16 research outputs found
Postmarketing Safety Study Tool: A Web Based, Dynamic, and Interoperable System for Postmarketing Drug Surveillance Studies
Postmarketing drug surveillance is a crucial aspect of the clinical research activities in pharmacovigilance and pharmacoepidemiology. Successful utilization of available Electronic Health Record (EHR) data can complement and strengthen postmarketing safety studies. In terms of the secondary use of EHRs, access and analysis of patient data across different domains are a critical factor; we address this data interoperability problem between EHR systems and clinical research systems in this paper. We demonstrate that this problem can be solved in an upper level with the use of common data elements in a standardized fashion so that clinical researchers can work with different EHR systems independently of the underlying information model. Postmarketing Safety Study Tool lets the clinical researchers extract data from different EHR systems by designing data collection set schemas through common data elements. The tool interacts with a semantic metadata registry through IHE data element exchange profile. Postmarketing Safety Study Tool and its supporting components have been implemented and deployed on the central data warehouse of the Lombardy region, Italy, which contains anonymized records of about 16 million patients with over 10-year longitudinal data on average. Clinical researchers in Roche validate the tool with real life use cases.Publisher's Versio
From Raw Data to FAIR Data: The FAIRification Workflow for Health Research
BackgroundFAIR (findability, accessibility, interoperability, and reusability) guidingprinciples seek the reuse of data and other digital research input, output, and objects(algorithms, tools, and workflows that led to that data) making themfindable, accessible,interoperable, and reusable. GO FAIR - a bottom-up, stakeholder driven and self-governedinitiative-defined a seven-step FAIRificationprocessfocusingondata,butalsoindicatingtherequired work for metadata. This FAIRification process aims at addressing the translation ofraw datasets into FAIR datasets in a general way, without considering specific requirementsand challenges that may arise when dealing with some particular types of data.This work was performed in the scope of FAIR4Healthproject. FAIR4Health has received funding from the European Unionâs Horizon 2020 research and innovationprogramme under grant agreement number 824666
Applying the FAIR4Health Solution to Identify Multimorbidity Patterns and Their Association with Mortality through a Frequent Pattern Growth Association Algorithm
This article belongs to the Special Issue Addressing the Growing Burden of Chronic Diseases and Multimorbidity: Characterization and InterventionsThe current availability of electronic health records represents an excellent research opportunity on multimorbidity, one of the most relevant public health problems nowadays. However, it also poses a methodological challenge due to the current lack of tools to access, harmonize and reuse research datasets. In FAIR4Health, a European Horizon 2020 project, a workflow to implement the FAIR (findability, accessibility, interoperability and reusability) principles on health datasets was developed, as well as two tools aimed at facilitating the transformation of raw datasets into FAIR ones and the preservation of data privacy. As part of this project, we conducted a multicentric retrospective observational study to apply the aforementioned FAIR implementation workflow and tools to five European health datasets for research on multimorbidity. We applied a federated frequent pattern growth association algorithm to identify the most frequent combinations of chronic diseases and their association with mortality risk. We identified several multimorbidity patterns clinically plausible and consistent with the bibliography, some of which were strongly associated with mortality. Our results show the usefulness of the solution developed in FAIR4Health to overcome the difficulties in data management and highlight the importance of implementing a FAIR data policy to accelerate responsible health research.This study was performed in the framework of FAIR4Health, a project that has received funding from the European Unionâs Horizon 2020 research and innovation programme under grant agreement number 824666. Also, this research has been co-supported by the Carlos III National Institute of Health, through the IMPaCT Data project (code IMP/00019), and through the Platform for Dynamization and Innovation of the Spanish National Health System industrial capacities and their effective transfer to the productive sector (code PT20/00088), both co-funded by European Regional Development Fund (FEDER) âA way of making Europeâ, and by REDISSEC (RD16/0001/0005) and RICAPPS (RD21/0016/0019) from Carlos III National Institute of Health. This work was also supported by Instituto de InvestigaciĂłn Sanitaria AragĂłn and Carlos III National Institute of Health [RĂo Hortega Program, grant number CM19/00164].Peer reviewe
FAIR4Health: Findable, Accessible, Interoperable and Reusable data to foster Health Research
Due to the nature of health data, its sharing and reuse for research are limited by ethical, legal and technical barriers. The FAIR4Health project facilitated and promoted the application of FAIR principles in health research data, derived from the publicly funded health research initiatives to make them Findable, Accessible, Interoperable, and Reusable (FAIR). To confirm the feasibility of the FAIR4Health solution, we performed two pathfinder case studies to carry out federated machine learning algorithms on FAIRified datasets from five health research organizations. The case studies demonstrated the potential impact of the developed FAIR4Health solution on health outcomes and social care research. Finally, we promoted the FAIRified data to share and reuse in the European Union Health Research community, defining an effective EU-wide strategy for the use of FAIR principles in health research and preparing the ground for a roadmap for health research institutions. This scientific report presents a general overview of the FAIR4Health solution: from the FAIRification workflow design to translate raw data/metadata to FAIR data/metadata in the health research domain to the FAIR4Health demonstrators' performance.This research was financially supported by the European Unionâs Horizon 2020 research and innovation programme under the grant agreement No 824666 (project FAIR4Health). Also, this research has been co-supported by the Carlos III National Institute of Health, through the IMPaCT Data project (code IMP/00019), and through the Platform for Dynamization and Innovation of the Spanish National Health System industrial capacities and their effective transfer to the productive sector (code PT20/00088), both co-funded by European Regional Development Fund (FEDER) âA way of making Europeâ.Peer reviewe
Corrigendum to âA federated semantic metadata registry framework for enabling interoperability across clinical research and care domainsâ [J. Biomed. Inf. 46(5) (2013) 784â794]
A Semantic Transformation Methodology for the Secondary Use of Observational Healthcare Data in Postmarketing Safety Studies
Background: Utilization of the available observational healthcare datasets is key to complement and strengthen the postmarketing safety studies. Use of common data models (CDM) is the predominant approach in order to enable large scale systematic analyses on disparate data models and vocabularies. Current CDM transformation practices depend on proprietarily developed Extract-Transform-Load (ETL) procedures, which require knowledge both on the semantics and technical characteristics of the source datasets and target CDM.
Purpose: In this study, our aim is to develop a modular but coordinated transformation approach in order to separate semantic and technical steps of transformation processes, which do not have a strict separation in traditional ETL approaches. Such an approach would discretize the operations to extract data from source electronic health record systems, alignment of the source, and target models on the semantic level and the operations to populate target common data repositories.
Approach: In order to separate the activities that are required to transform heterogeneous data sources to a target CDM, we introduce a semantic transformation approach composed of three steps: (1) transformation of source datasets to Resource Description Framework (RDF) format, (2) application of semantic conversion rules to get the data as instances of ontological model of the target CDM, and (3) population of repositories, which comply with the specifications of the CDM, by processing the RDF instances from step 2. The proposed approach has been implemented on real healthcare settings where Observational Medical Outcomes Partnership (OMOP) CDM has been chosen as the common data model and a comprehensive comparative analysis between the native and transformed data has been conducted.
Results: Health records of similar to 1 million patients have been successfully transformed to an OMOP CDM based database from the source database. Descriptive statistics obtained from the source and target databases present analogous and consistent results.
Discussion and Conclusion: Our method goes beyond the traditional ETL approaches by being more declarative and rigorous. Declarative because the use of RDF based mapping rules makes each mapping more transparent and understandable to humans while retaining logic-based computability. Rigorous because the mappings would be based on computer readable semantics which are amenable to validation through logic-based inference methods.European Community (EC)Publisher's Versio
A Semantic Transformation Methodology for the Secondary Use of Observational Healthcare Data in Postmarketing Safety Studies
Background: Utilization of the available observational healthcare datasets is key to complement and strengthen the postmarketing safety studies. Use of common data models (CDM) is the predominant approach in order to enable large scale systematic analyses on disparate data models and vocabularies. Current CDM transformation practices depend on proprietarily developed ExtractâTransformâLoad (ETL) procedures, which require knowledge both on the semantics and technical characteristics of the source datasets and target CDM.Purpose: In this study, our aim is to develop a modular but coordinated transformation approach in order to separate semantic and technical steps of transformation processes, which do not have a strict separation in traditional ETL approaches. Such an approach would discretize the operations to extract data from source electronic health record systems, alignment of the source, and target models on the semantic level and the operations to populate target common data repositories.Approach: In order to separate the activities that are required to transform heterogeneous data sources to a target CDM, we introduce a semantic transformation approach composed of three steps: (1) transformation of source datasets to Resource Description Framework (RDF) format, (2) application of semantic conversion rules to get the data as instances of ontological model of the target CDM, and (3) population of repositories, which comply with the specifications of the CDM, by processing the RDF instances from step 2. The proposed approach has been implemented on real healthcare settings where Observational Medical Outcomes Partnership (OMOP) CDM has been chosen as the common data model and a comprehensive comparative analysis between the native and transformed data has been conducted.Results: Health records of ~1 million patients have been successfully transformed to an OMOP CDM based database from the source database. Descriptive statistics obtained from the source and target databases present analogous and consistent results.Discussion and Conclusion: Our method goes beyond the traditional ETL approaches by being more declarative and rigorous. Declarative because the use of RDF based mapping rules makes each mapping more transparent and understandable to humans while retaining logic-based computability. Rigorous because the mappings would be based on computer readable semantics which are amenable to validation through logic-based inference methods
A semantic backend for content management systems
The users of a content repository express the semantics they have in mind while defining the content items and their properties, and forming them into a particular hierarchy. However, this valuable semantics is not formally expressed, and hence cannot be used to discover meaningful relationships among the content items in an automated way. Although the need is apparent, there are several challenges in explicating this semantics in a fully automated way: first, it is difficult to distinguish between data and the metadata in the repository and secondly, not all the metadata defined, such as the file size or encoding type, contribute to the meaning. More importantly, for the developed solution to have practical value, it must address the constraints of the content management system (CMS) industry: CMS industry cannot change their repositories in production use and they need a generic solution not limited to a specific repository architecture. In this article, we address all these challenges through a set of tools developed which first semi-automatically explicate the content repository semantics to a knowledge-base and establish semantic bridges between this backend knowledge-base and the content repository. The repository content is dynamic; to be able to maintain the content repository semantics while new content is created, the changes in the repository semantics are reflected onto the knowledge-base through the semantic bridges. The tool set is complemented with a search engine that make use of the explicated semantics