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 scientific discovery process that provides a well-founded framework for integrating experimental data with preexisting knowledge and with automated inference tools. In order to demonstrate the usefulness and power of the proposed framework, we present its application to Genome-Wide Association Studies, and we use it to reproduce a portion of the initial analysis performed on the well-known WTCCC dataset. Finally, we describe a computational system we are developing, aimed at assisting translational research. The system, based on the proposed model, will be able to automatically plan and perform knowledge discovery steps, to keep track of the inferences performed, and to explain the obtained results.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Riva A,Nuzzo A,Stefanelli M,Bellazzi Rdoi
10.1016/j.jbi.2009.11.005subject
Has Abstractpub_date
2010-06-01 00:00:00pages
419-27issue
3eissn
1532-0464issn
1532-0480pii
S1532-0464(09)00151-8journal_volume
43pub_type
杂志文章abstract：:Computer-based clinical decision support (CDS) has been pursued for more than five decades. Despite notable accomplishments and successes, wide adoption and broad use of CDS in clinical practice has not been achieved. Many issues have been identified as being partially responsible for the relatively slow adoption and ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2017.12.005
更新日期：2018-02-01 00:00:00
abstract：BACKGROUND:Personal health information is a valuable resource to the advancement of research. In order to achieve a comprehensive reform of data infrastructure in Australia, both public engagement and building social trust is vital. In light of this, we conducted a study to explore the opinions, perceived risks and tru...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103222
更新日期：2019-07-01 00:00:00
abstract：:A software framework can reduce costs related to the development of an application because it allows developers to reuse both design and code. Recently, companies and research groups have announced that they have been employing health software frameworks. This paper presents the design, proof-of-concept implementation...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2016.06.002
更新日期：2016-08-01 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：PURPOSE:Negative life events, such as the death of a family member, an argument with a spouse or the loss of a job, play an important role in triggering depressive episodes. Therefore, it is worthwhile to develop psychiatric services that can automatically identify such events. This study describes the use of associati...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2011.01.006
更新日期：2011-08-01 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
abstract：OBJECTIVE:The goal of this study is to investigate entity recognition within Electronic Health Records (EHRs) focusing on Spanish and Swedish. Of particular importance is a robust representation of the entities. In our case, we utilized unsupervised methods to generate such representations. METHODS:The significance of...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.05.009
更新日期：2017-07-01 00:00:00
abstract：:A 1998 paper that delineated desirable characteristics, or desiderata for controlled medical terminologies attempted to summarize emerging consensus regarding structural issues of such terminologies. Among the Desiderata was a call for terminologies to be "concept oriented." Since then, research has trended toward the...
journal_title：Journal of biomedical informatics
pub_type： 评论,杂志文章
doi：10.1016/j.jbi.2005.11.008
更新日期：2006-06-01 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：: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：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：: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
更新日期：2003-08-01 00:00:00
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
更新日期：2011-06-01 00:00:00
abstract：:Human musculoskeletal system resources of the human body are valuable for the learning and medical purposes. Internet-based information from conventional search engines such as Google or Yahoo cannot response to the need of useful, accurate, reliable and good-quality human musculoskeletal resources related to medical ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2012.11.001
更新日期：2013-02-01 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：: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：: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
更新日期：2019-07-01 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：:Sensitive biomedical data is often collected from distributed sources, involving different information systems and different organizational units. Local autonomy and legal reasons lead to the need of privacy preserving integration concepts. In this article, we focus on anonymization, which plays an important role for ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.12.002
更新日期：2014-08-01 00:00:00
abstract：:To understand how healthcare technologies are used in practice and evaluate them, researchers have argued for adopting the theoretical framework of Distributed Cognition (DC). This paper describes the methods and results of a study in which a DC methodology, Distributed Cognition for Teamwork (DiCoT), was applied to s...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2012.02.003
更新日期：2012-06-01 00:00:00
abstract：INTRODUCTION:Most data extraction efforts in epidemiology are focused on obtaining targeted information from clinical trials. In contrast, limited research has been conducted on the identification of information from observational studies, a major source for human evidence in many fields, including environmental health...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2017.04.004
更新日期：2017-06-01 00:00:00
abstract：:The term registry is widely used to refer to any database storing clinical information collected as a byproduct of patient care. Despite the use of this single characterizing term (registry), these databases exist in various forms and support functions ranging from biomedical informatics and clinical research, to publ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2008.01.009
更新日期：2008-12-01 00:00:00
abstract：:The class of continuous time Bayesian network classifiers is defined; it solves the problem of supervised classification on multivariate trajectories evolving in continuous time. The trajectory consists of the values of discrete attributes that are measured in continuous time, while the predicted class is expected to ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2012.07.002
更新日期：2012-12-01 00:00:00
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
更新日期：2006-06-01 00:00:00
abstract：:Unnecessary antibiotic regimens in the intensive care unit (ICU) are associated with adverse patient outcomes and antimicrobial resistance. Bacterial infections (BI) are both common and deadly in ICUs, and as a result, patients with a suspected BI are routinely started on broad-spectrum antibiotics prior to having con...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2020.103540
更新日期：2020-09-01 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
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：: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：:The explosive growth of biomedical literature has created a rich source of knowledge, such as that on protein-protein interactions (PPIs) and drug-drug interactions (DDIs), locked in unstructured free text. Biomedical relation classification aims to automatically detect and classify biomedical relations, which has gre...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2019.103294
更新日期：2019-11-01 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
