当前位置： SCI文献检索 > JOURNAL OF BIOMEDICAL INFORMATICS期刊下所有文献 > TRAK ontology: defining standard care for the rehabilitation of knee conditions.

TRAK ontology: defining standard care for the rehabilitation of knee conditions.

Abstract：

:In this paper we discuss the design and development of TRAK (Taxonomy for RehAbilitation of Knee conditions), an ontology that formally models information relevant for the rehabilitation of knee conditions. TRAK provides the framework that can be used to collect coded data in sufficient detail to support epidemiologic studies so that the most effective treatment components can be identified, new interventions developed and the quality of future randomized control trials improved to incorporate a control intervention that is well defined and reflects clinical practice. TRAK follows design principles recommended by the Open Biomedical Ontologies (OBO) Foundry. TRAK uses the Basic Formal Ontology (BFO) as the upper-level ontology and refers to other relevant ontologies such as Information Artifact Ontology (IAO), Ontology for General Medical Science (OGMS) and Phenotype And Trait Ontology (PATO). TRAK is orthogonal to other bio-ontologies and represents domain-specific knowledge about treatments and modalities used in rehabilitation of knee conditions. Definitions of typical exercises used as treatment modalities are supported with appropriate illustrations, which can be viewed in the OBO-Edit ontology editor. The vast majority of other classes in TRAK are cross-referenced to the Unified Medical Language System (UMLS) to facilitate future integration with other terminological sources. TRAK is implemented in OBO, a format widely used by the OBO community. TRAK is available for download from http://www.cs.cf.ac.uk/trak. In addition, its public release can be accessed through BioPortal, where it can be browsed, searched and visualized.

journal_name

J Biomed Inform

journal_title

Journal of biomedical informatics

authors

Button K,van Deursen RW,Soldatova L,Spasić I

doi

10.1016/j.jbi.2013.04.009

subject

Has Abstract

pub_date

2013-08-01 00:00:00

pages

615-25

issue

4

eissn

1532-0464

issn

1532-0480

pii

S1532-0464(13)00052-X

journal_volume

46

pub_type

杂志文章

相关文献

JOURNAL OF BIOMEDICAL INFORMATICS文献大全
  • Does the use of structured reporting improve usability? A comparative evaluation of the usability of two approaches for findings reporting in a large-scale telecardiology context.

    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

    authors： Lacerda TC,von Wangenheim CG,von Wangenheim A,Giuliano I

    更新日期：2014-12-01 00:00:00

  • Enhancing phylogeography by improving geographical information from GenBank.

    abstract：:Phylogeography is a field that focuses on the geographical lineages of species such as vertebrates or viruses. Here, geographical data, such as location of a species or viral host is as important as the sequence information extracted from the species. Together, this information can help illustrate the migration of the...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2011.06.005

    authors： Scotch M,Sarkar IN,Mei C,Leaman R,Cheung KH,Ortiz P,Singraur A,Gonzalez G

    更新日期：2011-12-01 00:00:00

  • A hybrid of whale optimization and late acceptance hill climbing based imputation to enhance classification performance in electronic health records.

    abstract：:Electronic health records (EHR) are a major source of information in biomedical informatics. Yet, missing values are prominent characteristics of EHR. Prediction on dataset with missing values results in inaccurate inferences. Nearest neighbour imputation based on lazy learning approach is a proven technique for missi...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2019.103190

    authors： Nagarajan G,Dhinesh Babu LD

    更新日期：2019-06-01 00:00:00

  • Extending the Fellegi-Sunter probabilistic record linkage method for approximate field comparators.

    abstract：:Probabilistic record linkage is a method commonly used to determine whether demographic records refer to the same person. The Fellegi-Sunter method is a probabilistic approach that uses field weights based on log likelihood ratios to determine record similarity. This paper introduces an extension of the Fellegi-Sunter...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2009.08.004

    authors： DuVall SL,Kerber RA,Thomas A

    更新日期：2010-02-01 00:00:00

  • Combining glass box and black box evaluations in the identification of heart disease risk factors and their temporal relations from clinical records.

    abstract：BACKGROUND:The determination of risk factors and their temporal relations in natural language patient records is a complex task which has been addressed in the i2b2/UTHealth 2014 shared task. In this context, in most systems it was broadly decomposed into two sub-tasks implemented by two components: entity detection, a...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2015.06.014

    authors： Grouin C,Moriceau V,Zweigenbaum P

    更新日期：2015-12-01 00:00:00

  • Annotating longitudinal clinical narratives for de-identification: The 2014 i2b2/UTHealth corpus.

    abstract：:The 2014 i2b2/UTHealth natural language processing shared task featured a track focused on the de-identification of longitudinal medical records. For this track, we de-identified a set of 1304 longitudinal medical records describing 296 patients. This corpus was de-identified under a broad interpretation of the HIPAA ...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2015.07.020

    authors： Stubbs A,Uzuner Ö

    更新日期：2015-12-01 00:00:00

  • Prediction of clinical risks by analysis of preclinical and clinical adverse events.

    abstract：:This study examines the ability of nonclinical adverse event observations to predict human clinical adverse events observed in drug development programs. In addition it examines the relationship between nonclinical and clinical adverse event observations to drug withdrawal and proposes a model to predict drug withdraw...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2015.02.008

    authors： Clark M

    更新日期：2015-04-01 00:00:00

  • Using UMLS to construct a generalized hierarchical concept-based dictionary of brain functions for information extraction from the fMRI literature.

    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

    authors： Hsiao MY,Chen CC,Chen JH

    更新日期：2009-10-01 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

  • Classification models for the prediction of clinicians' information needs.

    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

    authors： Del Fiol G,Haug PJ

    更新日期：2009-02-01 00:00:00

  • Balancing volume and duration of information consumption by physicians: The case of health information exchange in critical care.

    abstract：BACKGROUND:The realization of the potential benefits of health information exchange systems (HIEs) for emergency departments (EDs) depends on the way these systems are actually used. The attributes of volume of information and duration of information processing are important for the study of HIE use patterns in the ED,...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2017.05.007

    authors： Politi L,Codish S,Sagy I,Fink L

    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

  • Emerging medical informatics with case-based reasoning for aiding clinical decision in multi-agent system.

    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

    authors： Shen Y,Colloc J,Jacquet-Andrieu A,Lei K

    更新日期：2015-08-01 00:00:00

  • Benchmarking deep learning models on large healthcare datasets.

    abstract：:Deep learning models (aka Deep Neural Networks) have revolutionized many fields including computer vision, natural language processing, speech recognition, and is being increasingly used in clinical healthcare applications. However, few works exist which have benchmarked the performance of the deep learning models wit...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2018.04.007

    authors： Purushotham S,Meng C,Che Z,Liu Y

    更新日期：2018-07-01 00:00:00

  • Specifying computer-based counseling systems in health care: a new approach to user-interface and interaction design.

    abstract：:Computer-based counseling systems in health care play an important role in the toolset available for medical doctors to inform, motivate and challenge their patients according to a well-defined therapeutic goal. The design, development and implementation of such systems require close collaboration between users, i.e. ...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2008.10.005

    authors： Herzberg D,Marsden N,Kübler P,Leonhardt C,Thomanek S,Jung H,Becker A

    更新日期：2009-04-01 00:00:00

  • Desiderata for domain reference ontologies in biomedicine.

    abstract：:Domain reference ontologies represent knowledge about a particular part of the world in a way that is independent from specific objectives, through a theory of the domain. An example of reference ontology in biomedical informatics is the Foundational Model of Anatomy (FMA), an ontology of anatomy that covers the entir...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2005.09.002

    authors： Burgun A

    更新日期：2006-06-01 00:00:00

  • The Analytic Information Warehouse (AIW): a platform for analytics using electronic health record data.

    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

    authors： Post AR,Kurc T,Cholleti S,Gao J,Lin X,Bornstein W,Cantrell D,Levine D,Hohmann S,Saltz JH

    更新日期：2013-06-01 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

  • BioLattice: a framework for the biological interpretation of microarray gene expression data using concept lattice analysis.

    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

    authors： Kim J,Chung HJ,Jung Y,Kim KK,Kim JH

    更新日期：2008-04-01 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

  • A comparison of machine learning methods for the diagnosis of pigmented skin lesions.

    abstract：:We analyze the discriminatory power of k-nearest neighbors, logistic regression, artificial neural networks (ANNs), decision tress, and support vector machines (SVMs) on the task of classifying pigmented skin lesions as common nevi, dysplastic nevi, or melanoma. Three different classification tasks were used as benchm...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1006/jbin.2001.1004

    authors： Dreiseitl S,Ohno-Machado L,Kittler H,Vinterbo S,Billhardt H,Binder M

    更新日期：2001-02-01 00:00:00

  • Enhancing reuse of structured eligibility criteria and supporting their relaxation.

    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

    authors： Milian K,Hoekstra R,Bucur A,Ten Teije A,van Harmelen F,Paulissen J

    更新日期：2015-08-01 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

  • Temporal phenotyping of medically complex children via PARAFAC2 tensor factorization.

    abstract：OBJECTIVE:Our aim is to extract clinically-meaningful phenotypes from longitudinal electronic health records (EHRs) of medically-complex children. This is a fragile set of patients consuming a disproportionate amount of pediatric care resources but who often end up with sub-optimal clinical outcome. The rise in availab...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2019.103125

    authors： Perros I,Papalexakis EE,Vuduc R,Searles E,Sun J

    更新日期：2019-05-01 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

  • 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

  • The REDCap consortium: Building an international community of software platform partners.

    abstract：:The Research Electronic Data Capture (REDCap) data management platform was developed in 2004 to address an institutional need at Vanderbilt University, then shared with a limited number of adopting sites beginning in 2006. Given bi-directional benefit in early sharing experiments, we created a broader consortium shari...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2019.103208

    authors： Harris PA,Taylor R,Minor BL,Elliott V,Fernandez M,O'Neal L,McLeod L,Delacqua G,Delacqua F,Kirby J,Duda SN,REDCap Consortium.

    更新日期：2019-07-01 00:00:00

  • Task definition, annotated dataset, and supervised natural language processing models for symptom extraction from unstructured clinical notes.

    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

    authors： Steinkamp JM,Bala W,Sharma A,Kantrowitz JJ

    更新日期：2020-02-01 00:00:00

  • Classification of ADHD with bi-objective optimization.

    abstract：:Attention Deficit Hyperactive Disorder (ADHD) is one of the most common diseases in school aged children. In this paper, we consider using fMRI data with classification techniques to aid the diagnosis of ADHD and propose a bi-objective ADHD classification scheme based on L1-norm support vector machine (SVM). In our cl...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2018.07.011

    authors： Shao L,Xu Y,Fu D

    更新日期：2018-08-01 00:00:00

  • Methodological variations in lagged regression for detecting physiologic drug effects in EHR data.

    abstract：:We studied how lagged linear regression can be used to detect the physiologic effects of drugs from data in the electronic health record (EHR). We systematically examined the effect of methodological variations ((i) time series construction, (ii) temporal parameterization, (iii) intra-subject normalization, (iv) diffe...

    journal_title：Journal of biomedical informatics

    pub_type： 杂志文章

    doi：10.1016/j.jbi.2018.08.014

    authors： Levine ME,Albers DJ,Hripcsak G

    更新日期：2018-10-01 00:00:00