Abstract:
BACKGROUND:Knowledge Organization Systems (KOS) and their associated mappings play a central role in several decision support systems. However, by virtue of knowledge evolution, KOS entities are modified over time, impacting mappings and potentially turning them invalid. This requires semi-automatic methods to maintain such semantic correspondences up-to-date at KOS evolution time. METHODS:We define a complete and original framework based on formal heuristics that drives the adaptation of KOS mappings. Our approach takes into account the definition of established mappings, the evolution of KOS and the possible changes that can be applied to mappings. This study experimentally evaluates the proposed heuristics and the entire framework on realistic case studies borrowed from the biomedical domain, using official mappings between several biomedical KOSs. RESULTS:We demonstrate the overall performance of the approach over biomedical datasets of different characteristics and sizes. Our findings reveal the effectiveness in terms of precision, recall and F-measure of the suggested heuristics and methods defining the framework to adapt mappings affected by KOS evolution. The obtained results contribute and improve the quality of mappings over time. CONCLUSIONS:The proposed framework can adapt mappings largely automatically, facilitating thus the maintenance task. The implemented algorithms and tools support and minimize the work of users in charge of KOS mapping maintenance.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Dos Reis JC,Pruski C,Da Silveira M,Reynaud-Delaître Cdoi
10.1016/j.jbi.2015.04.001subject
Has Abstractpub_date
2015-06-01 00:00:00pages
153-73eissn
1532-0464issn
1532-0480pii
S1532-0464(15)00068-4journal_volume
55pub_type
杂志文章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::Patient monitoring algorithms that analyze multiple features from physiological signals can produce an index that serves as a predictive or prognostic measure for a specific critical health event or physiological instability. Classical detection metrics such as sensitivity and positive predictive value are often used ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2017.09.008
更新日期:2017-11-01 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::Bioinformatics research relies heavily on the ability to discover and correlate data from various sources. The specialization of life sciences over the past decade, coupled with an increasing number of biomedical datasets available through standardized interfaces, has created opportunities towards new methods in biome...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2013.10.001
更新日期:2014-02-01 00:00:00
abstract::Nowadays, artificial intelligence plays an integral role in medical and healthcare informatics. Developing an automatic question classification and answering system is essential for coping with constant advancements in science and technology. However, efficient online medical services are required to promote offline m...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2020.103525
更新日期:2020-09-01 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::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
更新日期:2015-08-01 00:00:00
abstract::Computer simulations have been used to model infectious diseases to examine the outcomes of alternative strategies for managing their spread. Methicillin resistant Staphylococcus aureus (MRSA) skin and soft tissue infections have become prominent in many communities and efforts are underway to reduce the spread of thi...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2010.03.013
更新日期:2010-08-01 00:00:00
abstract:MOTIVATION:A challenge in microarray data analysis is to interpret observed changes in terms of biological properties and relationships. One powerful approach is to make associations of gene expression clusters with biomedical ontologies and/or biological pathways. However, this approach evaluates only one cluster at a...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2007.10.003
更新日期:2008-04-01 00:00:00
abstract::Investigators in the translational research and systems medicine domains require highly usable, efficient and integrative tools and methods that allow for the navigation of and reasoning over emerging large-scale data sets. Such resources must cover a spectrum of granularity from bio-molecules to population phenotypes...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2011.07.006
更新日期:2011-12-01 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::The Foundational Model of Anatomy (FMA), initially developed as an enhancement of the anatomical content of UMLS, is a domain ontology of the concepts and relationships that pertain to the structural organization of the human body. It encompasses the material objects from the molecular to the macroscopic levels that c...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2003.11.007
更新日期:2003-12-01 00:00:00
abstract::Patient discharge summaries provide detailed medical information about individuals who have been hospitalized. To make a precise and legitimate assessment of the abundant data, a proper time layout of the sequence of relevant events should be compiled and used to drive a patient-specific timeline, which could further ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2013.09.007
更新日期:2013-12-01 00:00:00
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) con...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2008.07.003
更新日期:2009-02-01 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: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::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
更新日期:2017-09-01 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:OBJECTIVE:To develop a cost-efficient method for identifying adverse drug events (ADEs) and medication errors (MEs) identified using outpatient electronic medical records within ambulatory settings. DESIGN:Comparison of sensitivity and cost of "traditional" pharmacist based approach to identifying ADEs and MEs during ...
journal_title:Journal of biomedical informatics
pub_type: 临床试验,杂志文章,多中心研究
doi:10.1016/s1532-0464(03)00059-5
更新日期:2003-02-01 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::Agglomerating results from studies of individual biological components has shown the potential to produce biomedical discovery and the promise of therapeutic development. Such knowledge integration could be tremendously facilitated by automated text mining for relation extraction in the biomedical literature. Relation...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2009.02.001
更新日期:2009-10-01 00:00:00
abstract::The Guideline Interchange Format (GLIF) is a model for representation of sharable computer-interpretable guidelines. The current version of GLIF (GLIF3) is a substantial update and enhancement of the model since the previous version (GLIF2). GLIF3 enables encoding of a guideline at three levels: a conceptual flowchart...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2004.04.002
更新日期:2004-06-01 00:00:00
abstract::Identification of co-referent entity mentions inside text has significant importance for other natural language processing (NLP) tasks (e.g. event linking). However, this task, known as co-reference resolution, remains a complex problem, partly because of the confusion over different evaluation metrics and partly beca...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2013.03.007
更新日期:2013-06-01 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::This paper proposes a new framework for the selection of tag SNPs based on haplotypes instead of on a single SNP. The tag SNPs found by this framework form a set of haplotypes completely predictive of the alleles of all untyped SNPs. We refer to this problem as MTMH, which is defined as follows: given a set of SNPs, f...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2008.04.003
更新日期:2008-12-01 00:00:00
abstract::We address the assignment of ICD-10 codes for causes of death by analyzing free-text descriptions in death certificates, together with the associated autopsy reports and clinical bulletins, from the Portuguese Ministry of Health. We leverage a deep neural network that combines word embeddings, recurrent units, and neu...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2018.02.011
更新日期:2018-04-01 00:00:00
abstract::In this paper we propose a novel approach to the design and implementation of knowledge-based decision support systems for translational research, specifically tailored to the analysis and interpretation of data from high-throughput experiments. Our approach is based on a general epistemological model of the scientifi...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2009.11.005
更新日期:2010-06-01 00:00:00
abstract:BACKGROUND:The association of genotyping information with common traits is not satisfactorily solved. One of the most complex traits is pain and association studies have failed so far to provide reproducible predictions of pain phenotypes from genotypes in the general population despite a well-established genetic basis...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2013.07.010
更新日期:2013-10-01 00:00:00
abstract::Real-time Obstructive Sleep Apnea (OSA) episode detection and monitoring are important for society in terms of an improvement in the health of the general population and of a reduction in mortality and healthcare costs. Currently, to diagnose OSA patients undergo PolySomnoGraphy (PSG), a complicated and invasive test ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2014.02.015
更新日期:2014-06-01 00:00:00
abstract:BACKGROUND:Correlation of data within electronic health records is necessary for implementation of various clinical decision support functions, including patient summarization. A key type of correlation is linking medications to clinical problems; while some databases of problem-medication links are available, they are...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2013.11.010
更新日期:2014-04-01 00:00:00