Abstract:
BACKGROUND:High-quality clinical data and biological specimens are key for medical research and personalized medicine. The Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC) aims to facilitate access to such biological resources. The accompanying ADOPT BBMRI-ERIC project kick-started BBMRI-ERIC by collecting colorectal cancer data from European biobanks. OBJECTIVES:To transform these data into a common representation, a uniform approach for data integration and harmonization had to be developed. This article describes the design and the implementation of a toolset for this task. METHODS:Based on the semantics of a metadata repository, we developed a lexical bag-of-words matcher, capable of semiautomatically mapping local biobank terms to the central ADOPT BBMRI-ERIC terminology. Its algorithm supports fuzzy matching, utilization of synonyms, and sentiment tagging. To process the anonymized instance data based on these mappings, we also developed a data transformation application. RESULTS:The implementation was used to process the data from 10 European biobanks. The lexical matcher automatically and correctly mapped 78.48% of the 1,492 local biobank terms, and human experts were able to complete the remaining mappings. We used the expert-curated mappings to successfully process 147,608 data records from 3,415 patients. CONCLUSION:A generic harmonization approach was created and successfully used for cross-institutional data harmonization across 10 European biobanks. The software tools were made available as open source.
journal_name
Appl Clin Informjournal_title
Applied clinical informaticsauthors
Mate S,Kampf M,Rödle W,Kraus S,Proynova R,Silander K,Ebert L,Lablans M,Schüttler C,Knell C,Eklund N,Hummel M,Holub P,Prokosch HUdoi
10.1055/s-0039-1695793subject
Has Abstractpub_date
2019-08-01 00:00:00pages
679-692issue
4issn
1869-0327journal_volume
10pub_type
杂志文章abstract:BACKGROUND:Although obesity is a growing problem, primary care physicians often inadequately address it. The objective of this study is to examine the prevalence of obesity documentation in the patient's problem list for patients with eligible body mass indexes (BMI) as contained in the patients' electronic medical rec...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2016-07-RA-0115
更新日期:2017-01-25 00:00:00
abstract:BACKGROUND:Several disease specific registers are operated by members of the 'TMF - Technology, Methods, and Infrastructure for Networked Medical Research', an umbrella organization of research networks in Germany. OBJECTIVE:To describe the coverage and the current state as well as financial and organizational issues ...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2010-04-RA-0024
更新日期:2010-11-24 00:00:00
abstract:BACKGROUND:Although diagnostic error (DE) is a significant problem, it remains challenging for clinicians to identify it reliably and to recognize its contribution to the clinical trajectory of their patients. The purpose of this work was to evaluate the reliability of real-time electronic health record (EHR) reviews u...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.1055/s-0040-1713750
更新日期:2020-05-01 00:00:00
abstract:UNLABELLED:Nationwide Children's Hospital established an i2b2 (Informatics for Integrating Biology & the Bedside) application for sleep disorder cohort identification. Discrete data were gleaned from semistructured sleep study reports. The system showed to work more efficiently than the traditional manual chart review ...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2014-11-RA-0106
更新日期:2015-05-27 00:00:00
abstract:OBJECTIVE:Efforts to promote adoption of electronic health records (EHRs) have focused on primary care physicians, who are now expected to exchange data electronically with other providers, including specialists. However, the variation of EHR adoption among specialists is underexplored. METHODS:We conducted a retrospe...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2013-02-RA-0015
更新日期:2013-05-22 00:00:00
abstract:OBJECTIVES:The authors investigated the impact of computerized provider order entry (CPOE) on the delivery times of analgesia and subsequent patient outcomes. We hypothesized that patients would report less pain and use less pain medications compared with the previous paper-based system. METHODS:Two groups of patients...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2014-12-RA-0114
更新日期:2015-09-23 00:00:00
abstract:BACKGROUND:The 2013 American College of Cardiology / American Heart Association Guidelines for the Treatment of Blood Cholesterol emphasize treatment based on cardiovascular risk. But finding time in a primary care visit to manually calculate cardiovascular risk and prescribe treatment based on risk is challenging. We ...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2016-07-RA-0114
更新日期:2017-02-08 00:00:00
abstract:BACKGROUND:Although patients who work and have related health issues are usually first seen in primary care, providers in these settings do not routinely ask questions about work. Guidelines to help manage such patients are rarely used in primary care. Electronic health record (EHR) systems with worker health clinical ...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.1055/s-0040-1715895
更新日期:2020-08-01 00:00:00
abstract:: ...
journal_title:Applied clinical informatics
pub_type: 社论
doi:10.1055/s-0038-1676332
更新日期:2018-10-01 00:00:00
abstract:OBJECTIVE:The Instrument for Evaluating Human-Factor Principles in Medication-Related Decision Support Alerts (I-MeDeSA) was developed recently in the US with a view towards improving considerations of human-factor principles when designing alerts for clinical decision support (CDS) systems. This study evaluated the ge...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2014-01-RA-0005
更新日期:2014-06-18 00:00:00
abstract:OBJECTIVE:To understand clinician adoption of CDS tools as this may provide important insights for the implementation and dissemination of future CDS tools. MATERIALS AND METHODS:Clinicians (n=168) at a large academic center were randomized into intervention and control arms to assess the impact of strep and pneumonia...
journal_title:Applied clinical informatics
pub_type: 杂志文章,随机对照试验
doi:10.4338/ACI-2014-04-RA-0043
更新日期:2014-09-17 00:00:00
abstract:BACKGROUND:Medication dose adjustment is crucial for patients with renal dysfunction (RD). The assessment of renal function is generally mandatory; however, the renal function may change during the hospital stay and the manual assessment is sometimes challenging. OBJECTIVE:We developed the clinical decision support sy...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.1055/s-0040-1721056
更新日期:2020-10-01 00:00:00
abstract:BACKGROUND: Prediabetes and type 2 diabetes mellitus (T2DM) are one of the major long-term health conditions affecting global healthcare delivery. One of the few effective approaches is to actively manage diabetes via a healthy and active lifestyle. OBJECTIVES: This research is focused on early detection of prediabete...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.1055/s-0040-1719043
更新日期:2021-01-01 00:00:00
abstract:OBJECTIVE:To evaluate the health information technology (HIT) workforce knowledge and skills needed by HIT employers. METHODS:Statewide face-to-face and online focus groups of identified HIT employer groups in Austin, Brownsville, College Station, Dallas, El Paso, Houston, Lubbock, San Antonio, and webinars for rural ...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2012-09-RA-0035
更新日期:2012-12-05 00:00:00
abstract:BACKGROUND:Electronic prescribing (e-prescribing) technology was introduced as an alternative to handwritten prescriptions allowing health care professionals to send prescriptions directly to pharmacies. While the technology has many advantages, such as improving pharmacy workflow and reducing medication errors, some l...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.1055/s-0039-1691840
更新日期:2019-05-01 00:00:00
abstract:OBJECTIVE:Venous thromboembolism (VTE) prophylaxis is an important consideration for hospitalized older adults, and the Padua Prediction Score (PPS) is a risk prediction tool used to prioritize patient selection. We developed an automated PPS (APPS) algorithm using electronic health record (EHR) data. This study examin...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.1055/s-0038-1670678
更新日期:2018-07-01 00:00:00
abstract:BACKGROUND:The assessment of user preferences for performance characteristics of patient-oriented clinical prediction models is lacking. It is unknown if complex statistical aspects of prediction models are readily understandable by a general audience. OBJECTIVE:A pilot study was conducted among nonclinical audiences ...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.1055/s-0038-1669457
更新日期:2018-07-01 00:00:00
abstract:BACKGROUND:Kidney disease is under-documented in physician notes. The use of template-guided notes may improve physician recognition of kidney disease early in training. OBJECTIVE:The objective of this study was to determine whether a computerized inpatient renal template note with clinical decision support improves r...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2013-07-RA-0048
更新日期:2013-11-13 00:00:00
abstract:BACKGROUND:As healthcare moves towards technology-driven population health management, clinicians must adopt complex digital platforms to access health information and document care. OBJECTIVES:This study explored information literacy, a set of skills required to effectively navigate population health information syst...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2016-06-RA-0083
更新日期:2017-02-15 00:00:00
abstract:BACKGROUND:Care-management tools are typically utilized for chronic disease management. Sonoma County government agencies employed advanced health information technologies, artificial intelligence (AI), and interagency process improvements to help transform health and health care for socially disadvantaged groups and o...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.1055/s-0040-1715894
更新日期:2020-08-01 00:00:00
abstract:BACKGROUND:Routine implementation of instruments to capture patient-reported outcomes could guide clinical practice and facilitate health services research. Audio interviews facilitate self-interviews across literacy levels. OBJECTIVES:To evaluate time burden for patients, and factors associated with response times fo...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2014-09-RA-0073
更新日期:2015-03-18 00:00:00
abstract:OBJECTIVE:Based on US. Centers for Disease Control and Prevention recommendations, New York State enacted legislation in 2010 requiring healthcare providers to offer non-targeted human immunodeficiency virus (HIV) testing to all patients aged 13-64. Three New York City adult emergency departments implemented an electro...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2013-09-RA-0075
更新日期:2014-03-26 00:00:00
abstract:BACKGROUND:Important information to support healthcare quality improvement is often recorded in free text documents such as radiology reports. Natural language processing (NLP) methods may help extract this information, but these methods have rarely been applied outside the research laboratories where they were develop...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2016-08-RA-0129
更新日期:2016-11-09 00:00:00
abstract:OBJECTIVES:Unwarranted variance in healthcare has been associated with prolonged length of stay, diminished health and increased cost. Practice variance in the management of asthma can be significant and few investigators have evaluated strategies to reduce this variance. We hypothesized that selective redesign of orde...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2011-01-RA-0002
更新日期:2012-02-08 00:00:00
abstract:OBJECTIVES:Telemonitoring of vital signs is an established option in treatment of patients with chronic heart failure (CHF). In order to allow for early detection of atrial fibrillation (AF) which is highly prevalent in the CHF population telemonitoring programs should include electrocardiogram (ECG) signals. It was th...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2010-12-RA-0078
更新日期:2011-11-23 00:00:00
abstract::Patient-generated health data are coming into broader use across the health care spectrum and hold great promise as a means to improve care and health outcomes. At the same time, rapid evolution in the social media and mobile health (mHealth) market has promoted an environment in which creation and transmission of per...
journal_title:Applied clinical informatics
pub_type: 杂志文章,评审
doi:10.4338/ACI-2014-09-R-0082
更新日期:2015-01-14 00:00:00
abstract:BACKGROUND:Accurate prediction of future patient census in hospital units is essential for patient safety, health outcomes, and resource planning. Forecasting census in the Neonatal Intensive Care Unit (NICU) is particularly challenging due to limited ability to control the census and clinical trajectories. The fixed a...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2015-09-RA-0127
更新日期:2016-05-04 00:00:00
abstract:OBJECTIVES:To assess the impact of introducing a new Picture Archiving and Communication System (PACS) and Radiology Information System (RIS) on: (i) Medical Imaging work processes; and (ii) turnaround times (TATs) for x-ray and CT scan orders initiated in the Emergency Department (ED). METHODS:We employed a mixed met...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2015-01-RA-0014
更新日期:2015-07-08 00:00:00
abstract:OBJECTIVES:Discharging patients from the Neonatal Intensive Care Unit (NICU) can be delayed for non-medical reasons including the procurement of home medical equipment, parental education, and the need for children's services. We previously created a model to identify patients that will be medically ready for discharge...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.4338/ACI-2015-09-RA-0114
更新日期:2016-02-24 00:00:00
abstract:OBJECTIVE:To evaluate informatics-enabled quality improvement (QI) strategies for promoting time spent on face-to-face communication between ophthalmologists and patients. METHODS:This prospective study involved deploying QI strategies during implementation of an enterprise-wide vendor electronic health record (EHR) i...
journal_title:Applied clinical informatics
pub_type: 杂志文章
doi:10.1055/s-0040-1701255
更新日期:2020-01-01 00:00:00