Abstract：
:Evaluating automated indexing applications requires comparing automatically indexed terms against manual reference standard annotations. However, there are no standard guidelines for determining which words from a textual document to include in manual annotations, and the vague task can result in substantial variation among manual indexers. We applied grounded theory to emergency department reports to create an annotation schema representing syntactic and semantic variables that could be annotated when indexing clinical conditions. We describe the annotation schema, which includes variables representing medical concepts (e.g., symptom, demographics), linguistic form (e.g., noun, adjective), and modifier types (e.g., anatomic location, severity). We measured the schema's quality and found: (1) the schema was comprehensive enough to be applied to 20 unseen reports without changes to the schema; (2) agreement between author annotators applying the schema was high, with an F measure of 93%; and (3) the authors made complementary errors when applying the schema, demonstrating that the schema incorporates both linguistic and medical expertise.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Chapman WW,Dowling JNdoi
10.1016/j.jbi.2005.06.004keywords:
subject
Has Abstractpub_date
2006-04-01 00:00:00pages
196-208issue
2eissn
1532-0464issn
1532-0480pii
S1532-0464(05)00070-5journal_volume
39pub_type
杂志文章abstract：:Anticancer drug-associated side effect knowledge often exists in multiple heterogeneous and complementary data sources. A comprehensive anticancer drug-side effect (drug-SE) relationship knowledge base is important for computation-based drug target discovery, drug toxicity predication and drug repositioning. In this s...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2014.10.002
更新日期：2015-02-01 00:00:00
abstract：OBJECTIVE:Clinical care guidelines recommend that newly diagnosed prostate cancer patients at high risk for metastatic spread receive a bone scan prior to treatment and that low risk patients not receive it. The objective was to develop an automated pipeline to interrogate heterogeneous data to evaluate the use of bone...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103184
更新日期：2019-06-01 00:00:00
abstract：:Stomach cancer is one of the leading causes of cancer-related deaths worldwide. More than 80% diagnosis of this cancer occur at later stages leading to low 5-year survival rate. This emphasizes the need to have better prognostic techniques for stomach cancer. In this regard, the Next-Generation Sequencing of whole gen...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103254
更新日期：2019-09-01 00:00:00
abstract：:In the United States, about 600,000 people die of heart disease every year. The annual cost of care services, medications, and lost productivity reportedly exceeds 108.9 billion dollars. Effective disease risk assessment is critical to prevention, care, and treatment planning. Recent advancements in text analytics hav...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.08.011
更新日期：2015-12-01 00:00:00
abstract：:This research aims to depict the methodological steps and tools about the combined operation of case-based reasoning (CBR) and multi-agent system (MAS) to expose the ontological application in the field of clinical decision support. The multi-agent architecture works for the consideration of the whole cycle of clinica...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.06.012
更新日期：2015-08-01 00:00:00
abstract：:Dialogue systems for health communication hold out the promise of providing intelligent assistance to patients through natural interfaces that require no training to use. But in order to make the development of such systems cost effective, we must be able to use generic techniques and components which are then special...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2006.02.004
更新日期：2006-10-01 00:00:00
abstract：:Over the last 8 years, the National Cancer Institute (NCI) has launched a major effort to integrate molecular and clinical cancer-related information within a unified biomedical informatics framework, with controlled terminology as its foundational layer. The NCI Thesaurus is the reference terminology underpinning the...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2006.02.013
更新日期：2007-02-01 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：:The ultimate goal of genomics research is to describe the network of molecules and interactions that govern all biological functions and disease processes in cells. Nonlinear interactions among genes in terms of their logic relationships play a key role for deciphering the networks of molecules that underlie cellular ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2007.11.006
更新日期：2008-08-01 00:00:00
abstract：OBJECTIVE:To report the results of a systematic literature review concerning the security and privacy of electronic health record (EHR) systems. DATA SOURCES:Original articles written in English found in MEDLINE, ACM Digital Library, Wiley InterScience, IEEE Digital Library, Science@Direct, MetaPress, ERIC, CINAHL and...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2012.12.003
更新日期：2013-06-01 00:00:00
abstract：:Patient recruitment is one of the most important barriers to successful completion of clinical trials and thus to obtaining evidence about new methods for prevention, diagnostics and treatment. The reason is that recruitment is effort consuming. It requires the identification of candidate patients for the trial (the p...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.05.005
更新日期：2015-08-01 00:00:00
abstract：BACKGROUND:One of the major concerns of the biomedical community is the increasing prevalence of antimicrobial resistant microorganisms. Recent findings show that the diversification of colony morphology may be indicative of the expression of virulence factors and increased resistance to antibiotic therapeutics. To tra...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.03.007
更新日期：2015-06-01 00:00:00
abstract：:Federal funds have supported Nurse Practitioner (NP) education and the establishment of nurse-managed centers. Yet, important questions are raised about the quality and appropriate scope of NP care. Few NP-patient encounters are documented in the largest national surveys of ambulatory care, sponsored by the National C...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2003.09.016
更新日期：2003-08-01 00:00:00
abstract：:Building classification models from clinical data using machine learning methods often relies on labeling of patient examples by human experts. Standard machine learning framework assumes the labels are assigned by a homogeneous process. However, in reality the labels may come from multiple experts and it may be diffi...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.08.007
更新日期：2013-12-01 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：:Methods for surveillance of adverse events (AEs) in clinical settings are limited by cost, technology, and appropriate data availability. In this study, two methods for semi-automated review of text records within the Veterans Administration database are utilized to identify AEs related to the placement of central ven...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2006.06.003
更新日期：2007-04-01 00:00:00
abstract：:Since the genome project in 1990s, a number of studies associated with genes have been conducted and researchers have confirmed that genes are involved in disease. For this reason, the identification of the relationships between diseases and genes is important in biology. We propose a method called LGscore, which iden...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.01.003
更新日期：2015-04-01 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：OBJECTIVE:Evaluate the quality of clinical order practice patterns machine-learned from clinician cohorts stratified by patient mortality outcomes. MATERIALS AND METHODS:Inpatient electronic health records from 2010 to 2013 were extracted from a tertiary academic hospital. Clinicians (n = 1822) were stratified into lo...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.09.005
更新日期：2018-10-01 00:00:00
abstract：OBJECTIVE:To create an analytics platform for specifying and detecting clinical phenotypes and other derived variables in electronic health record (EHR) data for quality improvement investigations. MATERIALS AND METHODS:We have developed an architecture for an Analytic Information Warehouse (AIW). It supports transfor...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.01.005
更新日期：2013-06-01 00:00:00
abstract：UNLABELLED:Responding to public health emergencies requires rapid and accurate assessment of workforce availability under adverse and changing circumstances. However, public health information systems to support resource management during both routine and emergency operations are currently lacking. We applied scenario-...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2011.07.004
更新日期：2011-12-01 00:00:00
abstract：:Outbreaks of infectious diseases such as influenza are a significant threat to human health. Because there are different strains of influenza which can cause independent outbreaks, and influenza can affect demographic groups at different rates and times, there is a need to recognize and characterize multiple outbreaks...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.08.003
更新日期：2017-09-01 00:00:00
abstract：OBJECTIVES:RxNorm is a standardized nomenclature for clinical drug entities developed by the National Library of Medicine. In this paper, we audit relations in RxNorm for consistency and completeness through the systematic analysis of the graph of its concepts and relationships. METHODS:The representation of multi-ing...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2009.04.004
更新日期：2009-06-01 00:00:00
abstract：:Clinical archetypes provide a means for health professionals to design what should be communicated as part of an Electronic Health Record (EHR). An ever-growing number of archetype definitions follow this health information modelling approach, and this international archetype resource will eventually cover a large num...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2011.12.001
更新日期：2012-06-01 00:00:00
abstract：:Named entity recognition is an extremely important and fundamental task of biomedical text mining. Biomedical named entities include mentions of proteins, genes, DNA, RNA, etc which often have complex structures, but it is challenging to identify and classify such entities. Machine learning methods like CRF, MEMM and ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2008.12.012
更新日期：2009-10-01 00:00:00
abstract：:Many interventions to improve the success of information technology (IT) implementations are grounded in behavioral science, using theories, and models to identify conditions and determinants of successful use. However, each model in the IT literature has evolved to address specific theoretical problems of particular ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2003.09.002
更新日期：2003-06-01 00:00:00
abstract：:The National Drug File - Reference Terminology (NDF-RT) is a large and complex drug terminology consisting of several classification hierarchies on top of an extensive collection of drug concepts. These hierarchies provide important information about clinical drugs, e.g., their chemical ingredients, mechanisms of acti...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.07.013
更新日期：2017-09-01 00:00:00
abstract：BACKGROUND:A tool that can predict the estimated glomerular filtration rate (eGFR) in routine daily care can help clinicians to make better decisions for kidney transplant patients and to improve transplantation outcome. In this paper, we proposed a hybrid prediction model for predicting a future value for eGFR during ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103116
更新日期：2019-03-01 00:00:00
abstract：:The discovery of implicit connections between terms that do not occur together in any scientific document underlies the model of literature-based knowledge discovery first proposed by Swanson. Corpus-derived statistical models of semantic distance such as Latent Semantic Analysis (LSA) have been evaluated previously a...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2009.09.003
更新日期：2010-04-01 00:00:00
abstract：BACKGROUND:Word embeddings have been prevalently used in biomedical Natural Language Processing (NLP) applications due to the ability of the vector representations being able to capture useful semantic properties and linguistic relationships between words. Different textual resources (e.g., Wikipedia and biomedical lit...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.09.008
更新日期：2018-11-01 00:00:00
