Abstract:
INTRODUCTION:This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". BACKGROUND:The need for complementary access to multiple RDF databases has fostered new lines of research, but also entailed new challenges due to data representation disparities. While several approaches for RDF-based database integration have been proposed, those focused on schema alignment have become the most widely adopted. All state-of-the-art solutions for aligning RDF-based sources resort to a simple technique inherited from legacy relational database integration methods. This technique - known as element-to-element (e2e) mappings - is based on establishing 1:1 mappings between single primitive elements - e.g. concepts, attributes, relationships, etc. - belonging to the source and target schemas. However, due to the intrinsic nature of RDF - a representation language based on defining tuples < subject, predicate, object > -, one may find RDF elements whose semantics vary dramatically when combined into a view involving other RDF elements - i.e. they depend on their context. The latter cannot be adequately represented in the target schema by resorting to the traditional e2e approach. These approaches fail to properly address this issue without explicitly modifying the target ontology, thus lacking the required expressiveness for properly reflecting the intended semantics in the alignment information. OBJECTIVES:To enhance existing RDF schema alignment techniques by providing a mechanism to properly represent elements with context-dependent semantics, thus enabling users to perform more expressive alignments, including scenarios that cannot be adequately addressed by the existing approaches. METHODS:Instead of establishing 1:1 correspondences between single primitive elements of the schemas, we propose adopting a view-based approach. The latter is targeted at establishing mapping relationships between RDF subgraphs - that can be regarded as the equivalent of views in traditional databases -, rather than between single schema elements. This approach enables users to represent scenarios defined by context-dependent RDF elements that cannot be properly represented when adopting the currently existing approaches. RESULTS:We developed a software tool implementing our view-based strategy. Our tool is currently being used in the context of the European Commission funded p-medicine project, targeted at creating a technological framework to integrate clinical and genomic data to facilitate the development of personalized drugs and therapies for cancer, based on the genetic profile of the patient. We used our tool to integrate different RDF-based databases - including different repositories of clinical trials and DICOM images - using the Health Data Ontology Trunk (HDOT) ontology as the target schema. CONCLUSIONS:The importance of database integration methods and tools in the context of biomedical research has been widely recognized. Modern research in this area - e.g. identification of disease biomarkers, or design of personalized therapies - heavily relies on the availability of a technical framework to enable researchers to uniformly access disparate repositories. We present a method and a tool that implement a novel alignment method specifically designed to support and enhance the integration of RDF-based data sources at schema (metadata) level. This approach provides an increased level of expressiveness compared to other existing solutions, and allows solving heterogeneity scenarios that cannot be properly represented using other state-of-the-art techniques.
journal_name
Methods Inf Medjournal_title
Methods of information in medicineauthors
Anguita A,García-Remesal M,de la Iglesia D,Graf N,Maojo Vdoi
10.3414/ME13-02-0020subject
Has Abstractpub_date
2015-01-01 00:00:00pages
50-5issue
1eissn
0026-1270issn
2511-705Xpii
13-02-0020journal_volume
54pub_type
杂志文章abstract:BACKGROUND:In the past decade, Medical Informatics (MI) and Bioinformatics (BI) have converged towards a new discipline, called Biomedical Informatics (BMI) bridging informatics methods across the spectrum from genomic research to personalized medicine and global healthcare. This convergence still raises challenging re...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:10.3414/ME11-01-0060
更新日期:2012-01-01 00:00:00
abstract:OBJECTIVES:Benchmarking statements provide a mechanism for making academic standards explicit within a subject area. They allow comparisons between courses to be based on learning outcomes rather than by defining a curriculum. No such statement has been produced for informatics. In the absence of any established benchm...
journal_title:Methods of information in medicine
pub_type: 杂志文章,评审
doi:10.1160/me0442
更新日期:2007-01-01 00:00:00
abstract:OBJECTIVES:We discuss supervised classification techniques applied to medical diagnosis based on gene expression profiles. Our focus lies on strategies of adaptive model selection to avoid overfitting in high-dimensional spaces. METHODS:We introduce likelihood-based methods, classification trees, support vector machin...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:The UMLS assigns semantic types to all its integrated concepts. The semantic types are widely used in various natural language processing tasks in the biomedical domain, such as named entity recognition, semantic disambiguation, and semantic annotation. Due to the size of the UMLS, erroneous semantic type as...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:10.3414/ME17-01-0120
更新日期:2018-02-01 00:00:00
abstract:OBJECTIVE:Introducing the Special Topic of Methods of Information in Medicine on pervasive healthcare, with selected papers from the Pervasive Healthcare Conference at Tampere, Finland, January 30 to February 1, 2008. METHODS:Describing pervasive healthcare as field. Reporting about the content of the selected papers ...
journal_title:Methods of information in medicine
pub_type: 社论
doi:
更新日期:2008-01-01 00:00:00
abstract::Appropriateness and necessity research of various procedures in medicine may be the most complex field of innovation in healthcare and technology assessment. Nevertheless, the appropriateness of the indication of any medical intervention is probably more important than the outcome since even ideal quality components o...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:
更新日期:2000-08-01 00:00:00
abstract:OBJECTIVE:Joint data analysis is a key requirement in medical research networks. Data are available in heterogeneous formats at each network partner and their harmonization is often rather complex. The objective of our paper is to provide a generic approach for the harmonization process in research networks. We applied...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:10.3414/ME14-02-0030
更新日期:2015-01-01 00:00:00
abstract:OBJECTIVE:Record linkage may create powerful datasets with which investigators can conduct comparative effectiveness studies evaluating the impact of tests or interventions on health. All linkages of health care data files to date have used protected health information (PHI) in their linkage variables. A technique to l...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:10.3414/ME14-01-0093
更新日期:2015-01-01 00:00:00
abstract::This editorial is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Evidence-based Health informatics: How do we know what we know?", written by Elske Ammenwerth [1]. Health informatics uses and applications have crept up on health systems over half a century, starting as simple a...
journal_title:Methods of information in medicine
pub_type: 评论,社论
doi:10.3414/ME14-10-0139
更新日期:2015-01-01 00:00:00
abstract:OBJECTIVES:As a preliminary for the design of Computer-Based Patient Records, the aim of this paper is to build an understanding of the roles physical artifacts like paper-based patient records play in supporting cognition and collaboration in the health-care settings. METHOD:A small ethnographically-informed study wa...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:
更新日期:2003-01-01 00:00:00
abstract:OBJECTIVE:To present a geometric ruler to determine predictive values of binary diagnostic test results from prevalence, sensitivity and specificity without calculation. METHODS:On logarithmic scale the relationships between pre-/post-test odds and the likelihood ratio as well as sensitivity, specificity and the likel...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:10.3414/ME14-01-0091
更新日期:2015-01-01 00:00:00
abstract:OBJECTIVES:In the field of open electronic health records (EHRs), openEHR as an archetype-based approach is being increasingly recognised. It is the objective of this paper to shortly describe this approach, and to analyse how openEHR archetypes impact on health professionals and semantic interoperability. METHODS:Ana...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:10.1160/ME5001
更新日期:2007-01-01 00:00:00
abstract::This paper presents a tutorial introduction to the handling of uncertainty and decision-making in medical reasoning systems. It focuses on the central role of uncertainty in all of medicine and identifies the major themes that arise in research papers. It then reviews simple Bayesian formulations of the problem and pu...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:
更新日期:1995-03-01 00:00:00
abstract::Requirements and approaches of Software Engineering education in the field of Medical Informatics are described with respect to the impact of (1) experiences characterizing the "software misery", (2) status and tendencies in software methodology, and (3) educational status and needs in computer science education influ...
journal_title:Methods of information in medicine
pub_type: 杂志文章,评审
doi:
更新日期:1989-11-01 00:00:00
abstract:INTRODUCTION:This article is part of the Focus Theme of Methods of Information in Medicine on "Biosignal Interpretation: Advanced Methods for Studying Cardiovascular and Respiratory Systems". OBJECTIVES:The aim of this study is to assess the reliability of the estimated Nocturnal Heart Rate (HR), recorded through a be...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:10.3414/ME13-02-0053
更新日期:2014-01-01 00:00:00
abstract:OBJECTIVES:a) To present a regional health care communication system developed in the North Karelia Hospital District with the help of two EU funded information technology projects namely the TERVE project (1) which was implemented at the national level financed by the regional subsidy 6 of the ERDF and the CHIN projec...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:
更新日期:2002-01-01 00:00:00
abstract::Medical care and medical education can be supported more than in the past by using new tools and new premises for the effective linkage between bodies of knowledge and the use of that knowledge. The medical record can be converted from a source-oriented record to a problem-oriented record, enabling to trace not only w...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:
更新日期:1989-11-01 00:00:00
abstract::Surgical fluid replacement is a critical issue in medicine as the fluid volume excess or deficit can both complicate the patient's condition. Currently, the administration of fluid volume is carried out primarily based on the experience and expertise of the anaesthetist as there is no analytical method available to es...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:
更新日期:2001-03-01 00:00:00
abstract:OBJECTIVES:This study aimed at gaining comprehensive information on the current status of patient care and management applications used in German acute hospitals. Since the degree of ICT coverage in hospitals depends on the attitude of the key decision makers we also wanted to capture their plans and priorities and her...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:
更新日期:2005-01-01 00:00:00
abstract:OBJECTIVES:A low rate of newly developed pressure ulcers is considered as an important quality indicator in nursing. However, the result of a hospital depends not only on the quality of care but on the risk profile of its patients as well. Therefore, based on multiple logistic regression models we describe a method for...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:10.3414/ME10-01-0019
更新日期:2010-01-01 00:00:00
abstract:OBJECTIVES:Our objective is to investigate diabetes-related alteration of glucose control in diurnal fluctuations in normal daily life by detrended fluctuation analysis (DFA). METHODS:The fluctuations of glucose of 12 non-diabetic subjects and 15 diabetic patients were measured using a continuous glucose monitoring sy...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:
更新日期:2007-01-01 00:00:00
abstract:INTRODUCTION:This article is part of the Focus Theme of Methods of Information in Medicine on "Biosignal Interpretation: Advanced Methods for Studying Cardiovascular and Respiratory Systems". BACKGROUND:Adaptation of the QT-interval to changes in heart rate reflects on the body-surface electrocardiogram the adaptation...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:10.3414/ME13-02-0039
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Delayed patient recruitment is a common problem in clinical trials. According to the literature, only about a third of medical research studies recruit their planned number of patients within the time originally specified. OBJECTIVES:To provide a method to estimate patient accrual rates in clinical trials b...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:10.3414/ME0582
更新日期:2009-01-01 00:00:00
abstract::Continuous recording of intraluminal pressures for extended periods of time is currently regarded as a valuable method for detection of esophageal motor abnormalities. A subsequent automatic analysis of the resulting motility data relies on strict mathematical criteria for recognition of pressure events. Due to great ...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:
更新日期:1994-03-01 00:00:00
abstract:OBJECTIVES:Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that ...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:10.3414/ME9302
更新日期:2010-01-01 00:00:00
abstract:OBJECTIVES:In this study, we evaluated the internal validity of EPICON, an application for grouping ICPC-coded diagnoses from electronic medical records into episodes of care. These episodes are used to estimate morbidity rates in general practice. METHODS:Morbidity rates based on EPICON were compared to a gold standa...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:
更新日期:2008-01-01 00:00:00
abstract:INTRODUCTION:This article is part of a Focus Theme of METHODS of Information in Medicine on Health Record Banking. BACKGROUND:Poor communication of health care information between health care providers (HCP) is still a major problem. One recent approach is the concept of Health Record Banking. OBJECTIVES:With this re...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:10.3414/ME13-02-0003
更新日期:2014-01-01 00:00:00
abstract::Often in drug trials only the objective, or the subjective responses of the subjects are investigated, depending on the kind of drug. It is, however, desirable to check both the objective and the subjective responses in every drug trial. The investigation of the objective symptoms which is especially necessary in psyc...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:
更新日期:1963-01-01 00:00:00
abstract:BACKGROUND:Until recently, genotype studies were limited to the investigation of single SNP effects due to the computational burden incurred when studying pairwise interactions of SNPs. However, some genetic effects as simple as coloring (in plants and animals) cannot be ascribed to a single locus but only understood w...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:10.3414/ME11-02-0049
更新日期:2013-01-01 00:00:00
abstract:OBJECTIVES:To provide a comprehensive bottom-up categorization of model-based segmentation techniques that allows to select, implement, and apply well-suited active contour models for segmentation of medical images, where major challenges are the high variability in shape and appearance of objects, noise, artifacts, pa...
journal_title:Methods of information in medicine
pub_type: 杂志文章
doi:
更新日期:2003-01-01 00:00:00