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Knowledge Representation and Management: Towards Patient Health Self-management

A.-M. Rassinoux
2012 IMIA Yearbook of Medical Informatics  
Delivering timely, friendly and secure access to functional, accurate, up-to-date and sustainable personal health records is a significant challenging task for supporting self-managed healthcare.  ...  One paper aims at exploiting domain-specific terminologies to improve the parsing of biomedical noun phrases, and another one aims at discovering rare diseases associations embedded into disparate textual  ...  Acknowledgement I greatly acknowledge the support of Martina Hutter and of the reviewers in the selection process of the IMIA Yearbook.  ... 
doi:10.1055/s-0038-1639442 fatcat:abldijr4hnegjbg7yksrobotby

Electronic Medical Records as a Tool in Clinical Pharmacology: Opportunities and Challenges

D M Roden, H Xu, J C Denny, R A Wilke
2012 Clinical Pharmacology and Therapeutics  
The development and increasing sophistication of electronic medical record (EMR) systems hold the promise of not only improving patient care but also providing unprecedented opportunities for discovery  ...  access to medical information and reducing costs associated with paper storage and retrieval.  ...  processing is especially important to detect diseases and events occurring at facilities outside the recording center and entered as part of the patient's past medical history and for discovery of rare  ... 
doi:10.1038/clpt.2012.42 pmid:22534870 pmcid:PMC3819803 fatcat:wa366oirjrdltdpzrdp5gblhtm

Chapter 13: Mining Electronic Health Records in the Genomics Era

Joshua C. Denny, Fran Lewitter, Maricel Kann
2012 PLoS Computational Biology  
Similarly, healthcare systems are increasingly adopting robust electronic health record (EHR) systems that not only can improve health care, but also contain a vast repository of disease and treatment  ...  However, to extract the large cohorts necessary for genome-wide association studies, natural language processing methods to process narrative text data may be needed.  ...  record systems'') N Hristidis V, editor (2009) Information discovery on electronic health records. 1st edition.  ... 
doi:10.1371/journal.pcbi.1002823 pmid:23300414 pmcid:PMC3531280 fatcat:ugktm6spyfe4tefawbwcgacrzu

Exome-Wide Rare Variant Analysis From the DiscovEHR Study Identifies Novel Candidate Predisposition Genes for Endometrial Cancer

Manu Shivakumar, Jason E. Miller, Venkata Ramesh Dasari, Radhika Gogoi, Dokyoon Kim
2019 Frontiers in Oncology  
In conclusion, our results using the single-source electronic health records (EHR) linked to genomic data highlights candidate genes and pathways associated with endometrial cancer and indicates rare variants  ...  We conducted exome-wide rare variant association using 472 cases and 4,110 controls in 60,000 patients (discovery cohort); and 261 cases and 1,531 controls from 30,000 patients (replication cohort).  ...  The high-throughput sequencing data coupled with longitudinal electronic health records (EHR) has been used for genetic research.  ... 
doi:10.3389/fonc.2019.00574 pmid:31338326 pmcid:PMC6626914 fatcat:6fn5quhhwfcvzf4cupdcnss5v4

The U.S. National Library of Medicine's Impact on Precision and Genomic Medicine [chapter]

Huan Mo, Joshua C. Denny
2022 Studies in Health Technology and Informatics  
NLM has been supporting the innovation of electronic health record systems to implement computability and secondary use for biomedical research, producing the scale of linked health and molecular datasets  ...  The hosting and curation of biomedical knowledge repositories and data by NLM enable quality information reachable for providers and researchers throughout the world.  ...  Acknowledgments The authors would like to thank Dr. Tracey Ferrara for her help in preparation of this manuscript.  ... 
doi:10.3233/shti210983 pmid:35102830 fatcat:rp32lsmnmbhnlkreelprfopoha

Pharmacogenetics and personal genomes

Michael J Wagner
2009 Personalized Medicine  
In order for this flood of information to not overwhelm both researchers and clinicians alike, a variety of new and expanded information management tools will be needed, including electronic medical records  ...  , bioinformatic algorithms for analyzing sequence data, information management systems for storing, retrieving and interpreting whole-genome sequence data, and pharmacogenetic decision tools for prescribers  ...  studies are linked to electronic medical and prescribing records.  ... 
doi:10.2217/pme.09.55 pmid:20190862 pmcid:PMC2826717 fatcat:z5dad7ojmnfjpdcbpmhlt645wi

The U.S. National Library of Medicine's impact on precision and genomic medicine

M.O. Huan, Joshua C. Denny
2022 Information Services and Use  
NLM has been supporting the innovation of electronic health record systems to implement computability and secondary use for biomedical research, producing the scale of linked health and molecular datasets  ...  The hosting and curation of biomedical knowledge repositories and data by NLM enable quality information reachable for providers and researchers throughout the world.  ...  Acknowledgements The authors would like to thank Dr. Tracey Ferrara for her help in preparation of this manuscript. This  ... 
doi:10.3233/isu-210144 pmid:35600119 pmcid:PMC9108560 fatcat:pm3jmshxdbazbj7cnllmnnoqzi

Extracting research-quality phenotypes from electronic health records to support precision medicine

Wei-Qi Wei, Joshua C Denny
2015 Genome Medicine  
The convergence of two rapidly developing technologies -high-throughput genotyping and electronic health records (EHRs) -gives scientists an unprecedented opportunity to utilize routine healthcare data  ...  However, the precise extraction of detailed disease and drug-response phenotype information hidden in EHRs is not an easy task.  ...  Acknowledgements The authors would like to acknowledge funding by the NIH (R01 LM010685, R01 GM103859 and R01 GM105688), NIH/NHLBI (5 U19 HL065962-14), and the American Heart Association (13POST16470018  ... 
doi:10.1186/s13073-015-0166-y pmid:25937834 pmcid:PMC4416392 fatcat:g4hiwcrxybatnc5s2ryrxxgw6y

Between Access and Privacy: Challenges in Sharing Health Data

Kenneth Goodman, Bradley Malin
2018 IMIA Yearbook of Medical Informatics  
risks of sharing new data increasingly utilized in research and the clinical setting (e.g., genomic), 4) new cryptographic techniques for querying clinical data for cohort discovery, and 5) novel game  ...  The papers introduce 1) consenting strategies for emerging environments, 2) software for searching and retrieving datasets in organizationally distributed environments, 3) approaches to measure the privacy  ...  We also wish to thank the external reviewers for the time and energy they devoted during the selection process.  ... 
doi:10.1055/s-0038-1641216 pmid:30157505 fatcat:wzc6dw3xqfehfggqkqsjjcirhm

Cohort study protocol: Bioresource in Adult Infectious Diseases (BioAID)

Laura J. Shallcross, Alexander Mentzer, Saadia Rahman, Graham S. Cooke, Shiranee Sriskandan, Mahdad Noursadeghi
2018 Wellcome Open Research  
The aim of the Bioresource in Adult Infectious Diseases (BioAID) is to provide a platform for biomarker discovery, trials and clinical service developments in the field of infectious diseases, by establishing  ...  The final cohort will be characterised using descriptive statistics including information on the number of cases that can be linked to biological and microbial samples to support future research studies  ...  Acknowledgements We are extremely grateful to all the patients who participated in BioAID, and to the scientists, clinical and laboratory staff who have contributed to the Bioresource.  ... 
doi:10.12688/wellcomeopenres.14690.1 pmid:30345383 pmcid:PMC6171553 fatcat:o5t7u3fknngnlhyg3ht6lxzije

Discovering Disease Associations by Integrating Electronic Clinical Data and Medical Literature

Antony B. Holmes, Alexander Hawson, Feng Liu, Carol Friedman, Hossein Khiabanian, Raul Rabadan, Andrey Rzhetsky
2011 PLoS ONE  
Electronic health record (EHR) systems offer an exceptional opportunity for studying many diseases and their associated medical conditions within a population.  ...  We apply ADAMS to the New York-Presbyterian Hospital's EHR to combine the information from the relational diagnosis tables and textual discharge summaries with those from PubMed and Wikipedia in order  ...  Author Contributions Conceived and designed the experiments: ABH AH CF HK RR. Performed the experiments: ABH AH FL HK. Analyzed the data: ABH AH HK RR.  ... 
doi:10.1371/journal.pone.0021132 pmid:21731656 pmcid:PMC3121722 fatcat:nc5rdg4qmbh2dkdr5kpnq3nn4e

Methods for safety signal detection in healthcare databases: a literature review

Mickael Arnaud, Bernard Bégaud, Nicolas Thurin, Nicholas Moore, Antoine Pariente, Francesco Salvo
2017 Expert Opinion on Drug Safety  
From this point of view, the SSA could appear as the most suitable method for signal detection in healthcare databases owing to its simple principle and its ability to provide a risk estimate.  ...  Areas covered: To review the methods proposed for safety signal detection in healthcare databases and their performance. Expert opinion: Fifteen different data mining methods were identified.  ...  The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the  ... 
doi:10.1080/14740338.2017.1325463 pmid:28490262 fatcat:w6tiqwm5vjg43cuatwn6sulkpi

Next-generation epidemiology: the role of high-resolution molecular phenotyping in diabetes research

Paul W. Franks, Hugo Pomares-Millan
2020 Diabetologia  
Epidemiologists have for many decades reported on the patterns and distributions of diabetes within and between populations and have helped to elucidate the aetiology of the disease.  ...  Many are banking on this massive volume of diverse molecular data for breakthroughs in drug discovery and predicting sensitivity to risk factors, response to therapies and susceptibility to diabetes complications  ...  and linkage with electronic health records.  ... 
doi:10.1007/s00125-020-05246-w pmid:32840675 fatcat:uvv37bmgdbbm3ocxcql6r5kz7u

Application of Big Data analysis in gastrointestinal research

Ka-Shing Cheung, Wai K Leung, Wai-Kay Seto
2019 World Journal of Gastroenterology  
While it retains most of the advantages and avoids some of the disadvantages of traditional observational studies (case-control and prospective cohort studies), it allows for phenomapping of disease heterogeneity  ...  Big Data in health care are defined as large datasets that are collected routinely or automatically, and stored electronically.  ...  information being automatically recording in electronic systems.  ... 
doi:10.3748/wjg.v25.i24.2990 pmid:31293336 pmcid:PMC6603810 fatcat:kcssyunozzeqbhwudcuep6lrf4

Accelerating Biomarker Discovery Through Electronic Health Records, Automated Biobanking, and Proteomics

Quinn S. Wells, Deepak K. Gupta, J. Gustav Smith, Sean P. Collins, Alan B. Storrow, Jane Ferguson, Maya Landenhed Smith, Jill M. Pulley, Sarah Collier, Xiaoming Wang, Dan M. Roden, Robert E. Gerszten (+1 others)
2019 Journal of the American College of Cardiology  
Newer molecular platforms can accelerate biomarker discovery, but they require significant resources for data and sample acquisition.  ...  Circulating biomarkers can facilitate diagnosis and risk stratification for complex conditions such as heart failure (HF).  ...  (A) Electronic algorithms are deployed in an electronic health record database for real-time identification of subjects with and without the phenotype of interest (e.g., heart failure).  ... 
doi:10.1016/j.jacc.2019.01.074 pmid:31047008 pmcid:PMC6501811 fatcat:etiuscloqjcb5iuh3csbr3migi
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