Abstract：
:The 2014 i2b2/UTHealth natural language processing shared task featured a track focused on the de-identification of longitudinal medical records. For this track, we de-identified a set of 1304 longitudinal medical records describing 296 patients. This corpus was de-identified under a broad interpretation of the HIPAA guidelines using double-annotation followed by arbitration, rounds of sanity checking, and proof reading. The average token-based F1 measure for the annotators compared to the gold standard was 0.927. The resulting annotations were used both to de-identify the data and to set the gold standard for the de-identification track of the 2014 i2b2/UTHealth shared task. All annotated private health information were replaced with realistic surrogates automatically and then read over and corrected manually. The resulting corpus is the first of its kind made available for de-identification research. This corpus was first used for the 2014 i2b2/UTHealth shared task, during which the systems achieved a mean F-measure of 0.872 and a maximum F-measure of 0.964 using entity-based micro-averaged evaluations.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Stubbs A,Uzuner Ödoi
10.1016/j.jbi.2015.07.020subject
Has Abstractpub_date
2015-12-01 00:00:00pages
S20-9eissn
1532-0464issn
1532-0480pii
S1532-0464(15)00182-3journal_volume
58 Supplpub_type
杂志文章abstract：OBJECTIVES:Major adverse cardiac events (MACE) of acute coronary syndrome (ACS) often occur suddenly resulting in high mortality and morbidity. Recently, the rapid development of electronic medical records (EMR) provides the opportunity to utilize the potential of EMR to improve the performance of MACE prediction. In t...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.01.001
更新日期：2017-02-01 00:00:00
abstract：:The Strategic Health IT Advanced Research Projects (SHARP) Program, established by the Office of the National Coordinator for Health Information Technology in 2010 supports research findings that remove barriers for increased adoption of health IT. The improvements envisioned by the SHARP Area 4 Consortium (SHARPn) wi...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2012.01.009
更新日期：2012-08-01 00:00:00
abstract：:Warfarin is an effective preventative treatment for arterial and venous thromboembolism, but requires individualised dosing due to its narrow therapeutic range and high individual variation. Many machine learning techniques have been demonstrated in this domain. This study evaluated the accuracy of the most promising ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2020.103634
更新日期：2021-01-01 00:00:00
abstract：:To extract biomedical information about bio-entities from the huge amount of biomedical literature, the first key step is recognizing their names in these literatures, which remains a challenging task due to the irregularities and ambiguities in bio-entities nomenclature. The recognition performances of the current po...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2008.01.002
更新日期：2008-08-01 00:00:00
abstract：:Previous research on standardization of eligibility criteria and its feasibility has traditionally been conducted on clinical trial protocols from ClinicalTrials.gov (CT). The portability and use of such standardization for full-text industry-standard protocols has not been studied in-depth. Towards this end, in this ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.06.001
更新日期：2013-10-01 00:00:00
abstract：:The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function....
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.01.008
更新日期：2015-04-01 00:00:00
abstract：:Medication errors are common and cause serious health issues during care transitions, particularly for older adults with multiple chronic conditions. In this paper, we discuss the design and evaluation of the Colorado Care Tablet, a Personal Health Application (PHA) that helps older adults and their lay caregivers man...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2010.05.007
更新日期：2010-10-01 00:00:00
abstract：BACKGROUND:The realization of the potential benefits of health information exchange systems (HIEs) for emergency departments (EDs) depends on the way these systems are actually used. The attributes of volume of information and duration of information processing are important for the study of HIE use patterns in the ED,...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.05.007
更新日期：2017-07-01 00:00:00
abstract：BACKGROUND:Understanding complexity in healthcare has the potential to reduce decision and treatment uncertainty. Therefore, identifying both patient and task complexity may offer better task allocation and design recommendation for next-generation health information technology system design. OBJECTIVE:To identify spe...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2016.10.018
更新日期：2017-07-01 00:00:00
abstract：:In this case study, we describe a method that has potential to provide systematic support for public health information management. Public health agencies depend on specialized information that travels throughout an organization via communication networks among employees. Interactions that occur within these networks ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2006.09.004
更新日期：2007-08-01 00:00:00
abstract：:The Breast Imaging Reporting and Data System (BI-RADS) was developed to reduce variation in the descriptions of findings. Manual analysis of breast radiology report data is challenging but is necessary for clinical and healthcare quality assurance activities. The objective of this study is to develop a natural languag...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.04.011
更新日期：2017-05-01 00:00:00
abstract：:In this paper, a Hidden Semi-Markov Model (HSMM) based approach is proposed to evaluate and monitor body motion during a rehabilitation training program. The approach extracts clinically relevant motion features from skeleton joint trajectories, acquired by the RGB-D camera, and provides a score for the subject's perf...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.12.012
更新日期：2018-02-01 00:00:00
abstract：:With the rise in chronic, behavior-related disease, computerized behavioral protocols (CBPs) that help individuals improve behaviors have the potential to play an increasing role in the future health of society. To be effective and widely used CBPs should be based on accepted behavioral theory. However, designing CBPs...
journal_title：Journal of biomedical informatics
pub_type： 临床试验,杂志文章
doi：10.1016/j.jbi.2004.12.001
更新日期：2005-08-01 00:00:00
abstract：:The major challenge in influenza vaccination is to predict vaccine efficacy. The purpose of this study was to design a model to enable successful prediction of the outcome of influenza vaccination based on real historical medical data. A non-linear neural network approach was used, and its performance compared to logi...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2010.04.011
更新日期：2010-10-01 00:00:00
abstract：:Causal inference often relies on the counterfactual framework, which requires that treatment assignment is independent of the outcome, known as strong ignorability. Approaches to enforcing strong ignorability in causal analyses of observational data include weighting and matching methods. Effect estimates, such as the...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2020.103515
更新日期：2020-09-01 00:00:00
abstract：OBJECTIVE:Clinical pathways (CPs) are widely studied methods to standardize clinical intervention and improve medical quality. However, standard care plans defined in current CPs are too general to execute in a practical healthcare environment. The purpose of this study was to create hospital-specific personalized CPs ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2014.07.017
更新日期：2014-12-01 00:00:00
abstract：:In absence of periodic systematic comparisons, biologists/bioinformaticians may be forced to make a subjective selection among the many protein-protein interaction (PPI) databases and tools. We conducted a comprehensive compilation and comparison of such resources. We compiled 375 PPI resources, short-listed 125 impor...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2020.103380
更新日期：2020-03-01 00:00:00
abstract：:Modern biomedical data mining requires feature selection methods that can (1) be applied to large scale feature spaces (e.g. 'omics' data), (2) function in noisy problems, (3) detect complex patterns of association (e.g. gene-gene interactions), (4) be flexibly adapted to various problem domains and data types (e.g. g...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.07.015
更新日期：2018-09-01 00:00:00
abstract：:Medical error is a leading cause of patient death in the United States. Among the different types of medical errors, harm to patients caused by doctors missing early signs of deterioration is especially challenging to address due to the heterogeneity of patients' physiological patterns. In this study, we implemented r...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2020.103425
更新日期：2020-07-01 00:00:00
abstract：RATIONALE:Templates in text notes pose challenges for automated information extraction algorithms. We propose a method that identifies novel templates in plain text medical notes. The identification can then be used to either include or exclude templates when processing notes for information extraction. METHODS:The tw...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2016.07.019
更新日期：2017-07-01 00:00:00
abstract：:Genomics has contributed to a growing collection of gene-function and gene-disease annotations that can be exploited by informatics to study similarity between diseases. This can yield insight into disease etiology, reveal common pathophysiology and/or suggest treatment that can be appropriated from one disease to ano...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2011.11.017
更新日期：2012-04-01 00:00:00
abstract：:One of the major problems in genomics and medicine is the identification of gene networks and pathways deregulated in complex and polygenic diseases, like cancer. In this paper, we address the problem of assessing the variability of results of pathways analysis identified in different and independent genome wide expre...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2009.09.005
更新日期：2010-06-01 00:00:00
abstract：:An open research question when leveraging ontological knowledge is when to treat different concepts separately from each other and when to aggregate them. For instance, concepts for the terms "paroxysmal cough" and "nocturnal cough" might be aggregated in a kidney disease study, but should be left separate in a pneumo...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2012.01.002
更新日期：2012-06-01 00:00:00
abstract：OBJECTIVE:Published clinical trials and high quality peer reviewed medical publications are considered as the main sources of evidence used for synthesizing systematic reviews or practicing Evidence Based Medicine (EBM). Finding all relevant published evidence for a particular medical case is a time and labour intensiv...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103321
更新日期：2019-12-01 00:00:00
abstract：:With a rapid progress in the field, a great many fMRI studies are published every year, to the extent that it is now becoming difficult for researchers to keep up with the literature, since reading papers is extremely time-consuming and labor-intensive. Thus, automatic information extraction has become an important is...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2009.04.003
更新日期：2009-10-01 00:00:00
abstract：:Rare diseases are often hard and long to be diagnosed precisely, and most of them lack approved treatment. For some complex rare diseases, precision medicine approach is further required to stratify patients into homogeneous subgroups based on the clinical, biological or molecular features. In such situation, deep phe...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103308
更新日期：2019-12-01 00:00:00
abstract：INTRODUCTION:The trend of an ageing and growing world population, particularly in developed countries, is expected to continue for decades to come causing an increase in demand for healthcare resources and services. Consequently, demand is growing faster than rises in funding. The UK government, in partnership with the...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2019.103102
更新日期：2019-02-01 00:00:00
abstract：INTRODUCTION:Heart disease remains a leading cause of global mortality. While acute myocardial infarction (colloquially: heart attack), has multiple proximate causes, proximate etiology cannot be determined by a blood-based diagnostic test. We enrolled a suitable patient cohort and conducted a non-targeted quantificati...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,多中心研究
doi：10.1016/j.jbi.2018.03.007
更新日期：2018-05-01 00:00:00
abstract：:Probabilistic record linkage is a method commonly used to determine whether demographic records refer to the same person. The Fellegi-Sunter method is a probabilistic approach that uses field weights based on log likelihood ratios to determine record similarity. This paper introduces an extension of the Fellegi-Sunter...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2009.08.004
更新日期：2010-02-01 00:00:00
abstract：BACKGROUND:Personal health information is a valuable resource to the advancement of research. In order to achieve a comprehensive reform of data infrastructure in Australia, both public engagement and building social trust is vital. In light of this, we conducted a study to explore the opinions, perceived risks and tru...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103222
更新日期：2019-07-01 00:00:00
