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. Given such information needs, we report upon the initial design and evaluation of an ontology-anchored integrative query tool, Research-IQ, which employs a combination of conceptual knowledge engineering and information retrieval techniques to enable the intuitive and rapid construction of queries, in terms of semi-structured textual propositions, that can subsequently be applied to integrative data sets. Our initial results, based upon both quantitative and qualitative evaluations of the efficacy and usability of Research-IQ, demonstrate its potential to increase clinical and translational research throughput.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Borlawsky TB,Lele O,Payne PRdoi
10.1016/j.jbi.2011.07.006subject
Has Abstractpub_date
2011-12-01 00:00:00pages
S56-62eissn
1532-0464issn
1532-0480pii
S1532-0464(11)00124-9journal_volume
44 Suppl 1pub_type
杂志文章abstract：:To improve the performance of Intensive Care Units (ICUs), the field of bio-statistics has developed scores which try to predict the likelihood of negative outcomes. These help evaluate the effectiveness of treatments and clinical practice, and also help to identify patients with unexpected outcomes. However, they hav...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103269
更新日期：2019-10-01 00:00:00
abstract：:The Radiology Gamuts Ontology (RGO)-an ontology of diseases, interventions, and imaging findings-was developed to aid in decision support, education, and translational research in diagnostic radiology. The ontology defines a subsumption (is_a) relation between more general and more specific terms, and a causal relatio...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2016.03.015
更新日期：2016-06-01 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：: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：BACKGROUND:One of the significant problems in the field of healthcare is the low survival rate of people who have experienced sudden cardiac arrest. Early prediction of cardiac arrest can provide the time required for intervening and preventing its onset in order to reduce mortality. Traditional statistical methods hav...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.10.008
更新日期：2018-12-01 00:00:00
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
更新日期：2020-07-01 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：: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：:Text categorization has been used extensively in recent years to classify plain-text clinical reports. This study employs text categorization techniques for the classification of open narrative forensic autopsy reports. One of the key steps in text classification is document representation. In document representation,...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.04.013
更新日期：2018-06-01 00:00:00
abstract：:The management of chronic and out-patients is a complex process which requires the cooperation of different agents belonging to several organizational units. Patients have to move to different locations to access the necessary services and to communicate their health status data. From their point of view there should ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2006.12.002
更新日期：2007-10-01 00:00:00
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：:Simulators for honing procedural skills (such as surgical skills and central venous catheter placement) have proven to be valuable tools for medical educators and students. While such simulations represent an effective paradigm in surgical education, there is an opportunity to add a layer of cognitive exercises to the...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2009.02.008
更新日期：2009-08-01 00:00:00
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
更新日期：2011-12-01 00:00:00
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
更新日期：2014-12-01 00:00:00
abstract：:Whenever a shared database resource, containing critical patient data, is created, protecting the contents of the database is a high priority goal. This goal can be achieved by developing a Query-By-Example (QBE) interface, designed to access a shared database, and embedding within the QBE a hierarchical security modu...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/s1532-0464(02)00524-5
更新日期：2002-06-01 00:00:00
abstract：:Many interventions to improve the success of information technology (IT) implementations are grounded in behavioral science, using theories, and models to identify conditions and determinants of successful use. However, each model in the IT literature has evolved to address specific theoretical problems of particular ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2003.09.002
更新日期：2003-06-01 00:00:00
abstract：:Health data exchange is a major challenge due to the sensitive information and the privacy issues entailed. Considering the European context, in which health data must be exchanged between different European Union (EU) Member States, each having a different national regulatory framework as well as different national h...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103183
更新日期：2019-06-01 00:00:00
abstract：:The Strategic Health IT Advanced Research Projects (SHARP) Program, established by the Office of the National Coordinator for Health Information Technology in 2010 supports research findings that remove barriers for increased adoption of health IT. The improvements envisioned by the SHARP Area 4 Consortium (SHARPn) wi...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2012.01.009
更新日期：2012-08-01 00:00:00
abstract：:Molecular Property Diagnostic Suite - Diabetes Mellitus (MPDSDM) is a Galaxy-based, open source disease-specific web portal for diabetes. It consists of three modules namely (i) data library (ii) data processing and (iii) data analysis tools. The data library (target library and literature) module provide extensive an...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.08.003
更新日期：2018-09-01 00:00:00
abstract：:Linkage analysis uses information from family pedigrees to map genes and locate disease genes on particular chromosomes. A recombination fraction denoted as theta is estimated as a measure of crossing over between two loci. Genetic linkage calculations are very time-consuming particularly for large family pedigrees, a...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1006/jbin.2002.1031
更新日期：2001-12-01 00:00:00
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
更新日期：2016-04-01 00:00:00
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
更新日期：2016-04-01 00:00:00
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
更新日期：2015-08-01 00:00:00
abstract：:Quantitative gait analysis allows clinicians to assess the inherent gait variability over time which is a functional marker to aid in the diagnosis of disabilities or diseases such as frailty, the onset of cognitive decline and neurodegenerative diseases, among others. However, despite the accuracy achieved by the cur...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2016.07.009
更新日期：2016-08-01 00:00:00
abstract：OBJECTIVE:To create an interoperable set of nursing diagnoses for use in the patient problem list in the EHR to support interoperability. DESIGN:Queries for nursing diagnostic concepts were executed against the UMLS Metathesaurus to retrieve all nursing diagnoses across four nursing terminologies where the concept was...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2011.12.003
更新日期：2012-08-01 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：: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：:Over the last 8 years, the National Cancer Institute (NCI) has launched a major effort to integrate molecular and clinical cancer-related information within a unified biomedical informatics framework, with controlled terminology as its foundational layer. The NCI Thesaurus is the reference terminology underpinning the...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2006.02.013
更新日期：2007-02-01 00:00:00
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
更新日期：2011-12-01 00:00:00
abstract：OBJECTIVE:Clinical care guidelines recommend that newly diagnosed prostate cancer patients at high risk for metastatic spread receive a bone scan prior to treatment and that low risk patients not receive it. The objective was to develop an automated pipeline to interrogate heterogeneous data to evaluate the use of bone...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103184
更新日期：2019-06-01 00:00:00
