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 annotations. This corpus in conjunction with the WSD set from the National Library of Medicine provided the basis for the evaluation of our method across multiple domains and for the comparison of our results to published ones. Noteworthy is that only 20% of the most relevant ambiguous terms within a domain overlap between the two domains, having more senses associated with them in the clinical space than in the biomedical literature space. Experimentation with 28 different feature sets rendered a system achieving an average F-score of 0.82 on the clinical data and 0.86 on the biomedical literature.

journal_name

J Biomed Inform

authors

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

doi

10.1016/j.jbi.2008.02.003

subject

Has Abstract

pub_date

2008-12-01 00:00:00

pages

1088-100

issue

6

eissn

1532-0464

issn

1532-0480

pii

S1532-0464(08)00024-5

journal_volume

41

pub_type

杂志文章
  • Towards an on-demand peer feedback system for a clinical knowledge base: a case study with order sets.

    abstract:OBJECTIVE:We have developed an automated knowledge base peer feedback system as part of an effort to facilitate the creation and refinement of sound clinical knowledge content within an enterprise-wide knowledge base. The program collects clinical data stored in our Clinical Data Repository during usage of a physician ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2007.05.006

    authors: Hulse NC,Del Fiol G,Bradshaw RL,Roemer LK,Rocha RA

    更新日期:2008-02-01 00:00:00

  • Decision-making model for early diagnosis of congestive heart failure using rough set and decision tree approaches.

    abstract::The accurate diagnosis of heart failure in emergency room patients is quite important, but can also be quite difficult due to our insufficient understanding of the characteristics of heart failure. The purpose of this study is to design a decision-making model that provides critical factors and knowledge associated wi...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2012.04.013

    authors: Son CS,Kim YN,Kim HS,Park HS,Kim MS

    更新日期:2012-10-01 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

  • An evaluation of clinical order patterns machine-learned from clinician cohorts stratified by patient mortality outcomes.

    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

    authors: Wang JK,Hom J,Balasubramanian S,Schuler A,Shah NH,Goldstein MK,Baiocchi MTM,Chen JH

    更新日期:2018-10-01 00:00:00

  • Heterogeneous database integration in biomedicine.

    abstract::The rapid expansion of biomedical knowledge, reduction in computing costs, and spread of internet access have created an ocean of electronic data. The decentralized nature of our scientific community and healthcare system, however, has resulted in a patchwork of diverse, or heterogeneous, database implementations, mak...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1006/jbin.2001.1024

    authors: Sujansky W

    更新日期:2001-08-01 00:00:00

  • RedMed: Extending drug lexicons for social media applications.

    abstract::Social media has been identified as a promising potential source of information for pharmacovigilance. The adoption of social media data has been hindered by the massive and noisy nature of the data. Initial attempts to use social media data have relied on exact text matches to drugs of interest, and therefore suffer ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2019.103307

    authors: Lavertu A,Altman RB

    更新日期:2019-11-01 00:00:00

  • Integrating cancer diagnosis terminologies based on logical definitions of SNOMED CT concepts.

    abstract::In oncology, the reuse of data is confronted with the heterogeneity of terminologies. It is necessary to semantically integrate these distinct terminologies. The semantic integration by using a third terminology as a support is a conventional approach for the integration of two terminologies that are not very structur...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2017.08.013

    authors: Nikiema JN,Jouhet V,Mougin F

    更新日期:2017-10-01 00:00:00

  • Analysis of microarray leukemia data using an efficient MapReduce-based K-nearest-neighbor classifier.

    abstract::Microarray-based gene expression profiling has emerged as an efficient technique for classification, prognosis, diagnosis, and treatment of cancer. Frequent changes in the behavior of this disease generates an enormous volume of data. Microarray data satisfies both the veracity and velocity properties of big data, as ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.03.002

    authors: Kumar M,Rath NK,Rath SK

    更新日期:2016-04-01 00:00:00

  • A novel web informatics approach for automated surveillance of cancer mortality trends.

    abstract::Cancer surveillance data are collected every year in the United States via the National Program of Cancer Registries (NPCR) and the Surveillance, Epidemiology and End Results (SEER) Program of the National Cancer Institute (NCI). General trends are closely monitored to measure the nation's progress against cancer. The...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.03.027

    authors: Tourassi G,Yoon HJ,Xu S

    更新日期:2016-06-01 00:00:00

  • Information extraction from biomedical text.

    abstract::Information extraction is the process of scanning text for information relevant to some interest, including extracting entities, relations, and events. It requires deeper analysis than key word searches, but its aims fall short of the very hard and long-term problem of full text understanding. Information extraction r...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/s1532-0464(03)00015-7

    authors: Hobbs JR

    更新日期:2002-08-01 00:00:00

  • Scenario-based design: a method for connecting information system design with public health operations and emergency management.

    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

    authors: Reeder B,Turner AM

    更新日期:2011-12-01 00:00:00

  • Game-based interventions for neuropsychological assessment, training and rehabilitation: Which game-elements to use? A systematic review.

    abstract::Game-based interventions (GBI) have been used to promote health-related outcomes, including cognitive functions. Criteria for game-elements (GE) selection are insufficiently characterized in terms of their adequacy to patients' clinical conditions or targeted cognitive outcomes. This study aimed to identify GE applied...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2019.103287

    authors: Ferreira-Brito F,Fialho M,Virgolino A,Neves I,Miranda AC,Sousa-Santos N,Caneiras C,Carriço L,Verdelho A,Santos O

    更新日期:2019-10-01 00:00:00

  • Modeling association detection in order to discover compounds to inhibit oral cancer.

    abstract::In the past, algorithms exploiting varying semantics in interactions between biological objects such as genes and diseases have been used in bioinformatics to uncover latent relationships within biological datasets. In this paper, we consider the algorithm Medusa in parallel with binary classification in order to find...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2018.07.005

    authors: Vittal S,Karthikeyan G

    更新日期:2018-08-01 00:00:00

  • Facilitating pre-operative assessment guidelines representation using SNOMED CT.

    abstract:OBJECTIVE:To investigate whether SNOMED CT covers the terms used in pre-operative assessment guidelines, and if necessary, how the measured content coverage can be improved. METHODS:Pre-operative assessment guidelines were retrieved from the websites of (inter)national anesthesia-related societies. The recommendations...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2010.07.009

    authors: Ahmadian L,Cornet R,de Keizer NF

    更新日期:2010-12-01 00:00:00

  • 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

  • Biomedical ontologies: what part-of is and isn't.

    abstract::Mereological relations such as part-of and its inverse has-part are fundamental to the description of the structure of living organisms. Whereas classical mereology focuses on individual entities, mereological relations in biomedical ontologies are generally asserted between classes of individuals. In general, this pr...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2005.11.003

    authors: Schulz S,Kumar A,Bittner T

    更新日期:2006-06-01 00:00:00

  • Multi-faceted informatics system for digitising and streamlining the reablement care model.

    abstract::Reablement is new paradigm to increase independence in the home amongst the ageing population. And it remains a challenge to design an optimal electronic system to streamline and integrate reablement into current healthcare infrastructure. Furthermore, given reablement requires collaboration with a range of organisati...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.05.008

    authors: Bond RR,Mulvenna MD,Finlay DD,Martin S

    更新日期:2015-08-01 00:00:00

  • A cascaded approach for Chinese clinical text de-identification with less annotation effort.

    abstract::With rapid adoption of Electronic Health Records (EHR) in China, an increasing amount of clinical data has been available to support clinical research. Clinical data secondary use usually requires de-identification of personal information to protect patient privacy. Since manually de-identification of free clinical te...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2017.07.017

    authors: Jian Z,Guo X,Liu S,Ma H,Zhang S,Zhang R,Lei J

    更新日期:2017-09-01 00:00:00

  • Unstructured medical image query using big data - An epilepsy case study.

    abstract::Big data technologies are critical to the medical field which requires new frameworks to leverage them. Such frameworks would benefit medical experts to test hypotheses by querying huge volumes of unstructured medical data to provide better patient care. The objective of this work is to implement and examine the feasi...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.12.005

    authors: Istephan S,Siadat MR

    更新日期:2016-02-01 00:00:00

  • A survey on literature based discovery approaches in biomedical domain.

    abstract::Literature Based Discovery (LBD) refers to the problem of inferring new and interesting knowledge by logically connecting independent fragments of information units through explicit or implicit means. This area of research, which incorporates techniques from Natural Language Processing (NLP), Information Retrieval and...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章,评审

    doi:10.1016/j.jbi.2019.103141

    authors: Gopalakrishnan V,Jha K,Jin W,Zhang A

    更新日期:2019-05-01 00:00:00

  • Impact of an electronic handoff documentation tool on team shared mental models in pediatric critical care.

    abstract:OBJECTIVE:To examine the impact of the implementation of an electronic handoff tool (the Handoff Tool) on shared mental models (SMM) within patient care teams as measured by content overlap and discrepancies in verbal handoff presentations given by different clinicians caring for the same patient. MATERIALS AND METHOD...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2017.03.004

    authors: Jiang SY,Murphy A,Heitkemper EM,Hum RS,Kaufman DR,Mamykina L

    更新日期:2017-05-01 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

  • A Hidden Semi-Markov Model based approach for rehabilitation exercise assessment.

    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

    authors: Capecci M,Ceravolo MG,Ferracuti F,Iarlori S,Kyrki V,Monteriù A,Romeo L,Verdini F

    更新日期:2018-02-01 00:00:00

  • Software tools for simultaneous data visualization and T cell epitopes and disorder prediction in proteins.

    abstract::We have developed EpDis and MassPred, extendable open source software tools that support bioinformatic research and enable parallel use of different methods for the prediction of T cell epitopes, disorder and disordered binding regions and hydropathy calculation. These tools offer a semi-automated installation of chos...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.01.016

    authors: Jandrlić DR,Lazić GM,Mitić NS,Pavlović MD

    更新日期:2016-04-01 00:00:00

  • Finding disease similarity based on implicit semantic similarity.

    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

    authors: Mathur S,Dinakarpandian D

    更新日期:2012-04-01 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

  • The EU-ADR corpus: annotated drugs, diseases, targets, and their relationships.

    abstract::Corpora with specific entities and relationships annotated are essential to train and evaluate text-mining systems that are developed to extract specific structured information from a large corpus. In this paper we describe an approach where a named-entity recognition system produces a first annotation and annotators ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2012.04.004

    authors: van Mulligen EM,Fourrier-Reglat A,Gurwitz D,Molokhia M,Nieto A,Trifiro G,Kors JA,Furlong LI

    更新日期:2012-10-01 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

  • Making sense: sensor-based investigation of clinician activities in complex critical care environments.

    abstract::In many respects, the critical care workplace resembles a paradigmatic complex system: on account of the dynamic and interactive nature of collaborative clinical work, these settings are characterized by non-linear, inter-dependent and emergent activities. Developing a comprehensive understanding of the work activitie...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2011.02.007

    authors: Kannampallil T,Li Z,Zhang M,Cohen T,Robinson DJ,Franklin A,Zhang J,Patel VL

    更新日期:2011-06-01 00:00:00

  • A term extraction tool for expanding content in the domain of functioning, disability, and health: proof of concept.

    abstract::Among the challenges in developing terminology systems is providing complete content coverage of specialized subject fields. This paper reports on a term extraction tool designed for the development and expansion of terminology systems concerned with functioning, disability, and health. Content relevant to this domain...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2003.09.005

    authors: Harris MR,Savova GK,Johnson TM,Chute CG

    更新日期:2003-08-01 00:00:00