Inductive creation of an annotation schema for manually indexing clinical conditions from emergency department reports.

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 Inform

authors

Chapman WW,Dowling JN

doi

10.1016/j.jbi.2005.06.004

keywords:

subject

Has Abstract

pub_date

2006-04-01 00:00:00

pages

196-208

issue

2

eissn

1532-0464

issn

1532-0480

pii

S1532-0464(05)00070-5

journal_volume

39

pub_type

杂志文章
  • Analysis of eligibility criteria representation in industry-standard clinical trial protocols.

    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

    authors: Bhattacharya S,Cantor MN

    更新日期:2013-10-01 00:00:00

  • Comparison with manual registration reveals satisfactory completeness and efficiency of a computerized cancer registration system.

    abstract::Automated software for cancer registration, called Open Registry and developed by ourselves was adopted by the Varese (population-based) Cancer Registry starting from 1997. Since the use of automated cancer registration is increasing, it is important to assess the quality and completeness of the automated data being p...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2007.03.003

    authors: Contiero P,Tittarelli A,Maghini A,Fabiano S,Frassoldi E,Costa E,Gada D,Codazzi T,Crosignani P,Tessandori R,Tagliabue G

    更新日期:2008-02-01 00:00:00

  • Semi-supervised medical entity recognition: A study on Spanish and Swedish clinical corpora.

    abstract:OBJECTIVE:The goal of this study is to investigate entity recognition within Electronic Health Records (EHRs) focusing on Spanish and Swedish. Of particular importance is a robust representation of the entities. In our case, we utilized unsupervised methods to generate such representations. METHODS:The significance of...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2017.05.009

    authors: Pérez A,Weegar R,Casillas A,Gojenola K,Oronoz M,Dalianis H

    更新日期:2017-07-01 00:00:00

  • Developing EHR-driven heart failure risk prediction models using CPXR(Log) with the probabilistic loss function.

    abstract::Computerized survival prediction in healthcare identifying the risk of disease mortality, helps healthcare providers to effectively manage their patients by providing appropriate treatment options. In this study, we propose to apply a classification algorithm, Contrast Pattern Aided Logistic Regression (CPXR(Log)) wit...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.01.009

    authors: Taslimitehrani V,Dong G,Pereira NL,Panahiazar M,Pathak J

    更新日期:2016-04-01 00:00:00

  • Integrated network analysis of symptom clusters across disease conditions.

    abstract::Identifying the symptom clusters (two or more related symptoms) with shared underlying molecular mechanisms has been a vital analysis task to promote the symptom science and precision health. Related studies have applied the clustering algorithms (e.g. k-means, latent class model) to detect the symptom clusters mostly...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2020.103482

    authors: Lu K,Yang K,Niyongabo E,Shu Z,Wang J,Chang K,Zou Q,Jiang J,Jia C,Liu B,Zhou X

    更新日期:2020-07-01 00:00:00

  • Use of morphological analysis in protein name recognition.

    abstract::Protein name recognition aims to detect each and every protein names appearing in a PubMed abstract. The task is not simple, as the graphic word boundary (space separator) assumed in conventional preprocessing does not necessarily coincide with the protein name boundary. Such boundary disagreement caused by tokenizati...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2004.08.001

    authors: Yamamoto K,Kudo T,Konagaya A,Matsumoto Y

    更新日期:2004-12-01 00:00:00

  • Challenges in clinical natural language processing for automated disorder normalization.

    abstract:BACKGROUND:Identifying key variables such as disorders within the clinical narratives in electronic health records has wide-ranging applications within clinical practice and biomedical research. Previous research has demonstrated reduced performance of disorder named entity recognition (NER) and normalization (or groun...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.07.010

    authors: Leaman R,Khare R,Lu Z

    更新日期:2015-10-01 00:00:00

  • Predicting the function of transplanted kidney in long-term care processes: Application of a hybrid model.

    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

    authors: Rashidi Khazaee P,Bagherzadeh M J,Niazkhani Z,Pirnejad H

    更新日期:2019-03-01 00:00:00

  • The use of logic relationships to model colon cancer gene expression networks with mRNA microarray data.

    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

    authors: Ruan X,Wang J,Li H,Perozzi RE,Perozzi EF

    更新日期:2008-08-01 00:00:00

  • Matching patients to clinical trials using semantically enriched document representation.

    abstract::Recruiting eligible patients for clinical trials is crucial for reliably answering specific questions about medical interventions and evaluation. However, clinical trial recruitment is a bottleneck in clinical research and drug development. Our goal is to provide an approach towards automating this manual and time-con...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2020.103406

    authors: Hassanzadeh H,Karimi S,Nguyen A

    更新日期:2020-05-01 00:00:00

  • LGscore: A method to identify disease-related genes using biological literature and Google data.

    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

    authors: Kim J,Kim H,Yoon Y,Park S

    更新日期:2015-04-01 00:00:00

  • MeSHy: Mining unanticipated PubMed information using frequencies of occurrences and concurrences of MeSH terms.

    abstract:MOTIVATION:PubMed is the most widely used database of biomedical literature. To the detriment of the user though, the ranking of the documents retrieved for a query is not content-based, and important semantic information in the form of assigned Medical Subject Headings (MeSH) terms is not readily presented or producti...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2011.05.009

    authors: Theodosiou T,Vizirianakis IS,Angelis L,Tsaftaris A,Darzentas N

    更新日期:2011-12-01 00:00:00

  • Identifying complexity in infectious diseases inpatient settings: An observation study.

    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

    authors: Roosan D,Weir C,Samore M,Jones M,Rahman M,Stoddard GJ,Del Fiol G

    更新日期:2017-07-01 00:00:00

  • Evaluating warfarin dosing models on multiple datasets with a novel software framework and evolutionary optimisation.

    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

    authors: Truda G,Marais P

    更新日期:2021-01-01 00:00:00

  • Genome-wide analysis of multi-view data of miRNA-seq to identify miRNA biomarkers for stomach cancer.

    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

    authors: Pant N,Rakshit S,Paul S,Saha I

    更新日期:2019-09-01 00:00:00

  • Annotating risk factors for heart disease in clinical narratives for diabetic patients.

    abstract::The 2014 i2b2/UTHealth natural language processing shared task featured a track focused on identifying risk factors for heart disease (specifically, Cardiac Artery Disease) in clinical narratives. For this track, we used a "light" annotation paradigm to annotate a set of 1304 longitudinal medical records describing 29...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.05.009

    authors: Stubbs A,Uzuner Ö

    更新日期:2015-12-01 00:00:00

  • A medical treatment based scoring model to detect abusive institutions.

    abstract::Medical abuse refers to a type of abnormal medical practice which is not in compliance with qualitative or ethical standards, such as excessive prescription or overbilling of medical services. Detection of such medical abuses is crucial, especially for the patients and insurance providers, because they become subject ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2020.103423

    authors: Lee J,Shin H,Cho S

    更新日期:2020-07-01 00:00:00

  • Word sense disambiguation across two domains: biomedical literature and clinical notes.

    abstract::The aim of this study is to explore the word sense disambiguation (WSD) problem across two biomedical domains-biomedical literature and clinical notes. A supervised machine learning technique was used for the WSD task. One of the challenges addressed is the creation of a suitable clinical corpus with manual sense anno...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2008.02.003

    authors: Savova GK,Coden AR,Sominsky IL,Johnson R,Ogren PV,de Groen PC,Chute CG

    更新日期:2008-12-01 00:00:00

  • An optimization based on simulation approach to the patient admission scheduling problem using a linear programing algorithm.

    abstract:BACKGROUND:As patient's length of stay in waiting lists increases, governments are looking for strategies to control the problem. Agreements were created with private providers to diminish the workload in the public sector. However, the growth of the private sector is not following the demand for care. Given this conte...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2014.08.007

    authors: Granja C,Almada-Lobo B,Janela F,Seabra J,Mendes A

    更新日期:2014-12-01 00:00:00

  • A framework for modeling health behavior protocols and their linkage to behavioral theory.

    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

    authors: Lenert L,Norman GJ,Mailhot M,Patrick K

    更新日期:2005-08-01 00:00:00

  • A graph-based approach to auditing RxNorm.

    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

    authors: Bodenreider O,Peters LB

    更新日期:2009-06-01 00:00:00

  • Selecting significant genes by randomization test for cancer classification using gene expression data.

    abstract::Gene selection is an important task in bioinformatics studies, because the accuracy of cancer classification generally depends upon the genes that have biological relevance to the classifying problems. In this work, randomization test (RT) is used as a gene selection method for dealing with gene expression data. In th...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2013.03.009

    authors: Mao Z,Cai W,Shao X

    更新日期:2013-08-01 00:00:00

  • Using natural language processing to extract mammographic findings.

    abstract:OBJECTIVE:Structured data on mammographic findings are difficult to obtain without manual review. We developed and evaluated a rule-based natural language processing (NLP) system to extract mammographic findings from free-text mammography reports. MATERIALS AND METHODS:The NLP system extracted four mammographic findin...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.01.010

    authors: Gao H,Aiello Bowles EJ,Carrell D,Buist DS

    更新日期:2015-04-01 00:00:00

  • Exploring the associations between drug side-effects and therapeutic indications.

    abstract::Drug therapeutic indications and side-effects are both measurable patient phenotype changes in response to the treatment. Inferring potential drug therapeutic indications and identifying clinically interesting drug side-effects are both important and challenging tasks. Previous studies have utilized either chemical st...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2014.03.014

    authors: Wang F,Zhang P,Cao N,Hu J,Sorrentino R

    更新日期:2014-10-01 00:00:00

  • Computer mediated reality technologies: A conceptual framework and survey of the state of the art in healthcare intervention systems.

    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

    authors: Ibrahim Z,Money AG

    更新日期:2019-02-01 00:00:00

  • Quantifying semantic similarity of clinical evidence in the biomedical literature to facilitate related evidence synthesis.

    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

    authors: Hassanzadeh H,Nguyen A,Verspoor K

    更新日期:2019-12-01 00:00:00

  • Health information technology adoption: Understanding research protocols and outcome measurements for IT interventions in health care.

    abstract:OBJECTIVE:To classify and characterize the variables commonly used to measure the impact of Information Technology (IT) adoption in health care, as well as settings and IT interventions tested, and to guide future research. MATERIALS AND METHODS:We conducted a descriptive study screening a sample of 236 studies from a...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.07.018

    authors: Colicchio TK,Facelli JC,Del Fiol G,Scammon DL,Bowes WA 3rd,Narus SP

    更新日期:2016-10-01 00:00:00

  • Computing with evidence Part II: An evidential approach to predicting metabolic drug-drug interactions.

    abstract::We describe a novel experiment that we conducted with the Drug Interaction Knowledge-base (DIKB) to determine which combinations of evidence enable a rule-based theory of metabolic drug-drug interactions to make the most optimal set of predictions. The focus of the experiment was a group of 16 drugs including six memb...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2009.05.010

    authors: Boyce R,Collins C,Horn J,Kalet I

    更新日期:2009-12-01 00:00:00

  • Lexical patterns, features and knowledge resources for coreference resolution in clinical notes.

    abstract::Generation of entity coreference chains provides a means to extract linked narrative events from clinical notes, but despite being a well-researched topic in natural language processing, general-purpose coreference tools perform poorly on clinical texts. This paper presents a knowledge-centric and pattern-based approa...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2012.02.012

    authors: Gooch P,Roudsari A

    更新日期:2012-10-01 00:00:00

  • An unsupervised and customizable misspelling generator for mining noisy health-related text sources.

    abstract:BACKGROUND:Data collection and extraction from noisy text sources such as social media typically rely on keyword-based searching/listening. However, health-related terms are often misspelled in such noisy text sources due to their complex morphology, resulting in the exclusion of relevant data for studies. In this pape...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2018.11.007

    authors: Sarker A,Gonzalez-Hernandez G

    更新日期:2018-12-01 00:00:00