unified framework proposed here takes this into account. The platform has been implemented and tested in context of the TRANSFoRm endeavour, a European project funded by the European commission. It aims at developing a LHS including clinical activities in primary care. The mediation model developed for the TRANSFoRm project, the Clinical Data Integration Model, is presented and discussed. Results from TRANSFoRm use-cases are presented. They illustrate how a unified data sharing platform can support and enhance prospective research activities in context of a LHS. In the end, the unified mediation framework presented here allows sufficient expressiveness for the TRANSFoRm needs. It is flexible, modular and the CDIM mediation model supports the requirements of a primary care LHS.Les systèmes de santé "apprenants" (SSA) présentent une approche complémentaire et émergente aux problèmes de la recherche translationnelle en couplant de près les soins de santé, la recherche et le transfert de connaissances. Afin de permettre un flot d’informations cohérent et optimisé, le système doit se doter d’une plateforme intégrée de partage de données. Le travail présenté ici vise à proposer une approche de partage de données unifiée pour les SSA. Les grandes approches d’intégration de données sont analysées en fonction du SSA. La sémantique des informations cliniques disponibles dans les sources biomédicales est la résultante des connaissances des modèles structurelles des sources mais aussi des connaissances des modèles terminologiques utilisés pour coder l’information. Les mécanismes de la plateforme unifiée qui prennent en compte cette interdépendance sont décrits. La plateforme a été implémentée et testée dans le cadre du projet TRANSFoRm, un projet européen qui vise à développer un SSA. L’instanciation du modèle de médiation pour le projet TRANSFoRm, le Clinical Data Integration Model est analysée. Sont aussi présentés ici les résultats d’un des cas d’utilisation de TRANSFoRm pour supporter la recherche afin de donner un aperçu concret de l’impact de la plateforme sur le fonctionnement du SSA. Au final, la plateforme unifiée d’intégration proposée ici permet un niveau d’expressivité suffisant pour les besoins de TRANSFoRm. Le système est flexible et modulaire et le modèle de médiation CDIM couvre les besoins exprimés pour le support des activités d’un SSA comme TRANSFoRm

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

Predictors of alcohol and other drug use among pregnant women in a peri-urban South African setting

Background: Alcohol and other drugs (AOD) use among pregnant women have been associated with adverse health outcomes for mother and child, during and after pregnancy. Factors associated with AOD use among women include age, poverty, unemployment, and interpersonal conflict. Few studies have looked at demographic, economic, and psychosocial factors as predictors of AOD use among pregnant women in low-income, peri-urban settings. The study aimed to determine the association between these risk factors and alcohol and drug use among pregnant women in Hanover Park, Cape Town. Methods: The study was undertaken at a Midwife Obstetric Unit providing primary-level maternity services in a resource-scarce area of South Africa. 376 adult women attending the unit were recruited and a multi-tool questionnaire administered. Demographic, socioeconomic and life events data were collected. The Expanded Mini-International Neuropsychiatric Interview Version 5.0.0 was used to assess alcohol abuse and other drugs use, depression, anxiety, and suicidal ideation. Descriptive and bivariate analyses were conducted to examine the associations between predictor variables. Non-parametric tests, Wilcoxon sum of rank test, Fisher Exact and two sample T test and multicollinearity tests were performed. Logistic regression was conducted to identify associations between the outcome of interest and key predictors. A probability value of p ≤ 0.05 was selected. Results: Of the total number of pregnant women sampled, 18 % reported current AOD use. Of these, 18 % were currently experiencing a major depressive episode, 19 % had a current anxiety diagnosis, and 22 % expressed suicidal ideation. Depression, anxiety, suicidality, food insecurity, interpersonal violence, relationship dynamics, and past mental health problems were predictors of AOD use. Conclusions: This study has confirmed the vulnerability of pregnant women in low-income, peri-urban settings to alcohol abuse and other drugs use. Further, the association between diagnosed depression and anxiety, suicidality, and AOD use among these women may reflect how complex environmental factors support the coexistence of multiple mental health problems. These problems place mothers and their infants at high risk for poor health and development outcomes. The results have implications for planning appropriate interventions