167,660 research outputs found

    ARGOS policy brief on semantic interoperability

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    Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained collections of coherent and quality-assured semantic resources, including models such as archetypes and templates that would (1) provide clinical context, (2) be mapped to interoperability standards for EHR data, (3) be linked to well specified, multi-lingual terminology value sets, and (4) be derived from high quality ontologies. Wide-scale engagement with professional bodies, globally, is needed to develop these clinical information standards

    OntoCR: A CEN/ISO-13606 clinical repository based on ontologies

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    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

    The state of the art in clinical knowledge management: An inventory of tools and techniques

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    Purpose To explore the need for, and use of, high-quality, collaborative, clinical knowledge management (CKM) tools and techniques to manage clinical decision support (CDS) content. Methods In order to better understand the current state of the art in CKM, we developed a survey of potential CKM tools and techniques. We conducted an exploratory study by querying a convenience sample of respondents about their use of specific practices in CKM. Results The following tools and techniques should be priorities in organizations interested in developing successful computer-based provider order entry (CPOE) and CDS implementations: (1) a multidisciplinary team responsible for creating and maintaining the clinical content; (2) an external organizational repository of clinical content with web-based viewer that allows anyone in the organization to review it; (3) an online, collaborative, interactive, Internet-based tool to facilitate content development; (4) an enterprise-wide tool to maintain the controlled clinical terminology concepts. Even organizations that have been successfully using computer-based provider order entry with advanced clinical decision support features for well over 15 years are not using all of the CKM tools or practices that we identified. Conclusions If we are to further stimulate progress in the area of clinical decision support, we must continue to develop and refine our understanding and use of advanced CKM capabilities

    PeptiCKDdb-peptide- and protein-centric database for the investigation of genesis and progression of chronic kidney disease

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    The peptiCKDdb is a publicly available database platform dedicated to support research in the field of chronic kidney disease (CKD) through identification of novel biomarkers and molecular features of this complex pathology. PeptiCKDdb collects peptidomics and proteomics datasets manually extracted from published studies related to CKD. Datasets from peptidomics or proteomics, human case/control studies on CKD and kidney or urine profiling were included. Data from 114 publications (studies of body fluids and kidney tissue: 26 peptidomics and 76 proteomics manuscripts on human CKD, and 12 focusing on healthy proteome profiling) are currently deposited and the content is quarterly updated. Extracted datasets include information about the experimental setup, clinical study design, discovery-validation sample sizes and list of differentially expressed proteins (P-value < 0.05). A dedicated interactive web interface, equipped with multiparametric search engine, data export and visualization tools, enables easy browsing of the data and comprehensive analysis. In conclusion, this repository might serve as a source of data for integrative analysis or a knowledgebase for scientists seeking confirmation of their findings and as such, is expected to facilitate the modeling of molecular mechanisms underlying CKD and identification of biologically relevant biomarkers.Database URL: www.peptickddb.com

    Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies

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    FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leadingmostly tomonogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS software that catalyzes development curation of national/ethnic genetic databases, (ii) the migration of all FINDbase data content into 90 distinct national/ethnicmutation databases, all built around Microsoft's PivotViewer (http://www.getpivot.com) software (iii) new data visualization tools and (iv) the interrelation of FINDbase with DruGeVar database with direct implications in clinical pharmacogenomics. The abovementioned updates further enhance the impact of FIND-base, as a key resource for Genomic Medicine applications

    Intuitive querying of e-Health data repositories

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    At the centre of the Clinical e-Science Framework (CLEF) project is a repository of well organised, detailed clinical histories, encoded as data that will be available for use in clinical care and in-silico medical experiments. An integral part of the CLEF workbench is a tool to allow biomedical researchers and clinicians to query – in an intuitive way – the repository of patient data. This paper describes the CLEF query editing interface, which makes use of natural language generation techniques in order to alleviate some of the problems generally faced by natural language and graphical query interfaces. The query interface also incorporates an answer renderer that dynamically generates responses in both natural language text and graphics

    Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies

    Get PDF
    FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leading mostly to monogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS software that catalyzes development curation of national/ethnic genetic databases, (ii) the migration of all FINDbase data content into 90 distinct national/ethnic mutation databases, all built around Microsoft’s PivotViewer (http://www.getpivot.com) software (iii) new data visualization tools and (iv) the interrelation of FINDbase with DruGeVar database with direct implications in clinical pharmacogenomics. The above mentioned updates further enhance the impact of FINDbase, as a key resource for Genomic Medicine applications

    Pre-service Middle School Teachers’ Knowledge of Algebraic Thinking

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    In this study we examined the relationship between 18 pre-service middle school teachers’ own ability to use algebraic thinking to solve problems and their ability to recognize and interpret the algebraic thinking of middle school students. We assessed the pre-service teachers’ own algebraic thinking by examining their solutions and explanations to multiple algebra-based tasks posed during a semester-long mathematics content course. We assessed their ability to recognize and interpret the algebraic thinking of students in two ways. The first was by analyzing the preservice teachers’ ability to interpret students’ written solutions to open-ended algebra-based tasks. The second was by analyzing their ability to plan, conduct, and analyze algebraic thinking (AT) interviews of middle school students during a concurrent semester-long, field-based education class. We used algebraic habits of mind as a framework to identify the algebraic thinking that pre-service teachers exhibited in their own problem solving, and we asked students to use them to analyze the algebraic thinking of middle school students. The data revealed that pre-service teachers’ AT abilities varied across different features of algebraic thinking. In particular, their ability to justify a rule was the weakest of seven AT features. The ability to recognize and interpret the algebraic thinking of students was strongly correlated with the strength of the pre-service teachers’ own algebraic thinking. Implications for mathematics teacher education are discussed

    Developing Predictive Molecular Maps of Human Disease through Community-based Modeling

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    The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics

    ImmPort, toward repurposing of open access immunological assay data for translational and clinical research

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    Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, Data Analysis, and Resources—for data archiving, dissemination, analyses, and reuse. To date, more than 300 studies have been made freely available through the ImmPort Shared Data portal , which allows research data to be repurposed to accelerate the translation of new insights into discoveries
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