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 73 records · Page 4Linked to original sources

PubMed2004

Wisconsin's environmental public health tracking network: information systems design for childhood cancer surveillance.

In this article we describe the development of an information system for environmental childhood cancer surveillance. The Wisconsin Cancer Registry annually receives more than 25,000 incident case reports. Approximately 269 cases per year involve children. Over time, there has been considerable community interest in understanding the role the environment plays as a cause of these cancer cases. Wisconsin's Public Health Information Network (WI-PHIN) is a robust web portal integrating both Health Alert Network and National Electronic Disease Surveillance System components. WI-PHIN is the information technology platform for all public health surveillance programs. Functions include the secure, automated exchange of cancer case data between public health-based and hospital-based cancer registrars; web-based supplemental data entry for environmental exposure confirmation and hypothesis testing; automated data analysis, visualization, and exposure-outcome record linkage; directories of public health and clinical personnel for role-based access control of sensitive surveillance information; public health information dissemination and alerting; and information technology security and critical infrastructure protection. For hypothesis generation, cancer case data are sent electronically to WI-PHIN and populate the integrated data repository. Environmental data are linked and the exposure-disease relationships are explored using statistical tools for ecologic exposure risk assessment. For hypothesis testing, case-control interviews collect exposure histories, including parental employment and residential histories. This information technology approach can thus serve as the basis for building a comprehensive system to assess environmental cancer etiology.

Automation↗

PubMed2005

Crossing heterogeneous information sources for better analysis of health and social care data.

In this paper we describe a methodology that emerged during an implementation of a health-and-social-care-oriented data repository, which consists in grouping information from heterogeneous and distributed information sources. We developed this methodology by first constructing a concrete data repository, containing information about elderly patients flows in the UK's long-term care (LTC) system. In our specific case, the role of the data repository is to allow knowledge extraction about consumption and behavioural tendencies in the elderly people population within the LTC system. These tendencies can be depicted in terms of survival behaviour (modelling), cost evolution, and bed use. Other types of knowledge that can be extracted are typical patient profiles, placement policy in term of rules and criteria effectively applied and, specific features of the business process behind the long-term care provision. A well-constructed data repository can support the discovery (analysis) of hidden aspects about the way patients are placed and accepted in the LTC, and also how the allocated resources are consumed. We argue that the use of this methodology could save time in similar undertakings or in other fields than health and social care.

Humans↗

PubMed2000

Current medicolegal and confidentiality issues in large, multicenter research programs.

The convenience of fast computers and the Internet have encouraged large collaborative research efforts by allowing transfers of data from multiple sites to a single data repository; however, standards for managing data security are needed to protect the confidentiality of participants. Through Dartmouth Medical School, in 1996-1998, the authors conducted a medicolegal analysis of federal laws, state statutes, and institutional policies in eight states and three different types of health care settings, which are part of a breast cancer surveillance consortium contributing data electronically to a centralized data repository. They learned that a variety of state and federal laws are available to protect confidentiality of professional and lay research participants. The strongest protection available is the Federal Certificate of Confidentiality, which supersedes state statutory protection, has been tested in court, and extends protection from forced disclosure (in litigation) to health care providers as well as patients. This paper describes the careful planning necessary to ensure adequate legal protection and data security, which must include a comprehensive understanding of state and federal protections applicable to medical research. Researchers must also develop rules or guidelines to ensure appropriate collection, use, and sharing of data. Finally, systems for the storage of both paper and electronic records must be as secure as possible.

Confidentiality↗

PubMed1995

Re-engineering care delivery to improve the health outcome of asthmatics in Campbelltown, New South Wales.

The pilot study for this project was established in February 1993 under a Health Communications Network initiative to improve the treatment results for asthmatics in Campbelltown, New South Wales. A user specific, standardized information environment was implemented across the community and hospital sectors linking General Practitioners, Specialist Consultants, and hospital doctors and nurses. The pilot included 20 General Practitioners, four pediatricians and respiratory physicians, and the nurses and doctors of a district hospital. ¿A multi-disciplinary team implemented the pilot, consisting of men and women from Campbelltown Health Service, Ernst & Young Health Services Consulting, and a major systems vendor. The team used process modeling tools to document the required changes to the roles and responsibilities of the individual practitioners and the impact of these changes on the cost of providing services and patient flow. Significant cost savings were anticipated from moving care out of the hospital and into the community. In the re-engineered environment, the General Practitioner became the case manager, responsible for guiding and coordinating the management of the patient's asthma, in consultation with the appropriate specialist consultants. The hospital continued to provide acute/emergency care. The level of sophistication of the information systems solutions was determined by the level of technical awareness of the users. Fax based communications were chosen to support the flow of timely and relevant information between the practitioners. A VAX based system was used as a data repository for the information collected by hospital staff and General Practitioners. The data repository acted as a clinical record for asthmatics who participated in the pilot. The clinical history of an asthmatic could then be viewed when a patient sought treatment from Campbelltown's Emergency Department during periods when the General Practitioner was not available. If a patient did seek emergency treatment, a record of the patient's visit was faxed immediately to the General Practitioner upon discharge from the hospital. Specialist consultants are independent practitioners in Australia. They were provided with a custom built application for their own personal computers. A key feature of this application was the automatic generation of letters to the General Practitioner to assist them in the management of asthmatics. The Specialist Consultants also identified a sub-group of high risk patients for whom additional clinical information was stored in the data repository at Campbelltown Hospital. Analysis of the patient information formed a core component of the project. Clinical outcomes for individual patients were forwarded to the General Practitioners regularly to assist them in their case management duties. System implementation in this re-engineered environment yielded the following: Strategies for managing the responses of clinicians and patients to the use of technology and a standardized information sharing environment. A means of assessing the system's impact on both the clinician-patient relationship and the professionals' relationship with other clinicians; The evolution of clinical use of information regarding individual patient's health outcome for the management of asthma; The integration of the information systems with policy and planning cycles for the Area Health Service; and The establishment of effective links with vendors of health service applications.

Asthma↗

PubMed1991

Using comparative clinical information to understand practice patterns and affect organizational change.

The University Hospital Consortium is collecting clinical, administrative and financial data from its members to develop a Clinical Information Network. The value of this collective data lies in how comparative information about peer hospitals and physicians in the same specialty can be used to influence practice. The raw data from each hospital is analyzed, classified, normalized and stored in a data repository which is easily accessible. This data becomes information when it is presented in a variety of ways, and is supported by a knowledge-base of health care rules. The "drilling down" technique to progressive levels of detail serves the needs of all levels in the organization--executives, managers, and analysts. The system combines the power of a mainframe for the data repository with the ease of use of a PC-based workstation. With an open-ended approach, the users can ask a variety of questions of the data, as well as perform statistical analysis, create graphical presentations and generate explanations of the analysis techniques.

Artificial Intelligence↗

PubMed1998

Scaling an expert system data mart: more facilities in real-time.

Clinical Data Repositories are being rapidly adopted by large healthcare organizations as a method of centralizing and unifying clinical data currently stored in diverse and isolated information systems. Once stored in a clinical data repository, healthcare organizations seek to use this centralized data to store, analyze, interpret, and influence clinical care, quality and outcomes. A recent trend in the repository field has been the adoption of data marts--specialized subsets of enterprise-wide data taken from a larger repository designed specifically to answer highly focused questions. A data mart exploits the data stored in the repository, but can use unique structures or summary statistics generated specifically for an area of study. Thus, data marts benefit from the existence of a repository, are less general than a repository, but provide more effective and efficient support for an enterprise-wide data analysis task. In previous work, we described the use of batch processing for populating data marts directly from legacy systems. In this paper, we describe an architecture that uses both primary data sources and an evolving enterprise-wide clinical data repository to create real-time data sources for a clinical data mart to support highly specialized clinical expert systems.

Computer Systems↗

PubMed1997

Use of relational database management system by clinicians to create automated MICU progress note from existent data sources.

We designed and built an application called MD Assist that compiles data from several hospital databases to create reports used for daily house officer rounding in the medical intensive care unit (MICU). After rounding, the report becomes the objective portion of the daily "SOAP" MICU progress note. All data used in the automated note was available in digital format residing in an institution wide Sybase data repository which had been built to fulfill data needs of the parent enterprise. From initial design of target output through actual creation and implementation in the MICU, MD Assist was created by physicians with only consultative help from information systems (IS). This project demonstrated a method for rapidly developing time saving, clinically useful applications using a comprehensive clinical data repository.

Database Management Systems↗

PubMed1998

Implementing enterprisewide databases: a challenge that can be overcome.

The evolving health care industry is placing new demands on its participants. Traditional institutional boundaries are being replaced by the need to cooperate, collaborate, and share increasingly scarce resources to provide high-quality care to patients. Information, which historically was coveted and protected, must now be shared by the multiple providers and organizations that together provide services. This need to share information has brought on the need for organizations to build common databases from which reports can be run, trends can be noted, and patient information can be drawn. Data warehouses and clinical data repositories are being recognized as solutions to issues of segregation of information. Both solutions are relatively new to health care, and there is acknowledgment that neither is simple to implement and that both represent new challenges to health care organizations. The article provides working definitions of the two solutions, describes at a high level some of the challenges associated with their implementation, and provides some of the key steps required to develop, implement, and realize the benefits of the clinical data repository or data warehouse.

Computer User Training↗

PubMed1997

Three perspectives on integrated clinical databases.

The dramatic transformation of health care organizations from independent local entities into regional and national integrated health care delivery enterprises has forced a reevaluation of the role of information systems. Until recently, nearly all clinical information systems were acquired to support financial and administrative services within single facilities. When independent facilities merge to form an integrated health system (IHS), they find that their unique computer systems do not allow for the sharing or combining of clinical data. However, new technologies are beginning to enable patient-specific data scattered among many information systems in many different hospitals and ambulatory care settings to be unified into a single database called a clinical data repository. The hope is that comprehensive electronic clinical records can enable IHSs to meet their goals of improving the quality and reducing the cost of health care. As the number of technological impediments to forming integrated clinical information systems rapidly decreases, nontechnologic issues surrounding the sharing of patient information become more prominent. The author focuses on the clinician's, the administrator's, and the patient's unique perspectives on the benefits and possible problems associated with clinical data repositories. He then describes how one IHS, together with an academic medical institution, has begun to grapple with many of these concerns through an effort called Project Spectrum. The goal of the project is the successful implementation of a comprehensive clinical data repository.

Clinical Medicine↗

PubMed1995

Data sharing in nursing research: advantages and challenges.

The sharing of data between investigators has received little attention in the nursing literature. Among other advantages, data sharing reinforces open scientific inquiry, encourages the development of multiple perspectives, and reduces respondent burden. However, ownership and control of the shared data, preservation of respondents' anonymity, and the costs of data sharing are among the issues that need to be addressed in agreements and contracts involving primary investigators, secondary investigators, and data repositories. The original researcher must spend time and energy to make data sharing possible. It is only when such efforts are acknowledged and rewarded that data sharing is likely to become a norm in the nursing profession. The authors argue that research data should be shared and nurse researchers should seek to have data from all publicly funded projects deposited in accessible data repositories. Nurse researchers need to incorporate plans for data sharing into their research programs and press for the infrastructures required to enable data sharing.

Authorship↗

PubMed2000

SAGEmap: a public gene expression resource.

We have constructed a public gene expression data repository and online data access and analysis, WWW and FTP sites for serial analysis of gene expression (SAGE) data. The WWW and FTP components of this resource, SAGEmap, are located at http://www.ncbi.nlm.nih. gov/sage and ftp://ncbi.nlm.nih.gov/pub/sage, respectively. We herein describe SAGE data submission procedures, the construction and characteristics of SAGE tags to gene assignments, the derivation and use of a novel statistical test designed specifically for differential-type analyses of SAGE data, and the organization and use of this resource.

Databases, Factual↗

PubMed2006

Small molecules, big players: the National Cancer Institute's Initiative for Chemical Genetics.

In 2002, the National Cancer Institute created the Initiative for Chemical Genetics (ICG), to enable public research using small molecules to accelerate the discovery of cancer-relevant small-molecule probes. The ICG is a public-access research facility consisting of a tightly integrated team of synthetic and analytical chemists, assay developers, high-throughput screening and automation engineers, computational scientists, and software developers. The ICG seeks to facilitate the cross-fertilization of synthetic chemistry and cancer biology by creating a research environment in which new scientific collaborations are possible. To date, the ICG has interacted with 76 biology laboratories from 39 institutions and more than a dozen organic synthetic chemistry laboratories around the country and in Canada. All chemistry and screening data are deposited into the ChemBank web site (http://chembank.broad.harvard.edu/) and are available to the entire research community within a year of generation. ChemBank is both a data repository and a data analysis environment, facilitating the exploration of chemical and biological information across many different assays and small molecules. This report outlines how the ICG functions, how researchers can take advantage of its screening, chemistry and informatic capabilities, and provides a brief summary of some of the many important research findings.

Antineoplastic Agents↗

PubMed2003

The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy.

The creation of structured shared data repositories for molecular data in the form of web-accessible databases like GenBank has been a driving force behind the genomic revolution. These resources serve not only to organize and manage molecular data being created by researchers around the globe, but also provide the starting point for data mining operations to uncover interesting information present in the large amount of sequence and structural data. To realize the full impact of the genomic and proteomic efforts of the last decade, similar resources are needed for structural and biochemical complexity in biological systems beyond the molecular level, where proteins and macromolecular complexes are situated within their cellular and tissue environments. In this review, we discuss our efforts in the development of neuroinformatics resources for managing and mining cell level imaging data derived from light and electron microscopy. We describe the main features of our web-accessible database, the Cell Centered Database (CCDB; http://ncmir.ucsd.edu/CCDB/), designed for structural and protein localization information at scales ranging from large expanses of tissue to cellular microdomains with their associated macromolecular constituents. The CCDB was created to make 3D microscopic imaging data available to the scientific community and to serve as a resource for investigating structural and macromolecular complexity of cells and tissues, particularly in the rodent nervous system.

Brain↗

PubMed2001

Three-dimensional computerised atlas of the rat brain stem precerebellar system: approaches for mapping, visualization, and comparison of spatial distribution data.

Comparisons of microscopical neuroanatomic data from different experiments and investigators are typically hampered by the use of different section planes and dissimilar techniques for data documentation. We have developed a framework for visualization and comparison of section-based, spatial distribution data, in brain stem nuclei. This framework provides opportunities for harmonized data presentation in neuroinformatics databases. Three-dimensional computerized reconstructions of the rat brain stem and precerebellar nuclei served as a basis for establishing internal coordinate systems for the pontine nuclei and the precerebellar divisions of the sensory trigeminal nuclei. Coordinate based diagrams were used for presentation of experimental data (spatial distribution of labelled neurons and axonal plexuses) from standard angles of view. Each nuclear coordinate system was based on a cuboid bounding box with a defined orientation. The bounding box was size-adjusted to touch cyto- and myeloarchitectonically defined boundaries of the individual nuclei, or easily identifiable nearby landmarks. We exemplify the use of these internal coordinate systems with dual retrograde neural tracing data from pontocerebellar and trigeminocerebellar systems. The new experimental data were combined, in the same coordinate based diagrams, with previously published data made available via a neuroinformatics data repository (www.nesys.uio.no/Database, see also www.cerebellum.org). Three-dimensional atlasing, internal nuclear coordinate systems, and consistent formats for presentation of neuroanatomic data in web-based data repositories, offer new opportunities for efficient analysis and re-analysis of neuroanatomic data.

Animals↗

PubMed1995

Repositories promise to quench growing thirst for health data.

Consolidation among providers and the growth of managed care are fueling the development of clinical data repositories. Repositories may be a key to integrated delivery systems' efforts to conduct research to boost outcomes and cut costs.

Delivery of Health Care, Integrated↗

PubMed1998

A NIDSEC primer: Part 2--Setting the standards.

The Nursing Information and Data Set Evaluation Center (NIDSEC), established by the American Nurses Association (ANA), recently published the criteria by which it evaluates information systems that support nursing practice documentation. These criteria include nomenclature, clinical content, clinical data repository and general system characteristics. This article focuses on two of the four dimensions of nursing data sets and the systems that contain them: clinical data repository and general system characteristics.

American Nurses' Association↗

PubMedDate not supplied

Automated mapping of observation codes using extensional definitions.

OBJECTIVE: To create "extensional definitions" of laboratory codes from derived characteristics of coded values in a clinical database and then use these definitions in the automated mapping of codes between disparate facilities. DESIGN: Repository data for two laboratory facilities in the Intermountain Health Care system were analyzed to create extensional definitions for the local codes of each facility. These definitions were then matched using automated matching software to create mappings between the shared local codes. The results were compared with the mappings of the vocabulary developers. MEASUREMENTS: The number of correct matches and the size of the match group were recorded. A match was considered correct if the corresponding codes from each facility were included in the group. The group size was defined as the total number of codes in the match group (e.g., a one-to-one mapping is a group size of two). RESULTS: Of the matches generated by the automated matching software, 81 percent were correct. The average group size was 2.4. There were a total of 328 possible matches in the data set, and 75 percent of these were correctly identified. CONCLUSIONS: Extensional definitions for local codes created from repository data can be utilized to automatically map codes from disparate systems. This approach, if generalized to other systems, can reduce the effort required to map one system to another while increasing mapping consistency.

Algorithms↗

PubMed2006

MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation.

BACKGROUND: The high-density oligonucleotide microarray (GeneChip) is an important tool for molecular biological research aiming at large-scale detection of small nucleotide polymorphisms in DNA and genome-wide analysis of mRNA concentrations. Local array data management solutions are instrumental for efficient processing of the results and for subsequent uploading of data and annotations to a global certified data repository at the EBI (ArrayExpress) or the NCBI (GeneOmnibus). DESCRIPTION: To facilitate and accelerate annotation of high-throughput expression profiling experiments, the Microarray Information Management and Annotation System (MIMAS) was developed. The system is fully compliant with the Minimal Information About a Microarray Experiment (MIAME) convention. MIMAS provides life scientists with a highly flexible and focused GeneChip data storage and annotation platform essential for subsequent analysis and interpretation of experimental results with clustering and mining tools. The system software can be downloaded for academic use upon request. CONCLUSION: MIMAS implements a novel concept for nation-wide GeneChip data management whereby a network of facilities is centered on one data node directly connected to the European certified public microarray data repository located at the EBI. The solution proposed may serve as a prototype approach to array data management between research institutes organized in a consortium.

Database Management Systems↗