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Implementation of a platform dedicated to the biomedical analysis terminologies management

Sylvie Cormont, Pierre-Yves Vandenbussche, Antoine Buemi, Jean Delahousse, Eric Lepage, Jean Charlet
2011 AMIA Annual Symposium Proceedings  
In this paper we describe in three steps (modeling, data migration and integration/verification) the implementation of a platform for publishing and maintaining the AP-HP laboratory data dictionary (AnaBio  ...  Assistance Publique - Hôpitaux de Paris (AP-HP) is implementing a new laboratory management system (LMS) common to the 12 hospital groups.  ...  In this way, it was necessary to acquire a biological analysis dictionary common to the whole production chain: order, analysis processing in the laboratory management systems (LMS) and transmission of  ... 
pmid:22195205 pmcid:PMC3243140 fatcat:fusvuwumc5f3lpy77uxxtgeede

Unsupervised Topic Modeling in a Large Free Text Radiology Report Repository

Saeed Hassanpour, Curtis P. Langlotz
2015 Journal of digital imaging  
The results of our system provide a target-based corpus and framework for information extraction and retrieval systems for radiology reports.  ...  Radiology report narrative contains a large amount of information about the patient's health and the radiologist's interpretation of medical findings.  ...  Acknowledgments The authors would like to thank Chuck Kahn, Kevin McEnery, and Brad Erickson for their work on compiling RadCore database and Daniel Rubin for his contribution to RadCore and providing  ... 
doi:10.1007/s10278-015-9823-3 pmid:26353748 pmcid:PMC4722022 fatcat:yh4tag7kyjfwhfjoucdduullxa

Practical implementation of a bridge between legacy EHR system and a clinical research environment

Dina Vishnyakova, Sylviane Bottone, Emilie Pasche, Christian Lovis
2014 Studies in Health Technology and Informatics  
Employing the bridge between Clinical Information System (CIS) and Clinical Research Environment (CRE) can provide functionality, which is not easily, implemented by traditional legacy EHR system.  ...  In this paper, the experience of such implementation at the University Hospitals of Geneva is described.  ...  Acknowledgements The research leading to these results has received support from the Innovative Medicines Initiative Joint Undertaking under grant agreement n° [115489], resources of  ... 
pmid:24743073 fatcat:b6w7mdi6ebcdxoowqck45xdhwy

Semantic Knowledge Base Construction from Radiology Reports

Eriksson Monteiro, Pedro Sernadela, Sérgio Matos, Carlos Costa, José Luís Oliveira
2016 Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies  
In order to leverage modern healthcare information systems, new strategies must be developed that address challenges such as extraction of relevant information, data redundancy, and the lack of associations  ...  The tremendous quantity of data stored daily in healthcare institutions demands the development of new methods to summarize and reuse available information in clinical practice.  ...  During the last decades, researchers have developed diverse solutions for improving information storage, management and retrieval in healthcare scenario (Thompson et al., 2014) (Belleau et al., 2008  ... 
doi:10.5220/0005709503450352 dblp:conf/biostec/MonteiroSMCO16 fatcat:vjk5e55zqnbk3p66m65trd5klm

Finding relevant free-text radiology reports at scale with IBM Watson Content Analytics: a feasibility study in the UK NHS

Alicja Piotrkowicz, Owen Johnson, Geoff Hall
2019 Journal of Biomedical Semantics  
Busy clinicians have limited time to read such large amounts of free-text and are at risk of information overload and consequently missing information vital to patient care.  ...  Automatically identifying relevant information at the point of care has the potential to reduce these risks but represents a considerable research challenge.  ...  The Unstructured Information Management Architecture (UIMA) [23] is implemented throughout the system and allows for adding of further components into the pipeline.  ... 
doi:10.1186/s13326-019-0213-5 pmid:31711538 pmcid:PMC6849164 fatcat:no7bmha2dve6jkfltxmd4fleia

POSTER ABSTRACTS from Third Annual Public Meeting: Mobilizing Computable Biomedical Knowledge ( MCBK 2020)

2020 Learning Health Systems  
into the MDR, 15 maintenance of metadata provenance and trajectory using approaches like blockchain, and data and process orchestration in ultra large scale systems.  ...  An operational definition is a computable piece of knowledge that is either implemented in a Computable Biomedical Knowledge (CBK) artifact, or is deployed as a service for which a computable API specification  ...  Remaining challenges include representing the extracted information in the standard vocabularies used in EHRs, dealing with mismatches of abstractions, and developing a workflow management system enabling  ... 
doi:10.1002/lrh2.10256 fatcat:cz6ijajvsng7xdqm7pezl2ibtu

Application Description and Policy Model in Collaborative Environment for Sharing of Information on Epidemiological and Clinical Research Data Sets

Elias César Araujo de Carvalho, Adelia Portero Batilana, Julie Simkins, Henrique Martins, Jatin Shah, Dimple Rajgor, Anand Shah, Scott Rockart, Ricardo Pietrobon, Simon I. Hay
2010 PLoS ONE  
A Model-based predictions of number of publications and funding resulting from combinations of different policy implementation strategies (for metadata and data sharing) were generated using System Dynamics  ...  Sharing of epidemiological and clinical data sets among researchers is poor at best, in detriment of science and community at large.  ...  Acknowledgments Team ''Research on Research'' Duke University Health System, USAtemplates for writing introduction and discussion sections of the manuscript [36] and templates for literature review  ... 
doi:10.1371/journal.pone.0009314 pmid:20174560 pmcid:PMC2824801 fatcat:pxq46vv265bi5ogcu6p5yfjruq

Emerging Data Management Roles for Health Librarians in Electronic Medical Records

Mary Corbett, Ariel Deardorff, Iris Kovar-Gough
2014 Journal of the Canadian Health Libraries Association  
Methods: To accomplish a state-of-the-art review, searches were conducted in the library and information science databases (LISTA, LISA), biomedical databases (MEDLINE, CINAHL, EMBASE), and on the web  ...  in system implementation, creating links to the medical literature, and using EMRs to provide patient health information.  ...  Many hospitals and healthcare centres in the United States have relied on librarians' database expertise when choosing and implementing EMR systems.  ... 
doi:10.5596/c14-022 fatcat:t3h7rn7qefbibj43l6wg4i7h3m

Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience

Jyotishman Pathak, Janey Wang, Sudha Kashyap, Melissa Basford, Rongling Li, Daniel R Masys, Christopher G Chute
2011 JAMIA Journal of the American Medical Informatics Association  
A web-based tool was also implemented to assist in semi-automatic mapping of data elements.  ...  In this study, the authors analyzed how a limited subset of phenotypic data is amenable to common definition and standardized collection, as well as how their adoption in large-scale epidemiological and  ...  Acknowledgments We thank Diane Reeves, Luke Rasmussen, Jennifer Pacheco, and several members of the PhenX Project for numerous fruitful discussions leading to this work.  ... 
doi:10.1136/amiajnl-2010-000061 pmid:21597104 pmcid:PMC3128396 fatcat:nesbi7ztfbgx7imlbbxsf36y4m

Inventory of infrastructures providing support for integration of cohort data [article]

Maria Panagiotopoulou, Sergei Gorianin
2020 Zenodo  
The SYNCHROS repository, already presented in Deliverable 2.3 and available at, was created to share key information on initiatives that harmonise and/or integrate cohort  ...  An important feature of all these initiatives is the type of infrastructure used to gather the information from the different cohorts and perform data analysis across them.  ...  Cohort studies, however, play an important role in informing biomedical research and healthcare and should not be hampered.  ... 
doi:10.5281/zenodo.6389765 fatcat:j7ukvrh6ivbfbdubdebjhl3dki

CERC: an interactive content extraction, recognition, and construction tool for clinical and biomedical text

Eva K Lee, Karan Uppal
2020 BMC Medical Informatics and Decision Making  
The system ranks sentences by relevance and includes features that can facilitate early detection of medical risks in a clinical setting.  ...  and extracting salient information from clinical and biomedical text.  ...  , Chris Kwan, Eunho Kwon, Di Liu, Joe Malecki, Autumn Phillips, and Peijue Zhang, who helped with the initial usage and testing of the anonymized data generated from the customizable information extraction  ... 
doi:10.1186/s12911-020-01330-8 pmid:33323109 fatcat:neac7vl5fncibnx3kxcktyqmba

IMIA LaMB WG event: 'Biomedical Semantics in the Big Data Era', Workshop at MEDINFO 2015 – São Paulo,Brazil

Roland Cornet, Stephane Meystre, Stefan Schulz, Patrick Ruch, Tomasz Adamusiak, Laszlo Balkanyi, Jianying Hu
2019 Zenodo  
The workshop of IMIA WG 'Language and Meaning in Biomedicine' was held at MEDINFO 2015 – São Paulo,Brazil.  ...  and unstructured content , by Tomasz Adamusiak - Summary and workshop organization, by Laszlo Balkanyi (2) a reader with a library of references for the MEDINFO 2015 workshop of IMIA LaMB Working Group  ...  Despite the use of simpIe Information Extraction strategies, our system exploits the redundancy of information in literature in order to provide a powerful Question Answering system.  ... 
doi:10.5281/zenodo.3398964 fatcat:ksn3rajzs5earbjd3kczdvrwdi

Using Electronic Data Capture for Cardiovascular Electrophysiology Invasive Procedures: An Important Step Towards Interoperable Clinical Registries

Mostafa Shanbehzadeh, Hadi Kazemi-Arpanahi, Hassan Bostan, Raoof Nopour
2020 Frontiers in Health Informatics  
Data collection applications were successfully develop as an a priori step in a clinical research for assisting data collection and management in a case of cardiovascular EP invasive procedures.  ...  The aim of this study was to design and implement an Electronic Data Capture (EDC) instruments to be use in context of cardiovascular invasive procedures.Material and Methods: This descriptive and developmental  ...  ACKNOWLEDGEMENTS The authors thank the deputy dean of research affairs, Abadan Faculty of Medical Sciences for financially supporting this project.  ... 
doi:10.30699/fhi.v9i1.236 fatcat:svnakn6nerhz3osjfeqzksdfn4

Clinical Research Informatics and Electronic Health Record Data

R. L. Richesson, M. M. Horvath, S. A. Rusincovitch
2014 IMIA Yearbook of Medical Informatics  
Considerations for the use of EHR data provide a starting point for practical applications and a CRI research agenda, which will be facilitated by CRI's key role in the infrastructure of a learning healthcare  ...  union of biomedical research and informatics.  ...  healthcare system as a continuous communication of data, information and knowledge between healthcare systems, researchers, and public.  ... 
doi:10.15265/iy-2014-0009 pmid:25123746 pmcid:PMC4287078 fatcat:zqiw3fciivfbpb6pqf77grla5e

Data Integration Challenges for Machine Learning in Precision Medicine

Mireya Martínez-García, Enrique Hernández-Lemus
2022 Frontiers in Medicine  
Computational approaches to medicine need to be able to efficiently manage, visualize and integrate, large datasets combining structure, and unstructured formats.  ...  A number of challenges arise in the design of successful designs to medical data analytics under currently demanding conditions of performance in personalized medicine, while also subject to time, computational  ...  EH-L acknowledges additional support from the 2016 Marcos Moshinsky Fellowship in the Physical Sciences.  ... 
doi:10.3389/fmed.2021.784455 pmid:35145977 pmcid:PMC8821900 fatcat:nxco4r4gsjdfnpbgoditxjptya
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