Abstract:
:We designed and implemented a generic search engine (Vaidurya), as part of our Digital clinical-Guideline Library (DeGeL) framework. Two search methods were implemented in addition to full-text search: (1) concept-based search, which relies on pre-indexing the guidelines in a clinically meaningful fashion, and (2) context-sensitive search, which relies on first semi-structuring the guidelines according to a given ontology, then searching for terms within specific labeled text segments. The Vaidurya engine is fully functional and is used within the DeGeL system. We describe the Vaidurya ontological and algorithmic framework; we also briefly summarize the results of a detailed evaluation in the clinical-guideline domain, demonstrating that both concept-based and context-sensitive ontology-independent search are highly feasible and significantly improve on free text search retrieval performance. We conclude by analyzing the limitations and advantages of the approach, and the steps that we have started to take to extend it based on user feedback.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Moskovitch R,Shahar Ydoi
10.1016/j.jbi.2008.07.003subject
Has Abstractpub_date
2009-02-01 00:00:00pages
11-21issue
1eissn
1532-0464issn
1532-0480pii
S1532-0464(08)00097-Xjournal_volume
42pub_type
杂志文章abstract:OBJECTIVE:This paper introduces a model that predicts future changes in systolic blood pressure (SBP) based on structured and unstructured (text-based) information from longitudinal clinical records. METHOD:For each patient, the clinical records are sorted in chronological order and SBP measurements are extracted from...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2015.06.024
更新日期:2015-12-01 00:00:00
abstract::We describe the process of introducing RFID technology in the trauma bay of a trauma center to support fast-paced and complex teamwork during resuscitation. We analyzed trauma resuscitation tasks, photographs of medical tools, and videos of simulated resuscitations to gain insight into resuscitation tasks, work practi...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2012.04.003
更新日期:2012-10-01 00:00:00
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
更新日期:2018-12-01 00:00:00
abstract::Clinical trials are typically conducted over a population within a defined time period in order to illuminate certain characteristics of a health issue or disease process. These cross-sectional studies give us a 'snapshot' of this disease process over a large number of people but do not allow us to model the temporal ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2012.11.003
更新日期:2013-04-01 00:00:00
abstract::Finding disease markers (classifiers) from gene expression data by machine learning algorithms is characterized by a high risk of overfitting the data due the abundance of attributes (simultaneously measured gene expression values) and shortage of available examples (observations). To avoid this pitfall and achieve pr...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2004.07.007
更新日期:2004-08-01 00:00:00
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
更新日期:2002-08-01 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::Evidence-based medicine is the most prevalent paradigm adopted by physicians. Clinical practice guidelines typically define a set of recommendations together with eligibility criteria that restrict their applicability to a specific group of patients. The ever-growing size and availability of health-related data is cur...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2018.06.001
更新日期:2018-07-01 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::As a result of recent advances in cancer research and "precision medicine" approaches, i.e. the idea of treating each patient with the right drug at the right time, more and more cancer patients are being cured, or might have to cope with a life with cancer. For many people, cancer survival today means living with a c...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2019.103342
更新日期:2020-01-01 00:00:00
abstract::One of the main reasons that leads to a low adoption rate of telemedicine systems is poor usability. An aspect that influences usability during the reporting of findings is the input mode, e.g., if a free-text (FT) or a structured report (SR) interface is employed. The objective of our study is to compare the usabilit...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2014.07.002
更新日期:2014-12-01 00:00:00
abstract::Community pharmacists are critically placed in the patient care chain being an extended frontline within primary healthcare networks across Europe. They are trained to ensure safe and effective medication use, a crucial and responsible role, extending beyond the common misconception limited to just providing timely ac...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2019.103336
更新日期:2019-12-01 00:00:00
abstract::Surgical planning for StereoElectroEncephaloGraphy (SEEG) is a complex and patient specific task, where the experience and medical workflow of each institution may influence the final planning choices. To account for this variability, we developed a data-based Computer Assisted Planning (CAP) solution able to exploit ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2020.103460
更新日期:2020-08-01 00:00:00
abstract:BACKGROUND:Detailed Clinical Model (DCM) approaches have recently seen wider adoption. More specifically, openEHR-based application systems are now used in production in several countries, serving diverse fields of application such as health information exchange, clinical registries and electronic medical record system...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2016.08.007
更新日期:2016-10-01 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::Due to increasing volume and unstructured nature of the scientific literatures in biomedical domain, most of the information embedded within them remain untapped. This paper presents a biomedical text analytics system, DiseaSE (Disease Symptom Extraction), to identify and extract disease symptoms and their association...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2019.103324
更新日期:2019-12-01 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::The centralized and public availability of molecular sequence and clinical trial data presents an opportunity to identify potentially valuable linkages across the bench-to-bedside "T1" translational barrier. In this study, we sought to leverage keyword metadata (Medical Subject Heading [MeSH] descriptors) to infer rel...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2009.10.003
更新日期:2010-06-01 00:00:00
abstract:INTRODUCTION:Machine learning (ML) and natural language processing have great potential to improve information extraction (IE) within electronic medical records (EMRs) for a wide variety of clinical search and summarization tools. Despite ML advancements, clinical adoption of real time IE tools for patient care remains...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2019.103354
更新日期:2020-02-01 00:00:00
abstract:OBJECTIVE:Clinicians face numerous information needs during patient care activities and most of these needs are not met. Infobuttons are information retrieval tools that help clinicians to fulfill their information needs by providing links to on-line health information resources from within an electronic medical record...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2008.07.001
更新日期:2009-02-01 00:00:00
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
更新日期:2012-10-01 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::With the increasing availability of genomic sequence data, numerous methods have been proposed for finding DNA motifs. The discovery of DNA motifs serves a critical step in many biological applications. However, the privacy implication of DNA analysis is normally neglected in the existing methods. In this work, we pro...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2013.12.016
更新日期:2014-08-01 00:00:00
abstract::The ubiquity and commoditisation of wearable biosensors (fitness bands) has led to a deluge of personal healthcare data, but with limited analytics typically fed back to the user. The feasibility of feeding back more complex, seemingly unrelated measures to users was investigated, by assessing whether increased levels...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2020.103610
更新日期:2020-12-01 00:00:00
abstract::Intensive care monitoring systems are typically developed from population data, but do not take into account the variability among individual patients' characteristics. This study develops patient-specific alarm algorithms in real time. Classification tree and neural network learning were carried out in batch mode on ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2008.03.011
更新日期:2008-06-01 00:00:00
abstract:BACKGROUND:Control systems engineering methods, particularly, system identification (system ID), offer an idiographic (i.e., person-specific) approach to develop dynamic models of physical activity (PA) that can be used to personalize interventions in a systematic, scalable way. The purpose of this work is to: (1) appl...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2018.01.010
更新日期:2018-03-01 00:00:00
abstract::One of the challenging problems in drug discovery is to identify the novel targets for drugs. Most of the traditional methods for drug targets optimization focused on identifying the particular families of "druggable targets", but ignored their topological properties based on the biological pathways. In this study, we...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2015.02.007
更新日期:2015-04-01 00:00:00
abstract::With recent advances in fluorescence microscopy imaging techniques and methods of gene knock down by RNA interference (RNAi), genome-scale high-content screening (HCS) has emerged as a powerful approach to systematically identify all parts of complex biological processes. However, a critical barrier preventing fulfill...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2008.04.007
更新日期:2009-02-01 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: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
更新日期:2016-10-01 00:00:00