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Integrated Data Management for Clinical Studies: Automatic Transformation of Data Models with Semantic Annotations for Principal Investigators, Data Managers and Statisticians

Martin Dugas, Susanne Dugas-Breit, Chris Mavergames
2014 PLoS ONE  
In addition, it supports semantic annotations, which enable precise definitions for data items.  ...  Citation: Dugas M, Dugas-Breit S (2014) Integrated Data Management for Clinical Studies: Automatic Transformation of Data Models with Semantic Annotations for Principal Investigators, Data Managers and  ...  Therefore R was chosen to represent the study data model for statistical analysis. The data model is represented by an R data frame.  ... 
doi:10.1371/journal.pone.0090492 pmid:24587378 pmcid:PMC3938746 fatcat:nux2yeui2bcipexzaym6rik4v4

Transform: Implementing a Learning Healthcare System in Europe through Embedding Clinical Research into Clinical Practice

Sarah N. Lim, Choi Keung, Lei Zhao, Vasa Curcin, Jean-Francois Ethier, Anita Burgun, Mark McGilchrist, Piotr Brodka, Wodzimierz Tuligowicz, Brendan C. Delaney, Theodoros N. Arvanitis, Anna Andreasson
2015 2015 48th Hawaii International Conference on System Sciences  
Pre-populating eCRFs from EHR Semantic Extension to ODM A study participant's clinical data space is represented by a generic reference model.  ...  a low-cost method for conducting large-scale pragmatic clinical trials [2, 30] .  ... 
doi:10.1109/hicss.2015.383 dblp:conf/hicss/KeungZCEBMBTDAA15 fatcat:sbr2ow7445blhnweot3c5dv5eq

TIM: A Semantic Web Application for the Specification of Metadata Items in Clinical Research

Matthias Löbe, Magnus Knuth, Roland Mücke
2009 Workshop on Semantic Web Applications and Tools for Life Sciences  
This paper presents a Semantic-Web-based application for specifying metadata items in clinical research and life sciences.  ...  We developed an ontology for item modeling and an application for managing a repository of items based on W3C standards.  ...  Application We present a tool called Trial Item Manager (TIM). It is based on Semantic Web technology and can be used to create CRFs and to manage clinical trial items.  ... 
dblp:conf/swat4ls/LobeKM09 fatcat:tqjmdnatcjgephlobdmkn7kg5u

ODMedit: uniform semantic annotation for data integration in medicine based on a public metadata repository

Martin Dugas, Alexandra Meidt, Philipp Neuhaus, Michael Storck, Julian Varghese
2016 BMC Medical Research Methodology  
values, vital signs, diagnostic tests etc.) are collected per patient in clinical trials.  ...  Conclusion: Uniform manual semantic annotation of data models is feasible in principle, but requires a large-scale collaborative effort due to the semantic richness of patient data.  ...  Availability of data and materials Data models of this manuscript are available at https://medical-datamodels.org Consent for publication Not applicable.  ... 
doi:10.1186/s12874-016-0164-9 pmid:27245222 pmcid:PMC4888420 fatcat:jkzalpccxbflbgikvzxf7plcai

Automated UMLS-Based Comparison of Medical Forms

Martin Dugas, Fleur Fritz, Rainer Krumm, Bernhard Breil, Bülent Yener
2013 PLoS ONE  
The scope of the proposed method is a comparison of these items by comparing their concept codes (coded in UMLS). Each data item is represented by item name, concept code and value domain.  ...  To enable data exchange for clinical care and research purposes there is a need to develop interoperable documentation systems with harmonized forms for data capture.  ...  Catalina Martínez Costa provided references for ontological analysis. Author Contributions  ... 
doi:10.1371/journal.pone.0067883 pmid:23861827 pmcid:PMC3701617 fatcat:sfgam7um7vdjbcr3bh4hkpmmha

The MedRed Ontology for Representing Clinical Data Acquisition Metadata [chapter]

Jean-Paul Calbimonte, Fabien Dubosson, Roger Hilfiker, Alexandre Cotting, Michael Schumacher
2017 Lecture Notes in Computer Science  
Electronic Data Capture (EDC) software solutions are progressively being adopted for conducting clinical trials and studies, carried out by biomedical, pharmaceutical and health-care research teams.  ...  Furthermore, we have validated the ontology with existing clinical studies in the context of the MedRed project, as well as a collection of metadata of well-known studies.  ...  Conclusion We presented the MedRed ontology for capturing metadata of clinical studies, following a set of design principles, and extending well-known recommendations.  ... 
doi:10.1007/978-3-319-68204-4_4 fatcat:dftxqwkdwzd2bjpt4qifmge2fi

CDEGenerator: an online platform to learn from existing data models to build model registries

Julian Varghese, Michael Fujarski, Stefan Hegselmann, Philipp Neuhaus, Martin Dugas
2018 Clinical Epidemiology  
Results: The analysis and item-tailoring module provides multilingual comparisons of semantically complex eligibility criteria of clinical trials.  ...  Objective: Best-practice data models harmonize semantics and data structure of medical variables in clinical or epidemiological studies.  ...  Disclosure The authors report no conflicts of interest in this work.  ... 
doi:10.2147/clep.s170075 pmid:30127646 pmcid:PMC6089100 fatcat:7xrv52x5jjhtpintzgtyvjhfji

How Can a Clinical Data Modelling Tool Be Used to Represent Data Items of Relevance to Paediatric Clinical Trials? Learning from the Conect4children (c4c) Consortium

Chima Amadi, Rebecca Leary, Avril Palmeri, Victoria Hedley, Anando Sen, Rahil Qamar Siddiqui, Dipak Kalra, Volker Straub
2022 Applied Sciences  
Models can be represented as an HTML document, mind map, or exported in various formats for import into a computer system.  ...  Data dictionaries for clinical trials are often created manually, with data structures and controlled vocabularies specific for a trial or family of trials within a sponsor's portfolio.  ...  Mind maps enable clinicians and other clinical trial personnel to better understand the stepwise format by which data dictionary items are represented for use in clinical trials [26] ; • The HTML summary  ... 
doi:10.3390/app12031604 fatcat:zss2hin3knckbfip5yg76fflse

Electronic Healthcare Record and clinical research in cardiovascular radiology. HL7 CDA and CDISC ODM interoperability

A El Fadly, C Daniel, C Bousquet, T Dart, P-Y Lastic, P Degoulet
2007 AMIA Annual Symposium Proceedings  
Informatics standards are different for EHR (HL7 CDA) and clinical research (CDISC ODM).  ...  Pompidou European Hospital (HEGP), cardiovascular radiology reports are captured twice, first in the Electronic Health Record (EHR) and then in a national clinical research server.  ...  It could be used as a core data standard for managing the workflow in clinical trials and for generating clinical trial software applications that share the same semantics and thus can exchange data more  ... 
pmid:18693829 pmcid:PMC2655824 fatcat:rkffz25dlrbe3hltq3qhww5jqq

Testing the therapeutic effects of transcranial direct current stimulation (tDCS) in semantic dementia: a double blind, sham controlled, randomized clinical trial

Clara Sanches, Richard Levy, Sarah Benisty, Lisette Volpe-Gillot, Marie-Odile Habert, Aurelie Kas, Sébastian Ströer, Nadya Pyatigorskaya, Anna Kaglik, Angelina Bourbon, Bruno Dubois, Raffaella Migliaccio (+2 others)
2019 Trials  
The primary objective of the present clinical trial (STIM-SD) is to evaluate the therapeutic efficacy of a multiday transcranial direct current stimulation (tDCS) regime on language impairment in patients  ...  The aim of this study is to assess the efficacy of tDCS for language/semantic disorders in semantic dementia.  ...  The authors thank the FRA foundation for logistic and equipment support and the Naturalia & Biologia Foundation for financial assistance for travel to and attendance at meetings.  ... 
doi:10.1186/s13063-019-3613-z pmid:31747967 pmcid:PMC6868701 fatcat:upi2r2if6ba3ppmzsdar74hq7e

Comparison and transformation between CDISC ODM and EN13606 EHR standards in connecting EHR data with clinical trial research data

Archana Tapuria, Philipp Bruland, Brendan Delaney, Dipak Kalra, Vasa Curcin
2018 Digital Health  
Data Model (CDISC ODM) used for clinical research.  ...  EN13606 can accommodate clinical information in a more structured manner with more constraints, whereas CDISC ODM is more suitable and specific for clinical trials and studies.  ...  Acknowledgements: We thanks the Institute of Medical Informatics, University of Mu¨nster, Germany, for allowing us to use the Medical Data Models portal.  ... 
doi:10.1177/2055207618777676 pmid:29942639 pmcid:PMC6016569 fatcat:2w4uha3lwnhv3fbm52r4tknfyq

Identifying the semantics of eligibility criteria of clinical trials based on relevant medical ontologies

Anca Bucur, Jasper van Leeuwen, David Perez-Rey, Raul Alonso Calvo, Brecht Claerhout, Kristof de Schepper
2012 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)  
At the same time, the assessment of the eligibility of a patient for a trial requires the (machineprocessable) understanding of the semantics of the eligibility criteria in order to further evaluate if  ...  The population suited to be enrolled in a trial is described by a set of free-text eligibility criteria that are both syntactically and semantically complex.  ...  In [6] an analysis has been carried out to estimate the coverage provided by SNOMED-CT for clinical research concepts that represented by the items present on case report forms (CRFs).  ... 
doi:10.1109/bibe.2012.6399762 dblp:conf/bibe/BucurLPACS12 fatcat:iuyya3xp5zbc3axrx36vrfnvhe

An ontologically founded architecture for information systems in clinical and epidemiological research

Alexandr Uciteli, Silvia Groß, Sergej Kireyev, Heinrich Herre
2011 Journal of Biomedical Semantics  
Clinical trials exhibit an important basis for clinical research, and the accurate specification of metadata and their documentation and application in clinical and epidemiological study projects represents  ...  An ontological foundation of an information system provides a semantic framework for the precise specification of those entities which are presented in this system.  ...  Acknowledgements The research of this paper is supported by the BMBF project "Specification and prototype implementation of a national metadata repository for clinical and epidemiological research in Germany  ... 
doi:10.1186/2041-1480-2-s4-s1 pmid:21995847 pmcid:PMC3194168 fatcat:dckirz7vuvakfoub5uwom2rq44

Facilitating Study and Item Level Browsing for Clinical and Epidemiological COVID-19 Studies [chapter]

Carsten Oliver Schmidt, Johannes Darms, Aliaksandra Shutsko, Matthias Löbe, Rajini Nagrani, Bastian Seifert, Birte Lindstädt, Martin Golebiewski, Sofiya Koleva, Theresa Bender, Christian Robert Bauer, Ulrich Sax (+9 others)
2021 Studies in Health Technology and Informatics  
Yet, it is difficult to obtain a good overview of studies across different medical fields of research such as clinical trials, epidemiology, and public health.  ...  Here, we describe a consensus metadata model to facilitate structured searches of COVID-19 studies and resources along with its implementation in three linked complementary web-based platforms.  ...  The CSH [16] enables to search for studies and for related study documents (Figure 2 ) based on information represented in the health studies data model.  ... 
doi:10.3233/shti210284 pmid:34042687 fatcat:kouydydo5jdilgidmjpbecwqt4

Differential patterns of contextual organization of memory in first-episode psychosis

Vishnu P. Murty, Rachel A. McKinney, Sarah DuBrow, Maria Jalbrzikowski, Gretchen L. Haas, Beatriz Luna
2018 npj Schizophrenia  
We employed an approach founded in a computational framework of free recall to quantify how individuals with first episode of psychosis (FEP, N = 97) and controls (CON, N = 55) use temporal and semantic  ...  In comparison to CON, FEP had reduced recall and less temporal clustering during free recall (p < 0.05, Bonferroni-corrected), and showed a trend towards greater semantic clustering (p = 0.10, Bonferroni-corrected  ...  For the post-hoc comparisons of semantic clustering and trial number, there was only one comparison.  ... 
doi:10.1038/s41537-018-0046-8 pmid:29449557 pmcid:PMC5814439 fatcat:q6t3oosn6vauvpnbsprswtfoue
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