SEARCH · PubMed Health

Results for “data repository”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources

PubMed1999

Using Boolean reasoning to anonymize databases.

This paper investigates how Boolean reasoning can be used to make the records in a database anonymous. In a medical setting, this is of particular interest due to privacy issues and to prevent the possible misuse of confidential information. As electronic medical records and medical data repositories get more common and widespread, the issue of making sensitive data anonymous becomes increasingly important. A theoretically well-founded algorithm is proposed that via cell suppression can be used to make a database anonymous before releasing or sharing it to the outside world. The degree of anonymity can be tailored according to the specific needs of the recipient, and according to the amount of trust we place in the recipient. Furthermore, the required measure of anonymity can be specified as far down as to the individual objects in the database. The algorithm can also be used for anonymization relative to a particular piece of information, effectively blocking deterministic inferences about sensitive database fields.

Adult↗

PubMed2000

Evaluation of a data warehouse in an academic health sciences center.

OBJECTIVES: The Clinical data repository (CDR) at the University of Virginia Health System is a data warehouse that provides direct access to data for clinical research and effective decision making. We undertook an evaluation of the CDR to understand factors affecting its adoption. DESIGN: We used a theoretical framework that is based on diffusion of innovation theory. Building on validated survey instruments, we developed a questionnaire and conducted interviews of key executive leaders. Fifty-three individuals with logon ids to the CDR completed our questionnaire. Twelve executive leaders were interviewed. MEASUREMENTS: The outcome variables were the initial and continued use of the CDR. Independent variables included attributes suggested by diffusion theory (i.e. relative advantage, complexity), knowledge and skills expected to correlate with computer usage, and the influence of communication channels. RESULTS: Our overall response rate was 82%. We identified characteristics of users associated with the initial decision to use the CDR. Compatibility with an individual's skills and work style was associated strongly with satisfaction and continued use. Secondly, the importance of organizational culture and the need for data was illuminated by management interviews. CONCLUSIONS: We have shown that diffusion of innovation theory can be used to help understand factors contributing to the success of a data warehouse in a healthcare setting. Our results suggest areas for future research and inquiry as the CDR evolves.

Academic Medical Centers↗

PubMedDate not supplied

An infrastructure for Integrated Electronic Health Record services: the role of XML (Extensible Markup Language).

BACKGROUND: The sharing of information resources is generally accepted as the key to substantial improvements in productivity and better quality of care. In addition, due to the greater mobility of the population, national and international healthcare networks are increasingly used to facilitate the sharing of healthcare-related information among the various actors of the field. In the context of HYGEIAnet, the regional health telematics network of Crete, an Integrated Electronic Health Record environment has been developed to provide integrated access to online clinical information, accessible throughout the island. OBJECTIVES: To make available comprehensive medical information about a patient by means of incorporating all the distributed and heterogeneous health record segments into an Integrated Electronic Health Record that can be viewed on-line through a unified user interface and visualization environment. METHODS: The technological approach for implementing this Integrated Electronic Health Record environment is based on the HYGEIAnet Reference Architecture, which provides the necessary framework for the reuse of services, components, and interfaces. Seamless presentation of information is achieved by means of the Extensible Markup Language (XML), while its underlying capabilities allow for dynamic navigation according to personalized end-user preferences and authorities. RESULTS: The Integrated Electronic Health Record environment developed in HYGEIAnet provides the basis for consistent and authenticated access to primary information over the Internet in order to support decision-making. Primary information is always kept at the place where it has been produced, and is maintained by the most appropriate clinical information system, contrasting traditional store and forward techniques, or centralized clinical data repositories. CONCLUSIONS: Since documents are much more easily accessible rather than data inside a database, Extensible Markup Language has the potential of becoming a very cheap technology provided, of course, that the underlying Healthcare Information Infrastructure exists. XML can be introduced incrementally and its implementation is completely transparent to the end user.

Databases as Topic↗

PubMedDate not supplied

Core data set. Importance to health services research, outcomes research, and policy research.

Development of consistent health care information has been hampered by the lack of a core data set that contains clinical information. The Uniform Hospital Discharge Set was developed to record individual discharge profiles derived from hospital billing systems. Using that information, some states developed data repositories. Government and health insurers maintain databases of claims paid. The data are not consistent, not readily available, may not contain all encounters, and are financial, not clinical. Wide variance in number of procedures in different geographic regions, variability in mortality rates, and variance in expenditures for particular conditions have been identified from those databases. However, they contain little information to assess the 'best' clinical practices regarding patient outcome. We describe specific limitations of current data sets and how health services research, outcomes research, and policy research, could be improved by a core data set, as well as recommendations about a core data set.

Data Collection↗

PubMed1996

The Iowa CHMIS (Community Health Management Information System): work in progress.

The Iowa Community Health Management Information System (CHMIS) is a legislatively authorized system that is designed to meet Iowa's shared information needs and reduce administrative costs. A public/private partnership has been planning this system for over three years, implementation is scheduled to begin in July 1996. At that time, certified transaction networks will route claims data between providers and payors, a subset of that data will be stored by a centralized data repository. As the system evolves, provider access will be expanded and additional data elements will be captured.

Community Networks↗

PubMed2003

DAVID: Database for Annotation, Visualization, and Integrated Discovery.

BACKGROUND: Functional annotation of differentially expressed genes is a necessary and critical step in the analysis of microarray data. The distributed nature of biological knowledge frequently requires researchers to navigate through numerous web-accessible databases gathering information one gene at a time. A more judicious approach is to provide query-based access to an integrated database that disseminates biologically rich information across large datasets and displays graphic summaries of functional information. RESULTS: Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://www.david.niaid.nih.gov) addresses this need via four web-based analysis modules: 1) Annotation Tool - rapidly appends descriptive data from several public databases to lists of genes; 2) GoCharts - assigns genes to Gene Ontology functional categories based on user selected classifications and term specificity level; 3) KeggCharts - assigns genes to KEGG metabolic processes and enables users to view genes in the context of biochemical pathway maps; and 4) DomainCharts - groups genes according to PFAM conserved protein domains. CONCLUSIONS: Analysis results and graphical displays remain dynamically linked to primary data and external data repositories, thereby furnishing in-depth as well as broad-based data coverage. The functionality provided by DAVID accelerates the analysis of genome-scale datasets by facilitating the transition from data collection to biological meaning.

Computational Biology↗

PubMed1999

Evaluation of a data warehouse in an academic health sciences center.

A data warehouse can provide significant benefits to a health care organization if successfully designed and implemented. The Clinical Data Repository (CDR) at the University of Virginia Health Sciences Center improves access to needed data for clinical research and effective decision making at many levels of the organization. We conducted an evaluation of the CDR using a survey questionnaire and interviews of key executive leaders. Our results suggest factors that influence the initial decision to use an information resource, examine the impact of communication channels, and highlight key issues that determine the continued use and ultimate success of a healthcare data warehouse.

Academic Medical Centers↗

PubMed2006

Inter-patient distance metrics using SNOMED CT defining relationships.

BACKGROUND: Patient-based similarity metrics are important case-based reasoning tools which may assist with research and patient care applications. Ontology and information content principles may be potentially helpful tools for similarity metric development. METHODS: Patient cases from 1989 through 2003 from the Columbia University Medical Center data repository were converted to SNOMED CT concepts. Five metrics were implemented: (1) percent disagreement with data as an unstructured "bag of findings," (2) average links between concepts, (3) links weighted by information content with descendants, (4) links weighted by information content with term prevalence, and (5) path distance using descendants weighted by information content with descendants. Three physicians served as gold standard for 30 cases. RESULTS: Expert inter-rater reliability was 0.91, with rank correlations between 0.61 and 0.81, representing upper-bound performance. Expert performance compared to metrics resulted in correlations of 0.27, 0.29, 0.30, 0.30, and 0.30, respectively. Using SNOMED axis Clinical Findings alone increased correlation to 0.37. CONCLUSION: Ontology principles and information content provide useful information for similarity metrics but currently fall short of expert performance.

Algorithms↗

PubMed1999

Variation in health care--the roles of the electronic medical record.

Variation in the use of clinical resources, outcomes, costs, access to health care and quality is a well recognized, ever present feature of health care. It is a phenomenon that affects all sectors of the health care delivery process and is important to clinicians, administrators and patients. As a phenomenon variation can be appropriate or inappropriate and the elimination of inappropriate variation is a fundamental principal behind continuous quality improvement in health care. The primary tools for the management of variation exists within the electronic medical record (EMR). The EMR utilizes the existing and evolving information storage technologies (data repositories) and information management tools (applications), to integrate the elements within this long-term data storage. Through this integration the EMR systems are able to provide knowledge representation in differing formats to the decision-makers and this will facilitate more accurate and appropriate decision-making with subsequent improvements in health care delivery.

Costs and Cost Analysis↗

PubMed2001

Pushing the quality envelope: a new outcomes management system.

This article is based on the authors' experience in designing and implementing outcomes management systems for large managed care organizations. Topics addressed include design of instruments, use of cost-effective technology, development of computerized decision-support tools, and methods for case-mix adjustment. The case-mix-adjustment models are based on a data repository of several thousand treatment cases with multiple measurement points across the course of treatment. Data from controlled and field studies are described. These data suggest that the outcomes management methods outlined in this article can result in significantly improved clinical outcomes and a more rational allocation of behavioral health care resources.

Cost-Benefit Analysis↗

PubMed2001

Pharmacogenetics research network and knowledge base: 1st annual scientific meeting.

The National Institute of General Medical Sciences of the National Institutes of Health recently established a collaborative group of scientists, called the Pharmacogenetics Research Network. Central to the network is a shared, state-of-the-art data repository, the Pharmacogenetics Knowledge Base (PharmGKB), which is housed at Stanford University. Network investigators deposit pharmacogenetic data into PharmGKB, after all individually identifying information has been removed. Contents of PharmGKB will be freely accessible to the scientific community, with the goal of forging new links between gene variation and drug response. An open scientific meeting was held recently to introduce the research community to the network and to invite academic and industry-based researchers to deposit data into PharmGKB. Featured at the meeting were summaries of research progress to date, as well as discussions of issues intimately related to pharmacogenetics research, namely ethics and relations with the biotechnology and pharmaceutical industries.

Animals↗

PubMed1999

Seamless integration of biological applications within a database framework.

There are more than two hundred biological data repositories available for public access, and a vast number of applications to process and interpret biological data. A major challenge for bioinformaticians is to extract and process data from multiple data sources using a variety of query interfaces and analytical tools. In this paper, we describe tools that respond to this challenge by providing support for cross-database queries and for integrating analytical tools in a query processing environment. In particular, we describe two alternative methods for integrating biological data processing within traditional database queries: (a) "light-weight" application integration based on Application Specific Data Types (ASDTs) and (b) "heavy-duty" integration of analytical tools based on mediators and wrappers. These methods are supported by the Object-Protocol Model (OPM) suite of tools for managing biological databases.

Computational Biology↗

PubMed2000

MedStage--platform for information and communication in healthcare.

This application report describes the technologies and strategies used by MedStage, an open infrastructure for secure telemedical internet applications. The infrastructure includes several technical and application frameworks including a public key infrastructure for providing professional security solutions, like certificate-based authentication, secure transport protocol, strong data encryption and digital signature. The key components are an universal healthcare data repository based on the work of CEN TC 251 with extensions for the storage of multimedia data, an exchangeable authorization management, an exchangeable patient index service based on CORBAmed PIDS and a set of XML-based import and export modules. Additionally there are prototype applications for home-monitoring, telereporting and personal health passport.

Computer Communication Networks↗

PubMed2001

What do patients do with access to their medical records?

We sought to study the phenomenon of patients having access to their own medical records in order to determine the impact on them and on their relationship with their health care providers. We created the Patient Clinical Information System (PatCIS) to interface with the clinical data repository at New York Presbyterian Hospital to allow patients to add to and review their medical data. We also provided educational resources and automated advice programs. We provided access to the system to thirteen subjects over a nineteen-month period and reviewed their activities in the system's usage log. We also collected data via questionnaire and telephone interview. We found that patients varied in their use of the system, from once a month or less to one or more times per day. All patients primarily used the system to review laboratory results. Both they and their physicians believed that use of the system enhanced the patients' understanding of their conditions and improved their communication with their physicians. There were no adverse events encountered during the study.

Adult↗

PubMed2002

The patient clinical information system (PatCIS): technical solutions for and experience with giving patients access to their electronic medical records.

As health records evolve into electronic form, increasing demand is being made to provide patients with access to them. We sought to study the character and impact of such access to determine how patients use such records, what cognitive effects it has on them, and how it affects their relationship with their health care providers. We created the Patient Clinical Information System (PatCIS) to interface with the clinical data repository at New York Presbyterian Hospital (NYPH) to allow patients to add to and review their medical data. We also provided educational resources and automated advice programs. We provided access to the system to thirteen subjects over a 36-month period and reviewed their activities in the system's usage log. We also collected data via questionnaire and telephone interview. We collected data for a total of 223 patient months. We found that patients varied in their use of the system, from once a month or less to one or more times per day. All patients primarily used the system to review laboratory results. Both they and their physicians believed that use of the system enhanced the patients' understanding of their conditions and improved their communication with their physicians. There were no adverse events encountered during the study.

Adult↗

PubMed2006

On-the-fly form generation and on-line metadata configuration--a clinical data management Web infrastructure in Java.

In this paper we describe the approach to build a web-based clinical data management infrastructure on top of an entity-attribute-value (EAV) database which provides for flexible definition and extension of clinical data sets as well as efficient data handling and high performance query execution. A "mixed" EAV implementation provides a flexible and configurable data repository and at the same time utilizes the performance advantages of conventional database tables for rarely changing data structures. A dynamically configurable data dictionary contains further information for data validation. The online user interface can also be assembled dynamically. A data transfer object which encapsulates data together with all required metadata is populated by the backend and directly used to dynamically render frontend forms and handle incoming data. The "mixed" EAV model enables flexible definition and modification of clinical data sets while reducing performance drawbacks of pure EAV implementations to a minimum. The system currently is in use in an electronic patient record with focus on flexibility and a quality management application (www.healthgate.at) with high performance requirements.

Austria↗

PubMedDate not supplied

An e-science environment for service crystallography--from submission to dissemination.

The U.K. National Crystallography Service (NCS) has developed a prototype e-science infrastructure for the provision of a small molecule crystallography service from sample receipt to results dissemination. This paper outlines the two strands of this service, which (a) enable a user to contribute in the conduction of an experiment and (b) provide an effective route for the archival and dissemination of the arising results. Access to use the NCS facilities and expertise and a mechanism to submit samples is granted through a secure Grid infrastructure, which seamlessly provides instantaneous feedback and the ability to remotely monitor and guide diffraction experiments and stage the diffraction data to a securely accessible location. Publication of all the data and results generated during the course of the experiment, from processed data to analyzed structures, is then enabled by means of an open access data repository. The repository publishes its content through established digital libraries' protocols, which enable harvester and aggregator services to make the data searchable and accessible.

Crystallography, X-Ray↗

PubMed2004

CEBS object model for systems biology data, SysBio-OM.

MOTIVATION: To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being developed to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users. Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential expression or differential profile technologies. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and protein-protein interaction analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics). RESULTS: To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the MicroArray Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation. The open source SysBio-OM model, which can be implemented on varied computing platforms is presented here. AVAILABILITY: A universal modeling language depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov/SysBioOM/. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. The database and interface are being built to implement the model and will be available for public use at http://cebs.niehs.nih.gov.

Database Management Systems↗