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The openEHR Genomics Project

Cecilia Mascia, Francesca Frexia, Paolo Uva, Gianluigi Zanetti, Luca Pireddu, Gideon Giacomelli, Christina Jaeger-Schmidt, Aurelie Tomczak, Simon Schumacher, Florian Kraecher, Roland Eils, Silje Ljosland Bakke (+1 others)
2020 Studies in Health Technology and Informatics  
This article introduces our work to create the openEHR Genomic Project and the set of genomic information models we developed to catch such complex structure and to preserve data provenance efficiently  ...  From the technological point of view, genomic data are big in size, have a complex granular nature and strongly depend on the computational steps of the generation and processing workflows.  ...  Acknowledgements The authors from CRS4 dedicate this work to the memory of Gianluigi Zanetti, whose legacy continues to inspire.  ... 
doi:10.3233/shti200199 pmid:32570423 fatcat:6vojwd45efa4dpy3lv5jfkkc5i

openEHR Mapper – A Tool to Fuse Clinical and Genomic Data Using the openEHR Standard [chapter]

Niklas Reimer, Hannes Ulrich, Hauke Busch, Ann-Kristin Kock-Schoppenhauer, Josef Ingenerf
2021 Studies in Health Technology and Informatics  
For data integration, we developed openEHR Mapper, a tool that allows to (i) process input data, (ii) communicate with the openEHR repository, and (iii) export the data to cBioPortal.  ...  We use the openEHR standard to create an expert-curated data model that is stored in a vendor-neutral format.  ...  Acknowledgement The project is funded by the German Federal Ministry of Education and Research (BMBF, grand id: 01ZZ1802Z).  ... 
doi:10.3233/shti210055 pmid:34042880 fatcat:qdcnp67mtjgbvj3hupwimfcu5e

Nutrigenomic Information in the openEHR Data Set

Gustavo Bacelar-Silva, Duarte Ferreira, Conceição Calhau, Pedro Vieira-Marques, Ricardo Cruz-Correia, Priscila Maranhão
2018 Applied Clinical Informatics  
Discussions about personalized nutrition have been on since the Human Genome Project, which has sequenced the human genome.  ...  Objective Finding the main clinical statements in the personalized nutrition field (nutrigenomics) to create the future-proof health information system to the openEHR server based on archetypes, as well  ...  Acknowledgments The authors would like to acknowledge-Project "NORTE-01-0145-FEDER-000016" (NanoSTIMA) is financed by the North Portugal Regional Operational Program (NORTE2020), under the PORTUGAL 2020  ... 
doi:10.1055/s-0038-1635115 pmid:29590680 pmcid:PMC5874138 fatcat:gygxqyeoqrdmfbvmnafrw2x2cu

OpenEHR modeling for genomics in clinical practice [article]

Cecilia Mascia, Paolo Uva, Simone Leo, Gianluigi Zanetti
2017 bioRxiv   pre-print
In this work we present a solution for integrating genomic data into electronic health records via openEHR archetypes.  ...  We introduce new genomics-specific archetypes based on the popular variant call format and show their applicability to a practical use case.  ...  ), known associations of the variant with diseases (e.g., OMIM, ClinVar) and allele frequency in reference populations (e.g., ESP6500, 1000 Genomes Project, gnomAD).  ... 
doi:10.1101/194720 fatcat:ippdgbyvkvfwdes2llrdxk7hre

Track Q. Interoperabilität für eine einrichtungsübergreifende Patientenversorgung

Marius R. Khan, Sabine Sachweh
2016 Biomedical Engineering  
To achieve this, the system needs user related input data from the digital social network of the project "QuartiersNETZ".  ...  Through an extension of the previous mentioned digital social network we additionally focus on bridging the gap between different stakeholder of the medical and nursing domain within the research project  ...  As part of the research project Hannover Medical School Translational Research Framework (HaMSTR), we test OpenEHR-based data storage for a clinical data warehouse (CDW) .  ... 
doi:10.1515/bmt-2016-5015 pmid:27682697 fatcat:sokw5usvcbah7icjkm5jyuw4ou

pyEHR: A scalable clinical data management toolkit for biomedical research projects

Luca Lianas, Francesca Frexia, Giovanni Delussu, Paolo Anedda, Gianluigi Zanetti
2014 2014 IEEE 16th International Conference on e-Health Networking, Applications and Services (Healthcom)  
The toolkit uses openEHR formalisms to guarantee the decoupling of clinical data descriptions from implementation details, and NoSQL technologies, or next-generation SQL ones, to provide scalable storage  ...  genome sequencing studies [9] - [11] and safety assessments of novel gene therapy approaches [12] .  ...  The latter issue is typical of longitudinal biomedical studies, where multiple, heterogeneous data types can become necessary within the time span of the project.  ... 
doi:10.1109/healthcom.2014.7001871 dblp:conf/healthcom/LianasFDAZ14 fatcat:7udkn2uqifaibdny7tratdos6q

The emergence of openness in open-source projects: the case of openEHR

Daniel Curto-Millet, Maha Shaikh
2017 Journal of Information Technology  
We draw on a very particular open source project primarily concerned with building rigorous clinical concepts to be used in electronic health records called openEHR. openEHR explains how openness is a  ...  concept that is purposely engaged with, and how, in this process of engagement, the very meaning of open matures and evolves within the project.  ...  Both processes are separate yet entangled, and become visible through the crises that the openEHR project experiences.  ... 
doi:10.1057/s41265-017-0042-x fatcat:p4r7ujr2xfbtbj37f5tgct7ahq

The Use of FHIR in Digital Health - A Review of the Scientific Literature

Moritz Lehne, Sandra Luijten, Paulina Vom Felde Genannt Imbusch, Sylvia Thun
2019 Studies in Health Technology and Informatics  
Here, we aim to address this gap and provide an overview of the main topics associated with FHIR in the scientific literature.  ...  We found that the topics most commonly discussed in the articles were related to data models, mobile and web applications as well as medical devices.  ...  OpenEHR publications were identified using the search term "openEHR" on Web of Science and PubMed.  ... 
doi:10.3233/shti190805 pmid:31483254 fatcat:gjh2kkrh7bbdbhiro7tyjk4d2q

Nutrition Information in Oncology - Extending the Electronic Patient-Record Data Set

Priscila A Maranhão, Ana Margarida Pereira, Conceição Calhau, Paula Ravasco, Federico Bozzetti, Alessandro Laviano, Liz Isenring, Elisa V Bandera, Maureen B Huhmann, Pedro Vieira-Marques, Ricardo J Cruz-Correia
2020 Journal of medical systems  
This study aimed at developing openEHR-archetypes representing clinical concepts in cancer nutrition-care, as well as to develop an openEHR-template including the aforementioned archetypes.  ...  ; 3) creating an example template with Template Designer; and 4) automatic conversion of the openEHR-template into a readily usable EHR using VCIntegrator.  ...  Acknowledgments The authors would like to acknowledge ODISSEIA -Oncology Information System project (POCI-05-5762-FSE-039021), financed by the North Portugal Regional Operational Programme (NORTE 2020)  ... 
doi:10.1007/s10916-020-01649-9 pmid:32986139 pmcid:PMC7520877 fatcat:7utpoyicjncwhc3echbhf6dfi4

HiGHmed – An Open Platform Approach to Enhance Care and Research across Institutional Boundaries

Björn Schreiweis, Sabine Rey, Ulrich Sax, Simone Scheithauer, Otto Rienhoff, Petra Knaup-Gregori, Udo Bavendiek, Christoph Dieterich, Benedikt Brors, Inga Kraus, Caroline Thoms, Dirk Jäger (+7 others)
2018 Methods of Information in Medicine  
We outline the basic principles and design goals of the open platform approach as well as the roles of standards and specifications such as IHE XDS, openEHR, SNOMED CT and HL7 FHIR.  ...  Other challenges including topics such as data quality, privacy regulations, and patient consent will be addressed throughout the project.  ...  and cancer genome sequencing.  ... 
doi:10.3414/me18-02-0002 pmid:30016813 pmcid:PMC6193407 fatcat:qxjethbbgzgwxgrgdgnhklahfy

OpenEHR and General Data Protection Regulation: Evaluation of Principles and Requirements

Duarte Gonçalves-Ferreira, Mariana Sousa, Gustavo M Bacelar-Silva, Samuel Frade, Luís Filipe Antunes, Thomas Beale, Ricardo Cruz-Correia
2019 JMIR Medical Informatics  
The openEHR principles conformed to 30% (15/50) of GDPR requirements. All the openEHR principles were aligned with GDPR requirements.  ...  The requirements were categorized and compared with the principles by experts on openEHR and GDPR. A total of 50 GDPR requirements and 8 openEHR design principles were identified.  ...  Acknowledgements The authors would like to acknowledge the project NanoSTIMA(NORTE-01-0145-FEDER-000016), which is financed by the North Portugal Regional Operational Programme (NORTE 2020), under the  ... 
doi:10.2196/medinform.9845 pmid:30907730 pmcid:PMC6452286 fatcat:xtua3s2ll5a5tfllx24m6k4iqi

The Evolving Role of Open Source Software in Medicine and Health Services

David Ingram, Sevket Seref Arikan
2013 Technology Innovation Management Review  
We give the example of the openEHR Foundation, which was established at University College London (UCL) in London, England, with members in 80 countries.  ...  The past five decades have witnessed immense coevolution of methods and tools of information technology, and their practical and experimental application within the medical and healthcare domain.  ...  -2011, including coordinating the EU GEHR Project, which laid the foundations for a standard health record architecture and the openEHR Foundation and community, internationally.  ... 
doi:10.22215/timreview648 fatcat:sa3777hxibbrbell6cqr5acebe

AQBE — QBE Style Queries for Archetyped Data

Shelly SACHDEVA, Daigo YAGINUMA, Wanming CHU, Subhash BHALLA
2012 IEICE transactions on information and systems  
These also require query interfaces at multiple levels and at the level of semi-skilled users.  ...  The new proposals propose an advanced (multi-level) DBMS architecture for repository services for health records of patients.  ...  To get clinical knowledge (information) from archetype, the "ADL parser", implemented in the openEHR Java Reference Implementation Project is being used [27] .  ... 
doi:10.1587/transinf.e95.d.861 fatcat:i7jh57zv4jgcdlbfgqftznmei4

EHDEN - D4.5 - Roadmap for interoperability solutions

Kees Van Bochove, Emma Vos, Maxim Moinat, Sebastiaan Van Sandijk, Tess Korthout, Peyman Mohtashani
2020 Zenodo  
The EHDEN project has explicitly chosen to standardize healthcare data for analysis using the OMOP Common Data Model, but other interoperability solutions, such as i2b2, CDISC, FHIR, openEHR, GA4GH etc  ...  The EHDEN project aims to make healthcare data in Europe Findable, Accessible, Interoperable and Reusable (FAIR) at an unprecedented level.  ...  for representing genomics data and patient consent.  ... 
doi:10.5281/zenodo.4474373 fatcat:3zw4vbrqyvhitc4pgqc2n2wiou

Archetype relational mapping - a practical openEHR persistence solution

Li Wang, Lingtong Min, Rui Wang, Xudong Lu, Huilong Duan
2015 BMC Medical Informatics and Decision Making  
openEHR specifications.  ...  System components such as ARM can greatly facilitate the adoption of openEHR architecture within EHR systems.  ...  Acknowledgements This work was supported by the National High-tech R&D Program of China (2012AA02A601).  ... 
doi:10.1186/s12911-015-0212-0 pmid:26541142 pmcid:PMC4636072 fatcat:dqyicksanfgihfawpv4zb5zzxy
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